title: wild type strain LAC rep 3

description: Gene expression data from_wild type strain LAC rep 3

source_name: wild type strain LAC rep 3


title: wild type strain 252 rep 2

status: Public on Mar 29 2011

type: RNA

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

country: USA

institute: NIH

description: Gene expression data from_wild type strain 252 rep 2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 40C on our custom Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Ft genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

molecule: total RNA

organism: Staphylococcus aureus

source_name: wild type strain 252 rep 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: standard broth cultures to log phase

extract_protocol: Total RNA was isolated by use of an RNeasy Mini Kit (Qiagen) recommended by a standard protocol.

tag: genotype/variation

value: wild type

tag: strain


title: agr mutant strain 252 rep 3

description: Gene expression data from_agr mutant strain 252 rep 3

source_name: agr mutant strain 252 rep 3

value: agr mutant


title: MCF-7_6hr_100nM-4-OHT_3

status: Public on Mar 30 2011

type: other

city: Louisville

first: Carolyn

middle: M

last: Klinge

state: KY

address: 580 S Preston St

department: Biochemistry & Molecular Biology

institute: University of Louisville School of Medicine

description:
CH1 raw data file: 1_Exiqon_13973533_S01_Cropped.txt
CH2 raw data file: 0_Exiqon_13973533_S01_Cropped.txt

hyb_protocol: Samples were sent to Exiqon where they were labeled and hybridized into the miRCURY LNA microarray (miRbase 11.0 human array)

scan_protocol: MiRNA analysis was performed by Exiqon

data_processing: LOESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Exiqon performed these calculations/analyses.

molecule: other

organism: Homo sapiens

source_name: Breast Cancer Cells treated with EtOH, E2, or 4-OHT

label_protocol: Cells were serum-starved for 48 h prior to 6 h treatment with Ethanol (EtOH- vehicle control), 10 nM estradiol (E2), or 100 nM 4-hydroxytamoxifen (4-OHT)

growth_protocol: MCF-7 cells were grown in IMEM with 5% FBS + 1% PS and were serum starved (5% dextran-coated charcoal stripped FBS in IMEM phenol red free medium) for 48 h prior to treatment

extract_protocol: RNA was extracted using miRVANA miRNA isolation kit from Ambion

treatment_protocol: Cells were treated with Ethanol (EtOH- vehicle control), 10 nM estradiol (E2), or 100 nM 4-hydroxytamoxifen (4-OHT) for 6 hr

tag: gender

value: female

tag: cell line

value: MCF-7 breast cancer cell line

tag: tamoxifen sensitivity

value: sensitive

tag: agent

source_name: Exiqon Common Reference Pool

tag: reference

value: Exiqon Common Reference Pool


title: wild type strain 252 rep 1

description: Gene expression data from_wild type strain 252 rep 1

source_name: wild type strain 252 rep 1


title: wild type strain LAC rep 1

description: Gene expression data from_wild type strain LAC rep 1

source_name: wild type strain LAC rep 1

value: LAC


title: Aged1

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

description:
Aged oocytes from Xenopus tropicalis, replicate 1
Gene expression data from aged X. tropicalis oocytes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Xenopus Tropicalis Genome arrays (Affymetrix Part No. 901100). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 400.

scan_protocol: Arrays were scanned in the Affymetrix GeneChip Scanner 3000 with G7 update

data_processing: The data were analyzed with MAS5 using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

organism: Xenopus tropicalis

source_name: Oocytes from Xenopus tropicalis

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

extract_protocol: RNA was extracted using the total RNA isolation kit from Peqlab

treatment_protocol: Oocytes were aged by incubation in Modified Barth's Solution for 3 hs.

tag: cell type

value: oocyte

tag: age

value: 3 h


title: Aged2

description:
Aged oocytes from Xenopus tropicalis, replicate 2
Gene expression data from aged X. tropicalis oocytes


title: DCAf3for12h

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

institute: University of Wuerzburg

hyb_protocol: hybridization for 16 hr at 42C using a Agilent hybridization oven, labeled targets from 500 ng total RNA were used for hybridization

scan_protocol: Arrays were scanned using the ScanArray 4000 (PerkinElmer)

data_processing: The data were analyzed with custom Bioconductor packages (under R) 1st median value of 4 replicates (flagged spots excluded) was calculated, 2nd normalization using a set of house keeping genes [c("12-1-2", "4-2-2", "12-2-2", "4-3-2", "12-3-2", "4-4-2", "12-4-2", "8-3-3", "16-3-3", "16-4-3", "8-1-2", "16-1-2")].

source_name: human whole blood from healthy blood donors

label_protocol: labeling according to the LabelStar Array Kit (Qiagen) manual

extract_protocol: purification from human dendritic cells using RNeasy Mini Kit and QiaShredder spin columns (Qiagen) as per the manufacturer’s instructions, followed by the amplification of RNA using the MessageAmp II aRNA Amplification Kit (Ambion)

value: human dendritic cells

tag: growth protocol

value: co-cultivation with Aspergillus fumigatus

tag: time


title: DCAf2for12h


title: Control2

description:
Fresh oocytes from Xenopus tropicalis, replicate 2
Gene expression data from fresh X. tropicalis oocytes

value: fresh


title: DCAf1for12h


title: 3' Poly(A) isolated liver Replicate 4

city: SaltLake City

first: Christopher

middle: Ian

last: Maxwell

state: UT

department: Internal Medicine / Gastroenterology

institute: University of Utah

description: 3' Poly(A) isolation replicate 4 of 4

hyb_protocol: Fluorescently labeled cDNA probes were heat denatured after being combined with cot-1 DNA, Agilent aCGH blocking agent and Agilent Hi-RPM hybridization solution. Microarray hybridizations were performed using Agilent SureHyb chambers incubated at 65ºC for 40 hours with a rotational speed of 20 rpm. Following incubation, the microarray slide was washed for 5 minutes in aCGH/ChIP-on-chip Wash Buffer 1 (0.5X SSPE, 0.005% N-lauroylsarcosine; room temperature) and 5 minute in aCGH/ChIP-on-chip Wash Buffer 2 (0.1X SSPE, 0.005% N-lauroylsarcosine; 31ºC). Microarray slides (Agilent ID# 014792) were briefly dipped in a solution of acetonitrile and dried. Two microarray slides each were used for labeled cDNA generated from 5' capped and 3' poly(A) RNA from two experimental replicate samples (HCV and normal liver). These slides were then stripped and used again with the other two experimental replicate samples.

scan_protocol: Scanned on an Agilent G2505B/C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.1.1.1).

data_processing: Agilent Feature Extraction Software (v 10.1.1.1) was used for background subtraction and LOWESS normalization.

source_name: Normal liver, pre-implant

label_protocol: cDNA was produced using a commercially available kit (Just cDNA Double-Stranded cDNA Synthesis Kit, Stratagene, La Jolla, CA). Random hexamers were used to prime first strand cDNA synthesis from both 5' capped and 3' poly(A) RNA samples. The cDNA product was labeled using an Agilent Genomic DNA Labeling Kit PLUS by incorporating fluorescently labeled nucleotides (Cy3-dUTP or Cy5-dUTP) using the exo-Klenow fragment. Following termination of the labeling reaction, fluorescently labeled cDNA probes were purified by isopropanol precipitation. Precipitated pellets were dried and then rehydrated in distilled water.

extract_protocol: 3'Poly(A) RNA isiolation: Total RNA extracted using Trizol following manufacturer's instructions. 3' poly(A) RNA was then purified with oligo(dT) beads (Oligotex®, Qiagen). The quantity of 3' poly(A) RNA was measured by NanoDrop analysis and its integrity confirmed with an Agilent 2100 Bioanalyzer.

tag: tissue

value: Normal liver

source_name: HCV-infected cirrhotic liver, explanted

value: HCV cirrhotic liver


title: DCAf3for9h

value: 9 h


title: DCAf1for9h


title: DCAf2for9h


title: DCAf3for6h

value: 6 h


title: 3' Poly(A) isolated liver Replicate 3

description: 3' Poly(A) isolation replicate 3 of 4


title: 3' Poly(A) isolated liver Replicate 1

description: 3' Poly(A) isolation replicate 1 of 4


title: Control1

description:
Fresh oocytes from Xenopus tropicalis, replicate 1
Gene expression data from fresh X. tropicalis oocytes


title: 3' Poly(A) isolated liver Replicate 2

description: 3' Poly(A) isolation replicate 2 of 4


title: 5' Cap isolated liver Replicate 3

description: 5' Cap isolation replicate 3 of 4

extract_protocol: 5'Cap RNA isolation: Total RNA extracted using Trizol following manufacturer's instructions. 5' capped RNAs were then purified using GST-eIF4EK119A recombinant protein bound to glutathione-agarose beads in microfuge tubes by batch purification. The quantity of 5' capped RNA was measured by NanoDrop analysis and its integrity confirmed with an Agilent 2100 Bioanalyzer.


title: prdm1 WT rep1

city: Aurora

first: KRISTIN

last: ARTINGER

state: CO

address: 12801 East 17th St

department: Craniofacial Biology

institute: University of Colorado Denver

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Arrays were read at a resolution of 2.5-3 microns  using GeneChip Scanner 3000 (Affimetrix).

data_processing: MAS 5.0

organism: Danio rerio

source_name: prdm1 WT, Whole embryo

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

growth_protocol: Zebrafish were maintained according to Westfield (1993) and staged by hours post fertilization (hpf) and morphology according to Kimmel (1995).

extract_protocol: prdm1a mutants phenotype were manually identified as wild-type or mutants.  All samples contained 5 ug of carrier glycogen and were prepared using Trizol. Samples were then treated with the RiobMinusâ„¢ rRNA reduction kit (Invitrogen), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

value: 25 hpf

value: embryo

tag: genotype


title: 5' Cap isolated liver Replicate 2

description: 5' Cap isolation replicate 2 of 4


title: DCAf2for6h


title: DCAf1for6h


title: Ppu_Soil_3CBplus_Rep1

city: Tsukuba

first: yong

last: wang

state: Ibaraki

address: 3-1-3 Kannondai

department: Environmental Biofunction Division

country: Japan

institute: National Institute for Agro-Environmental Sciences

description:
Accessions: NC_002947 + AB050198
This sample is the soil culture of Pseudomonas putida KT2440/pSL1 in the presence of 3-chlorobenzoate.

hyb_protocol: Hybridization was performed according to Roche NimbleGen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed according to Roche NimbleGen standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the ArrayStar software package, version 4.0 (DNASTAR, Madison, WI, USA).

organism: Pseudomonas putida KT2440

source_name: Pseudomonas putida KT2440/pSL1 in the presence of 3CB

label_protocol: Labeling was performed according to Roche NimbleGen standard operating protocol. See www.nimblegen.com.

growth_protocol: Pseudomonas putida KT2440/pSL1 was inoculated from a glycerol stock to a LB agar plate with kanamycin (50 µg/ml), and incubated at 30°C overnight. This strain was then subcultured overnight in LB medium with kanamycin (50 µg/ml) at 28°C. One ml of this liquid culture (OD600 = 1.0) was centrifuged to collect cells. After washing twice with 10 mM Na2HPO4/NaH2PO4 buffer (pH 6.8), cells were resuspended and diluted 10-fold. For RNA extraction, 0.5 ml of the diluted bacteria suspension were mixed with 4.5 g sterilized soil in 50-ml tubes, to which 3-chlorobenzoate (3CB) was added at a final concentration of 250 ppm in the case of 3CB+ samples. To ensure a homogeneous distribution of 3CB in the soil, 3CB was first mixed with Celite® powder (Wako, Osaka, Japan) as previously described (Morimoto et al. Microbes Environ. 20(3): 151-159.). The soil culture of the bacteria was incubated at 30ºC for 24 h (3CB- samples) or 48 h (3CB+ samples).

