title: 5mC NPC Chr7

source_name: methylated DNA fraction enriched by MIRA. DNA was isolated from NPC

value: neural progenitor cells, cortex

source_name: Input DNA from NPC


title: 5hmC after Hydroxymethyl Collector in NPC, Chr7

status: Public on Dec 31 2012

type: genomic

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

country: USA

institute: City of Hope National Medical Center

description: Cells were isolated by FACs sorting from nmouse cortex using GFP/RFP reported system at 15.5E embryonic development. GFP+ (under Nestin promoter), RFP - (Under Dbx promoter)

hyb_protocol: According to NimbleGen Kit

scan_protocol: Follow NimbleScan's default using Agilent Scanner

data_processing: Cy5/Cy3 log2 ratio scaled by NimbleScan software v2.5 with Tukey Biweight mean

molecule: genomic DNA

organism: Mus musculus

source_name: 5hmC enriched DNA fraction after pull-down with Hydroxymethyl Collector. DNA was isolated from NPC

label_protocol: According to standard NimbleGen Protocol

extract_protocol: For MIRA, sonicated DNA was incubated with MBD2b-GST and MBD3L1-His overnight at +4C. Methylated DNA was captured by using magnetic GST beads, purified and amplified by using LM-PCR. For ChIp-ChIp experiments, cells were fixed with 1% formaldehyde in PBS1x for 10 minutes at RT and briefly quest by adding of 0.125M Glycine.  Sonicated chromatin was incubated with appropriate antibodies overnight and captured by A/G agarose beads. Purified decrosslinked DNA was amplified by LM-PCR procedure. For hMeDIP, linker ligated DNA was denatured and incubated with 5hmC antibodies overnight at +4C with further purification with A/G plus beads and genome amplification by LM-PCR. For 5hmC enrichment with Hydroxymethyl Collector (Active Motif), sonicated DNA was glycosylated, labeled with biotin and purified according manufacturer instructions with further genome amplification by LM-PCR.

treatment_protocol: no treatment

tag: cell type

tag: age

tag: enrichment method

value: biotin capturing of glycosylated 5hmC DNA

tag: antibody

value: none, Input


title: 5hmC hMeDIP NPC Chr7

source_name: 5hmC enriched DNA fraction after pull-down with 5hmC antibodies.  DNA was isolated from NPC

value: hMeDIP


title: 1023 treatment vs DMSO control, replicate 2

type: RNA

city: Salt Lake City

first: Bryan

last: Welm

state: UT

address: 2000 Circle of Hope Drive

department: Oncological Science

institute: University of Utah, Huntsman Cancer Institute

description: Expression comparison in cells treated with compound 1023 vs DMSO control, replicate 2.

hyb_protocol: Labeled samples hybridized using standard Agilent two-color gene expression hybridization and wash protocols

scan_protocol: Microarray slides were scanned on an Agilent Technologies G2505B scanner at 5 micron resolution

data_processing:
Slide images were processed using Agilent Feature Extraction software version 9.5.1.1
Data filtered to remove control features and features flagged as nonuniform or population outlers. Remaining values for each unique probe sequence averaged.

molecule: total RNA

source_name: DMSO-treated aggregate primary mammary epithelial cells

label_protocol: Samples labeled using Agilent Two-Color Low RNA Input Linear Amplification Kit

growth_protocol: Aggregate primary mammary epithelial cells were embedded in extracellular matrix-Matrigel (BD) and grown with DMEM/F-12 (HyClone) supplemented with 5 mg/mL ITS-X (Gibco), Pen Strep Glutamine (Gibco), and 2.5 nM human FGF2 (Invitrogen).

extract_protocol: Total RNA isolated using Qiagen RNEasy kit.

treatment_protocol: Samples were dosed for 72 hours with either DMSO or 10 mM 1023.

tag: treatment

value: DMSO

source_name: 1023-treated aggregate primary mammary epithelial cells

value: compound 1023


title: Pleural and ascites fluids with chylothorax but without the ITGA9 G404S mutation and OK-432 treatmuent FC-r

city: Changhua

first: Gwo-Chin

last: Ma

address: 3F, 176, Zhanghua Rd.

department: Department of Genomic Medicine

country: Taiwan

institute: Changhua Christian Hospital

description: Transcriptional profile comparison of the pleural and ascites fluids in a reference fetal with chylothorax

hyb_protocol: 0.3 mg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60oC for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to a SurePrint G3 Human GE 8×60K oligo microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: Scanned on an Agilent G2565CA scanner, and images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Homo sapiens

source_name: Pleural fluid

label_protocol: 0.2 mg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 or Cy5 (CyDye, PerkinElmer, USA) during the in vitro transcription process.

extract_protocol: Cell lines were lyzed by Trizol® Reagent (Invitrogen, USA) first, and purified by RNeasy Mini Kit (Qiagen, Germany). RNA isolated was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 nano labchip kit (Agilent Technologies, USA).

tag: mutation

value: No ITGA9 mutation

value: No OK-432 treatment

source_name: Ascites fluid


title: ko Epithelium_OVA_rep2

city: San Francisco

first: Xiaozhu

last: Huang

address: 1550 4th St. Rock Hall, 5th FL. Rm 545

department: medicine

institute: UCSF

hyb_protocol: Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned on the Agilent scanner immediately after washing.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1 (Agilent) using default parameters. We used quantile normalization.

source_name: ko airway epithelium OVA challenged

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using Qiagen RNeasy micro kit following the manufacturer's recommendations.

treatment_protocol: wt and ko mice IP sensitized with 20 ug OVA or saline on day 1, 4 and 7, Intranasal challenged with 10 ug OVA or saline once per week for 9 weeks. Airway epithelium were harvested 24 hrs after last challenge

tag: agent

value: OVA

tag: tissue

value: airway epithelium

tag: strain

value: FvB

value: 6-8 weeks old-sensitization

tag: genotype/variation

value: beta6 knockout


title: ko Epithelium_OVA_rep3


title: 1023 treatment vs DMSO control, replicate 1

description: Expression comparison in cells treated with compound 1023 vs DMSO control, replicate 1.


