title: Samples at T4, replica 2

city: Valencia

first: David

last: Alabadi

state: Valencia

address: Av de los Naranjos s/n, Campus UPV, Edificio 8E

department: Biologia del Desarrollo

country: Spain

institute: Instituto de Biologia Molecular y Celular de Plantas (CSIC-UPV)

description: HS:gai-1 seedlings transferred to 37ºC for 30 min and sampled 4 h after the beginning of the treatment and labelled with Cy5 (replica 2), compared with wild type control seedlings that received the same treatment and labelled with Cy3 (replica 2).

hyb_protocol: DNA onto slides was rehydrated by placing the slide upside-down over a water bath at 60°C for 10 s, and snap dry onto a heat block at 65°C. Rehydration was repeated 3 times. DNA was immobilized by UV light by exposing the slides DNA-side-up to 65 mJ in a UV cross-linker (Stratagene). Slides were then washed twice in 0.1% SDS and 4 times in water, 2 min each wash at RT, and finally dipped in 96% ethanol for 1 min and dried by centrifugation at 2000 rpm 1 min at RT. Slides were prehybridized for 30 min at 42°C with 100 µL of prehybridization solution (6x SSC (Sigma), 1% BSA (Sigma) and 0.5% SDS (Sigma)), under a 60x22 mm coverslip LifterSlip (Erie Scientific) in a microarray hybridization chamber (ArrayIt Hybridization Cassette, Telechem). Slides were rinsed 5 times in H2O in a slide rack at RT and dried by centrifugation at 2000 rpm 1 min at RT. Slides were hybridized immediately. Both coupled aa-aRNA (Cy3 and Cy5) were mixed and fragmented in the presence of 20 µg of tRNA (Ambion) and 20 µg of poly(A) (Roche) using the RNA fragmentation Reagent (Ambion) as described by the manufacturer, in a final volume of 10 µL. Fragmented aa-aRNA was used directly in the hybridization mix, which contains 50 µL deionized formamide (Sigma), 30 µL 20x SSC, 5 µL 100x Denhardt´s solution (Sigma), and 5 µL 10% SDS in a final volume of 100 µL. Hybridization mixture was denatured at 95 °C for 5 min, spun briefly, and applied by capillarity between a pre-treated slide (see above) and a 60x42 mm coverslip LifterSlip. Slides were incubated o/n at 37°C in a microarray hybridization chamber (ArrayIt Hybridization Cassette, Telechem). Slides were washed sequentially once in 1x SSC 0.1% SDS 5 min at 30°C; once in 0.2x SSC 0.1% SDS 5 min at 30°C; twice in 0.1x SSC 2 min each at 30°C; and finally 0.01x SSC 10 sec at RT. Slides were dried by centrifugation at 2000 rpm 1 min at RT.

scan_protocol: Hybridized microarray slides were scanned at 532-nm for the Cy3 and 635-nm for the Cy5 dyes, with a GenePix 4000B scanner (Axon Molecular Devices, Sunnyvale CA), at 10-mm resolution and 100% laser power.

data_processing: Spot intensities were quantified using GenePix Pro 6.0 microarray-analysis software (Axon Molecular Devices, Sunnyvale CA). Spots with a net intensity in both channels lower than the median signal background plus twice standard deviations were removed as low signal spots.  Data were normalized by median global intensity using the GenePix Pro 6.0 software.

organism: Arabidopsis thaliana

label_protocol: RNA was amplified using the MessageAmp II aRNA Amplification kit (Ambion), basically as described by the manufacturer. 5-(3-aminoallyl)-UTP (aa-UTP) (Ambion) was incorporated into the amplified RNA (aRNA) at ratio 1:1 with UTP. After purification, 7.5 µg of aminoallyl-aRNA (aa-aRNA) were used in a coupling reaction with either fluorescent Cy3 or Cy5 as reactive N-hydroxyl succinimidal dyes (NHS-dyes) (Amersham Pharmacia Biotech, Piscataway, NJ). For this, each aliquot of Cy3 or Cy5 was dissolved in 20 µL of DMSO and used in four coupling reactions. aa-aRNA was dissolved in 15 µL of freshly-made 0.1 M NaCO3 pH 9.0, and mixed with 5 µl of either Cy-3 or Cy-5 dye. Coupling was allowed for 1 h at RT in the dark. Reaction was stopped with 35 µL of 100 mM sodium acetate pH 5.2 and incubated 5 min in the dark. Fluorescent aa-aRNA was purified using a MegaClear purification column (Ambion) as described by the manufacturer. Coupled aa-aRNA (250-300 pmol Cy dye in 5-7 µg aa-aRNA) was dried in a speedvac and dissolved in 2.5 µL of filtered water.

growth_protocol: Wild type Col-0 and HS:gai-1 seeds were surface sterilized and sown on sterile filter papers, placed on half-strength MS media plus 1% sucrose and stratified for 4 days at 4ºC in darkness. Germination of all seeds was induced by placing plates at 20ºC and under white fluorescent light (150 mmol m-2 s-1) for 8 h. Next, plates were wrapped in aluminum foil and kept in the dark at the same temperature for 64 h.

extract_protocol: Total RNA was extracted from frozen, whole etiolated seedlings, using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol: Plates were placed in a 37ºC oven for a total of 30 minutes and then returned to the 20ºC growth cabinet, always in complete darkness. Samples from wild type and the transgenic line were harvested 1, 2 or 4 h after the beginning of the treatment. Samples at time point 0 were harvested just before the treatment.

value: whole etiolated seedlings

value: 3 days

tag: treatment

value: 37ºC for 30 min, returned to 20ºC

tag: time point

value: 4 hr

source_name: Wild type seedlings transferred to 37ºC for 30 min and sampled 4 h after the beginning of the treatment

tag: ecotype

value: wild type


title: CRC-127

status: Public on Sep 01 2011

type: RNA

city: Beppu

first: Koshi

last: Mimori

state: Oita

address: 4546 Tsurumihara

department: Department of Surgery

country: Japan

institute: Kyushu university

hyb_protocol: Hybridization was carried out using the conditions specified in the Agilent Human Whole Genome Expression system.

scan_protocol: Fluorescence intensities were determined with an Agilent DNA Microarray Scanner.

data_processing: Expression levels were quantified by G2567AA Feature Extraction Software Version A.7.5.1 (Agilent Technologies), which used the  LOWESS (locally weighted linear regression curve fit) normalization method. Further analyses were performed using GeneSpring version 7.3.

molecule: total RNA

organism: Homo sapiens

source_name: colorectal cancer

label_protocol: Cyanine (Cy)-labeled cRNA was prepared using T7 linear amplification as described in the Agilent Low RNA Input Fluorescent Linear Amplification Kit Manual  (Agilent Technologies).

extract_protocol: Total RNA was extracted with QIAGEN RNeasy minElute Spin Column (QIAGEN, Inc., Valencia, CA) according to the manufacturer's protocols.

treatment_protocol: Laser micro-dissection

tag: gender

value: M

tag: age

tag: tumor-nodes-metastasis classification t

tag: tumor-nodes-metastasis classification n

tag: tumor-nodes-metastasis classification m


title: Samples at T4, replica 3

description: HS:gai-1 seedlings transferred to 37ºC for 30 min and sampled 4 h after the beginning of the treatment and labelled with Cy5 (replica 3), compared with wild type control seedlings that received the same treatment and labelled with Cy3 (replica 3).

tag: genotype

tag: tissue


title: Top fractions

city: Stanford

first: Linda

last: Yip

state: CA

address: 269 Campus Drive West, CCSR Building Rm. 2240

department: Medicine

country: USA

institute: Stanford University

description: Differential gene expression in top fraction

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit and the Agilent Microarray Hybridization Chamber as instructed by the manufacturer. Samples were hybridized for 17 h at 65ºC, and slides were washed with Gene Expression Wash Buffer (Agilent) according to maufacturer's instructions.

scan_protocol: Microarray chips were scanned using the DNA microarray scanner (Agilent Technologies) with the following parameters: 2 color scan; scan resolution 5 um, single pass, red and green dye channels. Data was extracted using Feature Extraction software (version 10.5.1.1)

data_processing: Lowess normalization was performed using the feature extraction software version 10.5.1.1.  Then this data was processed with Genespring 11.5 to generate the normalized log(2) ratio of the test (cy5-labeled)/reference(cy3-labelled) intensity values.

organism: Mus musculus

source_name: cultured lymph node stromal cells

label_protocol: 200 ng of total RNA was labeled RNAusing the Agilent low RNA input fluorescence linear amplification kit (Agilent Technologies) according to manufacturer's instructions.

growth_protocol: Cultured lymph node stromal cells (LNSCs) were grown in 10 cm culture dishes in DMEM containing 10% FCS until ~80% confluent.

extract_protocol: Total RNA was extracted by acid phenol/chloroform extraction following incubation with 250 μg/ml proteinase K (NEB) and 0.5% SDS at 37ºC for 30 min.  Extracted RNA was precipitated overnight at -20ºC with glycogen (Roche), 300 mM sodium acetate (pH5), and 3 volumes of ethanol.  RNA pellets were washed in 75% ethanol and reconstituted in nuclease free water.

treatment_protocol: Cells were transfected with 400 pmol of control or Eif4g3 siRNA in a volume of 10 ml media using Lipofectamine 2000. Media was changed at 24h after transfection, and cells were harvested at 48 h.

tag: strain

value: BALB/c

tag: cell type

tag: transfection

value: Eif4g3-siRNA treated

tag: polysome fraction

value: Top fractions

value: Control-siRNA treated


title: control medium (10% FBS): replicate 2

city: Tokyo

first: francois

middle: frederic

last: renault-mihara

address: 35 Shinanomachi, Shinjuku-ku

department: Physiology

institute: Keio University School of Medicine

description: Gene expression in control medium

hyb_protocol: Cy3-labeled cRNA (1000 ng) was hybridized to an Agilent Whole Mouse Gene Expression Microarray (#14868), as per the manufacturer’s protocol.

scan_protocol: Slides were scanned using the Agilent dual-laser DNA microarray scanner (G2565CA).

data_processing:
The data were extracted by the Agilent Feature Extraction software version 10.1. Normalization for each plot was performed as recommended by Agilent: Values below 0.01 were set to 0.01. Each measurement was divided by the 50.0th percentile of all measurements in that sample. Data were analyzed using Genespring GX software (Tomy Digital Biotechnologies).
Genes that were up- or down-regulated more than twofold were identified. Statistical comparisons between the control and Ro3303544 groups, or between the control and wash-out groups were performed using an unpaired t-test (unequal variances), and the threshold for statistical significance was set at p ≤0.05.

source_name: cortico-striatal astrocytes in primary culture

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared using the QuickAmp labeling kit (Agilent), according to the manufacturer’s instructions.

growth_protocol: Astrocytes in primary cultures were prepared as previously described (Araujo et al., 1993). Briefly, striatal and cortical cells from 1-day postnatal wild-type C57BL/6J mice were dissociated and plated on culture dishes coated with poly-L-ornithine (1.5 g/ml; MW 40,000, Sigma) in defined MEM-F12 medium consisting of a 1:1 mixture of MEM and F-12 nutrient (Invitrogen) supplemented with glucose (33 mM), L-glutamine (2 mM), sodium bicarbonate (3 mM), HEPES (pH 7.4, 5 mM), penicillin (50 IU/ml), streptomycin (5 g/ml) (all from Invitrogen), and 10% heat-inactivated fetal bovine serum (Nichirei Biosciences, Japan). The culture medium was changed every 3 days. When the cells were almost confluent, at around day 7, they were treated with 5 M cytosine arabinoside for 2 days, to deplete the contaminating microglial cells. Further stringent washes with PBS were performed to obtain high-purity cultures of astrocytes (less than 1% Iba1-positive contaminating microglial cells at 12 days in culture).

extract_protocol: Total RNA was isolated from astrocytes in primary culture upon the indicated treatments using Trizol®, following the manufacturer’s protocol, and further purified with the RNeasy mini kit (Qiagen). Two replicates were run per condition. RNA was quantified using a Nanodrop-1000 spectrophotometer (Nanodrop Technologies), and its quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). The RNA had an A260/280 ratio ≥ 2, and the RNA Integrity Number was ≥ 6.5.

treatment_protocol: After 13 days in vitro, cells were treated for 48 h with either 1 µM Ro3303544 (dissolved in growth medium), or an equivalent final concentration of DMSO, or treated for 48h with 1 µM Ro3303544 and wash-out for two additional days in growth medium.