extract_protocol: Firstly, total RNA was extracted from soil using a RNA PowerSoil Total RNA Isolation Kit (MO BIO Laboratories, Inc., Carlsbad, CA) according to the manufacturer’s instructions with a modification, in which a centrifugation (2,500 g for 10 min at room temperature) was conducted between the cell lysis and the phenol extraction to separate cell lysate from soil. Then, purification using a MicroSpin S-400 HR spin column (GE Healthcare, Little Chalfont, UK), DNase digestion using a TURBO DNA-free DNase (Ambion, Austin, TX) and purification using a RNA Clean & Concentrator™-5 (Zymo Research, Orange, CA, USA) were conducted as described previously (Wang et al. J Appl Microbiol 107:1168-1177). The integrity of RNA was assessed by agarose gel electrophoresis. The concentration of RNA was determined using a Nanodrop system (Nanodrop, Wilmington, DE). Finally, 100 ng RNA was used for amplification by a MessageAmp™ II-Bacteria Kit for Prokaryotic RNA Amplification (ABI Ambion, Japan).

value: contains an introduced plasmid, pSL1

tag: phenotype

value: degrades 3CB completely

tag: treatment

value: 3-chlorobenzoic acid (3CB)


title: Ppu_Soil_3CBminus_Rep3

description:
Accessions: NC_002947 + AB050198
This sample is the soil culture of Pseudomonas putida KT2440/pSL1 in the absence of 3-chlorobenzoate.

source_name: Pseudomonas putida KT2440/pSL1 in the absence of 3CB


title: prdm1 mutant rep2

source_name: prdm1 mutant, Whole embryo

value: prdm1 nulll mutant


title: Ppu_Soil_3CBplus_Rep2


title: Ppu_Soil_3CBminus_Rep2


title: DCAf3for3h


title: Ppu_Soil_3CBminus_Rep1


title: prdm1 mutant rep1


title: prdm1 WT rep2

value: wild type


title: 5' Cap isolated liver Replicate 1

description: 5' Cap isolation replicate 1 of 4


title: prdm1 WT rep3


title: DCAf2for3h


title: DCAf1for3h


title: polysome mRNA WT-3

city: Knoxville

first: Albrecht

last: von Arnim

state: TN

address: M407 Walters Life Sciences Building

department: Biochemistry, Cellular and Molecular Biology

institute: the University of Tennessee

description:
18-AVA030_WT_PL3

Based on our analysis, the data from replicates #1 and #2  more closely resemble each other than replicate #3. Microarray data were generated on the following dates:  replicate 1 and replicate 2:  5/13/2009, replicate 3: 12/2/2009.

hyb_protocol: cDNA samples were hybridized to the Affymetrix ATH1 array (July 01, 2002) according to the manufacturer's protocol (Affymetrix) by the  Affymetrix Microarry Core Facility of the University of Tennessee. Probe set ID, Locus and Description refer to the Arabidopsis thaliana genome release TAIR 9 (June 19, 2009).

scan_protocol: Array scanning was performed according to the manufacturer's instructions (Affymetrix) by the  Affymetrix Microarray Core Facility of the University of Tennessee.

data_processing: Data were GCRMA normalized. TL states (Log(2)[PL/NP]) were calculated (=Log(2)PL - Log(2)NP).

organism: Arabidopsis thaliana

source_name: wild type, polysome mRNA

label_protocol: cDNA were generated and labeled according to the standard protocol by the  Affymetrix Microarray Core Facility of the University of Tennessee, Knoxville.

growth_protocol: Medium: GM medium with 1% sucrose and 0.8% agar, in petri plates wrapped with parafilm that was pierced to allow gas exchange; Light: 16 h long day, from fluorescent bulbs at ~80umole/m2/second; Temperature: 22oC.

extract_protocol:
Harvest method: Under room light, flood seedlings with liquid Nitrogen and scrape off into liquid nitrogen with spatula; Timing: 4 hours after light on.

Polysome gradient and RNA purification were carried out essentially as decribed in Kim et al. (2007) Genome Biology 8:R60 (PMID 17439654). The top 6 fractions were pooled as non-polysomal (NP), and the bottom 6 fractions were pooled as polysomal (PL).

tag: ecotype

value: Columbia

value: 11 days

value: aerial part

tag: rna

value: polysome mRNA


title: DC3for12h

value: human dendritic cells

value: control


title: non-polysome mRNA WT-3

description:
17-AVA031_WT_NP3

Based on our analysis, the data from replicates #1 and #2  more closely resemble each other than replicate #3. Microarray data were generated on the following dates:  replicate 1 and replicate 2:  5/13/2009, replicate 3: 12/2/2009.

source_name: wild type, non-polysome mRNA

value: non-polysome mRNA


title: DC2for12h


title: Cholic acid 1st, Chol-Cy5 Py-Cy3

city: Vancouver

first: Hirofumi

last: Hara

state: BC

address: 2350 Health Science Mall

department: Microbilogy and Immunology

country: Canada

institute: University of British Columbia

description: To correct for non-specific (background) signal for each channel (each dye), the mean signal of 10% of the probes in each sub grid with the lowest intensity was subtracted from that of all probes in the corresponding sub grid.

hyb_protocol: The microarray slides were pre-hybridized using 5x SSC containing 0.1% SDS and 0.2% BSA for 45 minutes at 48oC and used immediately for hybridization in a GeneTac HybStation (Genomic Solution). The hybridization was carried out at 42oC for 18 hours with mixing using 120 μL per slide of SlideHyb#1 hybridization solution (Ambion). The post hybridization washing consisted of 3 cycles of 20 second incubations with each of the following solutions: 2x SSC plus 0.1% SDS (medium stringency) at 42oC; 0.1x SSC plus 0.05% SDS (high stringency) at 25oC; and 0.1x SSC (low stringency) at 25oC.

scan_protocol: The slides were scanned with a GenePix 4000B scanner (Axon Instruments). The spot intensities were quantified using Imagene 5.6 (BioDiscovery, Inc.).

data_processing: Expression ratios were normalized using the LOWESS method. Average normalized expression ratios (experiment/control) were calculated for each gene and tested for significant variation between treatments (ANOVA p < 0.05).

organism: Rhodococcus jostii RHA1

source_name: R. jostii RHA1, cholic acid

label_protocol: Cy5-labeled cDNA were prepared by indirect labeling.

extract_protocol: Total RNA isolation involved vortexing with glass beads, hot phenol plus SDS, precipitation of debris with acetate, phenol plus chloroform, precipitation of nucleic acids with acetate plus isopropanol, DNase treatment and purification with an RNeasy mini column (Qiagen).

tag: condition

value: grown on cholic acid

tag: sample type

value: experiment

source_name: R. jostii RHA1, pyruvate

label_protocol: Cy3-labeled cDNA were prepared by indirect labeling.

value: grown on pyruvate


title: Con KD ES cells, 5-hydroxymethylcytosine  by hMeDIP-chip, Rb Ab  (2/4)

type: genomic

city: Boston

first: Hao

last: Wu

state: Massachusetts

address: 149G Warren Alpert Building, 200 Longwood Avenue

department: Genetics

institute: Harvard Medical School/HHMI

hyb_protocol: 34 ug of Cy5- and Cy3-labeled samples were combined and hybridized to each mouse whole genome tiling microarray (Roche/NimbleGen 4-array set) for 16-20 h at 42 ˚C using NimbleGen hybridization System 4.

scan_protocol: Microarrays were scanned using the Agilent scanner at 5 micron resolution.

data_processing: Data were extracted and analyzed using NimbleScan v2.5 (Roche/NimbleGen).  For identifying regions associated with a significant enrichment of 5hmC in Con KD or Tet1 KD ES cells, a non-parametric one-sided Kolmogorov-Smirno (KS) test was used ([-log10 5hmC peak P-value]>2.3).

molecule: genomic DNA

organism: Mus musculus

source_name: Con KD ES cells, whole cell extract

label_protocol: Immunoprecipitated and input DNA were amplified using the Whole Genome Amplification Kit (Sigma), and 5 ug of amplified DNA were labeled (5’ Cy5- or Cy3-random nonamers, TriLink Biotechnologies) using the standard protocol (NimbleGen Arrays User’s Guide for ChIP-chip analysis).

growth_protocol: Mouse ES cells were maintained on gelatin-coated dishes in Glasgow Minimum Essential medium (GMEM; GIBCO), supplemented with 15% heat-inactivated fetal bovine serum, 55 mM b-mercaptoethanol (GIBCO), 2mM L-glutamine, 0.1mM MEM non-essential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of ESGRO (Chemicon) under feeder-free conditions.

extract_protocol: Genomic DNA was sequentially digested with proteinase K and RNase A, and purified by phenol/chloroform extraction. Purified DNA was sonicated to 200-1000 bp and heat-denatured (95 ˚C, 10 min).  An aliquot of sonicated genomic DNA was saved as input.  5μg fragmented genomic DNA was immunoprecipitated with 5 μg of rat monoclonal 5hmC Ab (Diagenode, cat# MAb-633HMC) or rabbit polyclonal 5hmC Ab (Active Motif, cat#39791) at 4 ˚C overnight in a final volume of 500 μl IP buffer [10 mM sodium phosphate (pH 7.0), 140 mM NaCl, 0.05% Triton X-100].  The DNA-antibody mixture was incubated with 30 μl protein G Dynabeads (Invitrogen) for 2 h at 4 ˚C and washed for three times with 1 ml IP buffer.  The beads were then treated with proteinase K for at least 3 h at 55 ˚C and the methylated DNA was purified by phenol-chloroform extraction followed by ethanol precipitation.

tag: tissue origin of primary cultures

value: Mouse ES cells

tag: strain

tag: antibody

source_name: Con KD ES cells, immunoprecipitated DNA by 5-hydroxymethylcytosine rabbit polyclonal antibody

tag: vendor

value: Active Motif

tag: cat#


title: DC3for9h

tag: cell type

value: 9 h


title: prdm1 mutant rep3

tag: age

value: 25 hpf

value: embryo


title: DC1for12h

tag: growth protocol


title: CBFb-SMMHCd179-221 animal 1, replicate 1

city: Bethesda

last: Pan

state: MD

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

source_name: Leukemic mice 3 weeks after birth

label_protocol: standard Affymetrix protocol

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

treatment_protocol: Cells were isolated from the spleens of leukemic mice

value: leukemic spleen cells

value: CBFb-SMMHCd179-221 chimera


title: 5' Cap isolated liver Replicate 4

description: 5' Cap isolation replicate 4 of 4

value: Normal liver

value: HCV cirrhotic liver


title: DC2for9h

tag: time


title: CBFb-SMMHC animal 2, replicate 2

source_name: Leukemic mice 2 months after ENU treatment

value: CBFb-SMMHC chimera


title: CBFb-SMMHCd179-221 animal 2, replicate 3


title: CBFb-SMMHCd179-221 animal 2, replicate 2


title: CBFb-SMMHC animal 2, replicate 3


title: CBFb-SMMHCd179-221 animal 2, replicate 1


title: DC3for6h

value: 6 h


title: CBFb-SMMHC animal 2, replicate 1


title: Con KDvsTet1 KD ES cells, DNA methylation by MeDIP-chip (2/4), exp2

description: IP/IP

data_processing: Data were extracted and analyzed using NimbleScan v2.5 (Roche/NimbleGen).  For identifying probes associated with a significant decrease in Ezh2 levels or a significant increase in DNA methylation level in Tet1 KD ES cells as compared to Con KD cells, a non-parametric one-sided Kolmogorov-Smirno (KS) test was used (KS score>1.3).

source_name: Con KD ES cells, immunoprecipitated DNA by 5-methylcytosine antibody

extract_protocol: MeDIP-chip was perfromed as previously described with minor modifications (Weber et al., 2005). Briefly, 5 ug sonicated, heat-denatured genomic DNA was immunoprecipitated with 5 ul of monoclonal antibody against 5-methylcytidine (Eurogentec) at 4 C overnight.  Immunoprecipitated methylated DNA was collected with 30 ul Dynal protein-G beads for 2 h at 4 C.  ChIP-chip assay was performed with about 10 million cells following Agilent mammalian ChIP-on-chip protocol (March, 2006). Briefly, cells were cross-linked with formaldehyde for 10 min at room temperature. Sonicated chromatin was immunoprecipitated overnight at 4 C with 10 ug immobilized (on 100 ul Dynal protein-G beads, Invitrogen) antibodies to Ezh2 (Active Motif, 39103).