title: wt Epithelium_OVA_rep3

source_name: wt airway epithelium OVA challenged

value: wildtype


title: ko Epithelium_saline_rep1

source_name: ko airway epithelium saline challenged

value: saline


title: wt Epithelium_OVA_rep4


title: wt Epithelium_OVA_rep1


title: ko Epithelium_saline_rep3


title: Pancreas FF A10-46_2N_Vim+

city: Scottsdale

first: Michael

middle: Thomas

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic Arizona

hyb_protocol: All labeling reactions were assessed using a Nanodrop assay (Nanodrop, Wilmington, DE) prior to mixing and hybridization to 400k CGH arrays (Agilent Technologies, Santa Clara, CA) for 40 hours in a rotating 65°C oven.

scan_protocol: All microarray slides were scanned using an Agilent 2565C DNA scanner, and the images were analyzed with Agilent Feature Extraction version 10.7 using default settings.

data_processing: The aCGH data was assessed with a series of QC metrics, dye normalized and centralized, and then analyzed using an aberration detection algorithm (ADM2) which is included in Agilent Genomic Workbench 6.5 software. The latter identifies all aberrant intervals in a given sample with consistently high or low log ratios based on the statistical score derived from the average normalized log ratios of all probes in the genomic interval multiplied by the square root of the number of these probes. This score represents the deviation of the average of the normalized log ratios from its expected value of zero and is proportional to the height h (absolute average log ratio) of the genomic interval and to the square root of the number of probes in the interval.

source_name: Fresh frozen tissue, pancreatic adenocarcinoma

label_protocol: Genomic DNAs from sorted FFPE samples were amplified using the Ovation® WGA FFPE System from NuGEN® Technologies (San Carlos, CA). DNA was processed in accordance with the Ovation® WGA FFPE standard protocol with an alternate T7 endonuclease fragmentation step. Resulting amplified product was either used as template for aCGH analysis or processed with the Nugen Encore ds-DNA module according to the supplier's instructions in order to generate double-stranded end repaired DNA as input for library suitable for next-generation sequencing. Extracted fresh frozen sourced genomic DNA was amplified using the phi29 based Illustra GenomiPhi V2 Amplification kit from GE Healthcare Bio-sciences Corp (Piscataway, NJ) according to our published protocols. A 100 ng aliquot of pooled 46,XX DNA (Promega, Madison, WI) was amplified with the matching amplification protocol to generate a suitable reference for each aCGH experiment using amplified DNA template. In all cases, the quality of the amplification product was assessed by gel electrophoresis.  Fresh frozen phi29 amplified and FFPE non-amplified DNAs were treated with DNAse 1 prior to Klenow-based labeling. High molecular weight phi29 templates were digested for 30 minutes while the smaller fragmented FFPE samples were digested for only 1 minute. In each case, 1ul of 10x DNase 1 reaction buffer and 2ul of DNase 1 dilution buffer were added to 7ul of DNA sample and incubated at room temperature,  then transferred to 70°C for 30 minutes to deactivate DNase 1. In contrast, the amplified FFPE sourced DNAs do not require DNase 1 treatment prior to Klenow-based labeling. Sample and reference templates were then labeled with Cy-5 dUTP and Cy-3 dUTP, respectively, using a BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to our published protocols.

growth_protocol: None.

extract_protocol: DNA from sorted nuclei was extracted using an amended protocol from the QIAamp® DNA Micro Kit from Qiagen (Valencia, CA). Briefly, each sorted sample was resuspended in 180ul buffer ATL and 20ul proteinase K, then incubated for 3 hours at 56°C for complete lysis. Samples were bound and washed according to QIAamp® DNA Micro Kit instructions, eluted into 50ul of H20, then precipitated overnight with 5ul 3 M sodium acetate and 180 ul 100% EtOH. Each sample was then centrifuged for 30 minutes at 20,000 x g, and washed in 1 ml of 70% EtOH for 30 minutes at 20,000 x g. The samples were carefully decanted and the DNA pellet was dried by speed vacuum then resuspended in a small volume (e.g. 10-50ul) of H20 for final concentrations suitable for accurate quantification.

treatment_protocol: Excess paraffin was removed with a scalpel from either side of 40-60um scrolls. Sectioning samples reduces accumulation of debris during the sorting process. Each sectioned piece was collected into individual microcentrifuge tubes, then washed three times with 1 ml Xylene for 5 minutes to remove remaining paraffin. Each sample was rehydrated in sequential ethanol washes (100% 5 minutes x2, then 95%, 70%, 50% and 30% ethanol) and washed 2 times in 1ml 1 mM EDTA pH 8.0. A 1 ml aliquot of 1 mM EDTA pH 8.0 was added to the samples and incubated at 95oC for 80 minutes to facilitate the removal of protein cross-links present in FFPE tissue. Samples were then cooled to room temperature for > 5 minutes, followed by addition of 300 ul PBS pH 7.4 and gentle centrifugation for 2 minutes at 3.6 x g. The supernatant was carefully removed and the pellet washed three times with 1 ml PBS pH 7.4/0.5mM CaCl2 to remove EDTA. Each sample was digested overnight (6-17 hours) in 1ml of a freshly prepared enzymatic cocktail containing 50 units/ml of collagenase type 3, 80 units/ml of purified collagenase, and 100 units/ml of hyaluronidase in PBS pH 7.4/0.5mM CaCl2 buffer. Each enzyme was rehydrated with PBS pH 7.4/0.5mM CaCl2 buffer, then stored at -200C immediately prior to addition to the cocktail mixture. Following overnight digestion, 500 ul NST was added to each sample to facilitate pelleting. Samples were centrifuged for 5 minutes at 3000 x g, after which pellets were resuspended in 750 ul of NST/10% fetal bovine serum and then passed through a 25 G needle 10-20 times. The samples were filtered through a 35 um mesh and collected into a 5 ml Polypropylene round bottom tube. The mesh was rinsed with an additional 750 ul of NST/10% fetal bovine serum and placed on ice while processing remaining samples. The total volume in the tube for each sample was approximately 1.5 ml. An equal volume of 20ug/ml DAPI was added to each tube to achieve a final concentration of 10ug/ml DAPI prior to flow sorting with a BD Influx cytometer with ultraviolet excitation (Becton-Dickinson, San Jose, CA). The optimal settings for sorting FFPE samples with the Influx sorter were as follows: Drop formation was achieved with piezzo amplitude of 6-10 volts and a drop frequency of 30 khertz. The sort mode was set to purity yield with a drop delay of 31.5-32. Sheath fluid pressure was typically 17-18 psi with a 100 um nozzle. For single parameter DNA content assays, DAPI emission was collected at >450nm. DNA content and cell cycle were then analyzed using the software program MultiCycle (Phoenix Flow Systems, San Diego, CA).