value: wild-type

value: 1-day postnatal

tag: condition

value: control medium


title: washed-out for 48h after an initial 48 h treatment with 1 micromolar Ro3303544: replicate 1

description: Gene expression after 48h wash-out (after an initial treatment with 1 µM Ro3303544)


title: treated 48h with 1 micromolar Ro3303544: replicate 1

description: Gene expression after 48h treatment 1 µM Ro3303544

value: after 48h treatment 1 µM Ro3303544


title: control medium (10% FBS): replicate 1

description: Gene expression in control medium


title: CRC-102

value: F


title: treated 48h with 1 micromolar Ro3303544: replicate 2


title: Samples at T4, replica 1

description: HS:gai-1 seedlings transferred to 37ºC for 30 min and sampled 4 h after the beginning of the treatment and labelled with Cy5 (replica 1), compared with wild type control seedlings that received the same treatment and labelled with Cy3 (replica 1).


title: CRC-101


title: Samples at T2, replica 2

description: HS:gai-1 seedlings transferred to 37ºC for 30 min and sampled 2 h after the beginning of the treatment and labelled with Cy5 (replica 2), compared with wild type control seedlings that received the same treatment and labelled with Cy3 (replica 2).

value: 2 hr

source_name: Wild type seedlings transferred to 37ºC for 30 min and sampled 2 h after the beginning of the treatment


title: Samples at T2, replica 3

description: HS:gai-1 seedlings transferred to 37ºC for 30 min and sampled 2 h after the beginning of the treatment and labelled with Cy5 (replica 3), compared with wild type control seedlings that received the same treatment and labelled with Cy3 (replica 3).


title: Samples at T1, replica 1

description: HS:gai-1 seedlings transferred to 37ºC for 30 min and sampled 1 h after the beginning of the treatment and labelled with Cy5 (replica 1), compared with wild type control seedlings that received the same treatment and labelled with Cy3 (replica 1).

value: 1 hr

source_name: Wild type seedlings transferred to 37ºC for 30 min and sampled 1 h after the beginning of the treatment


title: Samples at T1, replica 2

description: HS:gai-1 seedlings transferred to 37ºC for 30 min and sampled 1 h after the beginning of the treatment and labelled with Cy5 (replica 2), compared with wild type control seedlings that received the same treatment and labelled with Cy3 (replica 2).

value: whole etiolated seedlings


title: Samples at T1, replica 3

description: HS:gai-1 seedlings transferred to 37ºC for 30 min and sampled 1 h after the beginning of the treatment and labelled with Cy5 (replica 3), compared with wild type control seedlings that received the same treatment and labelled with Cy3 (replica 3).

value: 3 days


title: Samples at T2, replica 1

description: HS:gai-1 seedlings transferred to 37ºC for 30 min and sampled 2 h after the beginning of the treatment and labelled with Cy5 (replica 1), compared with wild type control seedlings that received the same treatment and labelled with Cy3 (replica 1).

value: 37ºC for 30 min, returned to 20ºC


title: Control samples at T0, replica 2

description: HS:gai-1 seedlings kept at 20ºC labelled with Cy5 (replica 2), compared with wild type control seedlings kept at 20ºC labelled with Cy3 (replica 2).

source_name: HS:gai-1 seedlings kept at 20ºC

value: untreated

value: 0 hr

source_name: Wild type control seedlings kept at 20ºC


title: Control samples at T0, replica 3

description: HS:gai-1 seedlings kept at 20ºC labelled with Cy5 (replica 3), compared with wild type control seedlings kept at 20ºC labelled with Cy3 (replica 3).

value: wild type


title: Normal oral tissue_ON82

type: genomic

city: Taoyuan

first: Chien-Hua

last: Peng

address: No. 5, Fu-Hsing ST.

country: Taiwan

institute: Chang Gung Memorial Hospital

description: Hybridized to Affymetrix SNP6.0

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: We used Partek to detect copy number variation. We used birdseed algorithm for calling SNP 6.0, which is suggested standard algorithm, and birdseed is embedded in software of Genotyping Console (GTC) or Affymetrix Power Tool (APT) which all provide by affymetrix company. The reported summarized intensity are separated into A intensity and B intensity, and results in calling into AA, AB, or BB categories.

label: Biotin

molecule: genomic DNA

source_name: Normal oral tissue

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: disease state

value: norml


title: F36VMpl transduced cord blood CD34+ cells cultured in the presence of Epo, biological replicate 3

city: Los Angeles

first: chintan

last: parekh

address: 610 Charles Young Drive

department: Pathology

institute: UCLA

description: Gene expression data from F36VMpl transduced cord blood CD34+ cells cultured in the presence of Epo

hyb_protocol: The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45 degree celcius for 16 hours.They were then washed and stained with a streptavidin phycoerythrin conjugate

scan_protocol: GeneChip Scanner 3000DX V.2

data_processing: dCHIP software (Department of biostatistics, Harvard School of Public Health, Boston, MA). The quantile method  was used to normalize gene expression values in a PM/MM model. Gene expression values from the sample NCID2 served as a baseline for normalization

label: biotin

label_protocol: The Total RNA (1 μg to 15 μg) was first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction.  Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and used as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.

growth_protocol: CB CD34+ cells transduced with F36VMpl-GFP were cultured on MS-5 stroma in lymphoid medium (RPMI 1640 [Irvine Scientific, Santa Ana, CA], 5% FCS [screened for B-cell cultures], 50 mM 2-ME, 50 U/mL penicillin/50 microgram/mL streptomycin,and 200 mM L-glutamie), either with CID alone, with Epo(5 international units/ ml) alone, or with Tpo (50 ng/ ml) alone. Transduced cells cultured on MS-5 stroma in the absence of either growth factors or CID served as controls. Three biologically independent experiments were performed. CD34+GFP+ cells were isolated by FACS after 7days of culture

extract_protocol: RNA was extracted using a Qiagen micro kit (Qiagen, Valencia, CA).

value: CD34+GFP+ cells isolated form culture on day 7

tag: genotype/variation

value: F36VMpl transduced


title: Control samples at T0, replica 1

description: HS:gai-1 seedlings kept at 20ºC labelled with Cy5 (replica 1), compared with wild type control seedlings kept at 20ºC labelled with Cy3 (replica 1).

tag: treatment


title: Normal oral tissue_ON51

description: Hybridized to Affymetrix SNP6.0


title: Normal oral tissue_ON66

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR4199

description: Hybridized to Affymetrix SNP6.0

source_name: OSCC  specimens

value: tumor


title: OSCC tumor_OR4207

description: Hybridized to Affymetrix SNP6.0


title: Normal oral tissue_ON64

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR4145

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR4181

description: Hybridized to Affymetrix SNP6.0


title: F36VMpl transduced cord blood CD34+ cells cultured in the presence of Tpo, biological replicate 3

description: Gene expression data from F36VMpl transduced cord blood CD34+ cells cultured in the presence of Tpo

treatment_protocol: CD34+GFP+ cells were isolated by FACS after 7days of culture


title: E5_vs_pMSG_96h_rep3 (mRNA)

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description: mRNA expression in E5 vs control cells after 96h induction

hyb_protocol: Hybridization was performed as described in the Agilent (Agilent Technologies, Rockville, MD) two color microarray-based gene expression analysis manual suggests. Hybridization for 16 h at +65 ºC. Washing was performed by the Agilent protocol 5 minutes in GE wash buffer 1 and one minute in GE wash buffer 2 (+37ºC). Arrays were dried with a 1 minute spin in a Spectrafuge mini (Labnet, Woodbridge, NJ).

scan_protocol: Default scanning performed with Axon 4200AL for Cy3 and Cy5 using resolution of five micrometer.

data_processing: quantile normalization of the log2 ratios

label_protocol: Cy5 and Cy3 indirect labelling using (Ambion, Austin, TX) amino allyl messageamp II aRNA amplification kit according to instructions.

growth_protocol: HaCaT-E5 and control cells were grown in D-MEM growth medium with 10% FBS and glutamine and antibiotics, and serum-starved 24h before treatment.

extract_protocol: Total RNA was isolated from confluent cell cultures using TriPure reagent (Roche Applied Science, Indianapolis, IN, USA)

treatment_protocol: E5 expression was induced by 1 mM dexamethasone treatment for different times.

value: skin keratinocytes

tag: cell line

value: HaCaT

value: vector control

tag: time

value: type 16 E5 oncogene


title: OSCC tumor_OR4119

description: Hybridized to Affymetrix SNP6.0


title: Normal oral tissue_ON68

description: Hybridized to Affymetrix SNP6.0


title: E5_vs_pMSG_96h_rep2 (mRNA)


title: F36VMpl transduced cord blood CD34+ cells cultured in the absence of CID or growth factors, biological replicate 3

description: Gene expression data from F36VMpl transduced cord blood CD34+ cells cultured in the absence of CID or growth factors


title: F36VMpl transduced cord blood CD34+ cells cultured in the presence of CID, biological replicate 3

description: Gene expression data from F36VMpl transduced cord blood CD34+ cells cultured in the presence of CID


title: OSCC tumor_OR4087

description: Hybridized to Affymetrix SNP6.0


title: Normal oral tissue_ON78

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR4058

description: Hybridized to Affymetrix SNP6.0


title: Normal oral tissue_ON81

description: Hybridized to Affymetrix SNP6.0


title: Normal oral tissue_ON80

description: Hybridized to Affymetrix SNP6.0


title: Normal oral tissue_ON79

description: Hybridized to Affymetrix SNP6.0


title: F36VMpl transduced cord blood CD34+ cells cultured in the presence of Epo, biological replicate 2


title: OSCC tumor_OR4130

description: Hybridized to Affymetrix SNP6.0


title: E5_vs_pMSG_72h_rep3 (mRNA)

description: mRNA expression in E5 vs control cells after 72h induction


title: E5_vs_pMSG_72h_rep2 (mRNA)


title: E5_vs_pMSG_72h_rep1 (mRNA)


title: F36VMpl transduced cord blood CD34+ cells cultured in the absence of CID or growth factors, biological replicate 2


title: OSCC tumor_OR4043

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR4041

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR4070

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR4146

description: Hybridized to Affymetrix SNP6.0


title: F36VMpl transduced cord blood CD34+ cells cultured in the presence of Tpo, biological replicate 2


title: E5_vs_pMSG_96h_rep1 (mRNA)


title: F36VMpl transduced cord blood CD34+ cells cultured in the presence of CID, biological replicate 2


title: OSCC tumor_OR4081

description: Hybridized to Affymetrix SNP6.0


title: E5_vs_pMSG_48h_rep2 (mRNA)

description: mRNA expression in E5 vs control cells after 48h induction


title: OSCC tumor_OR4155

description: Hybridized to Affymetrix SNP6.0


title: E5_vs_pMSG_48h_rep1 (mRNA)


title: F36VMpl transduced cord blood CD34+ cells cultured in the presence of Tpo, biological replicate 1


title: OSCC tumor_OR4060

description: Hybridized to Affymetrix SNP6.0


title: F36VMpl transduced cord blood CD34+ cells cultured in the absence of CID or growth factors, biological replicate 1


title: OSCC tumor_OR4052

description: Hybridized to Affymetrix SNP6.0


title: E5_vs_pMSG_24h_rep1 (mRNA)

description: mRNA expression in E5 vs control cells after 24h induction


title: OSCC tumor_OR4032

description: Hybridized to Affymetrix SNP6.0


title: Normal oral tissue_ON57

description: Hybridized to Affymetrix SNP6.0


title: F36VMpl transduced cord blood CD34+ cells cultured in the presence of CID, biological replicate 1


title: F36VMpl transduced cord blood CD34+ cells cultured in the presence of Epo, biological replicate 1


title: E5_vs_pMSG_48h_rep3 (mRNA)


title: E5_vs_pMSG_24h_rep2 (mRNA)


title: E5_vs_pMSG_4h_rep2 (mRNA)

description: mRNA expression in E5 vs control cells after 4h induction


title: A893_21

city: Sandwich

first: Glyn

last: Bradley

state: Kent

address: Ramsgate Road

country: United Kingdom

institute: Pfizer Ltd

description: Gene expression data from human endometrium.

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Data was RMA normalized and analyzed using Bioconductor in the R statistical environment.

source_name: Human endometrium

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

growth_protocol: Endometrial biopsies were taken from women by pipelle catheter, and glandular epithelium was laser capture microdissected.

