title: Effects of dexamethasone on human adipose tissue RL

data_processing: The data extracted with Mapix software (Innopsys) were normalized with the Lowess procedure without background subtraction by use of R. Features with a signal to background ratio strictly below 2 in both color as well as control spots were discarded. Value is the Log2 of normalized Green/Red value ratio.

value: male


title: pathogen isolates: Taiwan 80-2 (vir) - time: 216 hai - rep1

status: Public on Nov 28 2011

type: RNA

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

country: USA

institute: Iowa State University

description: PI462312  Taiwan 80-2 treatment 216 hours

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

label: biotin

molecule: total RNA

organism: Glycine max

source_name: leaf (pathogen isolates: Taiwan 80-2 (vir) - time: 216 hai)

label_protocol: Affy-Eukaryotic Target Preparation

extract_protocol: TRIzol-Qiagen

tag: pathogen isolates

value: Taiwan 80-2 (vir)

tag: time

tag: germplasm name

tag: organism part

tag: development stage

value: PO:0007134 A vegetative growth

tag: growth media

value: soil mix


title: Limb 4C Prox

type: genomic

city: Lausanne

first: Thomas

last: Montavon

address: SV 2843, Station 19

country: Switzerland

institute: EPFL

description: Prox interacting sequences from E12.5 mouse Forelimbs/autopods, Biological Rep. 1+2

hyb_protocol: 1μg of DNA was hybridzed per array for 16 hours at 45° at 60rpm using the Affymetrix hybridization kit.

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

data_processing:
Data were quantile normalized within 4C/input replicate groups and scaled to medial feature intensity of 100 using TAS software (Affymetrix). For each genomic position, a data set was generated consisting of all (PM-MM) pairs mapping within a sliding window of 250 bp.
signal.bar and pvalue.bar are generated by TAS software (Affymetrix). signal.bar contains log2(IP/Input) fold changes for each probe in a region 2*sliding window+1. pvalue.bar contains -10log10 (IP/Input) for each probe in a region 2*sliding window+1.

molecule: genomic DNA

organism: Mus musculus

label_protocol: 1 ug of 4C and input DNA was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix).

extract_protocol: Presumptive digits and forebrains were dissected from E12.5 mouse embryos, dissociated by collagenase treatment and fixed in 2 % formaldehyde for 10 minutes at room temperature. After cell lysis, nuclei were stored at -80°C. Pools of 16 autopods or 2 forebrains were digested with DpnII (New England Biolabs) and ligated in diluted conditions to promote intramolecular ligation events. DNA was purified by phenol/chloroform extraction followed by ethanol precipitation. Sequences ligated to the fragment of interest (interacting regions) were amplified by inverse PCR as described (Simonis et al., 2006), using the following primer pairs for each viewpoint: Hoxd13-F: 5'-GCACAGGCTCTTCGTCGT-3'; Hoxd13-R: 5'-CAAATTCGAGACAGCTCATCC-3'; Hoxd4-F: 5'-GTAGTTCAGAGCGGGGTTTG-3'; Hoxd4-R: 5'-GGCAGCTGGGATTAACACTTA-3'; IslandI-F: 5'-GGGACACGGTCCAATTTAAG-3'; IslandI-R: 5'-TGGAAAGGTCATGCGTGTT-3'; IslandIV-F: 5'-GGAATGACCAAGGGATACAAGA-3'; IslandIV-R: 5'-GGGTAAAGACTGCACAAGAGC-3'; Prox-F: 5'-GACGGCCACTCACATAATAAGA-3'; Prox-R: 5'-GGCTTGACAGCTGTGTAGTAGC-3'.. 200 ng of 4C template were amplified per reaction, using AmpliTaq DNA polymerase (Applied Biosystems). For each condition, 16 reactions were pooled and purified using Qiagen PCR clean-up kit.

tag: age

tag: developmental stage

value: embryo

tag: tissue

value: Forelimb/ autopod

tag: viewpoint

value: Prox

tag: genetic background

value: B6/CBA (F1)

source_name: Input DNA from E12.5 mouse limbs


title: 1st hybridization susceptible vs. Resistant tree

city: Vancouver

first: Sébastien

last: Verne

state: BC

address: 2424, Main Mall

department: Forest Sciences

country: Canada

institute: University of British Columbia

hyb_protocol: The slide was prewashed twice in 0.1% SDS at room temperature for 5 min., followed by two 2 min. washes in MilliQ-H2O, 3 min. at 95ºC in MilliQ-H2O, and dried by centrifugation (3 min at 2000 rpm in an IEC Centra CL2 centrifuge with rotor IEC 2367-00 in 50 mL conical tube). The cDNA probe was heat-denatured at 80ºC for 10 min, maintained at 65ºC prior to adding to a microarray slide that heated to 55ºC, and covered with a 22 x 60 mm glass coverslip.  First hybridization (cDNA hybdridization) used the ingredients of Genisphere Array350 kit (Genisphere, Hatfield, USA): 2X SDS Buffer; LNA dT blocker; nuclease-free water together with 2 ug of salmon testes DNA (Invitrogen).  The incubation condition for cDNA hybridization was 16h at 60ºC. The slide was washed in 2x SSC, 0.2% SDS at room temperature for 5 min to remove the coverslip, followed by 15 min at 65ºC in the same solution, and three washes (5 min. each) in 2x SSC at room temperature, and three washes (5 min. each) in 0.2x SSC at room temperature, and dried by centrifugation.  Second hybridization (3DNA hybridization) used the ingredients of Genisphere Array350 kit (Genisphere, Hatfield, USA): 2X SDS buffer; Cy3 3DNA dendrimer; Cy5 3DNA dendrimer; and nuclease-free water.  Incubation condition for 3DNA hybridization was 3 h at 60ºC, followed by washing and drying as described for the first hybridization.

scan_protocol: The slide was scanned using ScanArray Express (Perkin Elmer, Foster City, USA).The Cy3 and Cy5 cyanine fluors were excited with laser at 543 nm and 633 nm respectively. Scanning was consistently done with 90% laser power. The optimal photomultiplier tube (PMT) gain was set at the dynamic range of 60%<PMT<80% to minimize background intensity, and maximize the signal intensity while the number of saturated spots, excluding human positive spikes and GFP orientation marker, not exceeding 5% of each subgird. Fluorescent intensity data were quantified using the ImaGene 6 software (Biodiscovery, El Segundo, USA).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from the 20 microarray hybridizations were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays to arrive at the expression levels ratio between resistant and susceptible trees. A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to the 20 microarray slides. The model contained a fixed effect for resistance phenotype and random effect for individuals within resistance phenotype. P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

organism: Picea engelmannii x Picea glauca

label_protocol: Used Genisphere Array350 kit (Genisphere, Hatfield, USA) following the manufacturer protocol: 40 micrograms of total RNA for reverse transcription; Superscript II reverse transcriptase (Invitrogen); 5.0 pmole/ul RT Primer for Cy3/Alexa Fluor 546 or Cy5/Alexa Fluor 647; Cy5/Alexa Fluor 647 dye-labeled; hydrolyzed in 0.5 M NaOH / 0.05 M EDTA at 65ºC for 15 min; and neutralized in 1 M Tris-HCl (pH 7.5).

extract_protocol: Total RNA extraction used a modified version of the protocol described by Kolosova et al. (2004) Biotechniques 36: 821-824. The extracted RNA was quantified and quality checked using spectrophotometry and agarose gel electrophoresis; in respect to the wavelength of maximum absorption at 260 nm and 280 nm and the presence of sharp bright bands of 28s and 18s ribosomal subunits at ~4.5 kb and ~1.9 kb on 1% agarose gel.

treatment_protocol: Specimen (bark/phloem sources of tissue) collected from one lateral shoot of the individual tree was flash-frozen on the field by liquid nitrogen and kept in -80 ºC freezer until extraction.

value: bark tissue sampled from the shoots of mature trees grown under the same environment at the Picearetum of Kalamalka Research Station, Vernon, BC (collection established 1972-1973).

tag: phenotype


title: Effects of dexamethasone on human adipose tissue BL rep

city: Toulouse

first: Nathalie

last: Viguerie

address: Avenue Poulhes

country: France

institute: INSERM

description: Labeling and hybridization qualities were verified with Agilent’s spike in kit.

hyb_protocol: 850 ng of Cy5 labelled probe was cohybridized the same amount of Cy3 labelled probe. We used the whole human genome oligo microarray from Agilent with the gene expression hybridization kit according to the manufacturer's protocol.

scan_protocol: Micro-arrays were scanned on a InnoScan 700 scanner (Innopsys, Carbonne, France, EU) and data were extracted with Mapix software (Innopsys).

data_processing: The data extracted with Mapix software (Innopsys) were normalized with the Lowess procedure without background subtraction by use of R. Features with a signal to background ratio strictly below 2 in both color as well as control spots were discarded. Value is the Log2 of normalized Red/Green value ratio.

organism: Homo sapiens

source_name: Human adipose tissue, control

label_protocol: Total RNA quality was checked by capillary electrophoresis (Agilent 2100 bioanalyzer and RNA 6000 labChip Kit) and good quality RNA extracts only were used for microarray hybridization. Fluorescent probes were obtained by amplifying and labelling 500ng of RNA with the low RNA input linear amplification kit (Agilent).

extract_protocol: Total RNA was extracted with the RNeasy mini kit (Qiagen) according to manufacturer instructions.

tag: agent

value: control

tag: gender

value: subcutaneous abdominal adipose tissue

source_name: Human adipose tissue, 4-d dexamethasone treatment

value: 4-d dexamethasone


title: Limb 4C isI

description: Island I interacting sequences from E12.5 mouse Forelimbs/autopods, Biological Rep. 1+2

value: IslandI


title: Effects of dexamethasone on human skeletal muscle TF rep

source_name: Human vastus lateralis muscle, control

value: skeletal muscle

source_name: Human vastus lateralis muscle, 4-d dexamethasone treatment


title: Effects of dexamethasone on human skeletal muscle MH rep


title: Effects of dexamethasone on human skeletal muscle RL rep


title: Effects of dexamethasone on human skeletal muscle JO rep


title: Limb 4C Hoxd4

description: Hoxd4 interacting sequences from E12.5 mouse Forelimbs/autopod, Biological Rep. 1+2s

source_name: Hoxd4 interacting sequences from E12.5 mouse Forelimbs/autopods


title: Effects of dexamethasone on human adipose tissue BS


title: Effects of dexamethasone on human adipose tissue MA


title: Effects of dexamethasone on human adipose tissue BL


title: pathogen isolates: Taiwan 80-2 (vir) - time: 144 hai - rep1

description: PI462312  Taiwan 80-2 treatment 144 hours

source_name: leaf (pathogen isolates: Taiwan 80-2 (vir) - time: 144 hai)


title: pathogen isolates: Taiwan 80-2 (vir) - time: 24 hai - rep3

description: PI462312  Taiwan 80-2 treatment 24 hours

source_name: leaf (pathogen isolates: Taiwan 80-2 (vir) - time: 24 hai)

value: 24 hr


title: Limb 4C Hoxd13

description: Hoxd13 interacting sequences from E12.5 mouse Forelimbs/autopods, Biological Rep. 1+2


title: Brain 4C Prox

description: Prox interacting sequences in E12.5 mouse Forebrain, Biological Rep. 1+2

value: Forebrain


title: 19th hybridization susceptible vs. Resistant tree


title: Limb 4C isIV

description: Island IV interacting sequences from E12.5 mouse Forelimbs/autopods, Biological Rep. 1+2

value: IslandIV


title: Effects of dexamethasone on human skeletal muscle MS rep

value: male


title: Effects of dexamethasone on human skeletal muscle RV rep


title: pathogen isolates: Taiwan 80-2 (vir) - time: 72 hai - rep3

description: PI462312  Taiwan 80-2 treatment 72 hours

source_name: leaf (pathogen isolates: Taiwan 80-2 (vir) - time: 72 hai)

value: Taiwan 80-2 (vir)

value: 72 hr


title: pathogen isolates: Taiwan 80-2 (vir) - time: 72 hai - rep2

value: PO:0007134 A vegetative growth

value: soil mix


title: pathogen isolates: Taiwan 80-2 (vir) - time: 24 hai - rep2


title: pathogen isolates: Taiwan 80-2 (vir) - time: 24 hai - rep1


title: PNC-3

city: La Jolla

first: Dan

last: Zhou

state: CA

address: CMG 103, 9500 Gilman Drive, MC0735

department: Pediatrics

institute: University of California, San Diego, School of Medicine

description: Embryonic Primary Neurons

hyb_protocol: Hybridizations were carried out by using the Illumina gene expression system according to the manufacturer's instructions.