value: pancreatic adenocarcinoma

tag: sample type

value: fresh frozen tissue

source_name: Normal 46,XX reference

value: commercial pooled reference


title: ko Epithelium_saline_rep2


title: Pancreas FFPE-120-02

source_name: FFPE tissue, pancreatic adenocarcinoma

value: formalin-fixed paraffin-embedded tissue


title: ko Epithelium_OVA_rep4


title: ko Epithelium_saline_rep4


title: wt Epithelium_OVA_rep2


title: Pancreas FF A10-46_2N


title: Ovarian SCCO-006

source_name: FFPE tissue, ovarian small cell carcinoma

value: ovarian small cell carcinoma


title: Pancreas FF-120-57


title: Breast PS03 4398 B2

source_name: FFPE tissue, breast carcinoma

value: breast carcinoma


title: Pancreas SPIA-120-02


title: Bladder B2006.33251

source_name: FFPE tissue, bladder carcinoma

value: bladder carcinoma


title: Pancreas FFPE-A10-AT


title: wt Epithelium_saline_rep3

source_name: wt airway epithelium saline challenged


title: Pancreas SPIA-A10-AT


title: Pancreas FF A10-46_2N_CK+


title: Breast SS04 4239 A2


title: A185-PRE-High dose

city: Ho Chi Minh

first: Nguyen

middle: Hanh

last: Tien

address: 764 Vo Van Kiet

department: Dengue group

country: Viet Nam

institute: Oxford University Clinical Research Unit

description: SAMPLE 357

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The array intensity values were extracted using GenomeStudio software (v.1.6.0, Illumina Inc., USA) and processed with GeneSpring (v.11.5, Agilent Technologies Inc., USA). First measurements having intensity values less than 5.0 were corrected to 5.0, and then all signals were normalized to the 80th percentile by dividing each value by the 80th percentile value; only genes that were confidently detected in at least 60% of samples in one of the three treatment groups were used for the analysis.

label: Biotin

source_name: PRE-High dose

label_protocol: RNA was amplified and labeled with biotin using Illumina TotalPrep 96 RNA amplification kit.

extract_protocol: RNA was extracted from blood using PAXgene Blood RNA kit (PreAnalytiX, Switzeland) as instructions of manufacturer.

treatment_protocol: Patients were randomly treated with placebo, low-dose (0.5mg/kg) or high-dose (2mg/kg) of prednisolone. Maximum 3 (pre-treatment (PRE); post-treatment (POST) and follow up (FU) - 1 month since illness onset) and at least 2 samples (pre-treatment and post-treatment) were collected from each patient.

tag: disease status

value: Vietnamese dengue patients

tag: treated with

value: high-dose (2mg/kg) of prednisolone

tag: sample collection time

value: pre-treatment

value: blood

tag: patient id


title: wt Epithelium_saline_rep2

value: airway epithelium


title: TW16 shoot at 18 days post RTBV inoculation rep3

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

country: Japan

institute: NARO/HARC

description: Biological replication 3 of 3, RTBV infected TW16 at 18DPI

hyb_protocol: hybridization_Kit: in situ hybridization plus hybridization_Manufacturer: Agilent Technologies hybridization_Manual: Agilent Technologies

scan_protocol: Scanner: Agilent DNA microarray Scaner Manufacturer: Agilent Technologies Software: Scanner Control software Manufacturer: Agilent Technologies Manual: Agilent Technologies

data_processing:
Software: Feature Extraction ver 9.5
Manufacturer: Agilent Technologies
Manual: Agilent Technologies

organism: Oryza sativa Indica Group

label_protocol:
Kit: Low RNA Input Linear Amplification kit
Manufacturer: Agilent Technologies
Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol:
Growth environment: greenhouse study
Growth: pot culture (D: 120mm x H: 150mm)
Growth media: Soil collected fielf of International Rice Research Institute, Philippines. Alutoclaved prior to use
No of seedling per pot : 5
Light condition: Natural conditions
Tempareture: 28±3℃
Growth length: 18 day post inoculation

extract_protocol:
separation: trimming
extraction source: frozen
extraction source: shoots pooled from 5 individual plants
kit: Qiagen Rneasy maxi kit
manual: Qiagen

treatment_protocol:
Treatment method: Agrobacterium method
Growth environment: greenhouse study
growth stage: growth stage: 14-day old plant
Light condition: Natural conditions
Tempareture: 28±3℃
virus inoculation: Rice tungro bacilliform virus
virus inoculation: Inoculation with Agrobacterium strain pGV3850 containing the RTBV infectious clone (pRTBR1162) (Dasgupta et al., 1991)

tag: cultivar

value: TW16 is an RTSV-resistant near-isogenic line (BC5) made by cross between Taichung Native 1 (recurrent parent) and Utri Merah (donor parent).