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

tag: gender

value: female

tag: disease status

value: healthy

value: endometrium

tag: days from lh peak

tag: progesterone level


title: A893_19


title: E5_vs_pMSG_24h_rep3 (mRNA)


title: A893_17


title: E5_vs_pMSG_4h_rep1 (mRNA)


title: E5_vs_pMSG_2h_rep2 (mRNA)

description: mRNA expression in E5 vs control cells after 2h induction


title: E5_vs_pMSG_2h_rep3 (mRNA)


title: A893_20


title: A893_18


title: A893_16


title: E5_vs_pMSG_2h_rep1 (mRNA)


title: E5_vs_pMSG_0h_rep3 (mRNA)

description: mRNA expression in E5 vs control cells after 0h induction


title: A893_15


title: CRC-73

value: M

tag: age

tag: tumor-nodes-metastasis classification t

tag: tumor-nodes-metastasis classification n

tag: tumor-nodes-metastasis classification m


title: CRC-72

value: F


title: E5_vs_pMSG_0h_rep1 (mRNA)

tag: cell type


title: OSCC tumor_OR4004

description: Hybridized to Affymetrix SNP6.0


title: A893_13

tag: tissue


title: E5_vs_pMSG_0h_rep2 (mRNA)

tag: transfection


title: CRC-74


title: A893_14


title: OSCC tumor_OR3383

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR3407

description: Hybridized to Affymetrix SNP6.0


title: CRC-71


title: OSCC tumor_OR4003

description: Hybridized to Affymetrix SNP6.0


title: BY4742 YPD rep2

city: Albany

first: Randall

middle: Heywood

last: Morse

state: NY

institute: Wadsworth Center

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Affymetrix GeneChip Scanner 3000 was used according to mfr's recommendation

data_processing: Data was processed in Genespring 11.5.1.  RMA summarisation Algorithm. Fold-change data is provided as a Series supplementary file [*Note filtering was not the same for CSM data as for YPD data, so number of probes differs.  Also, fold changes are NOT log2.]

organism: Saccharomyces cerevisiae

source_name: Wild type yeast grown in YPD

label_protocol: Standard Affymetrix protocol

growth_protocol: Yeast were grown in YPD or CSM at 30C and RNA isolated from mid-log cultures.

extract_protocol: RNA purified using Masterpure Yeast RNA Purification Kit (Epicenter Technology, Madison, WI) and Rneasy purification kit (Qiagen)

tag: genotype

value: MATa his3Δ1 leu2Δ0 lys2Δ0 ura3Δ0


title: A893_12


title: A893_11


title: BY4742 YPD rep3


title: BY4742 YPD rep1


title: CRC-70


title: OSCC tumor_OR3294

description: Hybridized to Affymetrix SNP6.0

tag: disease state


title: OSCC tumor_OR3376

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR4015

description: Hybridized to Affymetrix SNP6.0


title: CRC-69


title: A893_10


title: gal11-myc med3∆ CSM rep3

source_name: gal11-myc med3∆ yeast grown in CSM

value: MATa his3Δ1 leu2Δ0 ura3Δ0 srb4Δ::kanMX GAL11-13MYC::HIS3MX  RY2844 (CEN LEU2 SRB4) med3Δ::URA3


title: A893_09


title: OSCC tumor_OR3306

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR3272

description: Hybridized to Affymetrix SNP6.0


title: CRC-66


title: CRC-68


title: CRC-67


title: gal11-myc med3∆ CSM rep2


title: A893_06


title: A893_07


title: gal11∆ med3∆ CSM rep3

source_name: gal11∆ med3∆ yeast grown in CSM

value: MATα med3Δ::kanMX4 med15Δ::kanMX4 his3Δ1 leu2Δ0 met15Δ0 ura3Δ0


title: gal11-myc med3∆ CSM rep1


title: gal11∆ med3∆ CSM rep2


title: CRC-65


title: gal11∆ med3∆ CSM rep1


title: OSCC tumor_OR3268

description: Hybridized to Affymetrix SNP6.0


title: A893_05


title: OSCC tumor_OR3244

description: Hybridized to Affymetrix SNP6.0


title: CRC-63


title: A893_04


title: OSCC tumor_OR3326

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR3289

description: Hybridized to Affymetrix SNP6.0


title: CRC-64


title: OSCC tumor_OR3243

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR3246

description: Hybridized to Affymetrix SNP6.0


title: CRC-62


title: OSCC tumor_OR3282

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR3265

description: Hybridized to Affymetrix SNP6.0


title: CRC-61


title: OSCC tumor_OR3283

description: Hybridized to Affymetrix SNP6.0


title: gal11-myc med3∆ YPD rep3

source_name: gal11-myc med3∆ yeast grown in YPD


title: CRC-60


title: Wild type CSM rep3

source_name: Wild type yeast grown in CSM

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0


title: Wild type CSM rep1


title: OSCC tumor_OR3233

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR3234

description: Hybridized to Affymetrix SNP6.0


title: CRC-59


title: OSCC tumor_OR3161

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR3179

description: Hybridized to Affymetrix SNP6.0


title: A893_01


city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

country: Germany

institute: University Tuebingen

description:
hh81_dmso_72h
Primary human hepatocytes from Donor 81 after 72h treatment with DMSO.

hyb_protocol: Standard Affymetrix hybridization protocol.

scan_protocol: Standard Affymetrix scanning protocol.

data_processing: All data preprocessing steps, i.e., normalization, background correction and detection of differentially expressed genes, were performed using standard procedures implemented in R Bioconductor.

source_name: Primary human hepatocytes, DMSO, 72h

label_protocol: Standard Affymetrix labeling protocol.

growth_protocol: Primary human hepatocytes were cultivated on 6-well plates in Williams medium E +10% FCS, Penicillin/Streptomycin (100U/ml), L-Glutamin (2mM), Dexamethasondihydrogenphosphat (0.025%v/v), Insulin (0.032 i.E.).

extract_protocol: Standard Qiagen RNA Isolation.

treatment_protocol: All samples were treated in Williams medium E, BSA (0.1%), Penicillin/Streptomycin (100U/ml), L-Glutamin (2mM), Dexamethasondihydrogenphosphat (0.025%v/v), ITS-X (5mg insulin, 3.35µg natriumselenit, 2,75 mg transferrin und 1mg ethanolamine). The concentration of atorvastatin was 40µM.

tag: donor

value: primary hepatocytes

value: DMSO

tag: time after treatment


title: gal11∆ med3∆ YPD rep3

source_name: gal11∆ med3∆ yeast grown in YPD


title: A893_03


description:
hh81_ato_48h
Primary human hepatocytes from Donor 81 after 48h treatment with atorvastatin.

source_name: Primary human hepatocytes, atorvastatin, 48h

tag: treatment

value: atorvastatin


title: gal11-myc med3∆ YPD rep1


description:
hh81_dmso_48h
Primary human hepatocytes from Donor 81 after 48h treatment with DMSO.

source_name: Primary human hepatocytes, DMSO, 48h


title: CRC-56

source_name: colorectal cancer


title: CRC-58


title: A893_02


title: gal11∆ med3∆ YPD rep2


title: OSCC tumor_OR3157

description: Hybridized to Affymetrix SNP6.0

value: tumor


title: CRC-57


title: OSCC tumor_OR3100

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR3116

description: Hybridized to Affymetrix SNP6.0


description:
hh81_ato_24h
Primary human hepatocytes from Donor 81 after 24h treatment with atorvastatin.

source_name: Primary human hepatocytes, atorvastatin, 24h


title: Wild type CSM rep2


title: CRC-55


description:
hh81_dmso_24h
Primary human hepatocytes from Donor 81 after 24h treatment with DMSO.

source_name: Primary human hepatocytes, DMSO, 24h


title: OSCC tumor_OR3149

description: Hybridized to Affymetrix SNP6.0


title: CRC-54


title: OSCC tumor_OR3115

description: Hybridized to Affymetrix SNP6.0


title: gal11-myc med3∆ YPD rep2


title: CRC-53


title: Wild type YPD rep2


title: gal11∆ med3∆ YPD rep1


title: Wild type YPD rep3


title: OSCC tumor_OR3191

description: Hybridized to Affymetrix SNP6.0


title: Wild type YPD rep1


title: CRC-52


description:
hh81_ato_12h
Primary human hepatocytes from Donor 81 after 12h treatment with atorvastatin.

source_name: Primary human hepatocytes, atorvastatin, 12h


title: OSCC tumor_OR3086

description: Hybridized to Affymetrix SNP6.0


description:
hh81_dmso_12h
Primary human hepatocytes from Donor 81 after 12h treatment with DMSO.

source_name: Primary human hepatocytes, DMSO, 12h


description:
hh81_ato_72h
Primary human hepatocytes from Donor 81 after 72h treatment with atorvastatin.

source_name: Primary human hepatocytes, atorvastatin, 72h


description:
hh81_dmso_6h
Primary human hepatocytes from Donor 81 after 6h treatment with DMSO.

source_name: Primary human hepatocytes, DMSO, 6h


title: CRC-51


description:
hh80_ato_72h
Primary human hepatocytes from Donor 80 after 72h treatment with atorvastatin.


title: rpb1-12XS2ACTD_LatA_biological replicate 3

city: London

first: Jim

last: Karagiannis

state: Ontario

address: 1151 Richmond St. N

department: Biology

country: Canada

institute: University of Western Ontario

description: Gene expression data for LatA treated rpb1-12XS2ACTD strains

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Yeast 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Analysis was performed using Genespring GX 10.0.1 software (Agilent).  CEL files were normalized with the RMA algorithm.  The data were grouped according to: genotype, representing rpb1-12XWTCTD or rpb1-12XS2ACTD, and drug, representing LatA or DMSO treatments.  All of the data could thus be classified as 1) rpb1-12XWTCTD, DMSO treated, 2) rpb1-12XWTCTD, LatA treated, 3) rpb1-12XS2ACTD, DMSO treated, and 4) rpb1-12XS2ACTD, LatA treated. To identify differentially regulated genes, data for these genes were inspected and data were filtered using Volcano plot analysis employing the Benjamin-Hochberg multiple testing correction.  Genes  showing statistically significant differences (p-value <0.05) and fold changes greater than 1.5 were identified as differentially regulated.

organism: Schizosaccharomyces pombe

source_name: rpb1-12XS2ACTD_LatA_0.5uM_3 hrs

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

growth_protocol: All strains were grown in liquid YES media with constant shaking.

extract_protocol: Total RNA extraction was performed using the Ribopure Yeast Kit (Ambion) according to the manufacturer's instructions.

treatment_protocol: Strains were treated with 0.5uM LatA or DMSO for 3 hours prior to RNA extraction.

tag: strain

tag: genotype/variation

value: site-directed CTD mutants


title: OSCC tumor_OR3088

description: Hybridized to Affymetrix SNP6.0

source_name: OSCC  specimens


title: CRC-50

tag: gender


title: rpb1-12XS2ACTD_LatA_biological replicate 2


title: rpb1-12XS2ACTD_LatA_biological replicate 1


description:
hh80_dmso_72h
Primary human hepatocytes from Donor 80 after 72h treatment with DMSO.


title: OSCC tumor_OR3084

description: Hybridized to Affymetrix SNP6.0


description:
hh80_dmso_48h
Primary human hepatocytes from Donor 80 after 48h treatment with DMSO.


title: rpb1-12XS2ACTD_DMSO_biological replicate 3

description: Gene expression data for DMSO treated rpb1-12XS2ACTD strains


title: CRC-48


title: rpb1-12XS2ACTD_DMSO_biological replicate 2


title: CRC-46


title: OSCC tumor_OR3076

description: Hybridized to Affymetrix SNP6.0


description:
hh80_dmso_24h
Primary human hepatocytes from Donor 80 after 24h treatment with DMSO.


title: CRC-49


description:
hh80_ato_24h
Primary human hepatocytes from Donor 80 after 24h treatment with atorvastatin.


title: CRC-47


description:
hh80_ato_48h
Primary human hepatocytes from Donor 80 after 48h treatment with atorvastatin.


title: rpb1-12XCTD_LatA_biological replicate 3

description: Gene expression data for LatA treated rpb1-12XCTD strains

source_name: rpb1-12XCTD_LatA_0.5uM_3 hrs

value: wild type CTD


title: OSCC tumor_OR3053

description: Hybridized to Affymetrix SNP6.0


description:
hh80_ato_12h
Primary human hepatocytes from Donor 80 after 12h treatment with atorvastatin.


title: CRC-45


title: OSCC tumor_OR3078

description: Hybridized to Affymetrix SNP6.0


title: CRC-44


title: OSCC tumor_OR3019

description: Hybridized to Affymetrix SNP6.0


title: rpb1-12XCTD_LatA_biological replicate 1


description:
hh80_dmso_12h
Primary human hepatocytes from Donor 80 after 12h treatment with DMSO.