scan_protocol: Illumina scanner

data_processing: Normalized average intensity of the bead type/target in the group using Cubic spline normalization with BeadStudio.

label: Biotin

source_name: Primary neuronal culture under normoxia

label_protocol: Illumina® TotalPrep™ RNA Amplification Kit following the manufacturer's instructions. Input amount: 100ng of total RNA.

extract_protocol: Total RNA was extracted from frozen tissues of using RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

value: brain

tag: strain

tag: cell type

value: embryonic primary neurons

tag: embryo age

tag: culture time

value: 8 days

tag: Sex

value: embryos, and used 1-2 litters per experiments, so most likely a mix of lames and females


title: pathogen isolates: Taiwan 80-2 (vir) - time: 72 hai - rep1

tag: pathogen isolates

tag: time

tag: germplasm name


title: Effects of dexamethasone on human skeletal muscle DL rep

value: control


title: PNC-2

description: Embryonic Primary Neurons


title: pathogen isolates: Taiwan 80-2 (vir) - time: 12 hai - rep3

description: PI462312  Taiwan 80-2 treatment 12 hours

source_name: leaf (pathogen isolates: Taiwan 80-2 (vir) - time: 12 hai)

value: 12 hr

tag: organism part

tag: development stage

tag: growth media


title: pathogen isolates: Taiwan 80-2 (vir) - time: 12 hai - rep2


title: Effects of dexamethasone on human skeletal muscle RV

value: 4-d dexamethasone

tag: tissue


title: Effects of dexamethasone on human skeletal muscle RL


title: Effects of dexamethasone on human skeletal muscle TF


title: Effects of dexamethasone on human skeletal muscle MH


title: Effects of dexamethasone on human skeletal muscle BS rep


title: pathogen isolates: Taiwan 80-2 (vir) - time: 12 hai - rep1


title: Brain RNA

type: mixed

description: Total RNA Forebrain, Biological Rep 1-2

hyb_protocol: 7μg of cDNA was hybridzed per array for 16 hours at 45° at 60rpm using the Affymetrix hybridization kit.

data_processing:
Data were quantile normalized within ChIP/input replicate groups and scaled to medial feature intensity of 100 using TAS software (Affymetrix). For each genomic position, a data set was generated consisting of all (PM-MM) pairs mapping within a sliding window of 80 bp.
signal.bar and pvalue.bar are generated by TAS software (Affymetrix). signal.bar contains log2(IP/Input) fold changes for each probe in a region 2*sliding window+1. pvalue.bar contains -10log10 (IP/Input) for each probe in a region 2*sliding window+1.

source_name: Total RNA from E12.5 mouse brain

label_protocol: rRNA was depleted using RiboMinus Human/Mouse Transcriptome Isolation kit (Affymetrix). After cRNA amplification, double-stranded cDNA was generated using the GeneChip Whole Transcript Amplified Double-Stranded Target Assay kit (Affymetrix) according to manufacturer’s instructions. cDNA was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix). The control genomic DNA samples were fragmented with DNAse I.

extract_protocol: Presumptive digits and forebrains were dissected from E12.5 mouse embryos and stored in RNAlater reagent (Qiagen). For each replicate, RNA was extracted from pools of 8 autopods or 2 forebrains using RNeasy mini-kit (Qiagen).

tag: age

tag: developmental stage

value: embryo

source_name: genomic DNA from mouse kidney

value: 3 month

tag: deveopmental stage

value: adult

value: kidney


title: pathogen isolates: Mock - time: 288 hai - rep2

description: PI462312  mock treatment 288 hours

source_name: leaf (pathogen isolates: Mock - time: 288 hai)

value: Mock


title: Brain 4C Hoxd13

description: Hoxd13 interacting sequences in E12.5 mouse Forebrain, Biological Rep. 1+2

value: Forebrain

tag: viewpoint

tag: genetic background

value: B6/CBA (F1)

value: Forelimb/ autopod


title: Brain 4C isI

description: Island I interacting sequences in E12.5 mouse Forebrain, Biological Rep. 1+2

value: IslandI


title: Brain 4C isIV

description: Island IV interacting sequences in E12.5 mouse Forebrain, Biological Rep. 1+2

value: IslandIV


title: pathogen isolates: Mock - time: 288 hai - rep1

description: PI462312  mock treatment 288 hours

value: PO:0007134 A vegetative growth

value: soil mix


title: Brain 4C Hoxd4

description: Hoxd4 interacting sequences in E12.5 mouse Forebrain, Biological Rep. 1+2


title: MMC-3

description: Neural stem cell (NSC) line C17.2

source_name: Mitomycin-treated neural stem cell (NSC) cultured under normoxia

tag: tissue of origin

value: brain

tag: strain

value: C57BL/6J x CD1

tag: cell line

value: neural stem cell (NSC) line C17.2

value: The culture by the time of RNA extraction is 8 days

value: cannot tell if originated from male or female


title: Effects of dexamethasone on human skeletal muscle FS rep

tag: agent

value: control

tag: gender

value: male

value: skeletal muscle

value: 4-d dexamethasone


title: pathogen isolates: Mock - time: 288 hai - rep3

description: PI462312  mock treatment 288 hours

tag: pathogen isolates

value: Mock


title: MMC-1

description: Neural stem cell (NSC) line C17.2

tag: Sex


title: PNC-1

description: Embryonic Primary Neurons

tag: cell type

value: embryonic primary neurons

tag: embryo age

tag: culture time

value: 8 days

value: embryos, and used 1-2 litters per experiments, so most likely a mix of lames and females


title: MMC-2

description: Neural stem cell (NSC) line C17.2


title: Limb RNA

description: Total RNA Forelimbs/autopods, Biological Rep 1-2

source_name: Total RNA from E12.5 mouse limb

value: embryo

value: Forelimb/ autopod

value: 3 month

value: adult

value: kidney


title: Effects of dexamethasone on human skeletal muscle MS


title: Limb RNAP2

description: RNAP2 ChIP Forelimbs/autopods, Biological Rep 1-2

data_processing:
Data were quantile normalized within ChIP/input replicate groups and scaled to medial feature intensity of 100 using TAS software (Affymetrix). For each genomic position, a data set was generated consisting of all (PM-MM) pairs mapping within a sliding window of 250 bp.
signal.bar and pvalue.bar are generated by TAS software (Affymetrix). signal.bar contains log2(IP/Input) fold changes for each probe in a region 2*sliding window+1. pvalue.bar contains -10log10 (IP/Input) for each probe in a region 2*sliding window+1.

source_name: RNA Pol2 ChIP DNA from E12.5 mouse autopods

label_protocol: 1 ug of ChIP and input DNA was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix).

extract_protocol: Presumptive digits and forebrains were dissected from E12.5 mouse embryos, fixed in 1% formaldehyde for 15 minutes at room temperature, washed three times with cold phosphate buffer solution (PBS) and stored at -80°C. Pools of 16 autopods or 2 forebrains were used for each experiment. ChIP was performed according to (Lee et al., 2006) using 2 μg of anti-H3K4me3 (ab8580, Abcam), H3K27me3 (17-622, Millipore), H3K4me1 (ab8895, Abcam), H3K27Ac (ab4729, Abcam), or RNAPII (8WG16, Covance) antibodies, and EZview Red protein G/A Affinity Gel (Sigma). Immunoprecipitated and whole cell extract DNA (input) were treated with RNAseA, proteinase K and purified by two rounds of extraction with phenol/chloroform/isoamyl alcohol. ChIP and input DNA were amplified using ligation-mediated PCR (Lee et al. 2006).

tag: antibody

value: RNAP2 8WG16

tag: antibody manufacturer

value: Covance

tag: antibody catalog number


title: pathogen isolates: Mock - time: 216 hai - rep3

description: PI462312  mock treatment 216 hours

source_name: leaf (pathogen isolates: Mock - time: 216 hai)

tag: time

tag: germplasm name

tag: organism part

tag: development stage

value: PO:0007134 A vegetative growth

tag: growth media

value: soil mix


title: NSC-3

description: Neural stem cell (NSC) line C17.2

source_name: Neural stem cell (NSC) cultured under normoxia

tag: tissue

value: brain

tag: strain

value: C57BL/6J x CD1

value: neural stem cell (NSC) line C17.2

value: not known if originated from male or female

tag: tag

value: Immortalized with c-myc, has the LacZ as a marker/tracer

tag: age

value: culture by the time of RNA extraction is 3-4 days (50% confluency)


title: Effects of dexamethasone on human skeletal muscle JO

tag: agent

value: 4-d dexamethasone

tag: gender

value: male

value: skeletal muscle

value: control


title: Effects of dexamethasone on human skeletal muscle FS


title: Effects of dexamethasone on human skeletal muscle DL


title: whole heart, adult, rep 2[MoGene[gene_level]]

city: Bad Nauheim

first: Pascal

last: Gellert

address: Ludwigstr. 43

department: Cardiac Development and Remodelling

country: Germany

institute: Max Planck Institut for Heart and Lung Research

description: whole heart – adult

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. • Transfer 200μl of hyb solution to each array, then tape holes. • Hybridize 17 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
RMA normalized, gene and exon level expression values from Affymetrix Power Tools
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps and MoGene-1_0-st-v1.r4.all.ps

source_name: whole heart – adult

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

growth_protocol: Mouse embryonic stem cells are differentiated into cardiomyocytes with DMEM based culture media supplied with 10% serum. Mouse hearts dissected from E17.5 and P1 mice.

extract_protocol: RNA was extracted from each samples (culture cells and tissues) with TRIzol reagent (Invitrogen).  Isolated RNAs were then treated with the RiobMinus rRNA reduction kit (Invitrogen), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

treatment_protocol: not applicable

value: Adult

value: whole heart


title: Limb H3K4me3

description: H3K4me3 ChIP Forelimbs/autopods, Biological Rep 1-2

source_name: H3K4me3 ChIP DNA from E12.5 mouse autopods

tag: developmental stage

value: embryo

value: Forelimb/ autopod

value: Abcam

source_name: Input DNA from E12.5 mouse limbs


title: Limb H3K4me1

description: H3K4me1 ChIP Forelimbs/autopods, Biological Rep 1-2

source_name: H3K4me1 ChIP DNA from E12.5 mouse autopods


title: Brain H3K4me1

description: H3K4me1 ChIP Brain, Biological Rep 1-2

source_name: H3K4me1 ChIP DNA from E12.5 mouse brain

value: Forebrain


title: Brain RNAP2

description: RNAP2 ChIP Brain, Biological Rep 1-2

source_name: RNA Pol2 ChIP DNA from E12.5 mouse brain

value: RNAP2 8WG16

value: Covance


title: pathogen isolates: Mock - time: 216 hai - rep2

description: PI462312  mock treatment 216 hours

tag: pathogen isolates

value: Mock

value: PO:0007134 A vegetative growth

value: soil mix


title: pathogen isolates: Mock - time: 144 hai - rep3

description: PI462312  mock treatment 144 hours

source_name: leaf (pathogen isolates: Mock - time: 144 hai)


title: Effects of dexamethasone on human skeletal muscle BL

description: Labeling and hybridization qualities were verified with Agilent’s spike in kit.