tag: knockdown

value: 5-methylcytosine antibody

tag: antibody manufacturer

value: Eurogentec

tag: antibody catalog #

source_name: Tet1 KD ES cells, immunoprecipitated DNA by 5-methylcytosine antibody


title: DC2for6h

source_name: human whole blood from healthy blood donors

value: human dendritic cells

value: control


title: Ppu_Soil_3CBplus_Rep3

tag: genotype

value: contains an introduced plasmid, pSL1

tag: phenotype

value: degrades 3CB completely

tag: treatment

value: 3-chlorobenzoic acid (3CB)


title: Con KDvsTet1 KD ES cells, Ezh2 ChIP-chip (2/4)

description: IP/IP

source_name: Tet1 KD ES cells, immunoprecipitated DNA by Ezh2 antibodies

value: Mouse ES cells

value: Ezh2 antibody

value: Active Motif

tag: antibody catalog number

value: 39103 (already discontinued by the vendor)

source_name: Con KD ES cells, immunoprecipitated DNA by Ezh2 antibodies


title: Tet1 KD ES cells, 5-hydroxymethylcytosine  by hMeDIP-chip, Rb Ab  (2/4)

source_name: Tet1 KD ES cells, whole cell extract

source_name: Tet1 KD ES cells, immunoprecipitated DNA by 5-hydroxymethylcytosine rabbit polyclonal antibody


title: DC3for3h

value: 3 h


title: DC1for6h


title: DC2for3h


title: DC1for3h


title: TesticularTissue_30mg.kg.day_rat7

city: Sophia Antipolis

first: Sophie

last: Ludwig

address: 355 Rue Dostoievski BP 153

department: Toxicology Research

country: France

institute: Bayer Cropscience

description: Gene expression in testes of rat treated 28 days with 30 mg/kg/day flutamide

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >15.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55µL of 2x GEx Hybridization Buffer HI-RPM was then added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Oligo Microarrays (G4131F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) , 1 minute with 37°C GE Wash buffer 2 (Agilent), 10 seconds with acetonitrile and 30 seconds with Stabilization and Drying Solution, then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 µm, Dye channel is set to Green and Green PMT is set to 100% (high) and 10% (low)).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.5.1.1  (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014879_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.
Ratio (treated/control) calculations and extraction of differentially expressed genes (probes) were then performed using GeneSpring software version 10.0 (Agilent Technologies). For normalization per array, the 75th percentile of the signal values taken from each microarray was used as the normalizing reference. Per gene normalization was based on calculating fold expression levels relative to the median of the control animals.

organism: Rattus norvegicus

source_name: Testicular tissue, 30 mg/kg/day flutamide, rat 7

label_protocol: Labeled cRNA targets were prepared using a Low RNA Input Linear Amplification Kit according to the “One-Color Microarray-Based Gene Expression Analysis” protocol provided by the manufacturer (Agilent Technologies). The resulting labeled cRNAs were purified using RNeasy Mini Kit to remove unlabeled products and quantified by absorbance at 260nm. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from individual control and treated testicular samples using RNeasy Mini kits (Qiagen, CA) in accordance with the manufacturer’s instructions.

treatment_protocol: Flutamide was administered to rats at a daily dose of 0, 0.2, 1, 6 and 30 mg/kg body weight, for 28 consecutive days. At necropsy, testes were excised from each rat, trimmed free of fat and connective tissue. Left testis was then decapsulated, and flash-frozen in liquid nitrogen prior storing at -80°C until transcriptomic analyses.

tag: gender

value: male

tag: tissue

value: testicular tissue

tag: dose flutamide

value: 30 mg/kg/day


title: TesticularTissue_30mg.kg.day_rat4

source_name: Testicular tissue, 30 mg/kg/day flutamide, rat 4


title: CBFb-SMMHC animal 1, replicate 1

value: leukemic spleen cells

value: CBFb-SMMHC chimera


title: TesticularTissue_30mg.kg.day_rat2

source_name: Testicular tissue, 30 mg/kg/day flutamide, rat 2


title: Cholic acid 2nd, Chol-Cy3 Py-Cy5

tag: strain

tag: condition

value: grown on cholic acid

tag: sample type

value: experiment

value: grown on pyruvate


title: TesticularTissue_30mg.kg.day_rat6

source_name: Testicular tissue, 30 mg/kg/day flutamide, rat 6


title: TesticularTissue_30mg.kg.day_rat5

source_name: Testicular tissue, 30 mg/kg/day flutamide, rat 5


title: Cholic acid 3rd, Chol-Cy5 Py-Cy3

source_name: R. jostii RHA1, cholic acid

source_name: R. jostii RHA1, pyruvate

value: control


title: TesticularTissue_30mg.kg.day_rat9

source_name: Testicular tissue, 30 mg/kg/day flutamide, rat 9


title: Con KDvsTet1 KD ES cells, DNA methylation by MeDIP-chip (2/4), exp1

description: IP/IP

tag: cell type

tag: antibody

value: 5-methylcytosine antibody

value: Eurogentec

value: immunoprecipitated DNA by 5-methylcytosine antibody


title: TesticularTissue_6mg.kg.day_rat8

description: Gene expression in testes of rat treated 28 days with 6 mg/kg/day flutamide

source_name: Testicular tissue, 6 mg/kg/day flutamide, rat 8

value: 6 mg/kg/day


title: TesticularTissue_30mg.kg.day_rat3

source_name: Testicular tissue, 30 mg/kg/day flutamide, rat 3


title: TesticularTissue_6mg.kg.day_rat9

source_name: Testicular tissue, 6 mg/kg/day flutamide, rat 9


title: TesticularTissue_30mg.kg.day_rat1

source_name: Testicular tissue, 30 mg/kg/day flutamide, rat 1


title: TesticularTissue_30mg.kg.day_rat8

source_name: Testicular tissue, 30 mg/kg/day flutamide, rat 8


title: DC1for9h

source_name: human whole blood from healthy blood donors

value: human dendritic cells

tag: growth protocol

value: 9 h


title: Con KD ES cells, DNA methylation by MeDIP-chip  (2/4)

description: IP/input

source_name: Con KD ES cells, whole cell extract

value: Mouse ES cells

value: input DNA

source_name: Con KD ES cells, immunoprecipitated DNA by 5-methylcytosine antibody


title: TesticularTissue_6mg.kg.day_rat6

source_name: Testicular tissue, 6 mg/kg/day flutamide, rat 6

value: male


title: OSU12-hisC, nurishment, biological rep 2

first: Bei-Wen

last: Ying

address: 1-1-1 Tennoudai

institute: University of Tsukuba

description:
20 h after histidine addition in minimal　medium
only two of the 3 custom tiling arrays (EcFS_1 and EcFS_2) were used in this study

hyb_protocol: Following fragmentation, 3 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing:
Microarray data were processed using custom scripts written in R based on the finite hybridisation (FH) model (Ono et al (2008) An improved physico-chemical model of hybridization on high-density oligonucleotide microarrays. Bioinformatics 24: 1278-1285.) and the thermodynamic model of non-specific binding (NSB) on short nucleotide microarrays (Furusawa et al, 2009).
log10 mRNA concentration (pM) data are provided as a supplementary file on the SERIES record.

organism: Escherichia coli

source_name: HisC rewired strain exponentially grown in the presence of histidine (1 mM)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Cells were transferred to the fresh minimal media, mM63, in the presence or absence of histidine. The initial cell concentrations were controlled as 104-105 cells/mL, and the final ones ~ 108 cells/mL within the exponential growth phase.

extract_protocol: Total RNAs were extracted using an RNeasy mini kit (Qiagen) in accordance with the manufacturer’s instructions.

treatment_protocol: The cell culture was put into cold phenol-ethanol solution (1 g of phenol in 10 mL of ethanol) prepared in advance. The cells were collected by centrifugation at 16,000 × g for 5 min at 4°C, and the pelleted cells were stored at –80°C prior to use.

value: DH1 ΔhisC::cat ΔintC::Ptrc-rfp-tetR-zeocinr ΔgalK::PtetA-gfp-hisC-kanr

tag: platform_id design


title: Tet1 KD ES cells, DNA methylation by MeDIP-chip  (2/4)

description: IP/input

source_name: Tet1 KD ES cells, whole cell extract

tag: knockdown

source_name: Tet1 KD ES cells, immunoprecipitated DNA by 5-methylcytosine antibody


title: TesticularTissue_6mg.kg.day_rat7

source_name: Testicular tissue, 6 mg/kg/day flutamide, rat 7

value: testicular tissue


title: OSU12-hisC, nurishment, biological rep 1


title: OSU12-hisC, starved, biological rep 2

description:
24 h after histidine depletion in minimal medium
only two of the 3 custom tiling arrays (EcFS_1 and EcFS_2) were used in this study

source_name: HisC rewired strain exponentially grown in the absence of histidine


title: TesticularTissue_6mg.kg.day_rat3

source_name: Testicular tissue, 6 mg/kg/day flutamide, rat 3


title: OSU12-hisC, starved, biological rep 1


title: TesticularTissue_6mg.kg.day_rat5

source_name: Testicular tissue, 6 mg/kg/day flutamide, rat 5


title: TesticularTissue_6mg.kg.day_rat2

source_name: Testicular tissue, 6 mg/kg/day flutamide, rat 2


title: TesticularTissue_1mg.kg.day_rat7

description: Gene expression in testes of rat treated 28 days with 1 mg/kg/day flutamide

source_name: Testicular tissue, 1 mg/kg/day flutamide, rat 7

value: 1 mg/kg/day


title: TesticularTissue_1mg.kg.day_rat5

source_name: Testicular tissue, 1 mg/kg/day flutamide, rat 5


title: TesticularTissue_1mg.kg.day_rat4

source_name: Testicular tissue, 1 mg/kg/day flutamide, rat 4


title: TesticularTissue_6mg.kg.day_rat1

source_name: Testicular tissue, 6 mg/kg/day flutamide, rat 1


title: TesticularTissue_1mg.kg.day_rat6

source_name: Testicular tissue, 1 mg/kg/day flutamide, rat 6


title: TesticularTissue_1mg.kg.day_rat1

source_name: Testicular tissue, 1 mg/kg/day flutamide, rat 1


title: TesticularTissue_0.2mg.kg.day_rat6

description: Gene expression in testes of rat treated 28 days with 0.2 mg/kg/day flutamide

source_name: Testicular tissue, 0.2 mg/kg/day flutamide, rat 6

value: 0.2 mg/kg/day


title: OSU11, nurishment, biological rep 3

source_name: Control strain exponentially grown in the presence of histidine (1 mM)

value: DH1 ΔhisC::cat ΔintC::Ptrc-rfp-tetR-zeocinr ΔgalK::PtetA-gfp-kanr


title: OSU12-hisC, starved, biological rep 3


title: TesticularTissue_1mg.kg.day_rat3

source_name: Testicular tissue, 1 mg/kg/day flutamide, rat 3


title: TesticularTissue_0.2mg.kg.day_rat8

source_name: Testicular tissue, 0.2 mg/kg/day flutamide, rat 8


title: TesticularTissue_0.2mg.kg.day_rat7

source_name: Testicular tissue, 0.2 mg/kg/day flutamide, rat 7


title: TesticularTissue_0.2mg.kg.day_rat5

source_name: Testicular tissue, 0.2 mg/kg/day flutamide, rat 5


title: OSU11, nurishment, biological rep 2


title: N5_normal_rep1

city: Guangzhou

first: Yifeng

last: Luo

state: Guangdong

address: 58 Zhongshan 2nd Road

department: Institute of Respiratory Diseases of Sun Yat-sen University

country: China

institute: The First Affiliated Hospital of Sun Yat-sen University

description: Gene expression of prostate benign tissue

hyb_protocol: Following the Agilent products processing protocol.

data_processing: Raw data are imported using the GeneSpring GX 11 software, then normalized under the setting of percentile shift normalization algorithm.

source_name: benign prostatic hyperplasia tissue

extract_protocol: Total RNA was prepared using the mirVana RNA Isolation Kit (Applied Biosystem) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Tissue are fast protected by Liquid nitrogen and then kept in -80℃. Frozen tissue are confirmed by HE staining.

value: prostate

tag: age

tag: psa

tag: gleason

value: no data


title: TesticularTissue_1mg.kg.day_rat2

source_name: Testicular tissue, 1 mg/kg/day flutamide, rat 2


title: N4_normal_rep1

scan_protocol: Following the Agilent products processing protocol.