value: shoot

tag: infection

value: RTBV inoculation

tag: time

value: 18 days post inoculation

growth_protocol:
Growth environment: greenhouse study
Growth: pot culture (D: 120mm x H: 150mm)
Growth media: Soil collected fielf of International Rice Research Institute, Philippines. Alutoclaved prior to use
No of seedling per pot : 5
Light condition: Natural conditions
Tempareture: 25±3℃
Growth length: 18 day post inoculation

treatment_protocol:
Treatment method: Agrobacterium method
Growth environment: greenhouse study
growth stage: growth stage: 14-day old plant
Light condition: Natural conditions
Tempareture: 28±3℃
virus inoculation: Mock inoculation
virus inoculation: Inoculation with Agrobacterium strain pGV3850 devoid of the RTBV infectious clone (Dasgupta et al., 1991)

value: mock inoculation


title: wt Epithelium_saline_rep4

value: saline

value: FvB

tag: age

value: 6-8 weeks old-sensitization

value: wildtype


title: A185-POST-High dose

description: SAMPLE 358

source_name: POST-High dose

value: post-treatment


title: TW16 shoot at 18 days post RTBV inoculation rep2

description: Biological replication 2 of 3, RTBV infected TW16 at 18DPI


title: Pancreas FFPE B03.3733

value: pancreatic adenocarcinoma

value: formalin-fixed paraffin-embedded tissue

value: commercial pooled reference


title: Pancreas FF-11164

value: fresh frozen tissue


title: ko Epithelium_OVA_rep1

value: OVA

value: beta6 knockout


title: Breast PS02 1557 E3-10K

value: breast carcinoma


title: wt Epithelium_saline_rep1

value: airway epithelium


title: TW16 shoot at 12 days post RTBV inoculation rep2

description: Biological replication 2 of 3, RTBV infected TW16 at 12DPI

growth_protocol:
Growth environment: greenhouse study
Growth: pot culture (D: 120mm x H: 150mm)
Growth media: Soil collected fielf of International Rice Research Institute, Philippines. Alutoclaved prior to use
No of seedling per pot : 5
Light condition: Natural conditions
Tempareture: 28±3℃
Growth length: 12 day post inoculation

value: TW16 is an RTSV-resistant near-isogenic line (BC5) made by cross between Taichung Native 1 (recurrent parent) and Utri Merah (donor parent).

value: shoot

value: 12 days post inoculation

growth_protocol:
Growth environment: greenhouse study
Growth: pot culture (D: 120mm x H: 150mm)
Growth media: Soil collected fielf of International Rice Research Institute, Philippines. Alutoclaved prior to use
No of seedling per pot : 5
Light condition: Natural conditions
Tempareture: 25±3℃
Growth length: 12 day post inoculation


title: TW16 shoot at 18 days post RTBV inoculation rep1

description: Biological replication 1 of 3, RTBV infected TW16 at 18DPI

value: RTBV inoculation

value: 18 days post inoculation

value: mock inoculation


title: TW16 shoot at 12 days post RTBV inoculation rep3

description: Biological replication 3 of 3, RTBV infected TW16 at 12DPI


title: Pancreas FF-A10-46


title: Breast PS02 1557 E3-25K-duplicate


title: Breast PS02 1557 E3-50K


title: Breast PS02 1557 E3-25K


title: Breast PS02 1557 E3-50K-duplicate


title: Pancreas A10-74-CELL LINE

source_name: Cell line, pancreatic adenocarcinoma

tag: cell line

tag: cell type

value: pancreatic adenocarcinoma cells

value: cell line


title: Breast PS02 1557 E3-10K-duplicate


title: A019-PRE-High dose

description: SAMPLE 355

value: Vietnamese dengue patients

value: high-dose (2mg/kg) of prednisolone

value: pre-treatment

value: blood


title: A015-POST-Low dose

description: SAMPLE 353

source_name: POST-Low dose

value: low-dose (0.5mg/kg) of prednisolone

value: post-treatment


title: A015-FU-Low dose

description: SAMPLE 354

source_name: FU-Low dose

value: follow up; 1 month after illness-onset


title: TW16 shoot at 9 days post RTBV inoculation rep1

description: Biological replication 1 of 3, RTBV infected TW16 at 9DPI

growth_protocol:
Growth environment: greenhouse study
Growth: pot culture (D: 120mm x H: 150mm)
Growth media: Soil collected fielf of International Rice Research Institute, Philippines. Alutoclaved prior to use
No of seedling per pot : 5
Light condition: Natural conditions
Tempareture: 28±3℃
Growth length: 9 day post inoculation

value: 9 days post inoculation

growth_protocol:
Growth environment: greenhouse study
Growth: pot culture (D: 120mm x H: 150mm)
Growth media: Soil collected fielf of International Rice Research Institute, Philippines. Alutoclaved prior to use
No of seedling per pot : 5
Light condition: Natural conditions
Tempareture: 25±3℃
Growth length: 9 day post inoculation


title: TW16 shoot at 9 days post RTBV inoculation rep2

description: Biological replication 2 of 3, RTBV infected TW16 at 9DPI


title: TW16 shoot at 12 days post RTBV inoculation rep1

description: Biological replication 1 of 3, RTBV infected TW16 at 12DPI


title: A011-FU-Placebo

description: SAMPLE 351

source_name: FU-Placebo

value: placebo


title: A011-POST-Placebo

description: SAMPLE 350

source_name: POST-Placebo


title: A015-PRE-Low dose

description: SAMPLE 352

source_name: PRE-Low dose


title: A011-PRE-Placebo

description: SAMPLE 349

source_name: PRE-Placebo


title: TW16 shoot at 6 days post RTBV inoculation rep3

description: Biological replication 3 of 3, RTBV infected TW16 at 6DPI

growth_protocol:
Growth environment: greenhouse study
Growth: pot culture (D: 120mm x H: 150mm)
Growth media: Soil collected fielf of International Rice Research Institute, Philippines. Alutoclaved prior to use
No of seedling per pot : 5
Light condition: Natural conditions
Tempareture: 28±3℃
Growth length: 6 day post inoculation

value: TW16 is an RTSV-resistant near-isogenic line (BC5) made by cross between Taichung Native 1 (recurrent parent) and Utri Merah (donor parent).