data_processing: The data extracted with Mapix software (Innopsys) were normalized with the Lowess procedure without background subtraction by use of R. Features with a signal to background ratio strictly below 2 in both color as well as control spots were discarded. Value is the Log2 of normalized Red/Green value ratio

source_name: Human vastus lateralis muscle, 4-d dexamethasone treatment

source_name: Human vastus lateralis muscle, control


title: pathogen isolates: Mock - time: 144 hai - rep1

description: PI462312  mock treatment 144 hours


title: pathogen isolates: Mock - time: 216 hai - rep1

description: PI462312  mock treatment 216 hours


title: NSC-2

description: Neural stem cell (NSC) line C17.2

value: brain

value: C57BL/6J x CD1

tag: cell line

value: neural stem cell (NSC) line C17.2

tag: Sex

value: not known if originated from male or female

value: Immortalized with c-myc, has the LacZ as a marker/tracer


title: whole heart, P1, rep 2 [MoGene[gene_level]]

description: whole heart – P1

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials.  Heat cocktails at 99C for 5 minutes, then 42C for 5 minutes centrifuge at max speed for 1 minute, Transfer 200ul of hyb solution to each array, then tape holes, Hybridize 17 hours at 45C at 60rpm. Fluidics washing is FS450_0001.

source_name: whole heart – P1

tag: tissue/cell  type


title: WildType_Replicate2

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

description: WildType Replicate 2

hyb_protocol: After a two-hour reaction, 1.5 μg of purified, Cy3-labeled cRNA were hybridized to an oligonucleotide C. elegans Microarray (015061, 4x44K, Agilent Technologies) for 17 hours at 65˚C, then washed according to manufacturer's protocol.

scan_protocol: Slides were scanned using an Agilent G2505B scanner, and data were extracted using the Feature Extraction software version 9.5 (Agilent Technologies).

data_processing: Median signal intensities from the Feature Extraction Software were converted to log2 and quantile normalized using the R package “limma”.

organism: Caenorhabditis elegans

source_name: WildType Replicate 2

label_protocol: 600 ng of total RNA were reverse-transcribed and amplified, thereby incorporating Cyanine 3-CTP nucleotides, using the Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's recommendations (Agilent One-Color Microarray-Based Gene Expression Analysis, protocol version 5.5, February 2007; Agilent Technologies).

growth_protocol: For the microarray studies 80 to 100 L4 and young adult worms raised at 21°C were used.

extract_protocol: Total RNA was extracted using the standard Trizol method following the manufacturer’s protocol.

tag: genotype

value: WT

value: whole worm


title: Effects of dexamethasone on human skeletal muscle BS

value: 4-d dexamethasone

value: male

value: skeletal muscle

value: control


title: pathogen isolates: Mock - time: 72 hai - rep3

description: PI462312  mock treatment 72 hours

source_name: leaf (pathogen isolates: Mock - time: 72 hai)

tag: time

value: 72 hr


title: pathogen isolates: Mock - time: 144 hai - rep2

description: PI462312  mock treatment 144 hours

tag: germplasm name


title: Brain H3K27Ac

description: H3K27Ac ChIP Brain, Biological Rep 1-2

source_name: H3K27Ac ChIP DNA from E12.5 mouse brain

value: embryo

value: Forebrain

tag: antibody

tag: antibody manufacturer

value: Abcam

tag: antibody catalog number

value: Forelimb/ autopod


title: pathogen isolates: Mock - time: 72 hai - rep2

description: PI462312  mock treatment 72 hours

value: Mock

tag: organism part

tag: development stage

value: PO:0007134 A vegetative growth

tag: growth media

value: soil mix


title: WildType_Replicate3

description: WildType Replicate 3

source_name: WildType Replicate 3

tag: strain

tag: tissue


title: whole heart, adult, rep 1[MoGene[gene_level]]

description: whole heart – adult

tag: age

value: Adult

value: whole heart


title: WildType_Replicate1

description: WildType Replicate 1

source_name: WildType Replicate 1


title: pathogen isolates: Mock - time: 72 hai - rep1

description: PI462312  mock treatment 72 hours


title: whole heart, E17.5, rep 2 [MoGene[gene_level]]

description: whole heart – E17.5

source_name: whole heart – E17.5


title: NSC-1

description: Neural stem cell (NSC) line C17.2

source_name: Neural stem cell (NSC) cultured under normoxia

value: brain

value: C57BL/6J x CD1

value: neural stem cell (NSC) line C17.2

value: not known if originated from male or female

tag: tag

value: Immortalized with c-myc, has the LacZ as a marker/tracer

value: culture by the time of RNA extraction is 3-4 days (50% confluency)


title: whole heart, P1, rep 1  [MoGene[gene_level]]

description: whole heart – P1


title: WildType_Replicate4

description: WildType Replicate 4

source_name: WildType Replicate 4

value: WT

value: whole worm


title: pathogen isolates: Mock - time: 24 hai - rep3

description: PI462312  mock treatment 24 hours

source_name: leaf (pathogen isolates: Mock - time: 24 hai)

tag: pathogen isolates

value: 24 hr


title: cardiac bodies, rep 1 [MoGene[gene_level]]

description: cardiac bodies

source_name: cardiac bodies

value: 14 day

value: cardiac bodies (cell culture)


title: Hpl2_KO_Mutant_Replicate2

description: Hpl2 KnockOut Mutant Replicate 2

source_name: Hpl2 KnockOut Mutant Replicate 2


title: His24_KO_Mutant_Replicate1

description: His24 KnockOut Mutant Replicate 1

source_name: His24 KnockOut Mutant Replicate 1


title: pathogen isolates: Mock - time: 12 hai - rep3

description: PI462312  mock treatment 12 hours

source_name: leaf (pathogen isolates: Mock - time: 12 hai)

value: 12 hr


title: embryonic bodies, rep 1 [MoGene[gene_level]]

description: embryonic bodies

source_name: embryonic bodies

value: 7 days

value: embryonic bodies (cell culture)


title: whole heart, E17.5, rep 1 [MoGene[gene_level]]

description: whole heart – E17.5


title: cardiac bodies, rep 2 [MoEx[exon_level]]

description:
cardiac bodies
probe_group_file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps and MoEx-1_0-st-v1.r2.dt1.mm9.core.ps

data_processing: RMA normalized, gene and exon level expression values from Affymetrix Power Tools

growth_protocol: Mouse embryonic stem cells are differentiated into cardiomyocytes with DMEM based culture media supplied with 10% serum.

extract_protocol: RNA was extracted from each samples with TRIzol reagent (Invitrogen). Isolated RNAs were then treated with the RiobMinus rRNA reduction kit (Invitrogen), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).


title: cardiac bodies, rep 2 [MoGene[gene_level]]

description: cardiac bodies


title: pathogen isolates: Mock - time: 24 hai - rep2

description: PI462312  mock treatment 24 hours

value: Mock

value: PO:0007134 A vegetative growth

value: soil mix


title: cardiac bodies, rep 1 [MoEx[exon_level]]


title: His24_KO_Mutant_Replicate2

description: His24 KnockOut Mutant Replicate 2

source_name: His24 KnockOut Mutant Replicate 2


title: embryonic bodies, rep 1 [MoEx[exon_level]]

description:
embryonic bodies
probe_group_file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps and MoEx-1_0-st-v1.r2.dt1.mm9.core.ps


title: Hpl1_KO_Mutant_Replicate1

description: Hpl1 KnockOut Mutant Replicate 1

source_name: Hpl1 KnockOut Mutant Replicate 1


title: embryonic bodie, rep 2 [MoGene[gene_level]]

description: embryonic bodies


title: Hpl2_KO_Mutant_Replicate1

description: Hpl2 KnockOut Mutant Replicate 1

source_name: Hpl2 KnockOut Mutant Replicate 1


title: Hpl1_KO_Mutant_Replicate2

description: Hpl1 KnockOut Mutant Replicate 2

source_name: Hpl1 KnockOut Mutant Replicate 2


title: undifferentiated ES cells, rep 2 [MoEx[exon_level]]

description:
undifferentiated ES cells
probe_group_file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps and MoEx-1_0-st-v1.r2.dt1.mm9.core.ps

source_name: undifferentiated ES cells

value: 0 days

value: undifferentiated ES (cell culture)


title: embryonic bodie, rep 2 [MoEx[exon_level]]


title: Limb H3K27Ac

description: H3K27Ac ChIP Forelimbs/autopods, Biological Rep 1-2

source_name: H3K27Ac ChIP DNA from E12.5 mouse autopods

tag: developmental stage

value: embryo

value: Forelimb/ autopod

value: Abcam

source_name: Input DNA from E12.5 mouse limbs


title: undifferentiated ES cells, rep 2 [MoGene[gene_level]]

description: undifferentiated ES cells


title: pathogen isolates: Mock - time: 12 hai - rep1

description: PI462312  mock treatment 12 hours


title: pathogen isolates: Mock - time: 24 hai - rep1

description: PI462312  mock treatment 24 hours


title: undifferentiated ES cells, rep 1 [MoGene[gene_level]]

description: undifferentiated ES cells


title: Effects of dexamethasone on human skeletal muscle BL rep

source_name: Human vastus lateralis muscle, control

tag: agent

value: control

tag: gender

value: male

value: skeletal muscle

source_name: Human vastus lateralis muscle, 4-d dexamethasone treatment

value: 4-d dexamethasone


title: pathogen isolates: Mock - time: 12 hai - rep2

description: PI462312  mock treatment 12 hours


title: undifferentiated ES cells, rep 1 [MoEx[exon_level]]