source_name: benign prostate tissue of prostate cancer


title: TesticularTissue_0.2mg.kg.day_rat4

source_name: Testicular tissue, 0.2 mg/kg/day flutamide, rat 4


title: TesticularTissue_6mg.kg.day_rat4

source_name: Testicular tissue, 6 mg/kg/day flutamide, rat 4


title: N2_normal_rep1

label_protocol: Following the Agilent products processing protocol.


title: TesticularTissue_0.2mg.kg.day_rat3

source_name: Testicular tissue, 0.2 mg/kg/day flutamide, rat 3


title: N1_normal_rep1


title: TesticularTissue_0mg.kg.day_rat9

description: Gene expression in testes of control rat treated 28 days with vehicle

source_name: Testicular tissue, 0 mg/kg/day flutamide, rat 9

value: 0 mg/kg/day


title: TesticularTissue_0.2mg.kg.day_rat2

source_name: Testicular tissue, 0.2 mg/kg/day flutamide, rat 2


title: TesticularTissue_0mg.kg.day_rat8

source_name: Testicular tissue, 0 mg/kg/day flutamide, rat 8


title: OSU11, starved, biological rep 3

source_name: Control strain exponentially grown in the absence of histidine

tag: genotype


title: OSU11, starved, biological rep 2


title: OSU11, nurishment, biological rep 1


title: TesticularTissue_0.2mg.kg.day_rat1

source_name: Testicular tissue, 0.2 mg/kg/day flutamide, rat 1


title: OSU11, starved, biological rep 1


title: C2_cancer_rep1

description: Gene expression of prostate cancer

source_name: prostate cancer tissue


title: C4_cancer_rep1

description: Gene expression of prostate cancer


title: TesticularTissue_0mg.kg.day_rat7

source_name: Testicular tissue, 0 mg/kg/day flutamide, rat 7


title: TesticularTissue_0mg.kg.day_rat4

source_name: Testicular tissue, 0 mg/kg/day flutamide, rat 4


title: C1_cancer_rep1

description: Gene expression of prostate cancer


title: TesticularTissue_0mg.kg.day_rat3

source_name: Testicular tissue, 0 mg/kg/day flutamide, rat 3


title: C5_cancer_rep1

description: Gene expression of prostate cancer


title: TesticularTissue_0mg.kg.day_rat5

source_name: Testicular tissue, 0 mg/kg/day flutamide, rat 5


title: TesticularTissue_0mg.kg.day_rat2

source_name: Testicular tissue, 0 mg/kg/day flutamide, rat 2


title: OSU12-hisC, nurishment, biological rep 3

source_name: HisC rewired strain exponentially grown in the presence of histidine (1 mM)


title: s_48h_A_mR

status: Public on Mar 28 2011

city: Berlin

first: Nathanael

last: Raschzok

address: Augustenburger Platz 1

department: Department of Surgery; Campus Charite Mitte / Campus Virchow Klinikum

institute: Charité - Universitätsmedizin Berlin

hyb_protocol: Hybridisation was performed by the febit GmbH. The elongation was done with Klenow Fragment and biotinylated nucleotides at 37° C for 15 minutes. Finally, the Biochip was washed automatically.

scan_protocol: Scan was performed by the febit GmbH using a Geniom Realtime Analyzer (GRTA, febit, Heidelberg, Germany). For maximum sensitivity, febit used biotin and its detection with streptavidin-phycoerythrin (SAPE), in combination with febit’s consecutive Signal Enhancement (CSE) procedure. For a more detailed description please read febit protocol 010. The feature recognition (using Cy3 filter set) and signal calculation were done automatically within milliseconds. The Geniom Technology showed accurate detection of miRNA profiles. The data correlates well with qPCR data. There was no photo bleaching thus enabling repeated measurements and multiple detection of each Biochip.

data_processing: Data processing was performed by the febit GmbH. Intensity values were measured by a CCD camera. The raw intensity values thus corresponded to the intensity of each single feature. Background correction was performed by subtracting the array-wise background. Replica were compressed by the median of all replica. For normalization, median or mean normalization, quantile normalization and variance stabilizing normalization were performed.

label_protocol: Labeling was performed by the febit GmbH. The microfluidic-based primer extension assay was used for labelling. This assay utilizes the bound miRNAs as a primer for an enzymatic elongation with labeled nucleotides.

extract_protocol: Total RNA, including the miRNA fraction, was isolated using the miRNeasy Mini Kit (QIAGEN, Valencia, CA, USA) according to the vendors description.

treatment_protocol: 70% partial hepatectomy according to Higgins and Anderson or sham laparotomy were performed prior to tissue harvesting

value: Wistar

value: liver

tag: time point after hepatectomy


title: s_48h_B_mR


title: s_48h_C_mR


title: TesticularTissue_0mg.kg.day_rat1

source_name: Testicular tissue, 0 mg/kg/day flutamide, rat 1


title: s_12h_A_mR


title: s_12h_B_mR


title: s_24h_A_mR


title: s_24h_B_mR


title: s_24h_C_mR


title: s_12h_C_mR


title: 5d_C_mR


title: 5d_B_mR


title: 5d_A_mR


title: 48h_B_mR


title: 48h_C_mR


title: 24h_C_mR


title: 48h_A_mR


title: 24h_A_mR


title: 24h_B_mR


title: 12h_C_mR


title: 12h_B_mR


title: 12h_A_mR


title: 6h_C_mR


title: 6h_B_mR


title: 2h_C_mR


title: 2h_B_mR


title: 2h_A_mR


title: TesticularTissue_0mg.kg.day_rat6

source_name: Testicular tissue, 0 mg/kg/day flutamide, rat 6


title: 6h_A_mR


title: 0h_B_mR


title: 0h_C_mR


title: digoxin, WT, biological replicate 2

city: New York

first: Jun

last: Huh

state: NY

address: 540 1st avenue

institute: NYU medical school

description: cells cultured under Th17 condition for 48 hours

hyb_protocol: According to Affymetrix protocols

scan_protocol: According to Affymetrix protocols

data_processing: GeneSpring GX11.5, RMA, normalized to baseline to median of control (DMSO, WT) samples

source_name: Digoxin treated wildtype CD4 T cells

label_protocol: According to Affymetrix protocols

growth_protocol: Naïve CD4 T cells were FACS sorted and cultured on CD3/CD28 antibodies in RPMI based medium

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

tag: genotype/variation

value: wildtype

tag: treatment

value: Digoxin treated


title: Mela1 spheroid cells, gene expression_1

city: Paris

first: Reem

last: Al-Daccak

address: Bat Bazin - 1 Av Claude Vellefaux

institute: INSERM

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: Mela1 spheroid cells

growth_protocol: Melanoma cells were grown for 12 days either under serum-free neural crest stem culture conditions (spheroid cells) or under classical serum-containing conditions (adherent cells).

extract_protocol: Total RNA from SLM8 and Mela1 spheroid and adherent cells was extracted using Trizol then labeled with reagents from Affymetrix. Hybridization cocktails containing fragmented, end-labeled single-stranded cDNA were prepared.

treatment_protocol: not applicable

tag: melanoma

value: primary stage IV-cutaneous melanoma lesion (Mela1)

tag: melanoma cell type

value: spheroid cells


title: digoxin, KO, biological replicate 2

source_name: Digoxin treated RORγt-deficient CD4 T cells

tag: strain

value: RORγt-deficient


title: Mela1 spheroid cells, gene expression_2


title: Mela1 spheroid cells, gene expression_3


title: 0h_A_mR

tag: gender

tag: tissue


title: Mela1 adherent cells, gene expression_3

source_name: Mela1 adherent cells

value: adherent cells


title: 28987302 - H3K27me3_WT_I_INPUT vs H3K27me3_WT_I_IP

city: Lyon

first: François

last: ROUDIER

address: 46 Allée d'Italie

department: Biologie

institute: Ecole Normale Supérieure de Lyon

description: Epigenomic mapping in fie

hyb_protocol: H3K27me3_WT_I_IP Cy5 / H3K27me3_WT_I_INPUT Cy3 : 80pmol.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 700V,laser power 100%

data_processing: For the ChIP-chip data we performed a normalization step by an ANOVA model (Kerr et.al,2002) to remove technical biases.Let Yplfts be the log2 intensity of the probe s on the chip p and the array l, with treatment t and fluorochrome f.The considered model is: Yplfts=mu+ap+bl+abpl+cf+acpf+Eplfts, where ap+bl+abpl is the support effect (chip, array and interactions), cf is the fluorochrome effect, acpf  is the chip*fluorochrome interaction and the errors Eplfts are centered Gaussian variables.We estimated the parameters of the model and we removed quantified biases from the raw data.The IP and INPUT intensities for each biological replicate were then averaged on the dye-swap to remove gene-specific dye biases.To analyze data, we use ChIPmix, a method proposed by Martin-Magniette et al.(2008) that we have adapted to study several biological replicates simultaneously. The method investigates the relationship between IP and Input by a mixture model of regressions. For a probe, available observation are the two measurements IP and INPUT for the two biological replicates. These latter are assumed to be independent by definition. The (unknown) status of a probe is characterized through a label Z which is 1 if the probe is enriched and 0 if it is normal (not enriched).

label_protocol: labelling Cy3 and Cy5 indirect, amplification=yes, DNA  .

growth_protocol: seedling - 20 days on MS agar plates at 22 degrees C. Cool white light at 100 uEm-2s-1, 16 hour photoperiod.

treatment_protocol: no treatment

tag: antibody catalog #

tag: antibody manufacturer

value: Upstate-Millipore

tag: antibody lot #

value: WT

tag: genetic background

value: seedling


title: 33160402fie - H3K4me3_fie_II_IP vs H3K4me3_fie_II_INPUT

description: Epigenomic mapping in fie

hyb_protocol: H3K4me3_fie_II_INPUT Cy5 / H3K4me3_fie_II_IP Cy3 : 80pmol.

growth_protocol: seedling - 20 days on MS agar plate at 22 degrees C. Cool white light at 100 uEm-2s-1, 16 hour photoperiod.

tag: antibody

value: fie mutant


title: Mela1 adherent cells, gene expression_1


title: 28985302 - H3K4me3_WT_I_IP vs H3K4me3_WT_I_INPUT

description: Epigenomic mapping in fie

hyb_protocol: H3K4me3_WT_I_INPUT Cy5 / H3K4me3_WT_I_IP Cy3 : 80pmol.


title: 33176102WT - H3K27me3_WT_II_INPUT vs H3K27me3_WT_II_IP

description: Epigenomic mapping in fie

hyb_protocol: H3K27me3_WT_II_IP Cy5 / H3K27me3_WT_II_INPUT Cy3 : 80pmol.


title: 28989702 - H3K27me3_WT_I_IP vs H3K27me3_WT_I_INPUT

description: Epigenomic mapping in fie

hyb_protocol: H3K27me3_WT_I_INPUT Cy5 / H3K27me3_WT_I_IP Cy3 : 80pmol.


title: 33160702fie - H3K27me3_fie_II_INPUT vs H3K27me3_fie_II_IP

description: Epigenomic mapping in fie

hyb_protocol: H3K27me3_fie_II_IP Cy5 / H3K27me3_fie_II_INPUT Cy3 : 80pmol.


title: 33171902WT - H3K4me3_WT_II_IP vs H3K4me3_WT_II_INPUT

description: Epigenomic mapping in fie

hyb_protocol: H3K4me3_WT_II_INPUT Cy5 / H3K4me3_WT_II_IP Cy3 : 80pmol.


title: Mela1 adherent cells, gene expression_2

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001


title: 33171920fie - H3K4me3_fie_II_INPUT vs H3K4me3_fie_II_IP

description: Epigenomic mapping in fie

hyb_protocol: H3K4me3_fie_II_IP Cy5 / H3K4me3_fie_II_INPUT Cy3 : 80pmol.


title: 28983902 - H3K4me3_fie_I_IP vs H3K4me3_fie_I_INPUT

description: Epigenomic mapping in fie

hyb_protocol: H3K4me3_fie_I_INPUT Cy5 / H3K4me3_fie_I_IP Cy3 : 80pmol.


title: 28990902 - H3K27me3_fie_I_IP vs H3K27me3_fie_I_INPUT

description: Epigenomic mapping in fie

hyb_protocol: H3K27me3_fie_I_INPUT Cy5 / H3K27me3_fie_I_IP Cy3 : 80pmol.