value: 6 days post inoculation

growth_protocol:
Growth environment: greenhouse study
Growth: pot culture (D: 120mm x H: 150mm)
Growth media: Soil collected fielf of International Rice Research Institute, Philippines. Alutoclaved prior to use
No of seedling per pot : 5
Light condition: Natural conditions
Tempareture: 25±3℃
Growth length: 6 day post inoculation


title: TW16 shoot at 6 days post RTBV inoculation rep2

description: Biological replication 2 of 3, RTBV infected TW16 at 6DPI

value: shoot


title: TW16 shoot at 6 days post RTBV inoculation rep1

description: Biological replication 1 of 3, RTBV infected TW16 at 6DPI

value: RTBV inoculation


title: A007-FU-Low dose

description: SAMPLE 345


title: TN1 shoot at 12 days post RTBV inoculation rep3

description: Biological replication 3 of 3, RTBV infected TN1 at 12DPI

value: Taichung Native 1 (TN1)

value: 12 days post inoculation


title: A008-POST-High dose

description: SAMPLE 347


title: TN1 shoot at 18 days post RTBV inoculation rep3

description: Biological replication 3 of 3, RTBV infected TN1 at 18DPI

value: 18 days post inoculation

value: mock inoculation


title: TN1 shoot at 18 days post RTBV inoculation rep2

description: Biological replication 2 of 3, RTBV infected TN1 at 18DPI


title: A008-PRE-High dose

description: SAMPLE 346

value: Vietnamese dengue patients


title: TN1 shoot at 12 days post RTBV inoculation rep2

description: Biological replication 2 of 3, RTBV infected TN1 at 12DPI


title: TN1 shoot at 18 days post RTBV inoculation rep1

description: Biological replication 1 of 3, RTBV infected TN1 at 18DPI


title: A119-PRE-High dose

description: SAMPLE 343

value: high-dose (2mg/kg) of prednisolone


title: TN1 shoot at 12 days post RTBV inoculation rep1

description: Biological replication 1 of 3, RTBV infected TN1 at 12DPI


title: A118-POST-Placebo

description: SAMPLE 342


title: A118-PRE-Placebo

description: SAMPLE 341

value: pre-treatment


title: TN1 shoot at 9 days post RTBV inoculation rep2

description: Biological replication 2 of 3, RTBV infected TN1 at 9DPI


title: TN1 shoot at 9 days post RTBV inoculation rep3

description: Biological replication 3 of 3, RTBV infected TN1 at 9DPI


title: TN1 shoot at 9 days post RTBV inoculation rep1

description: Biological replication 1 of 3, RTBV infected TN1 at 9DPI


title: A114-FU-Low dose

description: SAMPLE 337

value: blood


title: A117-FU-Low dose

description: SAMPLE 340

value: low-dose (0.5mg/kg) of prednisolone


title: A117-PRE-Low dose

description: SAMPLE 338


title: TW16 shoot at 9 days post RTBV inoculation rep3

description: Biological replication 3 of 3, RTBV infected TW16 at 9DPI


title: TN1 shoot at 6 days post RTBV inoculation rep3

description: Biological replication 3 of 3, RTBV infected TN1 at 6DPI


title: A110-POST-High dose

description: SAMPLE 333

value: post-treatment


title: A110-FU-High dose

description: SAMPLE 334

source_name: FU-High dose

value: follow up; 1 month after illness-onset


title: A119-POST-High dose

description: SAMPLE 344


title: TN1 shoot at 6 days post RTBV inoculation rep1

description: Biological replication 1 of 3, RTBV infected TN1 at 6DPI


title: A114-POST-Low dose

description: SAMPLE 336


title: A109-POST-High dose

description: SAMPLE 330


title: A108-FU-Low dose

description: SAMPLE 328


title: A109-PRE-High dose

description: SAMPLE 329


title: A117-POST-Low dose

description: SAMPLE 339


title: A109-FU-High dose

description: SAMPLE 331


title: A108-PRE-Low dose

description: SAMPLE 326


title: A107-FU-Placebo

description: SAMPLE 325


title: A114-PRE-Low dose

description: SAMPLE 335


title: A108-POST-Low dose

description: SAMPLE 327


title: A107-PRE-Placebo

description: SAMPLE 323


title: A104-FU-High dose

description: SAMPLE 322


title: A180-POST-Low dose

description: SAMPLE 319


title: A104-POST-High dose

description: SAMPLE 321


title: A180-FU-Low dose

description: SAMPLE 320


title: A107-POST-Placebo

description: SAMPLE 324


title: A024-POST-Low dose

description: SAMPLE 356


title: A180-PRE-Low dose

description: SAMPLE 318


title: A178-FU-Placebo

description: SAMPLE 317


title: A110-PRE-High dose

description: SAMPLE 332


title: Ad-PDEF

city: Charleston

first: Dennis

last: Watson

address: 68 President Street

institute: Medical Univeristy of South Carolina

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPL13A, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control (i.e., Ad-FLI1/Parental) ratios.