tag: tissue/cell  type


title: Severe stress condition, 75 days after germination

status: Public on Nov 27 2011

city: Hyderabad

first: Markandeya

last: Gorantla

state: Andhra Pradesh

address: University of Hyderabad

department: Department of Plant Science

country: India

institute: university of Hyderabad

description: A4 - 75 Days

hyb_protocol: The dye-labeled cDNA once quantified, equal amounts of cDNA from tester and reference samples were pooled and was precipitated by adding 1/10th of Sodium acetate and 2.5 volumes of ethanol, the cDNA populations are spun at  8000 RPM for 10 min. to pellet down the cDNA, extreme care was taken not to disturb the pellet while decanting. The pellet was washed with 70% ethanol and dried in a speedvac, and the pellet was directly dissolved in 50ul of low temperature hybridization buffer from Sigma. We have developed protocols that give reproducible, high-quality hybridization results while maximizing the measured fluorescence from the array. Aminosilane-coated slides bind DNA with high efficiency. Prior to hybridization, the free amine groups on the slide were blocked or inactivated to avoid nonspecific binding of labeled cDNA to the slide which can deplete the probe and produce high background. The slides were blocked in Sodium Borate and Succinic anhydride, a solution of 0.5M Sodium Borate was prepared by dissolving Sodium Borate by heating until it got dissolved and ph was adjusted to 8.0. Simultaneously 900mg succinic anhydride was dissolved in 47ml of 1 methyl 2 pyrillidone (Sigma Aldrich), in a 50ml falcon tube and as soon as the last flake of succinic anhydride was dissolved 2.2ml, 0.5M Sodium Borate was added and was mixed well. Microarray slides stored at 4 deg C were allowed to come to room temperature, the required number of slides were dipped in the above solution and kept for shaking on an orbital shaker for 15 min, and care was taken that the printed side does not touch each other, the slides were placed in opposite direction such that the non printed side touches each other. This was Scaled up if more than 2 slides were processed using a Lipshaw slide holder and jar. After 15 min the slides were washed in 0.1% SDS for 2 min in a clean glass jar (Lipshaw dish staining assembly) the SDS solution was removed and a brief 10sec wash was performed with milliQ water, and were transferred to a fresh dish jar containing  2XSSC,  the slides were washed twice with 2X SSC for 2 min each. Denaturation was performed by dipping the slides in boiling hot water at 95 deg C and incubating them for 2 min. The denatured DNA was fixed by transferring the slides in ice cold 200 pint 95% ethanol (Aldrich), care was taken to avoid shattering of slides due to sudden transfer of slides from boiling hot water to ice cold ethanol. Slides were retained in ice cold ethanol for 2 to 3 min before being transferred to a 50ml falcon tube with a tissue paper at the bottom and the slides. The slides were spun without cap at 1000RPM for 5 min at RT, there is every possibility that the slide coating could peel off but the substrate we selected withstood the pre-hybridization conditions and all the slides processed did not peel. After spinning the slides were immediately used for hybridization. Data from each fluorescence channel was collected and stored as a 16-bit TIFF image. The two images were loaded on to the two different channels of Quantarray and grids were generated taking printing style in to the consideration. Overlay of the two channel intensities revealed the hybridization was good and more or less similar intensities were observed in adjacent in-slide replicates. A total of 48 blocks with 324 features in each were generated with 12 rows and 4 columns in each covering all the ~15550 features including controls. A total of 15550 cells were generated with 5 - 23 pixel spot size adjusted as to cover all the features of the superimposed slide. In house custom perl scripts were written to facilitate the annotation to the features on the array. Annotation including gene function, chromosome Bac/Pac location, map positions, unigene cluster, functional classification, and redundancy were provided to facilitate further analysis with ease. All the grids were processed and spots were quantified in the cells eliminating local background. The spots with poor quality in either of the slide were flagged off and were eliminated during the normalization. The intensities captured at the saturated level were excluded from further analysis and quantified spots from each analysis were stored for further analysis. The labeled cDNA dissolved in low temperature hybridization buffer from sigma, two blocking agents yeast tRNA (Sigma) at a concentration of 20ug per hybridization, and 2ug poly DA (Sigma) per hybridization were used to block non-specific hybridization, these two were mixed with the labeled target and was denatured at 95 deg C for 5 minutes, during this period the pre-hybridized slides were heated to bring the slides to 45 deg C for hybridization. After denaturation the labeled probe was applied to a pre-hybridized microarray slide and covered with 22mm x 60mm plastic hybrid-slips (Sigma, Schleicher and Schuell Gmbh). Once the coverslip is properly placed without any air bubble trapped between the slide and the coverslip, the slides were inverted (array side down) and kept inside a 50ml falcon tube, which we used as an makeshift hybridization chamber, a small piece of tissue paper was soaked with 1ml of 3x SSC and was kept inside the bottom of falcon tube to maintain humidity during hybridization and to avoid drying of the target, which will make the coverslip stick to the slide and result in failure of hybridization. We placed the 50ml falcon tube in hybridization bottle (Amersham Pharmacia) and with support on two sides with bottle holders these units were dipped in hot water bath set at 50 deg C. Weight rings were used between the bottles to avoid floating of the hybridization bottles. Hybridization was allowed to carry out for 16 hours in dark at 50 Deg C. The slides from the water bath were taken out after 16 hours of hybridization and these slides were carefully dipped in wash buffer 1 (1x SSC , 0.03% SDS), the slides were shaken gently until the coverslip come off by itself, in any case care was taken not to take of the coverslips manually, but rather was allowed to soak in the buffer for some more time by shaking gently. Once the coverslips come off, the slides were transferred to wash buffer 2 (0.2x SSC)  and the slides were washed  for 2 min by gently shaking and then transferred to wash buffer 3 (0.05x SSC) these slides were further washed with gently agitation for 5 min. The slides were then transferred to a 50ml falcon tube and with its lid open were spun at 1000 RPM for 5 min in order to dry the slides for scanning. Extreme care was taken that the slides are not dried between transfers.

scan_protocol: Scanning of the hybridized slide was done using ScanArray 3000 (Genomic solutions). Hybridized slides are scanned first in the high wave length channel (594nm and 647nm), and then the lower wavelength (488nm and 555nm), as high wave length channel dyes are more susceptible to photo-degradation than lower wavelength channels. Data from each fluorescence channel was collected and stored as a 16-bit TIFF image. To quantify the right intensities slides were scanned as soon as possible after washing. The slides were scanned at appropriate PMT gain and 100% laser power, the slides were scanned at various PMT gains from low to high at 30 microns scan resolution, then appropriate PMT settings for both the dye wavelength was standardized. Scanning was done at PMTs where we could observe 20 to 30 white spots as such the overall intensities are good. This was determined by observing the RI (Ratio Vs Intensity) plot of intensities. Once the right PMT gains for both the channels were determined, the slides were scanned at 10micron resolution. During quantification we used the highest threshold limits for spot intensity calculation and ANOVA for performed for these low PMT and High PMT technical replicates. During quantification care was taken that the week spots and saturated spots are flagged off during intensity calculation. To minimize the background fluorescence, care was taken such that the background fluorescence is as low as possible, using appropriate blocking agents. Scanned images generated from microarray experiment were quantified with Quantarray (GSI Lumonics), software.

data_processing: Total intensity normalization was first applied to all the data points assuming the initial RNA taken for the hybridization is equal in both the samples. It has been observed based on pre- and post-normalized RI plot (log ratio intensity vs. log intensity product) the factor calculation for scaling up the data was not appropriate. Keeping the systemic errors like systematic dependence of log2 values on the intensity, the Lowess (LOcally WEighted linear regreSSion) normalization technique was applied to all the data points and compared with the total intensity normalized plots. Lowess normalization factor was calculated considering internal controls as housekeeping genes and applied to whole data using avadis3.3 (Strand Life Sciences, India). The genes were hierarchically clustered after normalization at experiment level initially and k-means clustered subsequently. The normalized data from each developmental stage (7 DAS to 33 DAS) within the stress level (A2, A3, A4) were taken for calculating fold change of gene expression. Mean shift normalization was used for experiment normalization, considering all the data points for each of the analysis.  Hierarchical clustering was carried out for genes and experiments in every analysis. Ten to twenty significant clusters from hierarchically clustered data were identified and further used for k-means clustering. Fold change value of gene expression was calculated using exponent of log value in each of the analysis and clusters with significant fold change difference were identified.

label: Alexa 488

organism: Oryza sativa Indica Group

source_name: rice seedlings, control, 75 DAG

label_protocol:
Probes for microarray analysis are prepared from RNA templates by first strand synthesis of cDNA containing amino-allyl-labeled nucleotide dCTP and amino-hexyl modified dATP for both control and stress samples, followed by a covalent coupling to the NHS-ester of the appropriate Cyanine fluor. This method has proven highly efficient for labeling all kinds of tissues from rice for expression analysis. Among the number of reverse transcriptases used, including AMV and MMLV we  have found that Superscript III RT (Life Technologies; Cat# L-1014-02) generates probes with significantly greater activity. Coupling of modified cDNA with fluorescent probes was done by photostable Alexafluor  fluorescent dyes (we have used Alexafluor 488 for control labeling and Alexafluor 594 NHS ester dyes for coupling stressed samples). The photosensitivity of dyes was minimized by avoiding exposure to light during labeling, hybridization, washing, and scanning processes. Upon receipt, these NHS ester dyes were stored in light-proof tubes and stored at -20C until needed. All reactions were carried out in foil-wrapped tubes and all hybridizations and washes in foil-wrapped containers.
First strand amino modified cDNA synthesis for  labeling, the quality of total RNA for both control and stressed experimental sample, were quantitated and suspended 40ug of total RNA in not more than 10ul DEPC treated water. Anchored oligo DT primer was used; this oligo (20mer oligo DT) primed with equal concentrations of A, C, G, or T, allowed proper priming of the primer to the 5’ end of the cDNA, this helped us in avoiding reverse transcription of long stretches of dT in cDNA. Five microgram of anchored primer was mixed with 40ug of total RNA and the reaction was incubated for 5’min at 700c, following which the reaction was snap cooled for 1 min on ice, to which the following components were added, 5x first strand buffer - 6.0ul, 10mM dNTP mix (contains modified aminoallyl dUTP and aminohexyl dATP - 1.5ul, RNAse out 20units/ul - 1.5ul Super script RT III 400 units/ul - 2.0ul. DEPC treated water was added to make-up a final volume of 30.0 ul.  The above RXN was Incubate for 2 hours at 42 deg in a thermocycler.
Once first strand amino modified cDNA synthesis was achieved, alkaline hydrolysis and neutralization was performed. To the amino modified cDNA, 15 ul 1N NaoH was added to denature the RNA through hydrolysis from RNA-DNA hybrid and was incubated for 10’min at 70 deg C for complete RNA denaturation. To this, 15ul of 1N HCL was added to neutralize the pH and mixed gently. To the above reaction, 20ul Sodium Acetate, pH 5.2 was added and mixed gently. Once the  cDNA is generated with amino-modified nucleotides the cDNA was purified to remove unincorporated dNTPs and hydrolyzed RNA, using bind wash elute SNAP columns (Life Technologies) as per manufacturers instructions following which, the cDNA was O/N ethanol precipitated by adding 1/10th volume Sodium Acetate and 2.5 volumes ethanol the  aminoallyl and aminohexyl modified cDNA  was further   centrifuged at 12000 RPM for 10 min to pellet it down and the pellet was washed with 70% ethanol and dried down in speedvac (Savant). The pellet was dissolved in 6ul sterile water. For coupling of the dye, the dye vails (Alexa fluor dyes) were allowed to come down to room temperature in order to avoid condensation of water inside the vial. The dyes were dissolved in 4ul of DMSO. For coupling 10ul of 2x coupling buffer (sodium bicarbonate) was added to modified cDNA to bring the final concentration to 1x, to the above reaction 4ul of the dissolved dye was added and allowed to couple overnight in dark at room temperature. Further, the cDNA was purified by bind wash elute SNAP columns (Life Technologies) as per manufacturers instructions to remove any unreacted free dye molecules.

growth_protocol: Rice seeds were surface sterilized, washed and germinated in a growth chamber. Fifteen-day-old seedlings were transplanted in the field for drought stress induction. The transplanted seedlings were grown in 100% field capacity with 2cm standing water until day 30. Micronutrients and urea were determined for each plot and  were dissolved in 1 lit water which was used to fertigate all the plots.

extract_protocol: Total RNA was isolated from leaf and panicle samples collected at different time intervals after stress treatment using Trizol (Chirgwin et al., 1979; Chomczynski and Sacchi, 1987) from Life Technologies with minor modifications. The harvested tissues were stored immediately in RNA later (Ambion) and stored at 4 deg C for 24 hours and after which the RNA latter was removed and the samples were quick frozen in liquid nitrogen and stored at –70 Deg C. Five grams of freshly harvested or frozen tissues were ground in liquid nitrogen to a fine powder, transferred to 50ml tubes with 15ml of Trizol in it. The sample was suspended well in Trizol and incubated at room temperature for 5 minutes. Cellular debris was removed by centrifugation at 4000rpm (2700g) for 15min at 4 Deg C. The supernatant was transferred to a fresh RNAase-free 50ml oakridge tube. To it, 3ml of chloroform (0.2ml/1ml Trizol) was added and shaken vigorously for 1 minute. After which the suspension was incubated at room temperature for 5 minutes. The samples were centrifuged at 4000rpm (2700 g) for 15min at 4 Deg C to remove proteins and high molecular weight DNA, following centrifugation three different layers are observed. The top supernatant layer contains RNA, the intermittent layer is a denatured protein layer, and the lower layer is high molecular weight DNA. The upper aqueous layer was carefully removed without disturbing the protein layer and was transferred to a fresh RNAase free oakridge tube. To this equal volume of isopropanol was added to precipitate the RNA and was incubated at RT for 15 minutes. Following which the precipitated sample was centrifuged at 15,000rpm (21,000g) for 15 minutes to pellet the RNA. The supernatant was discarded and the pellet resuspended in 70% ethanol. The RNA pellet was resuspended in diethylpyrocarbonate (DEPC) treated water. The quality of the total RNA was determined through 1.2% denatured agarose formaldehyde gel and concentration estimated spectrophotometrically. For labeling at university of Georgia the samples were resuspended in 1/10th volume DEPC treated sodium acetate and 2.5 volumes ethanol. Prior to labeling the precipitated RNA was spun at 12000 RPM for 10 min and washed with 70% ethanol. The RNA was dried in a savant rotary vapor trap and resuspended in RNAase free milliQ water for labeling.