title: 33160702WT - H3K27me3_WT_II_IP vs H3K27me3_WT_II_INPUT

description: Epigenomic mapping in fie

hyb_protocol: H3K27me3_WT_II_INPUT Cy5 / H3K27me3_WT_II_IP Cy3 : 80pmol.


title: 28989202 - H3K27me3_fie_I_INPUT vs H3K27me3_fie_I_IP

description: Epigenomic mapping in fie

hyb_protocol: H3K27me3_fie_I_IP Cy5 / H3K27me3_fie_I_INPUT Cy3 : 80pmol.


title: DMSO, KO, biological replicate 2

source_name: DMSO treated RORγt-deficient CD4 T cells

value: DMSO treated


title: 28990802 - H3K4me3_WT_I_INPUT vs H3K4me3_WT_I_IP

description: Epigenomic mapping in fie

hyb_protocol: H3K4me3_WT_I_IP Cy5 / H3K4me3_WT_I_INPUT Cy3 : 80pmol.


title: 28985402 - H3K4me3_fie_I_INPUT vs H3K4me3_fie_I_IP

description: Epigenomic mapping in fie

hyb_protocol: H3K4me3_fie_I_IP Cy5 / H3K4me3_fie_I_INPUT Cy3 : 80pmol.


title: 33160402WT - H3K4me3_WT_II_INPUT vs H3K4me3_WT_II_IP

description: Epigenomic mapping in fie

hyb_protocol: H3K4me3_WT_II_IP Cy5 / H3K4me3_WT_II_INPUT Cy3 : 80pmol.


title: SLM8 spheroid cells, gene expression_3

source_name: SLM8 spheroid cells

value: melanoma lymph node metastasis (SLM8)


title: 33176102fie - H3K27me3_fie_II_IP vs H3K27me3_fie_II_INPUT

description: Epigenomic mapping in fie

hyb_protocol: H3K27me3_fie_II_INPUT Cy5 / H3K27me3_fie_II_IP Cy3 : 80pmol.


title: DMSO, WT, biological replicate 2

hyb_protocol: According to Affymetrix protocols

source_name: DMSO treated wildtype CD4 T cells


title: digoxin, KO, biological replicate 1


title: SLM8 spheroid cells, gene expression_2


title: SLM8 spheroid cells, gene expression_1


title: CD8 rejecting vs naive

city: London

first: Diane

middle: Marylin

last: Scott

address: Du Cane Road

department: Immunobiology

country: United Kingdom

institute: Imperial College London

hyb_protocol: Plates were run on the 7900HT sequence detection system using 384 well block (Applied Biosystems).

scan_protocol: Standard cycling conditions were used (95ºC 10mins followed by 40 cycles of 95 ºC for 15sec and 60 ºC for 1 min).

data_processing:
Ct data was analysed using a modified version of Global Pattern Recognition™ algorithm, GPR 2.0 (http://array.lonza.com/gpr/). Where there is no difference between the Ct values of test and control cells, the genes are considered as ‘normalisers’. Each gene is compared to every normaliser in succession and the ΔCt is calculated (ΔCT Gene = CT Gene  -CT Normaliser). The ΔCts for the control and experimental groups are then compared by a two-tailed unpaired Student’s T test.
P-value: calculated using GPR 2.0 (http://array.lonza.com/gpr/): The ΔCts for the control and experimental groups were compared using a two-tailed unpaired Student’s T test, comparing at least three replicates for each experimental group.
Fold Change: Comparison of gene expression level with that of the 10 best 'normaliser' genes
Rank: numerical ranking of gene.with respect to lowest P-value

label: Sybr Green

source_name: CD8 T cells, naïve

label_protocol: Power Sybr green master mix, 1814.4μl DEPC treated water (Ambion) and 201.6μl cDNA diluted 1:10 with DEPC treated water was made and 10μl added to each well. Each plate was prepared in triplicate.

extract_protocol: RNA was extracted from pooled frozen cell pellets or pooled cells immediately after sorting, using a PicoPure kit  according to manufacturers instructions. cDNA was made from 100ng RNA using a MessageSensor RT kit with 10mM random hexamer primers (Ambion) and incubations at 43ºC for 60mins followed by 95ºC for 10mins.

treatment_protocol: Cells were sorted using FACSVantage Diva: Naïve CD4 cells: spleen and LN cells fromTCR transgenic mice were stained with anti-Vβ6 FITC, anti-CD4 PerCP, anti-CD45RB PE and anti-CD25 APC and sorted for the CD4+, Vβ6+, CD45RB+, CD25- population. Experimental CD4 T cells: Five days after adoptive transfer of CFSE-labelled TCR transgenic cells and peptide or peptide plus LPS treatment, recipient spleen and LN cells were depleted using anti-CD8 and anti-B220 Dynabeads. Cells were stained with anti Thy1.2 PE and sorted. NaIve CD8 T cells: spleen and LN cells from WT B6 female mice were stained with anti-CD44 FITC, anti-TCRβ PE, anti-CD62L APC and anti-CD8 Pacific Blue and sorted for the CD8+TCR+CD62LhighCD44low population. HY specific CD8+ T cells were sorted from pooled spleen and LN suspensions from peptide treated or untreated B6 female mice 22 days after skin grafting or 10 to 15 days after male spleen cell transfer. Cells were incubated with HYDbUty-PE tetramer and anti-CD8-APC and sorted.

tag: cell type

value: CD8 T cells, naïve

source_name: CD8 T cells,  HY tetramer positive from rejecting mice


title: CD8 tolerant vs naive

source_name: CD8 T cells,  HY tetramer positive from tolerant mice


title: DMSO, WT, biological replicate 1


title: DMSO, KO, biological replicate 1


title: SLM8 adherent cells, gene expression_3

source_name: SLM8 adherent cells


title: Peptide+LPS vs naïve expt 2

source_name: TCR transgenic CD4 T cells, naïve

value: TCR transgenic CD4 T cell:naïve

source_name: TCR transgenic CD4 T cells, from adoptive transfer peptide+LPS treated mice

value: TCR transgenic CD4 T cell: from LN and spleen peptide+LPS treated female


title: digoxin, WT, biological replicate 1


title: bcatGOF  mouse kidney E12.5, biological rep 3

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

institute: University of Toronto

description:
Hoxb7-Cre:EGFP mice ( Zhao, et al. (2004) Dev Biol 276:403-415) were crossed with mice containing loxP sites flanking exon 3 of the ß-catenin allele (ß-catdelta3/delta3) (Harada,et al. (2002) Cancer Res 62:1971-1977) to generate ß-catenin gain-of-function mutant mice specifc to the uteric bud, termed ß-catGOF-UB .Eighteen ß-catGOF-UB mutant kidneys and 9 WT kidneys were micro-dissected at E12.5. Mutant kidneys were divided into three random pools (n=3) consisting of 6 kidneys each.
Expression data for mouse ß-catGOF-UB mutant kidneys embryonic day E12.5

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse MOE430v2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: mutant mouse embryonic kidney day 12.5

label_protocol: one cycle amplification as per Affymetrix protocol from 1ug of total RNA

extract_protocol: Samples were stored in RNAlater RNA stabilization reagent (Qiagen, Canada) and then isolated using the RNeasy Micro kit (Qiagen, Canada).

treatment_protocol: tissue was disected, imaged by digital microscopy and randomly sorted into one of three sample vials

value: ß-catenin gain-of-function mutant (ß-catGOF-UB)

value: kidney (uteric bud)

tag: developmental stage

value: embryo

tag: age

value: 12.5 days


title: Peptide+LPS vs naïve expt 1


title: Peptide vs naïve expt 2

source_name: TCR transgenic CD4 T cells, from adoptive transfer peptide treated mice

value: TCR transgenic CD4 T cell: from LN and spleen peptide treated female


title: 33162502WT - H3K4me3_WT_II_INPUT vs H3K4me3_WT_II_IP

description: Epigenomic mapping in fie

tag: genotype


title: Peptide vs naïve expt 1


title: SLM8 adherent cells, gene expression_1


title: 33162502fie - H3K4me3_fie_II_IP vs H3K4me3_fie_II_INPUT

description: Epigenomic mapping in fie

hyb_protocol: H3K4me3_fie_II_INPUT Cy5 / H3K4me3_fie_II_IP Cy3 : 80pmol.


title: Peptide+LPS vs naïve expt 3


title: SLM8 adherent cells, gene expression_2


title: DNA

status: Public on Mar 27 2011

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

hyb_protocol: Samples were hybridised at the NASC Microarray Core Facility according to manufacturer's instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) using an Affymetrix 3000 7G scanner.

data_processing: The RNA data was analysed using the Genspring GX 11 Software (Agilent technologies) using the RMA probe summarisation algorithm, using a CDF file produced from the Aloe gDNA hybridisation result with a hybridisation threshold of 250. Each gene signal was then normalised to the median of the gene signal across all samples.

organism: Aloe vera

source_name: Leaf

label_protocol: 500ng of genomic DNA was labelled using the Invitrogen DNA labelling kit as per manufactures' instructions

growth_protocol: A mature Aloe plant obtained from a local garden centre, was grown in the laboratory at room temperature.

extract_protocol: Genomic DNA was extracted using the Qiagen DNeasy plant mini kit according to the manufactures' instructions.

value: Leaf


title: MCF7.siC.ZNF 3

city: Cambridge

first: Suraj

last: Menon

address: Li Ka Shing Center, Robinson Way

institute: Cambridge Research Institute, Cancer Research UK

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were log base 2 quantile normalised the beadarray package in R

source_name: MCF-7 human cell lines

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

growth_protocol: The ER-positive breast cancer cell line MCF-7 (from ATCC) was cultured in DMEM supplemented with 10% v/v Fetal Bovine Serum and penicillin/streptomycin (all from Gibco, Invitrogen) according to manufacturer’s recommendations.

extract_protocol: Total RNA was extracted using miRNeasy (Qiagen) following manufacturer’s recommendations, its yield and purity monitored by spectroscopy at 260, 280 and 230 nm using the NanoDrop (Thermo Scientific) and its integrity prior to microarrays analysis verified by a Bioanalyzer trace (Agilent).

treatment_protocol: An 1804 bp fragment of the ZNF703 mRNA spanning the entire open reading frame and native stop codon was amplified from HCC-1500 cDNA using ZNF-for-Not1 and ZNF-rev-Not1 primers (see table below). The NotI-digested fragment was cloned into the NotI site of HIV-ZsGreen [#Welm, CellStemCell 2008] and the construct verified by sequencing. The parental vector was used as a negative control. Cleared virus-containing supernatants from transfected HEK-293T cells were obtained as described in (Welm et al., 2008) and used directly without further concentration or titration. Sub-confluent MCF-7 cultures were infected twice on consecutive days in the presence of 1 μg/ml polybrene (Sigma). Infected cells were sorted by GFP expression using FACS Aria SORP (BD Biosciences) to eliminate non-infected cells.For knock-down experiments, sub-confluent cultures were transfected with either a siZNF pool (100 nM each siRNA1: GCUUGACCCUGCCGGGAUU & siRNA2: CUUACAAGCUGGGAAUAUA; Thermo Scientific Dharmacon RNAi Technologies) or a negative control non-targeting siRNA (100 nM, #1027281, Qiagen) in OptiMEM (Gibco, Invitrogen) using Lipofectamine 2000 (Invitrogen) according to manufacturer’s instructions. The transfection medium was replaced by culture medium after 6 hours, and after 48 hours protein, total RNA and chromatin were extracted from replicate samples.

tag: sirna

value: siC

tag: overexpression

value: ZNF


title: MCF7.siC.hiv 3

value: hiv


title: bcatGOF  mouse kidney E12.5, biological rep 1


title: bcatGOF  mouse kidney E12.5, biological rep 2


title: MCF7.siZNF.hiv 3

value: siZNF


title: MCF7.siZNF.ZNF 3


title: MCF7.siC.ZNF 2


title: 28905202 - H3K4me3_WT_I_IP vs H3K4me3_WT_I_INPUT

description: Epigenomic mapping in fie

hyb_protocol: H3K4me3_WT_I_INPUT Cy5 / H3K4me3_WT_I_IP Cy3 : 80pmol.