label: SYBR Green

label_protocol: PCR assays were performed using the Human Cancer Pathway Finder PCR assay panel (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions. Reverse transcription was performed from 2000 ng total RNA using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR were performed (Light Cycler 480, Roche) with 45 cycles at 94 oC for 15 seconds and 60 oC for 60 seconds.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit.

value: adenocarcinoma

tag: activation agent

value: Ad-GFP-PDEF

value: 72 hours


title: Ad-GFP

description: Test

value: Ad-GFP


title: Parental

description: Control

value: Control


title: 4dpf_eye_rep1

city: Dublin

first: Breandan

last: Kennedy

address: Belfield

department: UCD School of Biomolecular and Biomedical Science

country: Ireland

institute: UCD Conway Institute, University College Dublin

description: Eyes from 4dpf zebrafish embryo, replicate 1

hyb_protocol: Hybridization, washing and staining were done according to a standard procedure from Affymetrix.

scan_protocol: Scanning was done according to a standard procedure from Affymetrix.

data_processing: The signal intensity of the microarray was normalized and summarized using the Bioconductor package, gcrma, using default setting.

organism: Danio rerio

source_name: Wild type whole eye on 4dpf

label_protocol: Total RNA were labeled by Affymetrix GeneChip Two-Cycle Target Labeling protocol.

extract_protocol: Total RNA was extracted with Qiashredder columns and the RNeasy Minikit (Qiagen, Hilden, Germany) in an RNase-free environment.

value: eye


title: A178-PRE-Placebo

description: SAMPLE 315

value: placebo


title: A177-PRE-High dose

description: SAMPLE 312


title: Ad-FLI1

description: Test


title: A177-POST-High dose

description: SAMPLE 313


title: A177-FU-High dose

description: SAMPLE 314


title: 4dpf_eye_rep3

description: Eyes from 4dpf zebrafish embryo, replicate 3


title: A178-POST-Placebo

description: SAMPLE 316


title: 3dpf_eye_rep3

description: Eyes from 3dpf zebrafish embryo, replicate 3

source_name: Wild type whole eye on 3dpf


title: A010-FU-Placebo

description: SAMPLE 348


title: 4dpf_eye_rep2

description: Eyes from 4dpf zebrafish embryo, replicate 2


title: 5dpf_eye_rep3

description: Eyes from 5dpf zebrafish embryo, replicate 3

source_name: Wild type whole eye on 5dpf


title: A176-FU-Low dose

description: SAMPLE 311


title: A176-POST-Low dose

description: SAMPLE 310


title: PL2F8 4d replicate 2 HHC15

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

description: replicate 2

data_processing: The data were normalised using quantile normalisation with Genedata analyst and probes to the same gene were averaged using a perl script.

label: biotin

source_name: cell culture

label_protocol: Standard Illumina  protocol

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

tag: time since lif removal


title: PL2F8 6d replicate 2 HHC17

description: replicate 2


title: PL2F8 8d replicate 1 HHC18

description: replicate 1


title: testicular germ cell tumour cell line SUSA

city: London

first: Xueying

last: Mao

address: Charterhouse Square

country: United Kingdom

institute: Queen Mary

description: Hybridized to 10K SNP

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 7G.

data_processing: CEL files and CHP files generated by Affymetrix Genechip Operating Software. Very weakly hybridized SNPs were filtered by the same software. The signal intensity data from SNP array were analyzed by in-house software: GOLF.

source_name: testicular germ cell tumour cell line

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Fresh frozen samples were digested by Proteinase K and RNaseA. DNA was extracted from these samples using phenol/chroloform.

value: SUSA


title: A082-POST-Placebo

description: SAMPLE 309


title: 5dpf_eye_rep1

description: Eyes from 5dpf zebrafish embryo, replicate 1


title: testicular germ cell tumour cell line GCT27

description: Hybridized to 10K SNP


title: 3dpf_eye_rep1

description: Eyes from 3dpf zebrafish embryo, replicate 1


title: PL2F8 4d replicate 1 HHC14

description: replicate 1


title: PL2F8 2d replicate 2 HHC13

description: replicate 2


title: 3dpf_eye_rep2

description: Eyes from 3dpf zebrafish embryo, replicate 2


title: 5dpf_eye_rep2

description: Eyes from 5dpf zebrafish embryo, replicate 2


title: testicular germ cell tumour cell line 833K

description: Hybridized to 10K SNP


title: A080-POST-High dose

description: SAMPLE 306


title: PL2F8 0d replicate 1 HHC10

description: replicate 1


title: PL2F8 6d replicate 1 HHC16

description: replicate 1


title: A082-PRE-Placebo

description: SAMPLE 308


title: PL2F8 2d replicate 1 HHC12

description: replicate 1


title: AB2.2 8d replicate 1 HHC9

description: replicate 1


title: AB2.2 4d replicate 1 HHC5

description: replicate 1


title: AB2.2 6d replicate 1 HHC7

description: replicate 1


title: AB2.2 6d replicate 2 HHC8

description: replicate 2


title: PL2F8 0d replicate 2 HHC11

description: replicate 2


title: 92T testicular germ cell tumour

description: Hybridized to 10K SNP

source_name: testicular germ cell tumour

tag: comment

value: testicular germ cell tumour


title: A080-FU-High dose

description: SAMPLE 307

tag: tissue


title: A080-PRE-High dose

description: SAMPLE 305


title: TN1 shoot at 6 days post RTBV inoculation rep2

description: Biological replication 2 of 3, RTBV infected TN1 at 6DPI

value: Taichung Native 1 (TN1)