title: rpb1-12XCTD_LatA_biological replicate 2


title: OSCC tumor_OR2451

description: Hybridized to Affymetrix SNP6.0


description:
hh80_ato_6h
Primary human hepatocytes from Donor 80 after 6h treatment with atorvastatin.

source_name: Primary human hepatocytes, atorvastatin, 6h


title: rpb1-12XCTD_DMSO_biological replicate 3

description: Gene expression data for DMSO treated rpb1-12XCTD strains


title: CRC-43


title: CRC-41


description:
hh80_dmso_6h
Primary human hepatocytes from Donor 80 after 6h treatment with DMSO.


title: rpb1-12XS2ACTD_DMSO_biological replicate 1


description:
hh79_ato_72h
Primary human hepatocytes from Donor 79 after 72h treatment with atorvastatin.


title: rpb1-12XCTD_DMSO_biological replicate 1


title: CRC-42


description:
hh79_dmso_72h
Primary human hepatocytes from Donor 79 after 72h treatment with DMSO.


title: rpb1-12XCTD_DMSO_biological replicate 2


title: CRC-40


title: OSCC tumor_OR2461

description: Hybridized to Affymetrix SNP6.0


title: CRC-39


title: CRC-38


title: OSCC tumor_OR2442

description: Hybridized to Affymetrix SNP6.0


title: CRC-36


description:
hh79_ato_24h
Primary human hepatocytes from Donor 79 after 24h treatment with atorvastatin.


description:
hh79_dmso_48h
Primary human hepatocytes from Donor 79 after 48h treatment with DMSO.


title: CRC-37


title: OSCC tumor_OR2403

description: Hybridized to Affymetrix SNP6.0


description:
hh79_dmso_24h
Primary human hepatocytes from Donor 79 after 24h treatment with DMSO.


title: GS-1-EM0168, DON T24, experimental rep 1

city: Lethbridge

first: Nora

last: Foroud

state: Alberta

address: 5403 1st Ave South

institute: Agriculture and Agri-Foods Canada

description:
3E-T24-RI
Gene expression data from DON-inoculated spike, collected at 24 h after inoculation in GS-1-EM0168.

hyb_protocol: Following fragmentation, 15ug of cRNA was hybridized on a GeneChip Wheat Genome Array overnight for 16hr at 45°C and with 60rpm rotation. After 16 hours of hybridization, the GeneChips were stained with SAPE stain and Antibody solutions and washed with Wash Buffers A and Wash Buffers B in the Affymetrix Fluidics Station 450 using the EukGE-WS2v4 Fluidics Script protocol.

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

data_processing: CEL files were subjected to transformation and normalization using ArrayAssist (Stratagene) software, using default settings.  GCRMA followed by MAS5.0 algorithms were applied, a value of 16 was added to the transformed data (for variance stabilization) and the log2 value was then calculated.

organism: Triticum aestivum

source_name: GS-1-EM0168 spikelets from DON-inoculated spike, collected at 24 h after inoculation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: Plants were grown in a greenhouse (21/18oC, 16 h photoperiod). Plants were watered as needed and fertilized biweekly with 20-20-20 (N-P-K). At the 5-7 leaf stage, they were treated with Tilt™ (2.5 mL L-1 propiconazole, Syngenta Crop Protection Canada, Guelph, ON) and Intercept™ (0.004 g L-1of soil, Imidacloprid, Bayer Crop Science Canada, Toronto, ON) preventative measures against powdery mildew and aphids.

extract_protocol: Total RNA was extracted using the QIAGEN RNeasy® Plant Mini Kit with an on-column DNase digestion according to manufacturer's instructions.

treatment_protocol: Plants were moved to a mist-irrigated greenhouse (25oC, 95% humidity, 16 h photoperiod) one day prior to anthesis. Two spikelets (one on each row) near the center of the spike were point inoculated at anthesis, by injection of 10 μL inoculum directly into the florets on either side of the spike between 0700 and 1000 hours. The concentration for F. graminearum-containing inocula was 40,000 macroconida/mL, and for DON-containing inocula was 2 ppm.  At 3, 8, and 24 h after inoculation, up to three spikelets above and below the inoculation point were collected.  For zero-hour uninoculated controls, spikelets were collected between 0700 and 1000 hours at anthesis.

value: spikelets

value: DON inoculation

tag: treatment duration

value: 24 hrs


title: GS-1-EM0168, DON T24, experimental rep 3

description:
3E-T24-RIII
Gene expression data from DON-inoculated spike, collected at 24 h after inoculation in GS-1-EM0168.


title: GS-1-EM0168, DON T24, experimental rep 2

description:
3E-T24-RII
Gene expression data from DON-inoculated spike, collected at 24 h after inoculation in GS-1-EM0168.


title: OSCC tumor_OR2449

description: Hybridized to Affymetrix SNP6.0


title: CRC-35


description:
hh79_ato_12h
Primary human hepatocytes from Donor 79 after 12h treatment with atorvastatin.


title: GS-1-EM0168, DON T8, experimental rep 3

description:
3E-T8-RIII
Gene expression data from DON-inoculated spike, collected at 8 h after inoculation in GS-1-EM0168.

source_name: GS-1-EM0168 spikelets from DON-inoculated spike, collected at 8 h after inoculation

value: 8 hrs


title: GS-1-EM0168, DON T8, experimental rep 2

description:
3E-T8-RII
Gene expression data from DON-inoculated spike, collected at 8 h after inoculation in GS-1-EM0168.


title: OSCC tumor_OR2378

description: Hybridized to Affymetrix SNP6.0


title: CRC-34


description:
hh79_dmso_12h
Primary human hepatocytes from Donor 79 after 12h treatment with DMSO.


title: OSCC tumor_OR2348

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR2360

description: Hybridized to Affymetrix SNP6.0


title: GS-1-EM0168, DON T8, experimental rep 1

description:
3E-T8-RI
Gene expression data from DON-inoculated spike, collected at 8 h after inoculation in GS-1-EM0168.


title: OSCC tumor_OR2446

description: Hybridized to Affymetrix SNP6.0


description:
hh79_ato_48h
Primary human hepatocytes from Donor 79 after 48h treatment with atorvastatin.


title: CRC-33


title: CRC-32


description:
hh79_ato_6h
Primary human hepatocytes from Donor 79 after 6h treatment with atorvastatin.


title: OSCC tumor_OR2341

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR2332

description: Hybridized to Affymetrix SNP6.0


description:
hh67_ato_72h
Primary human hepatocytes from Donor 67 after 72h treatment with atorvastatin.


title: GS-1-EM0168, DON T3, experimental rep 2

description:
3E-T3-RII
Gene expression data from DON-inoculated spike, collected at 3 h after inoculation in GS-1-EM0168.

source_name: GS-1-EM0168 spikelets from DON-inoculated spike, collected at 3 h after inoculation

value: 3 hrs


title: CRC-30


title: OSCC tumor_OR2267

description: Hybridized to Affymetrix SNP6.0


description:
hh79_dmso_6h
Primary human hepatocytes from Donor 79 after 6h treatment with DMSO.


title: OSCC tumor_OR2328

description: Hybridized to Affymetrix SNP6.0


title: GS-1-EM0168, DON T3, experimental rep 1

description:
3E-T3-RI
Gene expression data from DON-inoculated spike, collected at 3 h after inoculation in GS-1-EM0168.


title: GS-1-EM0168, DON T3, experimental rep 3

description:
3E-T3-RIII
Gene expression data from DON-inoculated spike, collected at 3 h after inoculation in GS-1-EM0168.


title: CRC-29

value: M


description:
hh65_ato_72h
Primary human hepatocytes from Donor 65 after 72h treatment with atorvastatin.


title: OSCC tumor_OR2266

description: Hybridized to Affymetrix SNP6.0


description:
hh62_ato_72h
Primary human hepatocytes from Donor 62 after 72h treatment with atorvastatin.


title: GS-1-EM0168, FgTri5-/DON T24, experimental rep 3

description:
3D-T24-RIII
Gene expression data from FgTri5-/DON-inoculated spike, collected at 24 h after inoculation in GS-1-EM0168.

source_name: GS-1-EM0168 spikelets from FgTri5-/DON-inoculated spike, collected at 24 h after inoculation

value: FgTri5-/DON inoculation


title: CRC-28


title: OSCC tumor_OR2231

description: Hybridized to Affymetrix SNP6.0


title: CRC-27

value: F


title: CRC-31


description:
hh67_dmso_72h
Primary human hepatocytes from Donor 67 after 72h treatment with DMSO.

source_name: Primary human hepatocytes, DMSO, 72h


title: OSCC tumor_OR2309

description: Hybridized to Affymetrix SNP6.0


description:
hh65_dmso_72h
Primary human hepatocytes from Donor 65 after 72h treatment with DMSO.


title: GS-1-EM0168, FgTri5-/DON T24, experimental rep 2

description:
3D-T24-RII
Gene expression data from FgTri5-/DON-inoculated spike, collected at 24 h after inoculation in GS-1-EM0168.


title: GS-1-EM0168, FgTri5-/DON T8, experimental rep 3

description:
3D-T8-RIII
Gene expression data from FgTri5-/DON-inoculated spike, collected at 8 h after inoculation in GS-1-EM0168.

source_name: GS-1-EM0168 spikelets from FgTri5-/DON-inoculated spike, collected at 8 h after inoculation


title: GS-1-EM0168, FgTri5-/DON T24, experimental rep 1

description:
3D-T24-RI
Gene expression data from FgTri5-/DON-inoculated spike, collected at 24 h after inoculation in GS-1-EM0168.


title: OSCC tumor_OR2343

description: Hybridized to Affymetrix SNP6.0


description:
hh62_dmso_72h
Primary human hepatocytes from Donor 62 after 72h treatment with DMSO.


title: CRC-25

source_name: colorectal cancer


title: CRC-24


title: GS-1-EM0168, FgTri5-/DON T8, experimental rep 2

description:
3D-T8-RII
Gene expression data from FgTri5-/DON-inoculated spike, collected at 8 h after inoculation in GS-1-EM0168.


title: GS-1-EM0168, FgTri5-/DON T8, experimental rep 1

description:
3D-T8-RI
Gene expression data from FgTri5-/DON-inoculated spike, collected at 8 h after inoculation in GS-1-EM0168.


title: OSCC tumor_OR2133

description: Hybridized to Affymetrix SNP6.0


title: GS-1-EM0168, FgTri5-/DON T3, experimental rep 3

description:
3D-T3-RIII
Gene expression data from FgTri5-/DON-inoculated spike, collected at 3 h after inoculation in GS-1-EM0168.

source_name: GS-1-EM0168 spikelets from FgTri5-/DON-inoculated spike, collected at 3 h after inoculation


description:
hh65_ato_48h
Primary human hepatocytes from Donor 65 after 48h treatment with atorvastatin.

source_name: Primary human hepatocytes, atorvastatin, 48h


title: CRC-23


description:
hh62_ato_48h
Primary human hepatocytes from Donor 62 after 48h treatment with atorvastatin.


title: CRC-22


title: GS-1-EM0168, FgTri5-/DON T3, experimental rep 2

description:
3D-T3-RII
Gene expression data from FgTri5-/DON-inoculated spike, collected at 3 h after inoculation in GS-1-EM0168.


title: OSCC tumor_OR2138

description: Hybridized to Affymetrix SNP6.0


description:
hh67_dmso_48h
Primary human hepatocytes from Donor 67 after 48h treatment with DMSO.

source_name: Primary human hepatocytes, DMSO, 48h


title: OSCC tumor_OR2186

description: Hybridized to Affymetrix SNP6.0


title: GS-1-EM0168, FgTri5-/DON T3, experimental rep 1

description:
3D-T3-RI
Gene expression data from FgTri5-/DON-inoculated spike, collected at 3 h after inoculation in GS-1-EM0168.


title: OSCC tumor_OR2237

description: Hybridized to Affymetrix SNP6.0


description:
hh65_dmso_48h
Primary human hepatocytes from Donor 65 after 48h treatment with DMSO.


description:
hh62_dmso_48h
Primary human hepatocytes from Donor 62 after 48h treatment with DMSO.


description:
hh67_ato_48h
Primary human hepatocytes from Donor 67 after 48h treatment with atorvastatin.


title: CRC-26


title: OSCC tumor_OR2193

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR2069

description: Hybridized to Affymetrix SNP6.0


description:
hh67_ato_24h
Primary human hepatocytes from Donor 67 after 24h treatment with atorvastatin.

source_name: Primary human hepatocytes, atorvastatin, 24h


title: CRC-19


title: GS-1-EM0168, FgTri5- T24, experimental rep 2

description:
3C-T24-RII
Gene expression data from (FgTri5-)-inoculated spike, collected at 24 h after inoculation in GS-1-EM0168.