value: WT

value: seedling

value: Upstate-Millipore


title: 28904802 - H3K4me3_fie_I_IP vs H3K4me3_fie_I_INPUT

description: Epigenomic mapping in fie

value: fie mutant


title: Root rep2

institute: Nottingham Arabidopsis Stock Centre (NASC)

source_name: Root

label_protocol: 250ng of total RNA was labelled using the Affymetrix 3' IVT express kit as per manufactures' instructions

extract_protocol: Total RNA was extracted using the Qiagen Rneasy plant mini kit according to the manufactures' instructions.

value: Root


title: Root rep3


title: MCF7.siZNF.hiv 1


title: MCF7.siZNF.hiv 2


title: 33160802WT - H3K27me3_WT_II_IP vs H3K27me3_WT_II_INPUT

description: Epigenomic mapping in fie


title: 33151102WT - H3K27me3_WT_II_INPUT vs H3K27me3_WT_II_IP

description: Epigenomic mapping in fie

hyb_protocol: H3K27me3_WT_II_IP Cy5 / H3K27me3_WT_II_INPUT Cy3 : 80pmol.


title: MCF7.siC.hiv 2


title: 28905302 - H3K4me3_WT_I_INPUT vs H3K4me3_WT_I_IP

description: Epigenomic mapping in fie


title: MCF7.siZNF.ZNF 2


title: MCF7.siZNF.ZNF 1


title: 33323802WT - H3K4me3_WT_II_IP vs H3K4me3_WT_II_INPUT

description: Epigenomic mapping in fie

hyb_protocol: H3K4me3_WT_II_INPUT Cy5 / H3K4me3_WT_II_IP Cy3 : 80pmol.


title: MCF7.siC.hiv 1


title: Leaf rep2


title: MCF7.siC.ZNF 1


title: Leaf rep3


title: Cdc45ChIP_hsk1ts_30min

status: Public on Mar 26 2011

city: Tokyo

first: Yutaka

last: Kanoh

address: 2-1-6 Kamikitazawa, Setagaya-ku

department: Genome Medicine

institute: Tokyo Metropolitan Institute of Medical Science

hyb_protocol: 6µg of DNA was hybridized to Affymetrix S. pombe Tiling 1.0FR Array using Affymetrix recommend component. The arrays were hybridized for 16 hours at 42ºC at 60 rpm using an Affymetrix hybridization oven.

scan_protocol: Standard protocol by Affymetrix

data_processing:
As previously described in Methods in Enzymology, Elsevier Life Sciences (CA), vol.409,chapter 23,389-410 in “DNA Repair” (edited by J.Campbell 2006)
All Samples (ch1) were compared to the same input DNA control CEL file linked to the Series record.

organism: Schizosaccharomyces pombe

source_name: Flag ChIPed from the strain expressing 3Flag-fused Cdc45 and hsk1-89

label_protocol: About 10µg amplified DNA was fragmented to 50bp with DNase I, and the ends of the fragments were labeled with biotin-6N-ddATP by terminal transferase.

extract_protocol:
The cells (1.0 x 10E9 cells) which were synchronized at appropriate cell cycle were cross-linked with 1% formaldehyde for 15 minutes and were homogenized by Multi-beads Shocker (Yasui-kikai Co., Osaka). DNA was sheared to 600 bp by sonication. Immunoprecipitation was performed by using monoclonal anti-FLAG M2 antibody (SIGMA). After incubation of lysate with antibody and protein G beads (Dynal) for 4 h, beads were washed 6 times with the lysis buffer. Co-immunoprecipitated DNA was reverse-crosslinked and purified by QIAquick PCR Purification Kit (QIAGEN).
The purified Input, BrdUIP and ChIPed DNA were amplified by IVT as described previously (Liu, C. et al., 2003, BMC Genomics).

tag: cell cycle

value: Early S-phase in HU at 60min after release from metaphase arrst

tag: chip target

value: Cdc45 and hsk1-89

value: FLAG M2 mouse monoclonal (Sigma, Cat No:F-1804)

source_name: Input DNA from Metaphase arrested cells

extract_protocol:
The genomic DNA was extracted and purified from the arrested at M-phase in nda-KM311 cells. The genomic DNA was sheared by sonication.
The purified Input, BrdUIP and ChIPed DNA were amplified by IVT as described previously (Liu, C. et al., 2003, BMC Genomics).


title: Mrc1ChIP_hsk1ts_30min

source_name: Flag ChIPed from the strain expressing 5Flag-fused Mrc1 and hsk1-89

value: Mrc1 and hsk1-89


title: Mrc1ChIP_hsk1ts_30min_2


title: 33323802fie - H3K4me3_fie_II_INPUT vs H3K4me3_fie_II_IP

description: Epigenomic mapping in fie

hyb_protocol: H3K4me3_fie_II_IP Cy5 / H3K4me3_fie_II_INPUT Cy3 : 80pmol.


title: Leaf rep1


title: uninfected control, biological replicate 3

city: Davis

first: Michael

last: George

state: CA

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

description: Gene expression data from jejunal tissue

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 400.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000

data_processing: The data were analyzed with dChip

source_name: jejunal tissue collected by upper endoscopy

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

extract_protocol: Qiagen Rneasy kit was used to extract total RNA

treatment_protocol: treatment with highly active antiretroviral therapy was removed

value: jejunum

tag: disease state

value: HIV-


title: uninfected control, biological replicate 2


title: Mrc1ChIP_Wild_20min

source_name: Flag ChIPed from the strain expressing 5Flag-fused Mrc1


title: Mcm4ChIP_hsk1ts_240minHU

source_name: Flag ChIPed from the strain expressing 3Flag-fused Mcm4 and hsk1-89

value: Mcm4 and hsk1-89


title: HIV infected patient, biological replicate 1

value: HIV+


title: KO-HsfA1d/A1e, biological rep1

city: Tottori

first: Yukinori

last: Yabuta

address: 4-101 Koyama-Minami

institute: Tottori University

description: Gene expression data from Arabidopsis

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Expression ConsoleTM Version 1.1 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Arabisopsis double knockout mutant (KO-HsfA1d/A1e) rosette leaves harvested 2-week-old plants after HL treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3'IVT Express User Manual, Affymetrix).

growth_protocol: The wild-type plants and KO-HsfA1d/A1e mutants were grown (16 h light, 25°C/8 h dark, 22°C) on MS medium under a light intensity of 100 µE m-2 sec-1.

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

treatment_protocol: Two-week-old seedlings were subjected to light intensity stress (400 µE m-2 sec-1, 25°C) for 30 min.

value: rosette leaves

tag: strain

value: Columbia


title: Cdc45ChIP_Wild_30min

source_name: Flag ChIPed from the strain expressing 3Flag-fused Cdc45


title: Root rep1


title: 28744302 - H3K27me3_WT_I_IP vs H3K27me3_WT_I_INPUT

description: Epigenomic mapping in fie

hyb_protocol: H3K27me3_WT_I_INPUT Cy5 / H3K27me3_WT_I_IP Cy3 : 80pmol.


title: uninfected control, biological replicate 1


title: 28744402 - H3K27me3_fie_I_IP vs H3K27me3_fie_I_INPUT

description: Epigenomic mapping in fie

hyb_protocol: H3K27me3_fie_I_INPUT Cy5 / H3K27me3_fie_I_IP Cy3 : 80pmol.


title: wild-type, biological rep1

description: Gene expression data from Arabidopsis

source_name: Arabisopsis rosette leaves harvested 2-week-old plants after HL treatment

value: wild type


title: 28752502 - H3K27me3_WT_I_INPUT vs H3K27me3_WT_I_IP

description: Epigenomic mapping in fie

hyb_protocol: H3K27me3_WT_I_IP Cy5 / H3K27me3_WT_I_INPUT Cy3 : 80pmol.


title: CCRF-CEM 700uM prednisolone vs. control 4h treatment Experiment 3 Robust Loess

city: Athens

first: George

middle: I

last: Lambrou

state: Attiki

address: Thivon & Levadeias

department: First Department of Pediatrics

country: Greece

institute: National and Kapodistrian University of Athens

description:
This experiment has been performed in triplicates: This is the third experiment. In particular, it is the following pair: 0uM prednisolone (designated as ‘0’) vs. 700 uM prednisolone at 4 h (designated as ‘3’) and the experiment is designated as '0vs3_4h_Exp3'.
Samples are co-hybridized on the microarray chip. The ratio is obtained as treatment (Cy5) over reference (Cy3).

hyb_protocol: Hybridization was performed with the CyScribe Post-Labeling kit (RPN5660, GE Healthcare, former Amersham Inc.) as described by the manufacturer. The fluorescent dyes used were Cy3 and Cy5. cDNAs were purified with PCR product clean-up kit (# 28104, QIAGEN Inc.). Slides were activated at 55o C for 30 min in 1% BSA. Samples were applied on the slides, and let to hybridize overnight at 55o C. The following day, slides were washed in 200 ml 0.1× SSC and 0,1% SDS for 3× 5 min, in 200 ml 0.1× SSC for 2× 5 min  and in 200 ml ddH2O for 30 sec. Slides were dried by centrifugation at 1500 rpm for 3 min and scanned with a microarray scanner.

scan_protocol: Slides were scanned with a microarray scanner (ScanArray 4000XL) (Perkin Elmer Inc. MA, former GSI Lumonics, USA). Images were generated with ScanArray microarray acquisition software (GSI Lumonics, USA). Image analysis and raw data acquisition were performed with the ImaGene® software from BioDiscovery (California, USA).

data_processing:
Microarray Data preprocessing and Background Correction:
The well performing multiplicative background correction (MBC) approach, as proposed by (Zhang, Zhang et al. 2006), was followed. MBC, which represents a combination of simplicity and efficient performance as regards background correction, assumes that the background noise affects the spot intensities in a multiplicative manner. Thus, instead of subtracting the background intensities from the foreground intensities, MBC subtracts the logarithmic estimates of the background intensities from the logarithmic foreground.
In order to reduce the complexity of the data set, we followed the replicate averaging approach proposed by (Quackenbush 2002), where the replicates were averaged by taking their geometric mean.
Microarray Data Normalization:
The background corrected signal intensities were further normalized in order to mitigate the effect of extraneous, non-biological variation in the measured gene expression levels. The normalization approach followed was the robust version of the intensity-dependent scatter-plot smoother Loess (Cleveland 1979; Cleveland 1981; Yang, Chen et al. 2002) with a quadratic polynomial model, and a smoothing parameter equal to 10%, which was considered appropriate for the relatively small number of probes attached in the microarrays. In order to compare our method we have performed normalization with the rank invariant algorithm which did not perform as well as the Loess did.

source_name: CCRF-CEM cells with no treatment at 4h

growth_protocol: The T-Lymphoblastic Leukemia CCRF-CEM were grown in RPMI-1640 medium supplemented with 2mM L-Glutamine and Streptomycin/Penicillin 100 U/ml (Gibco), 15% FBS (Gibco) at 37 oC, 5% CO2 and ~100% humidity. Cells were allowed to grow to ~900-1.500×10^3 cells/ul for CCRF-CEM. Concentrations of prednisolone (Pharmacia) used were: 0μM (control), 10nM, 22μM, 700μM.

extract_protocol: RNA was isolated with Trizol (Invitrogen Inc.) according to the manufacturer’s instructions. RNA was further processed with RQ1 DNase (Promega Inc. Madison, WI, USA) as described by the manufacturer and then it was cleaned-up with the RNEasy Mini kit (#74104, QIAGEN Inc.). The amount of RNA isolated was measured with a NanoDrop 2000 (Thermo Scientific Inc.) spectrophotometer and RNA integrity was estimated by 2% agarose gel electrophoresis. Samples with a 1.8 to 2.0 A260/A280 ratio were selected. In addition, those that empirically showed a twice as bright 28S band than the 18S band on the gel were utilized. At least 40 μg of RNA from each sample was used.