treatment_protocol: The transplanted seedlings were grown in 100% field capacity with 2cm standing water until day 30. Field drought stress was initiated from day 31 at 100%, 60%, 40% and 15% field capacities designated as A1, A2, A3, and A4. It took 7 days for the onset of the actual drought for the experimental plots to reach their designated field capacities from 100% FC. Samples were collected at various stages and drought stress regimes based on the developmental stages of the plant. Under each stress regime, target samples were prepared from field drought stressed plants under A2, A3 and A4  stresses at vegetative (DAG 45, 52), pre-anthesis  (DAG 55), post-anthesis and seed setting stages (DAG 63, 67 , 71 & 75). A sampling of 5 leaves per plot were used to obtain high quality RNA samples for labeling and hybridization for all the above targets under all the stress regimes.

tag: subspecies

value: indica

tag: cultivar

value: Nagina 22 (N22)

value: leaves

tag: treatment

tag: treatment duration

value: 37 days

tag: days after germination

value: 75 days

label: Alexa 594

source_name: rice seedlings, severe stress, 75 DAG

value: severe drought stress


title: Severe stress condition, 63 days after germination

description: A4 - 63 Days

source_name: rice seedlings, control, 63 DAG

value: 25 days

value: 63 days

source_name: rice seedlings, severe stress, 63 DAG


title: Severe stress condition, 71 days after germination

description: A4 - 71 Days

source_name: rice seedlings, control, 71 DAG

value: 33 days

value: 71 days

source_name: rice seedlings, severe stress, 71 DAG


title: Severe stress condition, 67 days after germination

description: A4 - 67 Days

source_name: rice seedlings, control, 67 DAG

value: 29 days

value: 67 days

source_name: rice seedlings, severe stress, 67 DAG


title: Severe stress condition, 59 days after germination

description: A4 - 59 Days

source_name: rice seedlings, control, 59 DAG

value: 21 days

value: 59 days

source_name: rice seedlings, severe stress, 59 DAG


title: After 48 h replicate 3

city: Tsukuba

first: Hirohide

last: Uenishi

state: Ibaraki

address: 2-1-2 Kannondai

country: Japan

institute: National Institute of Agrobiological Sciences

description: Biological replicate 3 of 3, relative expression of the cells 6 d after the start of differentiation to the undifferentiated cells

hyb_protocol: The mixed labelled cRNAs were hybridized overnight to each array at 65 °C under constant rotation in the hybridization buffer supplied with the Gene Expression Hybridization Kit (Agilent).

scan_protocol: Arrays were washed by using a Gene Expression Wash Pack (Agilent) and scanned with a G2505B DNA microarray scanner (Agilent) in accordance with the manufacturer’s protocol.

data_processing: Linear and LOWESS normalized, background subtracted data obtained from log10 of processed Red signal/processed Green signal. Agilent Feature Extraction Software was used. After normalization within the array, signal intensity values were log10-transformed and the 75th percentile value was adjusted across the arrays. The value of the difference between the adjusted and unadjusted 75th percentile values was subtracted from the expression values of the spots on each array. Spot data that the Feature Extraction Software did not consider significantly different from or greater than background were discarded.

organism: Sus scrofa

source_name: PSPA, 48 h after the start of differentiation

label_protocol: Each total RNA (400 ng) was used to synthesize fluorescence-labelled complementary RNA (cRNA) by using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent) in accordance with the manufacturer’s protocol. Total RNAs of differentiated PSPA cells at various time points, and of the undifferentiated control, were labelled with cyanine-5 (Cy5) and cyanine-3 (Cy3), respectively. The labelled cRNA was purified by using a QIAGEN RNeasy Mini Kit (Qiagen).

growth_protocol: Cells were grown in a 5% CO2 humidified incubator at 37degreeC in DMEM supplemented with 10% FBS, 100U/mL penicillin, and 100 μg/mL streptomycin. The cells were trypsinised with phosphate-buffered saline (pH 7.4) containing 0.05% trypsin and 0.01% EDTA and were passaged every 4 days.

extract_protocol: Total RNA was extracted from PSPA cells at different time points after the start of differentiation by using RNeasy Lipid Tissue Midi Kit in accordance with the manufacturer's protocol.

treatment_protocol: After the cells had reached confluence, differentiation into adipocytes was induced by the use of differentiation medium, which was a high-glucose (4.5 g/L) DMEM containing 10% FBS, 5 μg/mL insulin, 0.25 μM dexamethasone, 33 microM biotin, 17 microM pantothenate, 5 mM octanoate, and antibiotics as previously described (Nakajima et al., Biochem. Biophys. Res. Comm. 309, 702-708, 2003). The differentiation medium was changed every second day.

tag: cell line

value: PSPA

tag: cell type

value: subcutaneous preadipocyte

tag: time

value: 48 h after the start of differentiation

source_name: PSPA, undifferentiated

value: control


title: After 6 d replicate 3

description: Biological replicate 3 of 3, relative expression of the cells 1 h after the start of differentiation to the undifferentiated cells

source_name: PSPA, 6 d after the start of differentiation

value: 6 d after the start of differentiation


title: After 2 h replicate 3

description: Biological replicate 3 of 3, relative expression of the cells 3 h after the start of differentiation to the undifferentiated cells

source_name: PSPA, 2 h after the start of differentiation

value: 2 h after the start of differentiation


title: Severe stress condition, 55 days after germination

description: A4 - 55 Days

source_name: rice seedlings, control, 55 DAG

value: indica

value: Nagina 22 (N22)

value: leaves

value: 17 days

value: 55 days

source_name: rice seedlings, severe stress, 55 DAG


title: Severe stress condition, 52 days after germination

description: A4 - 52 Days

source_name: rice seedlings, control, 52 DAG

value: 14 days

value: 52 days

source_name: rice seedlings, severe stress, 52 DAG

value: severe drought stress


title: Moderate stress condition, 75 days after germination

description: A3 - 75 Days

source_name: rice seedlings, control, 75 DAG

value: 37 days

value: 75 days

source_name: rice seedlings, moderate stress, 75 DAG

value: moderate drought stress


title: Severe stress condition, 45 days after germination

description: A4 - 45 Days

source_name: rice seedlings, control, 45 DAG

value: 7 days

value: 45 days

source_name: rice seedlings, severe stress, 45 DAG


title: After 4 h replicate 3

description: Biological replicate 3 of 3, relative expression of the cells 12 h after the start of differentiation to the undifferentiated cells

source_name: PSPA, 4 h after the start of differentiation

value: PSPA

value: subcutaneous preadipocyte

value: 4 h after the start of differentiation


title: After 3 h replicate 3

description: Biological replicate 3 of 3, relative expression of the cells 4 h after the start of differentiation to the undifferentiated cells

source_name: PSPA, 3 h after the start of differentiation

value: 3 h after the start of differentiation

value: control


title: After 12 h replicate 2

description: Biological replicate 2 of 3, relative expression of the cells 48 h after the start of differentiation to the undifferentiated cells

source_name: PSPA, 12 h after the start of differentiation

value: 12 h after the start of differentiation


title: Moderate stress condition, 52 days after germination

description: A3 - 52 Days

value: indica

value: Nagina 22 (N22)

value: leaves

source_name: rice seedlings, moderate stress, 52 DAG


title: After 3 h replicate 2

description: Biological replicate 2 of 3, relative expression of the cells 4 h after the start of differentiation to the undifferentiated cells


title: After 4 h replicate 2

description: Biological replicate 2 of 3, relative expression of the cells 12 h after the start of differentiation to the undifferentiated cells


title: Moderate stress condition, 55 days after germination

description: A3 - 55 Days

value: 17 days

value: 55 days

source_name: rice seedlings, moderate stress, 55 DAG


title: Moderate stress condition, 59 days after germination

description: A3 - 59 Days

source_name: rice seedlings, control, 59 DAG

value: 21 days

value: 59 days

source_name: rice seedlings, moderate stress, 59 DAG


title: After 1 h replicate 3

description: Biological replicate 3 of 3, relative expression of the cells 2 h after the start of differentiation to the undifferentiated cells

source_name: PSPA, 1 h after the start of differentiation

value: 1 h after the start of differentiation

source_name: PSPA, undifferentiated


title: Moderate stress condition, 63 days after germination

description: A3 - 63 Days

source_name: rice seedlings, control, 63 DAG

value: 25 days

value: 63 days

source_name: rice seedlings, moderate stress, 63 DAG

value: moderate drought stress


title: After 1 h replicate 2

description: Biological replicate 2 of 3, relative expression of the cells 2 h after the start of differentiation to the undifferentiated cells

value: PSPA


title: After 6 d replicate 2

source_name: PSPA, 6 d after the start of differentiation

value: subcutaneous preadipocyte

value: 6 d after the start of differentiation


title: After 48 h replicate 2

description: Biological replicate 2 of 3, relative expression of the cells 6 d after the start of differentiation to the undifferentiated cells

source_name: PSPA, 48 h after the start of differentiation

value: 48 h after the start of differentiation


title: Moderate stress condition, 71 days after germination

description: A3 - 71 Days

source_name: rice seedlings, control, 71 DAG

value: control

value: 33 days

value: 71 days

source_name: rice seedlings, moderate stress, 71 DAG


title: After 6 d replicate 1

description: Biological replicate 1 of 3, relative expression of the cells 1 h after the start of differentiation to the undifferentiated cells


title: Moderate stress condition, 45 days after germination

description: A3 - 45 Days

source_name: rice seedlings, control, 45 DAG

value: indica

value: Nagina 22 (N22)

value: 7 days

value: 45 days

source_name: rice seedlings, moderate stress, 45 DAG


title: Brain H3K4me3

description: H3K4me3 ChIP Brain, Biological Rep 1-2

source_name: H3K4me3 ChIP DNA from E12.5 mouse brain

value: embryo

value: Forebrain

tag: antibody

tag: antibody manufacturer

value: Abcam

tag: antibody catalog number

source_name: Input DNA from E12.5 mouse limbs

value: Forelimb/ autopod


title: After 2 h replicate 2

description: Biological replicate 2 of 3, relative expression of the cells 3 h after the start of differentiation to the undifferentiated cells

source_name: PSPA, 2 h after the start of differentiation

value: 2 h after the start of differentiation


title: Mild stress condition, 67 days after germination

description: A2 - 67 Days

source_name: rice seedlings, control, 67 DAG

tag: tissue

value: leaves

value: 29 days

value: 67 days

source_name: rice seedlings, mild stress, 67 DAG

value: mild drought stress


title: After 3 h replicate 1

description: Biological replicate 1 of 3, relative expression of the cells 4 h after the start of differentiation to the undifferentiated cells

source_name: PSPA, 3 h after the start of differentiation

value: PSPA

value: subcutaneous preadipocyte

value: 3 h after the start of differentiation


title: Mild stress condition, 59 days after germination

description: A2 - 59 Days

source_name: rice seedlings, control, 59 DAG

value: control

value: 21 days

value: 59 days

source_name: rice seedlings, mild stress, 59 DAG


title: Mild stress condition, 75 days after germination

description: A2 - 75 Days

source_name: rice seedlings, control, 75 DAG

value: indica

value: Nagina 22 (N22)

value: 37 days

value: 75 days

source_name: rice seedlings, mild stress, 75 DAG


title: Mild stress condition, 71 days after germination

description: A2 - 71 Days

value: 33 days

value: 71 days

source_name: rice seedlings, mild stress, 71 DAG


title: After 4 h replicate 1

description: Biological replicate 1 of 3, relative expression of the cells 12 h after the start of differentiation to the undifferentiated cells