source_name: GS-1-EM0168 spikelets from (FgTri5-)-inoculated spike, collected at 24 h after inoculation

value: FgTri5- inoculation


title: GS-1-EM0168, FgTri5- T24, experimental rep 1

description:
3C-T24-RI
Gene expression data from (FgTri5-)-inoculated spike, collected at 24 h after inoculation in GS-1-EM0168.


title: CRC-18


title: OSCC tumor_OR2470

description: Hybridized to Affymetrix SNP6.0


title: GS-1-EM0168, FgTri5- T8, experimental rep 3

description:
3C-T8-RIII
Gene expression data from (FgTri5-)-inoculated spike, collected at 8 h after inoculation in GS-1-EM0168.

source_name: GS-1-EM0168 spikelets from (FgTri5-)-inoculated spike, collected at 8 h after inoculation


description:
hh65_ato_24h
Primary human hepatocytes from Donor 65 after 24h treatment with atorvastatin.


description:
hh62_ato_24h
Primary human hepatocytes from Donor 62 after 24h treatment with atorvastatin.


title: GS-1-EM0168, FgTri5- T8, experimental rep 2

description:
3C-T8-RII
Gene expression data from (FgTri5-)-inoculated spike, collected at 8 h after inoculation in GS-1-EM0168.


title: GS-1-EM0168, FgTri5- T24, experimental rep 3

description:
3C-T24-RIII
Gene expression data from (FgTri5-)-inoculated spike, collected at 24 h after inoculation in GS-1-EM0168.


title: OSCC tumor_OR1458

description: Hybridized to Affymetrix SNP6.0


title: CRC-17


title: OSCC tumor_OR1414

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR1438

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR1427

description: Hybridized to Affymetrix SNP6.0


title: GS-1-EM0168, FgTri5- T8, experimental rep 1

description:
3C-T8-RI
Gene expression data from (FgTri5-)-inoculated spike, collected at 8 h after inoculation in GS-1-EM0168.


title: OSCC tumor_OR2006

description: Hybridized to Affymetrix SNP6.0


title: GS-1-EM0168, FgTri5- T3, experimental rep 2

description:
3C-T3-RII
Gene expression data from (FgTri5-)-inoculated spike, collected at 3 h after inoculation in GS-1-EM0168.

source_name: GS-1-EM0168 spikelets from (FgTri5-)-inoculated spike, collected at 3 h after inoculation


description:
hh62_dmos_24h
Primary human hepatocytes from Donor 62 after 24h treatment with DMSO.

source_name: Primary human hepatocytes, DMSO, 24h


description:
hh67_ato_12h
Primary human hepatocytes from Donor 67 after 12h treatment with atorvastatin.

source_name: Primary human hepatocytes, atorvastatin, 12h


title: GS-1-EM0168, FgTri5- T3, experimental rep 1

description:
3C-T3-RI
Gene expression data from (FgTri5-)-inoculated spike, collected at 3 h after inoculation in GS-1-EM0168.


description:
hh65_dmso_24h
Primary human hepatocytes from Donor 65 after 24h treatment with DMSO.


title: CRC-12


description:
hh65_ato_12h
Primary human hepatocytes from Donor 65 after 12h treatment with atorvastatin.


title: CRC-11


title: GS-1-EM0168, FgTri5- T3, experimental rep 3

description:
3C-T3-RIII
Gene expression data from (FgTri5-)-inoculated spike, collected at 3 h after inoculation in GS-1-EM0168.


title: OSCC tumor_OR1376

description: Hybridized to Affymetrix SNP6.0

source_name: OSCC  specimens


title: GS-1-EM0168, FgTri5+ T24, experimental rep 3

description:
3B-T24-RIII
Gene expression data from (FgTri5+)-inoculated spike, collected at 24 h after inoculation in GS-1-EM0168.

source_name: GS-1-EM0168 spikelets from (FgTri5+)-inoculated spike, collected at 24 h after inoculation

value: FgTri5+ inoculation


title: OSCC tumor_OR1343

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR1325

description: Hybridized to Affymetrix SNP6.0


description:
hh67_dmso_24h
Primary human hepatocytes from Donor 67 after 24h treatment with DMSO.


title: OSCC tumor_OR1394

description: Hybridized to Affymetrix SNP6.0


description:
hh62_ato_12h
Primary human hepatocytes from Donor 62 after 12h treatment with atorvastatin.


title: GS-1-EM0168, FgTri5+ T24, experimental rep 1

description:
3B-T24-RI
Gene expression data from (FgTri5+)-inoculated spike, collected at 24 h after inoculation in GS-1-EM0168.


description:
hh67_dmso_12h
Primary human hepatocytes from Donor 67 after 12h treatment with DMSO.

source_name: Primary human hepatocytes, DMSO, 12h


description:
hh65_dmso_12h
Primary human hepatocytes from Donor 65 after 12h treatment with DMSO.


title: OSCC tumor_OR1349

description: Hybridized to Affymetrix SNP6.0


title: GS-1-EM0168, FgTri5+ T24, experimental rep 2

description:
3B-T24-RII
Gene expression data from (FgTri5+)-inoculated spike, collected at 24 h after inoculation in GS-1-EM0168.


title: CRC-8


title: GS-1-EM0168, FgTri5+ T8, experimental rep 2

description:
3B-T8-RII
Gene expression data from (FgTri5+)-inoculated spike, collected at 8 h after inoculation in GS-1-EM0168.

source_name: GS-1-EM0168 spikelets from (FgTri5+)-inoculated spike, collected at 8 h after inoculation


title: GS-1-EM0168, FgTri5+ T8, experimental rep 3

description:
3B-T8-RIII
Gene expression data from (FgTri5+)-inoculated spike, collected at 8 h after inoculation in GS-1-EM0168.


description:
hh67_ato_6h
Primary human hepatocytes from Donor 67 after 6h treatment with atorvastatin.

source_name: Primary human hepatocytes, atorvastatin, 6h


title: CRC-7


title: OSCC tumor_OR1291

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR1320

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR1285

description: Hybridized to Affymetrix SNP6.0


title: CRC-5


title: CRC-9


title: GS-1-EM0168, FgTri5+ T3, experimental rep 1

description:
3B-T3-RI
Gene expression data from (FgTri5+)-inoculated spike, collected at 3 h after inoculation in GS-1-EM0168.

source_name: GS-1-EM0168 spikelets from (FgTri5+)-inoculated spike, collected at 3 h after inoculation


description:
hh62_dmso_12h
Primary human hepatocytes from Donor 62 after 12h treatment with DMSO.


title: OSCC tumor_OR1293

description: Hybridized to Affymetrix SNP6.0


title: CRC-3

value: Tis


description:
hh65_ato_6h
Primary human hepatocytes from Donor 65 after 6h treatment with atorvastatin.

value: primary hepatocytes


description:
hh67_dmso_6h
Primary human hepatocytes from Donor 67 after 6h treatment with DMSO.

source_name: Primary human hepatocytes, DMSO, 6h

value: DMSO


description:
hh62_ato_6h
Primary human hepatocytes from Donor 62 after 6h treatment with atorvastatin.

value: atorvastatin


description:
hh65_dmso_6h
Primary human hepatocytes from Donor 65 after 6h treatment with DMSO.


title: GS-1-EM0168, FgTri5+ T3, experimental rep 2

description:
3B-T3-RII
Gene expression data from (FgTri5+)-inoculated spike, collected at 3 h after inoculation in GS-1-EM0168.


title: GS-1-EM0168, FgTri5+ T8, experimental rep 1

description:
3B-T8-RI
Gene expression data from (FgTri5+)-inoculated spike, collected at 8 h after inoculation in GS-1-EM0168.


title: GS-1-EM0168, FgTri5+ T3, experimental rep 3

description:
3B-T3-RIII
Gene expression data from (FgTri5+)-inoculated spike, collected at 3 h after inoculation in GS-1-EM0168.


title: OSCC tumor_OR1240

description: Hybridized to Affymetrix SNP6.0

value: tumor


title: OSCC tumor_OR1272

description: Hybridized to Affymetrix SNP6.0


title: GS-1-EM0168, water T24, experimental rep 3

description:
3A-T24-RIII
Gene expression data from water-inoculated spike, collected at 24 h after inoculation in GS-1-EM0168.

source_name: GS-1-EM0168 spikelets from water-inoculated spike, collected at 24 h after inoculation

value: water inoculation


title: Dsim.MD239

city: Ithaca

first: Margarida

last: Cardoso Moreira

address: 526 Campus Road

department: Molecular Biology and Genetics

institute: Cornell University

hyb_protocol: Following labeling, 25ml of the terminal labeled solution were hybridized according to standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures using Affymetrix GeneChip Scanner 3000

data_processing:
The data was analyzed using R and Bioconductor. The data was first quantile normalized, and then the natural logarithm was recorded as “LNNORMINTENSITY”. Following initial processing, the probes representing the 5% most variable probes among the three replicates for the 14 lines were discarded. The data was then subjected to analysis using an HMM. Results of the HMM analysis are included in the GEO Sample table.
The *post.txt processed data supplementary file contains for each probe, its location in the D. simulans genome and its posterior probability of being duplicated (output from the Hiddem Markov Model)

organism: Drosophila simulans

label_protocol: Labeling was conducted following Affymetrix oligoarray target pre-processing as described bellow. There are two main steps: 1- Genomic DNA fragmentation and 2- Terminal labeling.    1- Genomic DNA fragmentation:  1.1- The following reaction mix was prepared:  6 ul 10x One-Phor-All buffer (1x)  25 ul of Genomic DNA  0.5 ul DNase I (0.168u/ul)  28.5 ul Nuclease-free ddH2O  1.2- The reaction was incubated at 37ºC for 10 minutes.  1.3- DNase I was inactivated at 100ºC for 10 minutes.  2- Terminal labeling was done using the Enzo BioArray terminal labeling kit with biotin-ddUTP (Affymetrix P/N 900181) to label 3' termini of the fragmentation products. The details of the protocol are described below.  2.1 The following reaction mix was prepared:  20 ul of reaction buffer (5x)  10 ul CoCl2 (10x)  4 ul Biotin-ddUTP (100x)  8 ul Terminal Deoxyribonucleotide transferase (50x)  54 ul of the fragmentation product (from the Genomic DNA fragmentation step)    2.2- The reaction was incubated at 37ºC for 60 minutes.  2.3- The reaction was stopped by adding 4 ul of 0.25M EDTA.  2.4- The target was then ready to be hybridized onto Tiling arrays.

growth_protocol: Flies were kept at room temperature in standard cornmeal-molasses-yeast medium. DNA was extracted from female virgins.

extract_protocol: Genomic DNA was extracted following the DNA purification protocol for 20-30 flies from PUREGENE with an added phenol-chloroform extraction step. DNA was extracted from 30 female virgin flies. After the protein precipitation step (and before the DNA precipitation step) a phenol-chloroform step was performed as follows: 1- an equal volume of pheno:chloroform:isoamyl:alcohol (25:24:1) was added to the solution containing DNA and mixed by inverting gently (50 times); 2- the solution was centrifuged at 14000rpm for two minutes; 3- the top aqueous layer was transferred to a new tube; 4- an equal volume of chloroform:isoamyl-alcohol (24:1) was added to the solution and mixed by inverting gently; 4- the solution was centrifuged at 14000rpm for two minutes; and 5- the top aqueous layer was transferred to a new tube. The PUREGENE DNA purification protocol was resumed starting in the DNA precipitation step. DNA was rehydrated using 50ml of DNA Hydration solution yielding a concentration of 400mg/ml.

treatment_protocol: No treatments were applied to the flies before DNA extraction.

tag: line


title: OSCC tumor_OR1219

description: Hybridized to Affymetrix SNP6.0


title: GS-1-EM0168, water T8, experimental rep 2

description:
3A-T8-RII
Gene expression data from water-inoculated spike, collected at 8 h after inoculation in GS-1-EM0168.

source_name: GS-1-EM0168 spikelets from water-inoculated spike, collected at 8 h after inoculation


title: Dsim.MD235


title: GS-1-EM0168, water T24, experimental rep 2

description:
3A-T24-RII
Gene expression data from water-inoculated spike, collected at 24 h after inoculation in GS-1-EM0168.


title: GS-1-EM0168, water T8, experimental rep 3

description:
3A-T8-RIII
Gene expression data from water-inoculated spike, collected at 8 h after inoculation in GS-1-EM0168.


title: OSCC tumor_OR1260

description: Hybridized to Affymetrix SNP6.0


description:
hh62_dmso_6h
Primary human hepatocytes from Donor 62 after 6h treatment with DMSO.