tag: agent

value: no treatment

tag: time point

tag: cell line

value: The CCRF-CEM (ALL) cell line was used as the model

tag: cell line provider

tag: cell line description

value: a CD4+ (Miranda, Wolf et al. 1996) and CD34+ presenting cell line (Naujokat, Sezer et al. 2000)

tag: origin

value: was initially obtained from peripheral blood

value: 2 year old

tag: ethnicity

value: Caucasian

tag: gender

value: female

tag: diagnosis

value: It was diagnosed as lymphosarcoma which progressed later on to acute leukemia (Foley, Lazarus et al. 1965)

tag: treatment

value: The child has undergone irradiation therapy and chemotherapy prior to obtaining the cell line. Although remission was achieved at various stages, the disease progressed rapidly (Foley, Lazarus et al. 1965).

tag: cell line characteristics

value: The cell line has been observed to undergone minor changes after long-term culture, except for the presence of dense granules in the nucleoli (Uzman, Foley et al. 1966). Finally, the CCRF-CEM cell line has been reported to manifest autocrine catalase activity which participates to its mechanisms of growth and progression (Sandstrom and Buttke 1993).

source_name: CCRF-CEM cells treated with 700uM Prednisolone at 4h

treatment_protocol: 700uM Prednisolone

value: 700uM Prednisolone

value: the European Collection of Cell Cultures (ECACC).


title: 33151102fie - H3K27me3_fie_II_IP vs H3K27me3_fie_II_INPUT

description: Epigenomic mapping in fie

hyb_protocol: H3K27me3_fie_II_INPUT Cy5 / H3K27me3_fie_II_IP Cy3 : 80pmol.

tag: antibody

tag: antibody catalog #

tag: antibody manufacturer

tag: antibody lot #

tag: genotype

value: fie mutant

tag: genetic background

tag: tissue

value: seedling

value: Upstate-Millipore


title: Mcm4ChIP_Wild_60minHU

source_name: Flag ChIPed from the strain expressing 3Flag-fused Mcm4

tag: cell cycle

value: Early S-phase in HU at 60min after release from metaphase arrst

tag: chip target

value: FLAG M2 mouse monoclonal (Sigma, Cat No:F-1804)


title: 33160802fie - H3K27me3_fie_II_INPUT vs H3K27me3_fie_II_IP

description: Epigenomic mapping in fie

hyb_protocol: H3K27me3_fie_II_IP Cy5 / H3K27me3_fie_II_INPUT Cy3 : 80pmol.


title: HIV infected patient, biological replicate 3

value: jejunum

tag: disease state

value: HIV+


title: 28905002 - H3K4me3_fie_I_INPUT vs H3K4me3_fie_I_IP

description: Epigenomic mapping in fie

hyb_protocol: H3K4me3_fie_I_IP Cy5 / H3K4me3_fie_I_INPUT Cy3 : 80pmol.


title: 28772402 - H3K27me3_fie_I_INPUT vs H3K27me3_fie_I_IP

description: Epigenomic mapping in fie

hyb_protocol: H3K27me3_fie_I_IP Cy5 / H3K27me3_fie_I_INPUT Cy3 : 80pmol.


title: AFI016

city: BKK

first: Thanavadee

last: Prachason

address: Division of Molecular Genetics, 10th floor Adulyadejvikrom Bld., Siriraj Hospital, Bangkoknoi

country: Thailand

institute: Mahidol University

data_processing: Using GeneSpring GX9 software, quantile normalization was applied to raw signal intensities (non-normalized data) exported from BeadStudio software; then baseline transformation to median of normal control samples was performed.

source_name: Malaria

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality of RNA was evaluated by gel electrophoresis.

tag: cell type

value: PBMCs

tag: disease group

value: Malaria

tag: age (years)

value: Male

tag: fever day


title: BrdUIP_Wild_60minHU

source_name: BrdU IPed from BrdU-incorporated DNA

extract_protocol:
Growing nda3-KM311 cells (1.0 x 10E9 cells) expressing Thymidine Kinase under control by Adh1 promoter  were arrested at metaphase and release in the presence of 200µM BrdU and 25mM HU. BrdU was incorporated into nascent DNA during the sub-sequential S-phase. The genomic DNA was extracted and purified by Qiagen Genomic DNA Buffer Set and Genomic-tip. BrdU-incorporated DNA after shearing and denature was immuno-precipitated by anti-bromodeoxyuridine (MBL) and purified by QIAquick PCR Purification Kit (QIAGEN).
The purified Input, BrdUIP and ChIPed DNA were amplified by IVT as described previously (Liu, C. et al., 2003, BMC Genomics).

value: BrdU

value: Anti-bromodeoxyuridine (MBL, Code No:MI-11-3, Clone:2B1)


title: CCRF-CEM 700uM prednisolone vs. control 4h treatment Experiment 2 Robust Loess

description:
This experiment has been performed in triplicates: This is the second experiment. In particular, it is the following pair: 0uM prednisolone (designated as ‘0’) vs. 700 uM prednisolone at 4 h (designated as ‘3’) and the experiment is designated as '0vs3_4h_Exp2'.
Samples are co-hybridized on the microarray chip. The ratio is obtained as treatment (Cy5) over reference (Cy3).

label_protocol: Hybridization was performed with the CyScribe Post-Labeling kit (RPN5660, GE Healthcare, former Amersham Inc.) as described by the manufacturer. The fluorescent dyes used were Cy3 and Cy5. cDNAs were purified with PCR product clean-up kit (# 28104, QIAGEN Inc.). Slides were activated at 55o C for 30 min in 1% BSA. Samples were applied on the slides, and let to hybridize overnight at 55o C. The following day, slides were washed in 200 ml 0.1× SSC and 0,1% SDS for 3× 5 min, in 200 ml 0.1× SSC for 2× 5 min  and in 200 ml ddH2O for 30 sec. Slides were dried by centrifugation at 1500 rpm for 3 min and scanned with a microarray scanner.

tag: agent

value: no treatment

tag: time point

tag: cell line

value: The CCRF-CEM (ALL) cell line was used as the model

tag: cell line provider

value: the European Collection of Cell Cultures (ECACC)

tag: cell line description

value: a CD4+ (Miranda, Wolf et al. 1996) and CD34+ presenting cell line (Naujokat, Sezer et al. 2000)

tag: origin

value: was initially obtained from peripheral blood

tag: age

value: 2 year old

tag: ethnicity

value: Caucasian

tag: gender

value: female

tag: diagnosis

value: It was diagnosed as lymphosarcoma which progressed later on to acute leukemia (Foley, Lazarus et al. 1965)


title: CCRF-CEM 10nM prednisolone vs. 700uM 4h treatment Experiment 1 Robust Loess

description:
This experiment has been performed in triplicates: This is the first experiment. In particular, it is the following pair: 10nM prednisolone (designated as ‘1’) vs. 700 uM prednisolone at 4 h (designated as ‘3’) and the experiment is designated as '1vs3_4h_Exp1'.
Samples are co-hybridized on the microarray chip. The ratio is obtained as treatment (Cy5) over reference (Cy3).

source_name: CCRF-CEM cells treated with 10nM at 4h

treatment_protocol: 10nM Prednisolone

value: 10nM prednisolone

tag: treatment

value: The child has undergone irradiation therapy and chemotherapy prior to obtaining the cell line. Although remission was achieved at various stages, the disease progressed rapidly (Foley, Lazarus et al. 1965).

tag: cell line characteristics

value: The cell line has been observed to undergone minor changes after long-term culture, except for the presence of dense granules in the nucleoli (Uzman, Foley et al. 1966). Finally, the CCRF-CEM cell line has been reported to manifest autocrine catalase activity which participates to its mechanisms of growth and progression (Sandstrom and Buttke 1993).

value: 700uM Prednisolone

value: the European Collection of Cell Cultures (ECACC).


title: CCRF-CEM 10nM prednisolone vs. control 4h treatment Experiment 1 Robust Loess

description:
This experiment has been performed in triplicates: This is the first experiment. In particular, it is the following pair: control (designated as ‘0’) vs. 10 nM prednisolone at 4 h (designated as ‘1’) and the experiment is designated as '0vs1_4h_Exp1'.
Samples are co-hybridized on the microarray chip. The ratio is obtained as treatment (Cy5) over reference (Cy3).

treatment_protocol: No treatment

source_name: CCRF-CEM cells treated with 10nM Prednisolone at 4h

value: 10nM Prednisolone


title: CCRF-CEM 22uM prednisolone vs. 700uM 72h treatment Robust Loess

description:
This experiment has been performed in a single experiment. In particular, it is the following pair: 22uM prednisolone (designated as ‘22’) vs. 700uM prednisolone at 72 h (designated as ‘700’) and the experiment is designated as '22vs700_72h_Exp1'.
Samples are co-hybridized on the microarray chip. The ratio is obtained as treatment (Cy5) over reference (Cy3).

source_name: CCRF-CEM cells treated with 22uM Prednisolone at 72h

treatment_protocol: 22uM Prednisolone

value: 22uM Prednisolone

source_name: CCRF-CEM cells treated with 700uM Prednisolone at 72h


title: CCRF-CEM 10nM prednisolone vs. control 4h treatment Experiment 3 Robust Loess

description:
This experiment has been performed in triplicates: This is the third experiment. In particular, it is the following pair: control (designated as ‘0’) vs. 10 nM prednisolone at 4 h (designated as ‘1’) and the experiment is designated as '0vs1_4h_Exp3'.
Samples are co-hybridized on the microarray chip. The ratio is obtained as treatment (Cy5) over reference (Cy3).


title: CCRF-CEM 700uM prednisolone vs. control 72h treatment Robust Loess

description:
This experiment has been performed in a single experiment. In particular, it is the following pair: 0uM prednisolone (designated as ‘0’) vs. 700uM prednisolone at 72 h (designated as ‘3’) and the experiment is designated as '0vs3_72h_Exp1'.
Samples are co-hybridized on the microarray chip. The ratio is obtained as treatment (Cy5) over reference (Cy3).

source_name: CCRF-CEM cells with no treatment at 72h


title: CCRF-CEM 10nM prednisolone vs. control 4h treatment Experiment 2 Robust Loess

description:
This experiment has been performed in triplicates: This is the second experiment. In particular, it is the following pair: control (designated as ‘0’) vs. 10 nM prednisolone at 4 h (designated as ‘1’) and the experiment is designated as '0vs1_4h_Exp2'.
Samples are co-hybridized on the microarray chip. The ratio is obtained as treatment (Cy5) over reference (Cy3).


title: Pool2

source_name: Pooled healthy control

value: PBMCs

value: Pooled healthy control

value: Female


title: AFI002

value: Malaria


title: AFI067

source_name: Murine typhus

value: Murine typhus


title: CCRF-CEM 700uM prednisolone vs. control 4h treatment Experiment 1 Robust Loess

description:
This experiment has been performed in triplicates: This is the first experiment. In particular, it is the following pair: 0uM prednisolone (designated as ‘0’) vs. 700 uM prednisolone at 4 h (designated as ‘3’) and the experiment is designated as '0vs3_4h_Exp3'.
Samples are co-hybridized on the microarray chip. The ratio is obtained as treatment (Cy5) over reference (Cy3).

value: no treatment

value: The CCRF-CEM (ALL) cell line was used as the model

value: the European Collection of Cell Cultures (ECACC)

value: a CD4+ (Miranda, Wolf et al. 1996) and CD34+ presenting cell line (Naujokat, Sezer et al. 2000)

value: was initially obtained from peripheral blood


title: CCRF-CEM 10nM prednisolone vs. 700uM 4h treatment Experiment 3 Robust Loess

description:
This experiment has been performed in triplicates: This is the third experiment. In particular, it is the following pair: 10nM prednisolone (designated as ‘1’) vs. 700 uM prednisolone at 4 h (designated as ‘3’) and the experiment is designated as '1vs3_4h_Exp3'.
Samples are co-hybridized on the microarray chip. The ratio is obtained as treatment (Cy5) over reference (Cy3).