source_name: PSPA, 4 h after the start of differentiation

value: 4 h after the start of differentiation

source_name: PSPA, undifferentiated


title: Moderate stress condition, 67 days after germination

description: A3 - 67 Days

value: leaves

source_name: rice seedlings, moderate stress, 67 DAG

value: moderate drought stress


title: After 12 h replicate 1

description: Biological replicate 1 of 3, relative expression of the cells 48 h after the start of differentiation to the undifferentiated cells

source_name: PSPA, 12 h after the start of differentiation

value: 12 h after the start of differentiation


title: Mild stress condition, 63 days after germination

description: A2 - 63 Days

source_name: rice seedlings, control, 63 DAG

value: 25 days

value: 63 days

source_name: rice seedlings, mild stress, 63 DAG

value: mild drought stress


title: Mild stress condition, 55 days after germination

description: A2 - 55 Days

source_name: rice seedlings, control, 55 DAG

value: 17 days

value: 55 days

source_name: rice seedlings, mild stress, 55 DAG


title: After 1 h replicate 1

description: Biological replicate 1 of 3, relative expression of the cells 2 h after the start of differentiation to the undifferentiated cells

source_name: PSPA, 1 h after the start of differentiation

value: PSPA

value: subcutaneous preadipocyte

value: 1 h after the start of differentiation

value: control


title: After 2 h replicate 1

description: Biological replicate 1 of 3, relative expression of the cells 3 h after the start of differentiation to the undifferentiated cells

source_name: PSPA, 2 h after the start of differentiation

value: 2 h after the start of differentiation


title: Mild stress condition, 52 days after germination

description: A2 - 52 Days

source_name: rice seedlings, control, 52 DAG

value: indica

value: Nagina 22 (N22)

value: 14 days

value: 52 days

source_name: rice seedlings, mild stress, 52 DAG


title: Mild stress condition, 45 days after germination

description: A2 - 45 Days

source_name: rice seedlings, control, 45 DAG

value: leaves

value: 7 days

value: 45 days

source_name: rice seedlings, mild stress, 45 DAG


title: After 48 h replicate 1

description: Biological replicate 1 of 3, relative expression of the cells 6 d after the start of differentiation to the undifferentiated cells

source_name: PSPA, 48 h after the start of differentiation

value: 48 h after the start of differentiation


title: 6_AGN193109+tRA_biological rep2

status: Public on Nov 26 2011

city: London

first: Qihe

last: Xu

address: 123, Coldharbour Lane

country: United Kingdom

institute: King's College London

description:
6_AGN193099+tRA
Gene expression data in mIMCD-3 cells treated with 1 μM AGN193109 + 0.2 μM tRA

hyb_protocol: 5.5 ug of cDNA were fargmented and labeled, and 2.3 ug of cDNA were hybridized on GeneChip Mouse Gene 1.0 ST arrays for 16 hr at 45 C, at a rotation of 60 rpm according to company's protocol (Affymetrix GeneChip WT Terminal Labelling and Hybridisation User Manual, Rev. 4). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to company's protocol (Affymetrix GeneChip Expression Wash, Stain and Scan User Manual for Cartridge Arrays, Rev. 3).

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

data_processing: CEL files were generated using Affymetrix GeneChip Command Console software, and the  data were analyzed and normalized using Robust Multichip Analysis (RMA) method with Affymetrix Expression Console software to generate CHP files. CHP files were then imported to Qlucore Omics Explorer to short-list target genes potentially regulated by AGN193109 and DEAB.

source_name: mIMCD-3 cells_1 μM AGN193109 + 0.2 μM tRA

label_protocol: Biotinylated cDNA were prepared from 500 ng total RNA according to company's protocol (Ambion WT Expression Kit for Affymetrix GeneChip Whole Transcript (WT) Expression Arrays, edition 05/2009).

growth_protocol: mIMCD-3 cells were routinely grown in DMEM-F12 containing penicillin (100 IU/ml), streptomycin (100 μg/ml) and amphotericin B (2.5 μg/ml), supplemented with 5% fetal calf serum, at 37C and 5% CO2. Cells were passaged at a ratio of 1:4-1:8.

extract_protocol: Total RNA was extracted using QIAshredder spin column and Rneasy Mini Kit according to manufacturer's instructions.

treatment_protocol: mIMCD-3 cells grown on 35 mm dishes and treatment protocols were as described before in "overall design"

value: mouse inner medullary collecting duct cells (mIMCD-3)


title: 18_DEAB+tRA_biological rep3

description:
DEAB+tRA_9
Gene expression data in mIMCD-3 cells treated with 25 μM DEAB + 0.01 μM tRA

source_name: mIMCD-3 cells_25 μM DEAB + 0.01 μM tRA


title: 10_vehicle_biological rep1

description:
VEH_1
Gene expression data in mIMCD-3 cells treated with vehicle

source_name: mIMCD-3 cells_vehicle (0.1% ethanol and 0.1% DMSO)


title: 14_DEAB_biological rep2

description:
DEAB_5
Gene expression data in mIMCD-3 cells treated with 25 μM DEAB

source_name: mIMCD-3 cells_25 μM DEAB


title: 9_AGN193109+tRA_biological rep3

description:
9_AGN193099+tRA
Gene expression data in mIMCD-3 cells treated with 1 μM AGN193109 + 0.2 μM tRA


title: 8_AGN193109_biological rep3

description:
8_AGN193109
Gene expression data in mIMCD-3 cells treated with 1 μM AGN193110

source_name: mIMCD-3 cells_1 μM AGN193110


title: 13_vehicle_biological rep2

description:
VEH_4
Gene expression data in mIMCD-3 cells treated with vehicle


title: 11_DEAB_biological rep1

description:
DEAB_2
Gene expression data in mIMCD-3 cells treated with 25 μM DEAB


title: 12_DEAB+tRA_biological rep1

description:
DEAB+tRA_3
Gene expression data in mIMCD-3 cells treated with 25 μM DEAB + 0.01 μM tRA


title: 15_DEAB+tRA_biological rep2

description:
DEAB+tRA_6
Gene expression data in mIMCD-3 cells treated with 25 μM DEAB + 0.01 μM tRA


title: 5_AGN193109_biological rep2

description:
5_AGN193109
Gene expression data in mIMCD-3 cells treated with 1 μM AGN193110


title: 4_vehicle_biological rep2

description:
4_VEH
Gene expression data in mIMCD-3 cells treated with vehicle


title: 16_vehicle_biological rep3

description:
VEH_7
Gene expression data in mIMCD-3 cells treated with vehicle


title: 05-53384a12 (M)

city: Tampere

first: Antti

last: Ylipää

address: Korkeakoulunkatu 1

country: Finland

institute: Tampere University of Technology

hyb_protocol: Samples were hybridized according to Agilent's protocol

scan_protocol: Arrays were scanned with Agilent's scanner using manufacturer's instructions.

data_processing: Data were extracted using Agilent Feature Extraction software (CGH-v4_91). Logratios were lowess-normalized. Ratio is always tumor/ref; dye-swaps were performed as necessary.

source_name: Commercial DNAs

label_protocol: Standard protocol for labeling genomic DNA

growth_protocol: Human primary tumor samples obtained by surgical resection

extract_protocol: Genomic DNA was extracted using the DNeasy kit from Qiagen cat# 69506 with minor modifications as mentioned in the Agilent aCGH protocol ULS Labeling Version 3.0.

treatment_protocol: Fresh-frozen (Tianjin cohort) or formalin-fixed and paraffin-embedded (MD Anderson cohort)

tag: source

value: Clontech Laboratories Inc

value: male

source_name: MPNST

value: MDACC


title: Pt55, larynx

city: Thessaloniki

first: elena

last: fountzilas

address: School of Medicine, Pathology Department

department: Medical Oncology

country: Greece

institute: Aristotle University of Thessaloniki, Greece

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: GenomeStudio v2009 was used to extract raw data and the lumi bioconductor package to perform quantile normalization. Analysis was performed using the BRB Array Tools software.

source_name: Patient 55, laryngeal cancer

label_protocol: RNA was labelled using the WG-DASL kit from Illumina.

extract_protocol: Rneasy FFPE kit, Qiagen.

treatment_protocol: Tumor-cell content of more than 50%. All slides were once more reviewed by a single specialist pathologist. Formalin-fixed, paraffin-embedded (FFPE) samples were cut into 1-3 mm cores.

value: laryngeal cancer

tag: grade

tag: age

value: not available

tag: disease-free survival (dfs)

value: 7 months

tag: disease-free survival (dfs) event

value: 1 (recurrence)

tag: dataset

value: training


title: 7_vehicle_biological rep3

description:
7_VEH
Gene expression data in mIMCD-3 cells treated with vehicle


title: Pt56, larynx

source_name: Patient 56, laryngeal cancer

value: 28 months

value: 0 (no recurrence)

value: validation


title: 17_DEAB_biological rep3

description:
DEAB_8
Gene expression data in mIMCD-3 cells treated with 25 μM DEAB


title: 0618083g1 (M)

tag: gender


title: 05-189092b7(F)

value: female


title: 3_AGN193109+tRA_biological rep1

description:
3_AGN193099+tRA
Gene expression data in mIMCD-3 cells treated with 1 μM AGN193109 + 0.2 μM tRA


title: 04-46768a10 (M)


title: 2_AGN193109_biological rep1

description:
2_AGN193109
Gene expression data in mIMCD-3 cells treated with 1 μM AGN193110


title: Pt54, larynx

source_name: Patient 54, laryngeal cancer

value: 13 months


title: 1_vehicle_biological rep1

description:
1_VEH
Gene expression data in mIMCD-3 cells treated with vehicle


title: 96-25006c2 (F)


title: 94-23965b2 (M)


title: Pt53, larynx

source_name: Patient 53, laryngeal cancer

value: 9 months


title: 96-45652a7 (M)


title: After 12 h replicate 3

description: Biological replicate 3 of 3, relative expression of the cells 48 h after the start of differentiation to the undifferentiated cells

source_name: PSPA, 12 h after the start of differentiation

value: PSPA

value: subcutaneous preadipocyte

value: 12 h after the start of differentiation

source_name: PSPA, undifferentiated

value: control


title: Pt51, larynx

source_name: Patient 51, laryngeal cancer

value: 2 months


title: Pt48, larynx

source_name: Patient 48, laryngeal cancer

value: 1 months


title: Pt46, larynx

source_name: Patient 46, laryngeal cancer

value: laryngeal cancer

value: 40 months


title: Pt50, larynx

source_name: Patient 50, laryngeal cancer

value: not available

value: 50 months


title: 94-5944c3) (M)

value: MDACC

value: male

value: Clontech Laboratories Inc


title: 04-16491d9) (M)


title: Pt45, larynx

source_name: Patient 45, laryngeal cancer

value: 32 months

value: 0 (no recurrence)

value: training


title: 98-27212 (M)


title: 96-07685 (F)

value: female


title: 04-62849b13) (F)


title: 06-13338 (F)


title: 86-4158 (F)


title: 97-13459a3 (F)


title: 96-44488b2) (F)


title: 94-44142 (M)


title: 05-14488 (M)


title: Pt47, larynx

source_name: Patient 47, laryngeal cancer

value: 21 months

value: validation


title: Pt52, larynx

source_name: Patient 52, laryngeal cancer

value: 3 months

value: 1 (recurrence)


title: 98-25401(F)


title: Pt49, larynx

source_name: Patient 49, laryngeal cancer

value: 16 months


title: 04-9571b7(F)


title: Pt41, larynx

source_name: Patient 41, laryngeal cancer


title: Pt40, larynx

source_name: Patient 40, laryngeal cancer

value: 59 months


title: Pt44, larynx

source_name: Patient 44, laryngeal cancer

value: laryngeal cancer

value: 10 months


title: Pt39, larynx

source_name: Patient 39, laryngeal cancer

value: not available

value: 22 months


title: Pt42, larynx

source_name: Patient 42, laryngeal cancer

value: 161 months


title: 90-30875 (F)