title: OSCC tumor_OR1019

description: Hybridized to Affymetrix SNP6.0


title: GS-1-EM0168, water T8, experimental rep 1

description:
3A-T8-RI
Gene expression data from water-inoculated spike, collected at 8 h after inoculation in GS-1-EM0168.


title: Dsim.MD222


title: Dsim.MD210


title: Dsim.MD197


title: GS-1-EM0168, water T24, experimental rep 1

description:
3A-T24-RI
Gene expression data from water-inoculated spike, collected at 24 h after inoculation in GS-1-EM0168.


title: Dsim.MD105


title: GS-1-EM0168, water T3, experimental rep 2

description:
3A-T3-RII
Gene expression data from water-inoculated spike, collected at 3 h after inoculation in GS-1-EM0168.

source_name: GS-1-EM0168 spikelets from water-inoculated spike, collected at 3 h after inoculation


title: OSCC tumor_OR1077

description: Hybridized to Affymetrix SNP6.0


title: GS-1-EM0168, water T3, experimental rep 1

description:
3A-T3-RI
Gene expression data from water-inoculated spike, collected at 3 h after inoculation in GS-1-EM0168.


title: Dsim.MD04


title: GS-1-EM0168, water T3, experimental rep 3

description:
3A-T3-RIII
Gene expression data from water-inoculated spike, collected at 3 h after inoculation in GS-1-EM0168.


title: GS-1-EM0168, uninoculated control, experimental rep 3

description:
3-T0-RIII
Gene expression data from uninoculated control spike, from GS-1-EM0168.

source_name: GS-1-EM0168 spikelets from uninoculated spike


title: GS-1-EM0168, uninoculated control, experimental rep 2

description:
3-T0-RII
Gene expression data from uninoculated control spike, from GS-1-EM0168.


title: OSCC tumor_OR1016

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR1058

description: Hybridized to Affymetrix SNP6.0


title: PC-9_7

city: Lexington

first: Esther

middle: P

last: Black

state: KY

address: 789 S Limestone

department: Pharmaceutical Sciences

institute: University of Kentucky

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human U133 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: NSCLC cell line

growth_protocol: NSCLC cell lines were cultured for 3d in 10% serum-containing RPMI 1640 with no drug treatment.

extract_protocol: RNA was extracted using Qiagen Rneasy column preparation

value: non small cell lung cancer cell (NSCLC)

tag: erlotinib sensitivity

value: Yes


title: K562

source_name: CML cell line

value: chronic myelogenous leukemia (CML)

value: No


title: Dsim.Valparaiso

description: Dsim.Valparaiso

source_name: Valparaiso

value: Valparaiso


title: GS-1-EM0040, DON T24, experimental rep 3

description:
2E-T24-RIII
Gene expression data from DON-inoculated spike, collected at 24 h after inoculation in GS-1-EM0040.

source_name: GS-1-EM0040 spikelets from DON-inoculated spike, collected at 24 h after inoculation

value: spikelets

value: DON inoculation

value: 24 hrs


title: Dsim.NewGuinea

description: Dsim.NewGuinea

source_name: New Guinea

value: New Guinea


title: OSCC tumor_OR1286

description: Hybridized to Affymetrix SNP6.0


title: GS-1-EM0168, uninoculated control, experimental rep 1

description:
3-T0-RI
Gene expression data from uninoculated control spike, from GS-1-EM0168.


title: OSCC tumor_OR0948

description: Hybridized to Affymetrix SNP6.0


title: Dsim.W74


title: GS-1-EM0040, DON T8, experimental rep 3

description:
2E-T8-RIII
Gene expression data from DON-inoculated spike, collected at 8 h after inoculation in GS-1-EM0040.

source_name: GS-1-EM0040 spikelets from DON-inoculated spike, collected at 8 h after inoculation

value: 8 hrs


title: GS-1-EM0040, DON T24, experimental rep 2

description:
2E-T24-RII
Gene expression data from DON-inoculated spike, collected at 24 h after inoculation in GS-1-EM0040.


title: OSCC tumor_OR0950

description: Hybridized to Affymetrix SNP6.0

source_name: OSCC  specimens


title: GS-1-EM0040, DON T8, experimental rep 2

description:
2E-T8-RII
Gene expression data from DON-inoculated spike, collected at 8 h after inoculation in GS-1-EM0040.


title: Dsim.Impala6

source_name: Impala 6

value: Impala 6


title: Dsim.SFSR2IIST


title: GS-1-EM0040, DON T24, experimental rep 1

description:
2E-T24-RI
Gene expression data from DON-inoculated spike, collected at 24 h after inoculation in GS-1-EM0040.


title: Dsim.MD72


title: GS-1-EM0040, DON T8, experimental rep 1

description:
2E-T8-RI
Gene expression data from DON-inoculated spike, collected at 8 h after inoculation in GS-1-EM0040.


title: 24hr incubated with CDRI-5g, rep2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description:
3c
Compound CDRI-5g  :  Saquib, M. et al. 2,3-Dideoxy hex-2-enolpyranosid-4-uloses as promising new-antitibercular agents : Design, synthesis, biological evaluation and SAR studies. Eur J. Med. Chem. 46 (2011) 2317-2223.

hyb_protocol: The labeled cRNA samples were hybridized on to an Agilent Custom Mycobacterium tuberculosis 8x15k Array designed by Genotypic Technology Pvt. Ltd. (AMADID: 019943). 300ng of Cy3 labeled sample and 300ng of Cy5 labeled sample were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327) and scanned using the Agilent Microarray Scanner G2505C at 5 micron resolution.

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1)

data_processing: The normalization was done using GeneSpring GX 11 Software 75th percentile shift normalization.

organism: Mycobacterium tuberculosis

source_name: 24hr incubated with CDRI-5g

label_protocol: Poly (A)-tails were added to the 3’-end of RNA by using A-plus Poly (A) polymerase tailing kit (Epicentre Biotechnologies).Then  the samples  were labeled using Agilent Quick-Amp labeling Kit (p/n:5190-0444).  Five hundred nanograms each of the samples were incubated with reverse transcription mix at 42°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3-CTP(Agilent) and Cy5-CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: M. tuberculosis H37Rv culture was grown to OD600= 0.02 in MB7H9 (Difco) medium. Culture was aliquoted into three different flask. One was used as a control and other two was added with 10 µg/ml compound CDRI-5g. After 12 h and 24 h of incubation culture from both the flask were pelleted and RNA was isolated by Qiagen RNA isolation kit.

extract_protocol: The total RNA isolated  using Qiagen Rneasy Minikit as per the manufacturer’s instructions

treatment_protocol: Compound CDRI-5g was added in the broth culture at 10 µg/ml concentration for 12 h and 24 h.


title: GS-1-EM0040, DON T3, experimental rep 3

description:
2E-T3-RIII
Gene expression data from DON-inoculated spike, collected at 3 h after inoculation in GS-1-EM0040.

source_name: GS-1-EM0040 spikelets from DON-inoculated spike, collected at 3 h after inoculation

value: 3 hrs


title: 12hr incubated with CDRI-5g, rep2

description:
3b
Compound CDRI-5g  :  Saquib, M. et al. 2,3-Dideoxy hex-2-enolpyranosid-4-uloses as promising new-antitibercular agents : Design, synthesis, biological evaluation and SAR studies. Eur J. Med. Chem. 46 (2011) 2317-2223.

source_name: 12hr incubated with CDRI-5g


title: Dsim.MD01


title: GS-1-EM0040, DON T3, experimental rep 2

description:
2E-T3-RII
Gene expression data from DON-inoculated spike, collected at 3 h after inoculation in GS-1-EM0040.


title: OSCC tumor_OR0936

description: Hybridized to Affymetrix SNP6.0


title: 12hr incubated with CDRI-5g, rep1

description:
2b
Compound CDRI-5g  :  Saquib, M. et al. 2,3-Dideoxy hex-2-enolpyranosid-4-uloses as promising new-antitibercular agents : Design, synthesis, biological evaluation and SAR studies. Eur J. Med. Chem. 46 (2011) 2317-2223.


title: Control-1

description:
2a
Compound CDRI-5g  :  Saquib, M. et al. 2,3-Dideoxy hex-2-enolpyranosid-4-uloses as promising new-antitibercular agents : Design, synthesis, biological evaluation and SAR studies. Eur J. Med. Chem. 46 (2011) 2317-2223.

source_name: Control


title: 24hr incubated with CDRI-5g, rep1

description:
2c
Compound CDRI-5g  :  Saquib, M. et al. 2,3-Dideoxy hex-2-enolpyranosid-4-uloses as promising new-antitibercular agents : Design, synthesis, biological evaluation and SAR studies. Eur J. Med. Chem. 46 (2011) 2317-2223.


title: GS-1-EM0040, FgTri5-/DON T24, experimental rep 2

description:
2D-T24-RII
Gene expression data from FgTri5-/DON-inoculated spike, collected at 24 h after inoculation in GS-1-EM0040.

source_name: GS-1-EM0040 spikelets from FgTri5-/DON-inoculated spike, collected at 24 h after inoculation

value: FgTri5-/DON inoculation


title: GS-1-EM0040, FgTri5-/DON T8, experimental rep 1

description:
2D-T8-RI
Gene expression data from FgTri5-/DON-inoculated spike, collected at 8 h after inoculation in GS-1-EM0040.

source_name: GS-1-EM0040 spikelets from FgTri5-/DON-inoculated spike, collected at 8 h after inoculation


title: P2_3

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

description:
NHNPs infected with Hairpin 2
4685238011_G

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: BeadStudio, quantile normalization

source_name: Human neural progenitor cells

label_protocol: Illumina protocol

growth_protocol: Human neural progenitor cells (NHNPs) were generated from a 17-week gestation aborted female fetus.  Differentiation of cells was carried out using neurobasal A media (Invitrogen), 2 ng/mL retinoic acid (Sigma-Aldrich), 10ng/mL BDNF (Peprotech), 10ng/mL NT3 (Peprotech), 10mM KCl (Fisher), 10uM forskolin (Sigma-Aldrich) and 1 ug/mL doxycycline (Sigma-Aldrich).  All cells were grown on surfaces coated overnight with 50 ug/mL polyornithine (Sigma-Aldrich) followed by 5 ug/mL laminin (Invitrogen) overnight.

extract_protocol: Qiagen RNAeasy kit

treatment_protocol: To knock down GRN in an inducible system, pTRIPZ vector was purchased from Open Biosystems (Huntsville, AL).  Their scrambled pTRIPZ vector was used as a control, their TRIPZ GRN hairpin was used to knock down GRN.  The other sequence of the other GRN hairpin was obtained from (Zhang et al., 2007), and was cloned into TRIPZ using the PCR shagging protocol (http://katahdin.cshl.org:9331/RNAi/html/rnai.html).NHNP cells were infected and selected using 0.5ug/mL puromycin (Sigma) 72 hours post-transduction.  Hairpins were induced when cells were seeded using 1 ug/mL doxycycline (Sigma-Aldrich).  These cells were differentiated for four weeks in the presence of doxycycline, after which RNA was harvested.

value: Human neural progenitor cells

tag: replicate

tag: construct

value: Hairpin 2


title: P1_4

description:
NHNPs infected with Hairpin 1
4685238011_F

value: Hairpin 1


title: GS-1-EM0040, FgTri5-/DON T8, experimental rep 3

description:
2D-T8-RIII
Gene expression data from FgTri5-/DON-inoculated spike, collected at 8 h after inoculation in GS-1-EM0040.


title: GS-1-EM0040, FgTri5-/DON T24, experimental rep 3

description:
2D-T24-RIII
Gene expression data from FgTri5-/DON-inoculated spike, collected at 24 h after inoculation in GS-1-EM0040.


title: GS-1-EM0040, FgTri5-/DON T24, experimental rep 1

description:
2D-T24-RI
Gene expression data from FgTri5-/DON-inoculated spike, collected at 24 h after inoculation in GS-1-EM0040.


title: OSCC tumor_OR0989

description: Hybridized to Affymetrix SNP6.0

value: tumor


title: GS-1-EM0040, DON T3, experimental rep 1

description:
2E-T3-RI
Gene expression data from DON-inoculated spike, collected at 3 h after inoculation in GS-1-EM0040.


title: OSCC tumor_OR0997

description: Hybridized to Affymetrix SNP6.0


title: C_3

description:
NHNPs infected with Scrambled Hairpin (Control)
4685238011_C

value: Control


title: Control-2

description:
3a
Compound CDRI-5g  :  Saquib, M. et al. 2,3-Dideoxy hex-2-enolpyranosid-4-uloses as promising new-antitibercular agents : Design, synthesis, biological evaluation and SAR studies. Eur J. Med. Chem. 46 (2011) 2317-2223.