source_name: CCRF-CEM cells treated with 10nM prednisolone at 4h

value: 10nM prednisolone

value: 2 year old

value: Caucasian

value: female

value: It was diagnosed as lymphosarcoma which progressed later on to acute leukemia (Foley, Lazarus et al. 1965)

source_name: CCRF-CEM cells treated with 700uM prednisolone at 4h

value: 700uM prednisolone


title: AFI003


title: AFI061


title: AFI066


title: HIV infected patient, biological replicate 2

source_name: jejunal tissue collected by upper endoscopy

tag: tissue

value: jejunum

tag: disease state

value: HIV+


title: CCRF-CEM 10nM prednisolone vs. 700uM 4h treatment Experiment 2 Robust Loess

description:
This experiment has been performed in triplicates: This is the second experiment. In particular, it is the following pair: 10nM prednisolone (designated as ‘1’) vs. 700 uM prednisolone at 4 h (designated as ‘3’) and the experiment is designated as '1vs3_4h_Exp2'.
Samples are co-hybridized on the microarray chip. The ratio is obtained as treatment (Cy5) over reference (Cy3).

value: The child has undergone irradiation therapy and chemotherapy prior to obtaining the cell line. Although remission was achieved at various stages, the disease progressed rapidly (Foley, Lazarus et al. 1965).

value: The cell line has been observed to undergone minor changes after long-term culture, except for the presence of dense granules in the nucleoli (Uzman, Foley et al. 1966). Finally, the CCRF-CEM cell line has been reported to manifest autocrine catalase activity which participates to its mechanisms of growth and progression (Sandstrom and Buttke 1993).

value: 700uM Prednisolone

value: the European Collection of Cell Cultures (ECACC).


title: roots buffer at 4d

city: Stanford

first: Adriana

middle: Parra

last: Rightmyer

address: 371 Serra Mall

department: Biology

institute: Stanford University

description:
A17_TCbuffer_4d
Gene expression data from roots harvested 4 day after buffer treatment.

hyb_protocol: Hybridization was performed as described in the Affymetrix technical manual, at the Stanford Protein and Nucleic Acid Facility (Stanford, CA).

scan_protocol: Scanning were performed as described in the Affymetrix technical manual.

data_processing: Pixel values were extracted from scan files by using Affymetrix MAS 5.0 software, and .CEL files were analyzed by using DCHIP 1.3. Probe sets specifying bacterial genes were masked before analysis. Expression analysis was performed as described in Mitra et al., 2004 (PMID 15220482). The data from the independent biological replicates for each condition were combined.

organism: Medicago truncatula

source_name: roots harvested 4 days after buffer treatment

label_protocol: Biotin-labeled cRNA was synthesized using the BioArray high yield RNA transcription labeling kit (Enzo diagnostics).

growth_protocol: Twenty M. truncatula plants were grown per Petri plate (240835, Nunc, Rochester, NY, USA) containing buffered nodulation medium (BNM; Ehrhardt et al., 1992), pH6.5 with 1 mM α-aminoisobutyric acid (AIB). Three plates were performed at this time point and treatment.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was used for double-stranded cDNA synthesis.

treatment_protocol: Plants were inoculated 6 d after planting with either 1 μl of a suspension of Rm1021 (optical density at 600 nm [OD600]=0.05) or 1 μl of 0.5X BNM as a mock control.

tag: cultivar

value: Jemalong A17

tag: genotype

value: wild-type

value: roots

tag: growth condition

value: BNM containing 1.15% (w/v) agar

value: 0.5X BNM as a mock control

tag: time after treatment

value: 4 days

tag: amount of total rna

value: 40 µg


title: roots buffer at 7d

description:
A17_TCbuffer_7d
Gene expression data from roots harvested 7 day after buffer treatment.

source_name: roots harvested 7 days after buffer treatment

value: BNM containing 2.5% (w/v) agar

value: 7 days


title: roots Rm1021 at 4d

description:
A17_Rm1021_4d
Gene expression data from roots harvested 4 day after Rm 1021 treatment.

source_name: roots harvested 4 days after Rm1021 treatment

value: Sinorhizobium meliloti Rm1021


title: Pool1

hyb_protocol: Standard Illumina hybridization protocol

tag: cell type

value: PBMCs

tag: disease group

value: Pooled healthy control

value: Male


title: AFI059

value: Murine typhus

tag: age (years)

value: Female

tag: fever day


title: roots buffer at 14d

description:
A17_TCbuffer_14d
Gene expression data from roots harvested 14 day after buffer treatment.

source_name: roots harvested 14 days after buffer treatment

value: 14 days


title: AFI058


title: Diclofenac treated THP-1 cells, biological replicate 1

city: Düsseldorf

first: Ingmar

last: Bruns

state: NRW

address: Moorenstr. 5

department: Hematology, Oncology and Clinical Immunology

institute: University of Düsseldorf

description: Gene expression data from Diclofenac treated THP-1 cells

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45°C on HG-U133A Gene Expression Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G

data_processing: CEL files were analyed using dChip after smooth spline normalization

source_name: THP-1 AML cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 µg total RNA

growth_protocol: Cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum

extract_protocol: Total RNA was harvested using the RNeasy Mini Kit from Qiagen

treatment_protocol: Cells were treated with 100 µM Diclofenac or equal amounts of DMSO for 48 hours

tag: cell line

value: monocytic leukemia


title: AFI004


title: Diclofenac treated THP-1 cells, biological replicate 2


title: AFI011


title: roots buffer at 1d

description:
A17_TCbuffer_1d
Gene expression data from roots harvested 1 day after buffer treatment.

value: Jemalong A17

value: 1 day

value: 30 µg


title: AFI023

source_name: Scrub typhus

value: Scrub typhus


title: AFI060


title: AFI027


title: roots Rm1021 at 1d

description:
A17_Rm1021_1d
Gene expression data from roots harvested 1 day after Rm 1021 treatment.

source_name: roots harvested 1 day after Rm1021 treatment

value: wild-type

value: roots

value: BNM containing 1.15% (w/v) agar


title: Diclofenac treated HL-60 cells, biological replicate 2

description: Gene expression data from Diclofenac treated HL-60 cells

source_name: HL60 AML cells

value: promyelocytic leukemia


title: AFI039

source_name: Dengue fever

value: Dengue fever


title: Heart_double_knockout_rep2

city: Shinjuku-ku

first: Keiko

last: Uchida

state: Tokyo

address: 35 Shinanomachi

institute: Keio University School of Medicine

hyb_protocol: cDNAs were hybridized on GeneChip arrays and the arrays were washed and stained in Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol (Expression Analysis Technical Manual P/N 702232 Rev.2).

scan_protocol: GeneChip arrays were scanned using Affymetrix GeneChip 3000 7G scanner.  GeneChip arrays were scanned using Affymetrix GeneChip 3000 7G scanner.

data_processing: RMA, Signal calculated by GCOS1.4 software

source_name: E9.25 knockout mouse

label_protocol: Fragmented and biotinylated cDNAs were prepared from the total RNA according to NuGEN protocol (FL-Ovation cDNA Biotin Module V2 USER GUIDE Version 04.05.07).

growth_protocol: Embryos were grown until embryonic day 9.25.

extract_protocol: Total RNA extraction using RNeasy (QIAgen) was performed according to the manufacturer's instructions.

treatment_protocol: Animals were housed under a 12 h light/12 h dark cycle and ad-lib access to food and water. Animals were sacrificed by cervical dislocation.

tag: strain

tag: genotype/variation


title: AFI052

tag: gender


title: AFI068


title: Heart_wildtype_rep1

source_name: E9.25 control mouse

value: wild type


title: Diclofenac treated HL-60 cells, biological replicate 1


title: skl1-1 roots TIBA at 21d

description:
skl_TIBA_21d
Gene expression data from roots harvested 21 day after TIBA treatment.

source_name: skl1-1 roots harvested 21 days after TIBA treatment

label_protocol: Bioarray high yield RNA transcription labeling kit (Enzo Diagnostics) following the manufacturer's instructions.

growth_protocol: Twenty Medicago truncatula plants were grown per Petri plate (240835, Nunc, Rochester, NY, USA) containing buffered nodulation medium (BNM; Ehrhardt et al. 1992), pH 6.5, with 1 µM α-aminoisobutyric acid (AIB). Three plates were performed at this time point and treatment.

treatment_protocol:
Roots were flooded 6 days after planting with 20 ml of solution containing the corresponding treatment. The excess of solution was removed at the bottom of the plate. Root tips were spot-inoculated with 1 µl of a suspension of Sinorhizobium meliloti exoA (RM7031) (OD600 = 0.05) or Sinorhizobium meliloti Rm1021 (OD600 = 0.05).

Root segments (5 cm) were harvested centered on the root tip mark at the moment of treatment: ATI, bacterial or mock. Root tips (if within the 5 cm segment) and lateral roots were removed. For each preparation, total RNA was isolated from approximately 60 root segments.

tag: background

value: BNM containing 2.5% (w/v) agar

tag: treatment

value: 200 µM TIBA

value: 21 day

value: 40 µg


title: roots NPA at 21d

description:
A17_NPA_21d
Gene expression data from roots harvested 21 day after NPA treatment.

source_name: roots harvested 21 days after NPA treatment

growth_protocol: Twenty Medicago truncatula plants were grown per Petri plate (240835, Nunc, Rochester, NY, USA) containing buffered nodulation medium (BNM; Ehrhardt et al. 1992), pH 6.5, with 1 µM α-aminoisobutyric acid (AIB). Four plates were performed at this time point and treatment.

tag: tissue

value: 200 µM NPA


title: skl1-1 roots buffer at 21d

description:
skl_buffer_21d
Gene expression data from roots harvested 21 day after buffer treatment.

source_name: skl1-1 roots harvested 21 days after buffer treatment

value: 0.5X BNM as a mock control


title: skl1-1 roots NPA at 21d

description:
skl_NPA_21d
Gene expression data from roots harvested 21 day after NPA treatment.

source_name: skl1-1 roots harvested 21 days after NPA treatment


title: Heart_double_knockout_rep1


title: skl1-1 roots Rm1021 at 21d

description:
skl_Rm1021_21d
Gene expression data from roots harvested 21 day after Rm 1021 treatment.

source_name: skl1-1 roots harvested 21 days after Rm1021 treatment

value: Sinorhizobium meliloti Rm1021


title: roots TIBA at 21d

description:
A17_TIBA_21d
Gene expression data from roots harvested 21 day after TIBA treatment.

source_name: roots harvested 21 days after TIBA treatment

value: Jemalong A17


title: roots buffer at 21d

description:
A17_buffer_21d
Gene expression data from roots harvested 21 day after buffer treatment.

source_name: roots harvested 21 days after buffer treatment

growth_protocol: Twenty Medicago truncatula plants were grown per Petri plate (240835, Nunc, Rochester, NY, USA) containing buffered nodulation medium (BNM; Ehrhardt et al. 1992), pH 6.5, with 1 µM α-aminoisobutyric acid (AIB). Five plates were performed at this time point and treatment.

value: 21 days


title: AFI049

value: PBMCs

value: Male


title: AFI028

value: Female


title: Heart_wildtype_rep2


title: AFI037


title: AFI038


title: roots TIBA at 7d

description:
A17_TIBA_7d
Gene expression data from roots harvested 7 day after TIBA treatment.

source_name: roots harvested 7 days after TIBA treatment

label_protocol: GeneChip IVT labeling kit (Affymetrix) following the manufacturer's instructions.

value: wild-type

value: roots

value: 7 day

value: 30 µg


title: roots exoA- at 21d

description:
A17_exoA-_21d
Gene expression data from roots harvested 21 day after S. meliloti exoA treatment.

source_name: roots harvested 21 days after exoA- treatment

value: Sinorhizobium meliloti exoA (RM7031)


title: AFI018

value: Dengue fever


title: roots NPA at 7d

description:
A17_NPA_7d
Gene expression data from roots harvested 7 day after NPA treatment.

source_name: roots harvested 7 days after NPA treatment

value: BNM containing 2.5% (w/v) agar


title: roots NPA at 1d

description:
A17_NPA_1d
Gene expression data from roots harvested 1 day after NPA treatment.

value: BNM containing 1.15% (w/v) agar

value: 1 day


title: roots buffer at 7d

description:
A17_buffer_7d
Gene expression data from roots harvested 7 day after buffer treatment.

source_name: roots harvested 7 days after buffer treatment


title: roots TIBA at 1d

description:
A17_TIBA_1d
Gene expression data from roots harvested 1 day after TIBA treatment.

value: 200 µM TIBA


title: roots buffer at 1d

description:
A17_buffer_1d
Gene expression data from roots harvested 1 day after buffer treatment.

value: 0.5X BNM as a mock control


title: AFI072

source_name: Malaria

value: Malaria