source_name: Commercial DNAs

source_name: MPNST

value: MDACC


title: Pt43, larynx

source_name: Patient 43, laryngeal cancer

value: 63 months


title: 05-48556G15 (M)

value: Clontech Laboratories Inc

value: male


title: Pt38, larynx

source_name: Patient 38, laryngeal cancer

value: 0 (no recurrence)


title: 03-54634 (M)


title: 98-22119 (M)


title: Pt33, larynx

source_name: Patient 33, laryngeal cancer

value: 107 months

value: training


title: Pt37, larynx

source_name: Patient 37, laryngeal cancer

value: 0 months

value: validation


title: Pt36, larynx

source_name: Patient 36, laryngeal cancer

value: 80 months


title: 96-02157A1 (M)


title: 13792-A1 (F)

value: Tianjin

value: female


title: Pt31, larynx

source_name: Patient 31, laryngeal cancer

value: laryngeal cancer

value: 46 months


title: 14087-A1(M)


title: Pt35, larynx

source_name: Patient 35, laryngeal cancer

value: 85 months


title: Pt27, larynx

source_name: Patient 27, laryngeal cancer

value: 134 months


title: 14231-A1 (F)


title: 14909-A1


title: 14829-A1


title: Pt26, larynx

source_name: Patient 26, laryngeal cancer


title: Pt34, larynx

source_name: Patient 34, laryngeal cancer

value: 18 months

value: 1 (recurrence)


title: Pt32, larynx

source_name: Patient 32, laryngeal cancer

value: not available

value: 101 months


title: Pt29, larynx

source_name: Patient 29, laryngeal cancer

value: 89 months


title: Pt28, larynx

source_name: Patient 28, laryngeal cancer

value: 92 months

value: 0 (no recurrence)


title: Pt21, larynx

source_name: Patient 21, laryngeal cancer

value: 41 months


title: 14671-A1(M)

value: male

value: Clontech Laboratories Inc


title: A547-1 (M)


title: Pt20, larynx

source_name: Patient 20, laryngeal cancer

value: 83 months

value: validation


title: Pt30, larynx

source_name: Patient 30, laryngeal cancer

value: training


title: BXH6-2

city: Baltimore

first: vikas

last: misra

state: MD

address: 615 N. Wolfe street, E6609

department: Environmental health sciences

institute: Johns Hopkins University School of public health

description: BXH6-2 Lung gene expression

hyb_protocol: Following fragmentation, 1 200 ul of hybridization cocktail containing 10 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manual- Affymetrix)

scan_protocol: Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.

data_processing: Data extraction was processed by Affy GeneChip® Operating Software v1.3 (Affymetrix).  Global scaling was equal to 500.  Normalization factor was equal to 1.

source_name: BXH6-2 Lung

label_protocol: cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module,cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).

growth_protocol: no growth protocol

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

treatment_protocol: no treatment

tag: BXH6 mouse strain (Jackson Lab)  gender- male, age- 8 weeks, n = 1, # of tissue = 1 tissue

value: Lung


title: Pt24, larynx

source_name: Patient 24, laryngeal cancer

value: laryngeal cancer

value: 31 months


title: Pt18, larynx

source_name: Patient 18, laryngeal cancer

value: 35 months


title: Pt23, larynx

source_name: Patient 23, laryngeal cancer

value: 28 months


title: 10081-1 (M)

source_name: MPNST

value: Tianjin

source_name: Commercial DNAs


title: 9162-1(M)


title: Pt17, larynx

source_name: Patient 17, laryngeal cancer

value: 123 months

value: 1 (recurrence)


title: Pt25, larynx

source_name: Patient 25, laryngeal cancer

value: 2 months


title: A934-1-1 (F)

value: female


title: F1-1

description: F1-1 Lung gene expression

source_name: F1-1 Lung

tag: BXHF1 mouse strain (Jackson Lab)  gender- male, age- 8 weeks, n = 1, # of tissue = 1 tissue


title: B6-2

description: B6-2 Lung gene expression

source_name: B6-2 Lung

tag: B6 (C57BL/6J) mouse strain (Jackson Lab)  gender- male, age- 8 weeks, n = 1, # of tissue = 1 tissue


title: Pt22, larynx

source_name: Patient 22, laryngeal cancer

value: 39 months

value: 0 (no recurrence)


title: B6-1

description: B6-1 Lung gene expression

source_name: B6-1 Lung


title: F1-2

description: F1-2 Lung gene expression

source_name: F1-2 Lung


title: C3-2

description: C3-2 Lung gene expression

source_name: C3-2 Lung

tag: C3 (C3H/HeJ) mouse strain (Jackson Lab)  gender- male, age- 8 weeks, n = 1, # of tissue = 1 tissue


title: Pt19, larynx

source_name: Patient 19, laryngeal cancer

value: 107 months


title: BXH6-1

description: BXH6-1 Lung gene expression

source_name: BXH6-1 Lung


title: Pt16, larynx

source_name: Patient 16, laryngeal cancer

value: 95 months


title: C3-1

description: C3-1 Lung gene expression

source_name: C3-1 Lung


title: 3783-1 (F)

value: Clontech Laboratories Inc


title: BXH9-2

description: BXH9-2 Lung gene expression

source_name: BXH9-2 Lung

tag: BXH9 mouse strain (Jackson Lab)  gender- male, age- 8 weeks, n = 1, # of tissue = 1 tissue


title: 7512-1(M)

value: male


title: Pt15, larynx

source_name: Patient 15, laryngeal cancer

value: 118 months

value: training


title: a1112-1(M)


title: Pt13, larynx

source_name: Patient 13, laryngeal cancer

value: laryngeal cancer


title: a757(M)

source_name: MPNST


title: BXH9-1

description: BXH9-1 Lung gene expression

source_name: BXH9-1 Lung

value: Lung


title: BXH8-2

description: BXH8-2 Lung gene expression

source_name: BXH8-2 Lung

tag: BXH8 mouse strain (Jackson Lab)  gender- male, age- 8 weeks, n = 1, # of tissue = 1 tissue


title: Pt14, larynx

source_name: Patient 14, laryngeal cancer

value: 20 months

value: validation


title: 2165-1(F)

value: Tianjin

source_name: Commercial DNAs


title: BXH8-1

description: BXH8-1 Lung gene expression

source_name: BXH8-1 Lung


title: Pt11, larynx

source_name: Patient 11, laryngeal cancer

value: 96 months


title: Pt10, larynx

source_name: Patient 10, laryngeal cancer

value: 34 months


title: Pt12, larynx

source_name: Patient 12, laryngeal cancer

value: 106 months


title: 4016-1(F)

value: female


title: Pt8, larynx

source_name: Patient 8, laryngeal cancer

value: 28 months


title: BXH7-2

description: BXH7-2 Lung gene expression

source_name: BXH7-2 Lung

tag: BXH7 mouse strain (Jackson Lab)  gender- male, age- 8 weeks, n = 1, # of tissue = 1 tissue


title: 1364-1(F)


title: BXH4-2

description: BXH4-2 Lung gene expression

source_name: BXH4-2 Lung

tag: BXH4 mouse strain (Jackson Lab)  gender- male, age- 8 weeks, n = 1, # of tissue = 1 tissue


title: 8532-1(F)


title: 13380-a1(F)


title: BXH7-1

description: BXH7-1 Lung gene expression

source_name: BXH7-1 Lung


title: 10273-1(M)


title: Pt9, larynx

source_name: Patient 9, laryngeal cancer

value: 92 months

value: 1 (recurrence)


title: 5367-1(M)


title: BXH2-2

description: BXH2-2 Lung gene expression

source_name: BXH2-2 Lung

tag: BXH2 mouse strain (Jackson Lab)  gender- male, age- 8 weeks, n = 1, # of tissue = 1 tissue


title: Pt7, larynx

source_name: Patient 7, laryngeal cancer

tag: tissue

value: 38 months


title: BXH4-1

description: BXH4-1 Lung gene expression

source_name: BXH4-1 Lung


title: BXH2-1

description: BXH2-1 Lung gene expression

source_name: BXH2-1 Lung


title: Pt6, larynx

source_name: Patient 6, laryngeal cancer

value: 81 months


title: BXH19-1

description: BXH19-1 Lung gene expression

source_name: BXH19-1 Lung

tag: BXH19 mouse strain (Jackson Lab)  gender- male, age- 8 weeks, n = 1, # of tissue = 1 tissue


title: a663-1(M)

source_name: MPNST

tag: source

value: male

value: Clontech Laboratories Inc


title: Pt4, larynx

source_name: Patient 4, laryngeal cancer

tag: grade

tag: age

value: 6 months


title: 8554-1(M)

source_name: Commercial DNAs


title: BXH19-2

description: BXH19-2 Lung gene expression

source_name: BXH19-2 Lung


title: T-cell ALL prä MLL_00226

status: Public on Nov 25 2011

city: New York

first: Hans-Ulrich

last: Klein

state: NY

department: Neurology

institute: Columbia University Medical Center

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)

source_name: mononuclear cells after Ficoll purification

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).

extract_protocol: The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.

tag: disease state

value: T-cell acute lymphoblastic leukemia

tag: gene fusion

value: no fusion

tag: genotype

tag: lineage

value: prä

tag: cell type

value: mononuclear cells


title: T-cell ALL cortical MLL_00229

value: cortical


title: Pt3, larynx

source_name: Patient 3, laryngeal cancer

value: laryngeal cancer

tag: disease-free survival (dfs)

value: 12 months

tag: disease-free survival (dfs) event

tag: dataset

value: training


title: Pt1, larynx

source_name: Patient 1, laryngeal cancer

value: 69 months

value: 0 (no recurrence)


title: T-cell ALL prä MLL_00227


title: Pt5, larynx

source_name: Patient 5, laryngeal cancer

value: 124 months

value: validation


title: Pt2, larynx

source_name: Patient 2, laryngeal cancer

value: 148 months


title: 5210-1(M)

value: Tianjin

tag: gender


title: T-cell ALL cortical MLL_00223


title: T-cell ALL cortical MLL_00224


title: T-cell ALL cortical MLL_00221


title: BXH14-2

description: BXH14-2 Lung gene expression

source_name: BXH14-2 Lung

tag: BXH14 mouse strain (Jackson Lab)  gender- male, age- 8 weeks, n = 1, # of tissue = 1 tissue

value: Lung


title: T-cell ALL prä MLL_00228


title: BXH10-2

description: BXH10-2 Lung gene expression

source_name: BXH10-2 Lung

tag: BXH10 mouse strain (Jackson Lab)  gender- male, age- 8 weeks, n = 1, # of tissue = 1 tissue


title: gregarious male CNS replicate 2 vs. gregarious male CNS replicate 3

city: Leuven

first: Jozef

last: Vanden Broeck

address: Naamsestraat 59

department: Animal Physiology and Neurobiology

country: Belgium

institute: KU Leuven

hyb_protocol: The labeled samples were hybridized onto the microarrays according to the design described under ‘Overall design’, and by using the Gene Expression Hybridization Kit (Agilent Technologies) following the manufacturer’s instructions. Hybridization was performed during 17 hr at 65°C. Next, the microarrays were washed twice in GE Wash Buffer 1 (Agilent) for 1 minute each and finally in GE Wash Buffer 2 at 37°C for 1 minute.

scan_protocol: Microarrays were scanned using a Genepix Personal 4100A confocal scanner (Axon Instruments) at a resolution of 5 µm and excitation wavelengths of 635 nm and 532 nm. The photomultiplier tube (PMT) voltages for separate wavelengths were adjusted to obtain an overall green/red ratio as close as possible to 1. Images were processed using GenePix Pro 6.0 software (Axon Instruments) for spot identification and quantification of the fluorescent signal intensities.