title: P2_4

description:
NHNPs infected with Hairpin 2
4685238011_H


title: C_4

description:
NHNPs infected with Scrambled Hairpin (Control)
4685238011_E


title: GS-1-EM0040, FgTri5-/DON T3, experimental rep 3

description:
2D-T3-RIII
Gene expression data from FgTri5-/DON-inoculated spike, collected at 3 h after inoculation in GS-1-EM0040.

source_name: GS-1-EM0040 spikelets from FgTri5-/DON-inoculated spike, collected at 3 h after inoculation


title: OSCC tumor_OR1008

description: Hybridized to Affymetrix SNP6.0


title: GS-1-EM0040, FgTri5-/DON T3, experimental rep 1

description:
2D-T3-RI
Gene expression data from FgTri5-/DON-inoculated spike, collected at 3 h after inoculation in GS-1-EM0040.


title: P1_3

description:
NHNPs infected with Hairpin 1
4685238011_A


title: GS-1-EM0040, FgTri5-/DON T3, experimental rep 2

description:
2D-T3-RII
Gene expression data from FgTri5-/DON-inoculated spike, collected at 3 h after inoculation in GS-1-EM0040.


title: Muller 3 Day PBS, biological rep3

city: Rockville

first: Radu

last: Cojocaru

state: MD

address: 5635 Fishers Lane, Suite 510

institute: Elsevier

hyb_protocol: Following fragmentation and labelling, 3.75 ug (for MOE 430 2.0) or 3 ug (for Exon 1.0 ST) of cDNA were hybridized at 45C for 18 hours.  GeneChips were washed and scanner in the Affymetrix FS450.

scan_protocol: GeneChips were scanner with an Affymetrix GCS3000 7G

data_processing: The data were analyzed using Partek Genomic Suite.

label_protocol: Biotinylated cDNA were prepared for the MOE 430 2.0arrays using Nugen Ovation RNA Amplification System V2 starting with 5 ng of total RNA.  For the Exon 1.0 ST arrays the Nugen WT-Ovation Pico RNA Amplification System starting with 500 pg total RNA for the Muller glia and 2 ng of total RNA for the microglia prior to strand switching using Nugen WT-Ovation Exon Module

extract_protocol: RNA was extracted using the RNeasy Mini kit (Qiagen, Valencia, CA)

value: Flow sorted Muller glial cells

value: PBS

tag: time

value: 3 d


title: GS-1-EM0040, FgTri5- T8, experimental rep 2

description:
2C-T8-RII
Gene expression data from (FgTri5-)-inoculated spike, collected at 8 h after inoculation in GS-1-EM0040.

source_name: GS-1-EM0040 spikelets from (FgTri5-)-inoculated spike, collected at 8 h after inoculation

value: FgTri5- inoculation


title: P2_2

description:
NHNPs infected with Hairpin 2
4685238001_G

tag: cell type


title: C_2

description:
NHNPs infected with Scrambled Hairpin (Control)
4685238001_H


title: P1_2

description:
NHNPs infected with Hairpin 1
4685238001_B


title: OSCC tumor_OR0816

description: Hybridized to Affymetrix SNP6.0


title: P1_1

description:
NHNPs infected with Hairpin 1
4685238001_A


title: C_1

description:
NHNPs infected with Scrambled Hairpin (Control)
4685238001_F


title: Muller 3 Day PBS, biological rep1


title: P2_1

description:
NHNPs infected with Hairpin 2
4685238001_D


title: GS-1-EM0040, FgTri5- T3, experimental rep 3

description:
2C-T3-RIII
Gene expression data from (FgTri5-)-inoculated spike, collected at 3 h after inoculation in GS-1-EM0040.

source_name: GS-1-EM0040 spikelets from (FgTri5-)-inoculated spike, collected at 3 h after inoculation

tag: tissue

value: spikelets


title: OSCC tumor_OR0923

description: Hybridized to Affymetrix SNP6.0


title: GS-1-EM0040, FgTri5+ T24, experimental rep 3

description:
2B-T24-RIII
Gene expression data from (FgTri5+)-inoculated spike, collected at 24 h after inoculation in GS-1-EM0040.

source_name: GS-1-EM0040 spikelets from (FgTri5+)-inoculated spike, collected at 24 h after inoculation

value: FgTri5+ inoculation


title: GS-1-EM0040, FgTri5- T8, experimental rep 3

description:
2C-T8-RIII
Gene expression data from (FgTri5-)-inoculated spike, collected at 8 h after inoculation in GS-1-EM0040.


title: GS-1-EM0040, FgTri5- T3, experimental rep 2

description:
2C-T3-RII
Gene expression data from (FgTri5-)-inoculated spike, collected at 3 h after inoculation in GS-1-EM0040.


title: GS-1-EM0040, FgTri5- T24, experimental rep 2

description:
2C-T24-RII
Gene expression data from (FgTri5-)-inoculated spike, collected at 24 h after inoculation in GS-1-EM0040.

source_name: GS-1-EM0040 spikelets from (FgTri5-)-inoculated spike, collected at 24 h after inoculation

value: 24 hrs


title: GS-1-EM0040, FgTri5- T24, experimental rep 1

description:
2C-T24-RI
Gene expression data from (FgTri5-)-inoculated spike, collected at 24 h after inoculation in GS-1-EM0040.


title: GS-1-EM0040, FgTri5- T24, experimental rep 3

description:
2C-T24-RIII
Gene expression data from (FgTri5-)-inoculated spike, collected at 24 h after inoculation in GS-1-EM0040.


title: GS-1-EM0040, FgTri5- T8, experimental rep 1

description:
2C-T8-RI
Gene expression data from (FgTri5-)-inoculated spike, collected at 8 h after inoculation in GS-1-EM0040.


title: Muller 3 Day PBS, biological rep2


title: OSCC tumor_OR0265

description: Hybridized to Affymetrix SNP6.0


title: OSCC tumor_OR0811

description: Hybridized to Affymetrix SNP6.0


title: GS-1-EM0040, FgTri5- T3, experimental rep 1

description:
2C-T3-RI
Gene expression data from (FgTri5-)-inoculated spike, collected at 3 h after inoculation in GS-1-EM0040.


title: GS-1-EM0040, FgTri5-/DON T8, experimental rep 2

description:
2D-T8-RII
Gene expression data from FgTri5-/DON-inoculated spike, collected at 8 h after inoculation in GS-1-EM0040.


title: H1650-9

source_name: NSCLC cell line

value: non small cell lung cancer cell (NSCLC)

value: Yes


title: Muller 3 Day CNTF, biological rep1

value: Ciliary neurotrophic factor


title: Muller 3 Day CNTF, biological rep2


title: Muller 3 Day CNTF, biological rep3


title: GS-1-EM0040, FgTri5+ T8, experimental rep 2

description:
2B-T8-RII
Gene expression data from (FgTri5+)-inoculated spike, collected at 8 h after inoculation in GS-1-EM0040.

source_name: GS-1-EM0040 spikelets from (FgTri5+)-inoculated spike, collected at 8 h after inoculation

value: 8 hrs


title: GS-1-EM0040, FgTri5+ T8, experimental rep 3

description:
2B-T8-RIII
Gene expression data from (FgTri5+)-inoculated spike, collected at 8 h after inoculation in GS-1-EM0040.


title: OSCC tumor_OR0752

description: Hybridized to Affymetrix SNP6.0


title: GS-1-EM0040, FgTri5+ T3, experimental rep 2

description:
2B-T3-RII
Gene expression data from (FgTri5+)-inoculated spike, collected at 3 h after inoculation in GS-1-EM0040.

source_name: GS-1-EM0040 spikelets from (FgTri5+)-inoculated spike, collected at 3 h after inoculation

value: 3 hrs


title: crb_400_het_m_9

description:
Cerebellum, Heterozygous mice, 9 MO
5388489005_E

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

source_name: Mouse Brain Tissue

label_protocol: Standard Illumina protocol

growth_protocol: Standard

extract_protocol: Qiagen RNAeasy

value: het

tag: region

value: crb

tag: timepoint

value: 9 month

value: M


title: GS-1-EM0040, FgTri5+ T24, experimental rep 2

description:
2B-T24-RII
Gene expression data from (FgTri5+)-inoculated spike, collected at 24 h after inoculation in GS-1-EM0040.

tag: genotype


title: OSCC tumor_OR1261

description: Hybridized to Affymetrix SNP6.0

source_name: OSCC  specimens

tag: disease state

value: tumor


title: OSCC tumor_OR0918

description: Hybridized to Affymetrix SNP6.0


title: hip_391_ko_m_9

description:
Hippocampus, KO mice, 9 MO
5388489005_F

value: ko

value: hip


title: ctx_625_wt_f_6

description:
Cortex, WT mice, 6 MO
5388489005_B

value: wt

value: ctx

value: 6 month

value: F


title: GS-1-EM0040, FgTri5+ T3, experimental rep 1

description:
2B-T3-RI
Gene expression data from (FgTri5+)-inoculated spike, collected at 3 h after inoculation in GS-1-EM0040.

value: spikelets

value: FgTri5+ inoculation


title: GS-1-EM0040, FgTri5+ T3, experimental rep 3

description:
2B-T3-RIII
Gene expression data from (FgTri5+)-inoculated spike, collected at 3 h after inoculation in GS-1-EM0040.


title: GS-1-EM0040, FgTri5+ T8, experimental rep 1

description:
2B-T8-RI
Gene expression data from (FgTri5+)-inoculated spike, collected at 8 h after inoculation in GS-1-EM0040.


title: ctx_665_wt_f_6

description:
Cortex, WT mice, 6 MO
5388489004_B


title: hip_648_ko_m_6

description:
Hippocampus, KO mice, 6 MO
5388489005_C


title: HEK293Tcells_si76_rep3

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

description: Gene expression from HEK293T cells after transfection with siRNA s18076 targeting Med26, replicate 3.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 and processed with AGCC v3.0 software.

data_processing: Array intensities were processed using the RMA algorithm in R/bioconductor. Bioconductor 2.6 and affy package affy_1.24.2

source_name: HEK293T cells

label_protocol: Biotinylated cRNA were prepared according to the Ambion MessageAmp III protocol from 300 ng total RNA (MessageAmp III Amplification kit Manual, 2007, Ambion).

growth_protocol: HEK293T cells were grown in 6 well tissue culture plates or 10 cm dishes for 48 hours after transfection.

extract_protocol: Total RNA was extracted using the standard Qiagen RNeasy cleanup protocol.

treatment_protocol: HEK293T cells in 6 well tissue culture plates (~1x105 cells/well) or 10 cm dishes (~2 x106 cells/dish) were transfected with 25 nM siRNAs targeting human Med26 (Ambion/Applied Biosystems, #4, s18074; #5, s18075; #6, s18076) or 25 nM siCONTROL NON-TARGETING siRNA #2 (Dharmacon D-001210-01) using X-tremeGENE siRNA Transfection Reagent (Roche) and grown for 48 hours.

tag: cell line

value: human embryonic kidney

tag: sirna

value: Med26 targeting s18076


title: A431

source_name: epidermoid carcinoma

value: epidermoid carcinoma

value: Yes


title: ctx_668_het_m_6

description:
Cortex, Heterozygous mice, 6 MO
5388489005_D

value: het


title: HEK293Tcells_si76_rep2

description: Gene expression from HEK293T cells after transfection with siRNA s18076 targeting Med26, replicate 2.


title: hip_457_ko_f_9

description:
Hippocampus, KO mice, 9 MO
5388489004_H


title: ctx_391_ko_m_9

description:
Cortex, KO mice, 9 MO
5388489002_H


title: crb_457_ko_f_9

description:
Cerebellum, KO mice, 9 MO
5388489005_A

value: crb


title: GS-1-EM0040, FgTri5+ T24, experimental rep 1

description:
2B-T24-RI
Gene expression data from (FgTri5+)-inoculated spike, collected at 24 h after inoculation in GS-1-EM0040.

tag: treatment

value: 24 hrs


title: ctx_648_ko_m_6

description:
Cortex, KO mice, 6 MO
5388489004_F

value: M


title: hip_668_het_m_6

description:
Hippocampus, Heterozygous mice, 6 MO
5388489004_G


title: GS-1-EM0040, water T8, experimental rep 2

description:
2A-T8-RII
Gene expression data from water-inoculated spike, collected at 8 h after inoculation in GS-1-EM0040.