value: shoot

value: RTBV inoculation

value: 6 days post inoculation

value: mock inoculation


title: AB2.2 2d replicate 2 HHC4

description: replicate 2


title: A078-FU-High dose

description: SAMPLE 304

value: Vietnamese dengue patients

value: high-dose (2mg/kg) of prednisolone

value: blood


title: 92N normal testis

description: Hybridized to 10K SNP

source_name: normal testis

value: normal testis


title: 90T testicular germ cell tumour

description: Hybridized to 10K SNP


title: AB2.2 0d replicate 2 HHC2

description: replicate 2


title: A078-POST-High dose

description: SAMPLE 303

value: post-treatment


title: AB2.2 0d replicate 1 HHC1

description: replicate 1


title: AB2.2 2d replicate 1 HHC3

description: replicate 1


title: A078-PRE-High dose

description: SAMPLE 302

source_name: PRE-High dose

value: pre-treatment


title: AB2.2 4d replicate 2 HHC6

description: replicate 2


title: A077-POST-Low dose

description: SAMPLE 300

value: low-dose (0.5mg/kg) of prednisolone


title: A394-P5

city: Birmingham

first: Steven

middle: L

last: Carroll

state: AL

address: SC930Ge, 1720 7th Ave South

department: Pathology

institute: University of Alabama at Birmingham

description: Sample 12

hyb_protocol: Slide hybridization and washing was performed using Agilent's standard protocol with their Oligo aCGH/ChIP Hybridization Kit (Agilent #5188-5220), OligoCHG Wash Buffers 1 and 2 (Agilent #5188-5226) and Stabilization and Drying Solution (Agilent #5185-5979).

scan_protocol: Arrays were scanned on a GenePix 4000B scanner per the manufacturer's protocol (Molecular Devices; Sunnyvale, CA).

data_processing: The data were analyzed using ‘Feature Extraction v9.5’ and ‘DNA Analytics v4.0’ software (Agilent Technologies). The analysis parameters used for the detection of genomic copy number changes included: linear dye normalization, ADM-2 aberration detection algorithm, and aberration filter of four sequential probes with a log2 ratio cutoff of 0.25.  All genomic breakpoints were mapped using mouse genome build NCBI37/mm9.

source_name: Genomic DNA from tumor A394 cells

label_protocol: Test (MPNST) and reference (Schwann cell) genomic DNA was labeled with Cy5-dUTP and Cy3-dUTP, respectively, using a Genomic DNA Enzymatic Labeling Kit (Agilent Technologies, Inc.; Santa Clara, CA) per the manufacturer’s recommendations.

growth_protocol: Tumor tissue was sterilely transferred to Hanks’ balanced salt solution, finely minced and then incubated in Dulbecco’s minimal essential medium supplemented with 10% fetal calf serum (DMEM10), 2 μM forskolin and 50 nM NRG1β; in preliminary experiments, we found that the latter two components facilitated the initial establishment of tumor cultures. Cells were allowed to grow out from explants until confluent.  Cultures were then split and maintained for no more than 5-8 passages in DMEM10 without forskolin or NRG1β.  Cultures of Schwann cells from wild-type and transgenic nerves were established identically, but were maintained continuously in DMEM10 supplemented with forskolin and NRG1β.

extract_protocol: Genomic DNA was isolated from early passage P0-GGFβ3 MPNST cells and wild-type mouse Schwann cells using the QIAamp DNA Mini Kit (Qiagen; Valencia, CA) per the manufacturer’s recommendations.

tag: strain background

value: C57BL/6J x SJL/J

value: P0-GGFβ3 transgenic

value: malignant peripheral nerve sheath tumor (MPNST) cells

source_name: Non-neoplastic Schwann cells

tag: strain

value: wild-type

value: Non-neoplastic Schwann cells


title: 88T testicular germ cell tumour

description: Hybridized to 10K SNP

value: testicular germ cell tumour


title: 87T testicular germ cell tumour

description: Hybridized to 10K SNP


title: A077-PRE-Low dose

description: SAMPLE 299


title: A382-P8

description: Sample 8

source_name: Genomic DNA from tumor A382 cells (passage 8)

tag: genotype/variation


title: 82T testicular germ cell tumour

description: Hybridized to 10K SNP


title: A382-P9

description: Sample 11

source_name: Genomic DNA from tumor A382 cells (passage 9)


title: 87N normal testis

description: Hybridized to 10K SNP


title: A077-FU-Low dose

description: SAMPLE 301

source_name: FU-Low dose

tag: disease status

value: follow up; 1 month after illness-onset


title: 88N normal testis

description: Hybridized to 10K SNP


title: B96-P8

description: Sample 9

source_name: Genomic DNA from tumor B96 cells


title: A390-P7

description: Sample 5

source_name: Genomic DNA from tumor A390 cells


title: A076-POST-High dose

description: SAMPLE 298

source_name: POST-High dose

tag: treated with


title: 82N normal testis

description: Hybridized to 10K SNP


title: B76-P13

description: Sample 10

source_name: Genomic DNA from tumor B76 cells


title: A161-PRE-High dose

description: SAMPLE 297

tag: sample collection time


title: A292-P8

description: Sample 7

source_name: Genomic DNA from tumor A292 cells


title: A18-P11

description: Sample 1

source_name: Genomic DNA from tumor A18 cells


title: 74T testicular germ cell tumour

description: Hybridized to 10K SNP


title: 231 Trig

description: Sample 2

source_name: Genomic DNA from tumor 231Trig cells


title: A160-FU-High dose

description: SAMPLE 296

source_name: FU-High dose

tag: patient id


title: B86-P6

description: Sample 3

source_name: Genomic DNA from tumor B86 cells


title: A160-POST-High dose

description: SAMPLE 295


title: 2T testicular germ cell tumour

description: Hybridized to 10K SNP

source_name: testicular germ cell tumour


title: A160-PRE-High dose

description: SAMPLE 294


title: B91-P9

description: Sample 6

source_name: Genomic DNA from tumor B91 cells


title: serum microRNA profile of case NPC-S5

city: Guangzhou

first: Jun

address: 651 Dongfeng Road East

country: China

institute: Sun Yat-sen University Cancer Center

description: serum samples from nasopharyngeal carcinoma patient with shorter-survival time