data_processing: The data were imported in a MIAME (Minimum Information About a Microarray Experiment) compliant database (www.islab.ua.ac.be/base/), developed by the Intelligent Systems Laboratory (University of Antwerp, Belgium) and maintained by the Ecophysiology, Biochemistry and Toxicology research group (University of Antwerp, Belgium). Statistical analysis of the microarray data was performed using the R package limma. Spots for which red or green FG < BG + 2SD  on all arrays, were deleted before analysis (FG: median foreground intensity, BG: average local background intensity, SD: standard deviation of local background intensities). Median intensity data were background corrected using a normal-exponential convolution model and were normalized by ‘Locally Weighed Scatterplot Smoothing’ (Loess).

organism: Schistocerca gregaria

source_name: pooled (5 individuals) gregarious CNS, biological replicate 2

label_protocol: Labeling of the samples was performed by using the Quick Amp Labeling Kit (Two Color, Agilent Technologies), according to the manufacturer’s instructions. For each sample, 2 µg total RNA was used for labeling. The fluorescently labeled samples were purified by means of the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

growth_protocol: Gregarious locusts were reared under crowed conditions in acrylic plastic cages (40 × 43 × 85 cm) under a 13 hour light / 11 hour dark photoperiod at 32°C. They were fed daily with fresh cabbage and oat flakes ad libitum. Solitarious locusts were reared individually for 30 successive generations in plastic boxes (15 × 8 × 7 cm), and received the same food as the crowd-reared animals. The solitarious breeding room had identical temperature and light conditions as the crowd-rearing room.

extract_protocol: Total RNA was extracted by using RNeasy Lipid Tissue Mini Kit (Qiagen) according to the manufacturer’s instructions. In addition, a DNase treatment (RNase-free DNase set, Qiagen) was performed to eliminate potential genomic DNA contamination.

value: male

value: adult, staged between 2 and 10 days after final eclosion

source_name: pooled (5 individuals) gregarious CNS, biological replicate 3


title: T-cell ALL cortical MLL_00219

value: T-cell acute lymphoblastic leukemia


title: T-cell ALL cortical MLL_00220

value: no fusion


title: solitarious male CNS replicate 2 vs. gregarious male CNS replicate 2

source_name: pooled (5 individuals) solitarious CNS, biological replicate 2


title: solitarious male CNS replicate 3 vs. gregarious male CNS replicate 2

source_name: pooled (5 individuals) solitariouis CNS, biological replicate 3


title: T-cell ALL cortical MLL_00222


title: 357-1(M)

value: Clontech Laboratories Inc


title: 5570-1(M)


title: gregarious male CNS replicate 3 vs. solitarious male CNS replicate 1

source_name: pooled (5 individuals) solitarious CNS, biological replicate 1


title: solitarious male CNS replicate 1 vs. solitariouis male CNS replicate 3

source_name: pooled (5 individuals) solitarious CNS, biological replicate 3


title: T-cell ALL mature MLL_00216

value: mature

value: mononuclear cells


title: solitarious male CNS replicate 1 vs. solitarious male CNS replicate 2


title: BXH10-1

description: BXH10-1 Lung gene expression

source_name: BXH10-1 Lung


title: gregarious male CNS replicate 1 vs. solitarious male CNS replicate 1

source_name: pooled (5 individuals) gregarious CNS, biological replicate 1


title: gregarious male CNS replicate 2 vs. gregarious male CNS replicate 1


title: solitarious female CNS replicate 1 vs. solitarious female CNS replicate 2

value: female


title: T-cell ALL mature MLL_00218


title: T-cell ALL prä MLL_00215

value: prä


title: CD8 T cells helped vs. helpless

city: Amsterdam

first: Monika

last: Wolkers

address: Plesmanlaan 125

department: Research

country: Netherlands

institute: Sanquin Research

hyb_protocol: The samples were then vacuum dried before being resuspended in 20µl of nuclease-free water, followed by addition of 40µl of hybridization solution (after dilution the concentrations were 25% formamide, 5X SSC, 0.1% SDS, 0.1mM DTT, 0.1µg/µl sheared salmon sperm DNA), heated to 95°C, before cooling to room temperature.  The hybridization pairs were then applied to a MEEBO slide printed on epoxy surface (purchased preprinted from Washington University), using a LifterSlip (Erie Scientific catalog #25X60 M series), placed into a Quantifoil µBox incubation chamber (Gel Company catalog #226), and incubated for 18 hours overnight in a 42°C water bath.  The following day, the slides were removed from the chamber and washed in the following manner in Lipshaw dishes (catalog #121) on an orbital shaker set at 100rpm: 5 minutes in wash #1 (2X SSC, 0.1% SDS, 0.1mM DTT, 42°C), 5 minutes in wash #2 (1X SSC, 0.1mM DTT, room temperature), 2 minutes in fresh wash #2, 1 minute in wash #3 (0.1X SSC, 0.1mM DTT, room temperature), and 1 minute in fresh #3.  The slides were then quickly transferred to a Slide Spinner (PGC, catalog #16-7002-00) and centrifuged for 30 seconds before quickly transferring to an Axon 4000B for scanning.

scan_protocol: Axon 4000B was used for scanning.  The images were preview scanned, balancing both channels until an overall Cy5/Cy3 ratio of 1 was achieved before a final data scan at 5µm was performed in GenePix.  The images were manually gridded, and then saved for analysis.

data_processing: Data were analysed using Spotfire Decision Site

source_name: Effector CD8+ CD44hi T cells (helped), activated for 4h with cognate peptide

label_protocol: The resulting aminoallyl cDNA was then resuspended in 4.5µl of 0.1M sodium carbonate, pH 9.0 (Fisher catalog #BP357-1) and indirectly labeled using 4.5µl of Cyanine 3 and Cyanine 5 (Amersham catalog #PA23001 and #PA25001), for reference and test samples respectively.  The labeling took place in the dark at room temperature for 1 hour, with the reactions stopped by addition of 35µl of 100mM sodium acetate, pH 5.5 (Ambion catalog #9740).  The resulting labeled samples were then purified using a Qiagen PCR purification kit (catalog #28106), eluted in 60µl of nuclease-free water (Ambion catalog #9937), OD checked on a NanoDrop 1000, and equilibrated on an equimolar basis.

growth_protocol:
At day 7 post immunization, Spleens and draining lymph nodes were harvested 7 days post immunization, and organs were mashed through a 70uM filter (BD). Single cell suspensions were washed and  CD8+ T cells were purified with the CD8 negative isolation kit (Miltenyi) according to the manufacturer’s protocol. Subsequently, CD8 T cells were labeled with aCD44-APC antibodies (BD), washed twice, and sorted by flow cytometry.
CD8+CD44hi T cells (5x10e6 per condition; i.e. helped and helpless) were restimulated in vitro with 2ug/ml E1B192-200 peptide in the presence of 20uM qVD-OPh (R&D Systems). Restimulation was performed in a concentration of 1x10e6 cells per 200ul.

extract_protocol: RNA was extracted using TriZol (Gibco BRL) according to the manufacturer's instructions.Total RNA (5µg) was amplified using Ambion’s MessageAmp kit (catalog #1751), yielding anti-sense RNA (aRNA).  5µg of aRNA was then converted to aminoallyl cDNA using Invitrogen SuperScript3 reverse transcriptase (1X SuperScript buffer, 10mM DTT, 0.5mM dATP, 0.5mM dCTP, 0.5mM dGTP, 0.3mM dTTP, 0.2mM aminoallyl-dUTP, 400U SuperScript3) for 3 hours at 42°C .  Aminoallyl cDNA was alkaline denatured to remove template, then purified using Microcon YM-30 columns, and vacuum dried.

treatment_protocol: C57BL/6J mice were treated with 100 ug GK1.5 intraperitoneally (helpless) or left untreated (helped) prior to subcutaneous immunization with 1x10e7 irradiated (3000 rad) TAP-/-Ad5E1-MEC. Each group consisted of 4 mice. 3 days post immunization, all mice were treated with 100 ug GK1.5.

tag: strain

value: 7 weeks

tag: source tissue

value: Spleen and Lymph nodes

value: helped CD8 T cells

source_name: Effector CD8+ CD44hi T cells (helpless), activated for 4h with cognate peptide

value: helpless CD8 T cells


title: solitarious female CNS replicate 2 vs. gregarious female CNS replicate 1


title: T-cell ALL prä MLL_00213

source_name: mononuclear cells after Ficoll purification


title: T-cell ALL prä MLL_00214


title: BXH14-1

description: BXH14-1 Lung gene expression

source_name: BXH14-1 Lung


title: gregarious female CNS replicate 2 vs. solitarious female CNS replicate 1


title: T-cell ALL cortical MLL_00217

value: cortical


title: gregarious female CNS replicate 1 vs. gregarious female CNS replicate 2


title: T-/myeloid mixed acute leukemia phenotype PICALM-MLLT10 fusion MLL_00207

value: PICALM-MLLT10 fusion


title: T-cell ALL PICALM-MLLT10 fusion MLL_00208


title: T-cell ALL PICALM-MLLT10 fusion MLL_00206


title: T-cell ALL prä MLL_00212


title: T-cell ALL prä MLL_00211


title: solitarious female CNS replicate 2 vs. solitarious female CNS replicate 3


title: solitarious female CNS replicate 3 vs. gregarious female CNS replicate 2


title: T-cell ALL PICALM-MLLT10 fusion MLL_00202


title: T-cell ALL PICALM-MLLT10 fusion MLL_00201


title: T-cell ALL PICALM-MLLT10 fusion MLL_00204


title: T-cell ALL prä MLL_00209


title: T-cell ALL PICALM-MLLT10 fusion MLL_00203


title: gregarious female CNS replicate 3 vs. solitarious female CNS replicate 2


title: T-cell ALL PICALM-MLLT10 fusion MLL_00205


title: gregarious female CNS replicate 2 vs. gregarious female CNS replicate 3


title: T-cell ALL prä MLL_00210


title: Hsbb-27-03

status: Public on Nov 24 2011

city: Princeton

first: Sudhir

last: Varma

state: NJ

address: 1215 Wessex Pl

institute: HiThru Analytics

description:
P3-8-Mf-1 Print ID:Hsbb-27
Sample name: 85988

hyb_protocol: Oligo arrays were hybridized to the cDNA probes in formamide based hybridization buffer (MWG's Coverslips Hybridization Buffer) at 42C overnight and subsequently washed in room temperature baths (2X SSC, 0.2% SDS; followed by 2X SSC, and then 0.2X SSC) for 12 min. each.  Fluorescent Cy3/Cy5 capture reagents were added to each array in MWG's Coverslips Hybridization Buffer.  Arrays were incubated for 3 hrs at 50C and washed as above.

scan_protocol: Axon's GenePix 4000B fluorescent scanner

data_processing: Data was processed using Partek Genomics Suite. Intensities in both channels were thresholded to 100, log2 transformation was done and duplicate probes averaged. Both channels of each array was median normalized. Control probes, as well as probes with mean < 7 or sd<0.7 were filtered out. Samples were again median normalized using the remaining probes.

source_name: MfAg Stimulated CD8+ cells

label_protocol: Ovation Aminoallyl RNA amplification and Labeling System (NuGen) was used to reverse transcribe 40 ng total RNA (37C 30 min; 75C 15 min). 2 ug of aminoallyl amplified cDNA was labeled with Cy3 dye (antigen samples) and Cy5 dye (unstimulated samples) using Amersham Post Labeling Reactive Dye Packs; Cy3 and Cy5 samples were combined for hybridization

growth_protocol: PBMCs were cultured for 18 hrs in RPMI media supplemented with 10% fetal calf serum

extract_protocol: Cells were harvested and purified for CD3+ T cells and then for CD4+ and CD8+ cells by Dynal magnetic bead separation; total RNA was extracted with Trizol followed by phase separation with chloroform; RNA was purified with RNeasy Kit (Qiagen) following manufacturer's instructions

treatment_protocol: Cells were left unstinmulated or stimulated with microfilarial (MfAg) or streptolysin O (SLO) antigens

tag: patient id

tag: patient type

value: Endemic

tag: technical replicates

source_name: Unstimulated CD8+ cells