source_name: GS-1-EM0040 spikelets from water-inoculated spike, collected at 8 h after inoculation

value: water inoculation

value: 8 hrs


title: crb_669_het_m_6

description:
Cerebellum, Heterozygous mice, 6 MO
5388489004_E


title: crb_404_wt_m_9

description:
Cerebellum, WT mice, 9 MO
5388489004_A

value: 9 month


title: GS-1-EM0040, water T8, experimental rep 3

description:
2A-T8-RIII
Gene expression data from water-inoculated spike, collected at 8 h after inoculation in GS-1-EM0040.


title: GS-1-EM0040, water T24, experimental rep 1

description:
2A-T24-RI
Gene expression data from water-inoculated spike, collected at 24 h after inoculation in GS-1-EM0040.

source_name: GS-1-EM0040 spikelets from water-inoculated spike, collected at 24 h after inoculation


title: GS-1-EM0040, water T3, experimental rep 2

description:
2A-T3-RII
Gene expression data from water-inoculated spike, collected at 3 h after inoculation in GS-1-EM0040.

source_name: GS-1-EM0040 spikelets from water-inoculated spike, collected at 3 h after inoculation

value: 3 hrs


title: crb_391_ko_m_9

description:
Cerebellum, KO mice, 9 MO
5388489004_D

value: ko


title: hip_680_ko_f_6

description:
Hippocampus, KO mice, 6 MO
5388489004_C

value: hip

value: 6 month


title: GS-1-EM0040, water T24, experimental rep 3

description:
2A-T24-RIII
Gene expression data from water-inoculated spike, collected at 24 h after inoculation in GS-1-EM0040.

value: spikelets


title: GS-1-EM0040, water T8, experimental rep 1

description:
2A-T8-RI
Gene expression data from water-inoculated spike, collected at 8 h after inoculation in GS-1-EM0040.


title: GS-1-EM0040, uninoculated control, experimental rep 3

description:
2-T0-RIII
Gene expression data from uninoculated control spike, from GS-1-EM0040.

source_name: GS-1-EM0040 spikelets from uninoculated spike


title: GS-1-EM0040, water T3, experimental rep 3

description:
2A-T3-RIII
Gene expression data from water-inoculated spike, collected at 3 h after inoculation in GS-1-EM0040.


title: GS-1-EM0040, water T24, experimental rep 2

description:
2A-T24-RII
Gene expression data from water-inoculated spike, collected at 24 h after inoculation in GS-1-EM0040.


title: GS-1-EM0040, water T3, experimental rep 1

description:
2A-T3-RI
Gene expression data from water-inoculated spike, collected at 3 h after inoculation in GS-1-EM0040.


title: crb_680_ko_f_6

description:
Cerebellum, KO mice, 6 MO
5388489002_G

value: F


title: hip_669_het_m_6

description:
Hippocampus, Heterozygous mice, 6 MO
5388489002_D


title: hip_393_het_m_9

description:
Hippocampus, Heterozygous mice, 9 MO
5388489002_E


title: GS-1-EM0040, uninoculated control, experimental rep 2

description:
2-T0-RII
Gene expression data from uninoculated control spike, from GS-1-EM0040.


title: crb_659_wt_f_6

description:
Cerebellum, WT mice, 6 MO
5388489002_C

value: wt


title: GS-1-EM0040, uninoculated control, experimental rep 1

description:
2-T0-RI
Gene expression data from uninoculated control spike, from GS-1-EM0040.


title: crb_648_ko_m_6

description:
Cerebellum, KO mice, 6 MO
5388489002_A


title: beta cells, FACS-purified from rats after 24h fast, biological replicate 2

city: Brussels

first: Geert

middle: A.

last: Martens

address: Laarbeeklaan 103

department: Diabetes Research Center

country: Belgium

institute: Vrije Universiteit Brussel

description:
Fast2
each biological replicate represents independent isolation from a pool of 5 rats

hyb_protocol: After fragmentation at 94°C for 35 min in fragmentation buffer (40mM Tris, 30mM magnesium acetate, 10mM potassium acetate), the labelled cRNA was hybridized for 16h to the Affymetrix HG133A

scan_protocol: Arrays were stained with phycoerythrin-streptavidin with the Affymetrix Fluidics Station 400, and scanned in the Affymetrix GeneArray2500scanner.

data_processing: Scanned arrays were analyzed with dChip model-based expression analysis to the array with the median intensity and correction for mismatch hybridization using the perfect match-mismatch correction model (PM-MM).

organism: Rattus norvegicus

source_name: FACS-purified beta cells from rats after 24h fast

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Rat beta (92 +- 3% insulin+) were FACS-purified from 10-weeks old Wistar rats and immediately snap frozen in liquid nitrogen, prior to total RNA extraction in batch, from all biological replicates.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA integrity verified on Bioanalyzer with minimal RIN cutoff = 8.

tag: strain

value: Wistar

value: male

tag: age

value: 10 weeks

value: freshly isolated FACS-purified pancreatic beta cells

tag: in vivo fed/fasted state

value: 24hr fasting


title: beta cells, FACS-purified from rats after 24h fast, biological replicate 3

description:
Fast3
each biological replicate represents independent isolation from a pool of 5 rats

tag: gender


title: Superb, DON T8, experimental rep 3

description:
1E-T8-RIII
Gene expression data from DON-inoculated spike, collected at 8 h after inoculation in 'Superb'.

source_name: Superb spikelets from DON-inoculated spike, collected at 8 h after inoculation

value: Superb

value: DON inoculation

tag: treatment duration


title: ctx_401_het_m_9

description:
Cortex, Heterozygous mice, 9 MO
5388489002_B

value: het

value: ctx

value: M

tag: replicate


title: HEK293Tcells_si75_rep3

description: Gene expression from HEK293T cells after transfection with siRNA s18075 targeting Med26, replicate 3.

value: human embryonic kidney

value: Med26 targeting s18075


title: Superb, DON T24, experimental rep 2

description:
1E-T24-RII
Gene expression data from DON-inoculated spike, collected at 24 h after inoculation in 'Superb'.

source_name: Superb spikelets from DON-inoculated spike, collected at 24 h after inoculation

value: 24 hrs


title: HEK293Tcells_si75_rep2

description: Gene expression from HEK293T cells after transfection with siRNA s18075 targeting Med26, replicate 2.


title: ctx_457_ko_f_9

description:
Cortex, KO mice, 9 MO
5406940006_H

value: ko

value: 9 month


title: HEK293Tcells_si74_rep2

description: Gene expression from HEK293T cells after transfection with siRNA s18074 targeting Med26, replicate 2.

value: Med26 targeting s18074


title: hip_665_wt_f_6

description:
Hippocampus, WT mice, 6 MO
5388489002_F

value: wt

value: hip

value: 6 month

value: F


title: HEK293Tcells_wt_rep2

description: Gene expression from HEK293T cells after transfection with non-targeting siRNA, replicate 2.

value: Dharmacon non-targeting #3


title: HEK293Tcells_si76_rep1

description: Gene expression from HEK293T cells after transfection with siRNA s18076 targeting Med26, replicate 1.

value: Med26 targeting s18076


title: Superb, DON T8, experimental rep 1

description:
1E-T8-RI
Gene expression data from DON-inoculated spike, collected at 8 h after inoculation in 'Superb'.

value: spikelets

value: Superb

value: 8 hrs


title: Superb, DON T8, experimental rep 2

description:
1E-T8-RII
Gene expression data from DON-inoculated spike, collected at 8 h after inoculation in 'Superb'.

value: DON inoculation


title: Superb, DON T3, experimental rep 3

description:
1E-T3-RIII
Gene expression data from DON-inoculated spike, collected at 3 h after inoculation in 'Superb'.

source_name: Superb spikelets from DON-inoculated spike, collected at 3 h after inoculation

value: 3 hrs


title: Superb, DON T24, experimental rep 3

description:
1E-T24-RIII
Gene expression data from DON-inoculated spike, collected at 24 h after inoculation in 'Superb'.


title: crb_649_ko_m_6

description:
Cerebellum, KO mice, 6 MO
5406940006_G

value: crb

value: M


title: beta cells, FACS-purified from rats after 24h fast, biological replicate 1

description:
Fast1
each biological replicate represents independent isolation from a pool of 5 rats

value: Wistar

value: male

value: 10 weeks

value: freshly isolated FACS-purified pancreatic beta cells

value: 24hr fasting


title: hip_383_wt_m_9

description:
Hippocampus, WT mice, 9 MO
5406940006_F

value: wt

value: hip

value: 9 month


title: HEK293Tcells_si75_rep1

description: Gene expression from HEK293T cells after transfection with siRNA s18075 targeting Med26, replicate 1.

value: human embryonic kidney

value: Med26 targeting s18075


title: HEK293Tcells_si74_rep1

description: Gene expression from HEK293T cells after transfection with siRNA s18074 targeting Med26, replicate 1.

value: Med26 targeting s18074


title: Superb, DON T24, experimental rep 1

description:
1E-T24-RI
Gene expression data from DON-inoculated spike, collected at 24 h after inoculation in 'Superb'.

value: spikelets

value: Superb

value: 24 hrs


title: HEK293Tcells_si74_rep3

description: Gene expression from HEK293T cells after transfection with siRNA s18074 targeting Med26, replicate 3.


title: HEK293Tcells_wt_rep3

description: Gene expression from HEK293T cells after transfection with non-targeting siRNA, replicate 3.

value: Dharmacon non-targeting #4


title: HEK293Tcells_wt_rep1

description: Gene expression from HEK293T cells after transfection with non-targeting siRNA, replicate 1.

value: Dharmacon non-targeting #2


title: Superb, DON T3, experimental rep 1

description:
1E-T3-RI
Gene expression data from DON-inoculated spike, collected at 3 h after inoculation in 'Superb'.

value: DON inoculation

value: 3 hrs


title: beta cells, FACS-purified from rats fed ad libitum, biological replicate 3

description:
Control3
each biological replicate represents independent isolation from a pool of 5 rats

source_name: FACS-purified beta cells from rats fed ad libitum

value: Wistar

value: male

value: ad libitum feeding


title: Superb, DON T3, experimental rep 2

description:
1E-T3-RII
Gene expression data from DON-inoculated spike, collected at 3 h after inoculation in 'Superb'.


title: ctx_434_ko_m_9

description:
Cortex, KO mice, 9 MO
5406940006_C

value: ko

value: ctx

value: M


title: beta cells, FACS-purified from rats fed ad libitum, biological replicate 2

description:
Control2
each biological replicate represents independent isolation from a pool of 5 rats

value: 10 weeks

value: freshly isolated FACS-purified pancreatic beta cells


title: beta cells, FACS-purified from rats fed ad libitum, biological replicate 1

description:
Control1
each biological replicate represents independent isolation from a pool of 5 rats


title: MB231.SL MDAMB231 breast cancer cell line rep 2

city: Bethesda

first: Jeffrey

middle: E

last: Green

address: Rm 4054, 37 Convent Drive

institute: NCI

description: gene expression data

hyb_protocol: cRNA were hybridized onto GeneChip Human Genome U133 Plus 2.0 Array

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

data_processing: Data were collected using Affymetrix GCOS software and then processed with GC-RMA and quantile normalization using Bioconductor gcrma package (http://www.bioconductor.org/packages/release/bioc/html/gcrma.html).

source_name: MDAMB231 human breast cancer cell line

label_protocol: Biotinylated cRNA were prepared accorded to standard affymetrix protocol

growth_protocol: MDAMB231 cell lines were grown in RPMI media with 5% FBS. M98040 and M99005 were grown in serum free mammary epithelial growth medium (MEGM) supplemented with growth factors in the MEGM SingleQuots (Lonza).

extract_protocol: Trizol extraction of RNA was performed according to manufacturers protocol

value: breast tumor cells


title: MB231.T MDAMB231 tumor xenograft rep1

description: gene expression data

source_name: MDAMB231 human breast cancer tumor xenograft

value: breat tumor cell xenograft tissue


title: crb_393_het_m_9

description:
Cerebellum, Heterozygous mice, 9 MO
5406940006_B

value: het

value: crb

value: 9 month


title: crb_677_het_f_6

description:
Cerebellum, Heterozygous mice, 6 MO
5406940006_D

value: 6 month

value: F


title: MB231.T MDAMB231 tumor xenograft rep2

description: gene expression data


title: crb_434_ko_m_9

description:
Cerebellum, KO mice, 9 MO
5406940006_A


title: crb_668_het_m_6

description:
Cerebellum, Heterozygous mice, 6 MO
5406940006_E


title: MB231.SL MDAMB231 breast cancer cell line rep 1

description: gene expression data


title: ctx_677_het_f_6

description:
Cortex, Heterozygous mice, 6 MO
5406940005_G