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US) at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA，Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: Nasopharyngeal carcinoma serum

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat#5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was isolated from 400 µl serum using TRIzol® LS reagent (Life Technologies, Carlsbad, CA, USA). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: survival time

value: shorter-survival time

tag: gender

value: male


title: A158-POST-Placebo

description: SAMPLE 292

source_name: POST-Placebo

value: placebo


title: serum microRNA profile of case NPC-L6

description: serum samples from nasopharyngeal carcinoma patient with longer-survival time

value: longer-survival time


title: serum microRNA profile of case NPC-L1


title: serum microRNA profile of case NPC-L8

value: female


title: serum microRNA profile of case NPC-L3


title: serum microRNA profile of case NPC-L5


title: serum microRNA profile of case NPC-S6


title: serum microRNA profile of case NPC-S4


title: serum microRNA profile of case NPC-S8


title: serum microRNA profile of case NPC-L7


title: serum microRNA profile of case NPC-L4


title: serum microRNA profile of case NPC-L2


title: 33T testicular germ cell tumour

description: Hybridized to 10K SNP


title: A158-PRE-Placebo

description: SAMPLE 291

source_name: PRE-Placebo

value: Vietnamese dengue patients

value: blood


title: A150-FU-Placebo

description: SAMPLE 290

source_name: FU-Placebo


title: A150-POST-Placebo

description: SAMPLE 289

value: post-treatment


title: A158-FU-Placebo

description: SAMPLE 293


title: A150-PRE-Placebo

description: SAMPLE 288

value: pre-treatment


title: serum microRNA profile of case NPC-S3


title: serum microRNA profile of case NPC-S7


title: serum microRNA profile of case NPC-S1


title: serum microRNA profile of case NPC-S2


title: A149-FU-High dose

description: SAMPLE 287

value: high-dose (2mg/kg) of prednisolone


title: La France-rep2

city: Chikusa-ku

first: Kenji

last: Nashima

state: Nagoya

address: Furo-cho

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

description: Pyrus communis - 'La France' - 2010 expt - 1 week before full bloom - receptacle - rep2

hyb_protocol: The labeled samples were hybridized to the oligoarray slides using Gene Expression Hybridization Kit (Agilent) as a hybridization buffer at 65°C for 17 h in a hybridization chamber. After hybridization, arrays were washed with Gene Expression Wash Buffer (Agilent) according to the manufacturer’s instructions.

scan_protocol: The dried slides were scanned by Agilent scanner. Raw data from scanning of the array was captured using Agilent Feature Extraction Ver. 10.7.1.1 (with Linear & Lowess normalization).

data_processing: Expression for each gene was calculated as the mean value of three biological replicates and the standard error of Global normalization settings were used with Subio platform with basic plug-in. See http://www.subio.jp/ for details. Briefly, the values were log transformed and were processed to global normalization with 75 percentile value.

organism: Pyrus communis

source_name: La France

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 10 to 50 ng RNA using the One-Color Low Input Quick Amp labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: European pear trees (Pyrus communis cv. ‘La France’ and its bud mutant ‘Giant Laf’) were managed according to standard orchard practices.

extract_protocol: Total RNAs were extracted using PicoPure RNA isolation kit (Molecular Devices) from receptacle which was isolated by using laser microdissection. Extracted RNA was purified using the RNeasy Mini Kit (Qiagen, Hilden, Germany) and the quality and purity were checked using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: cultivar

value: La France

value: Receptacle

tag: Stage

value: 1 week before full bloom

tag: sampling year


title: A149-POST-High dose

description: SAMPLE 286


title: A103-FU-Placebo

description: SAMPLE 284


title: A103-PRE-Placebo

description: SAMPLE 282


title: MCF7_DAC72h_EtOh6h_2

city: Huddinge

first: Milica

last: Putnik

address: Hälsovägen 7

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

description:
Sample name: MP10
A_EtOH

hyb_protocol: Array plates were washed and stained in the Affymetrix Gene Titan system.

scan_protocol: Array plates were scanned according to Affymetrix Gene Titan standard procedure.

data_processing:
Summarization: RMA, Normalization: Sketch-Quantile, Transformation: to linear scale
Software: Affymetrix Expression Console version 1.1

source_name: MCF7 cells, 72h 1μM DAC treatment, 6h EtOh treatment, rep 2

label_protocol: GeneChip 3' IVT Express kit starting with 200 ng of total RNA.

growth_protocol: MCF7 cells were seeded in plates and cultured  in phenol red-free DMEM supplemented with 2.5% dextran-coated charcoal-treated heat-inactivated FBS (Hyclone) for 72 h.

extract_protocol: RNeasy Mini Kit (Qiagen)

treatment_protocol: During these 72h, the cells were either not treated or treated with 1μM DAC (Sigma Aldrich). Culture medium with or without treatment was changed every 24h. The DAC-treated cells were subsequently treated with vehicle (ethanol, EtOh), and the non-treated cells were subsequently treated with either vehicle or 10nM E2 for 6h. Each treatment was done in four replicates.

tag: cell line

value: MCF7 breast cancer cells

tag: dac treatment

value: 72h 1μM DAC treatment

tag: post-dac treatment

value: 6h EtOH treatment


title: La France-rep3

description: Pyrus communis - 'La France' - 2010 expt - 1 week before full bloom - receptacle - rep3


title: La France-rep1

description: Pyrus communis - 'La France' - 2010 expt - 1 week before full bloom - receptacle - rep1


title: A104-PRE-High dose

description: SAMPLE 285

source_name: PRE-High dose


title: MCF7_control72h_E26h_1

description:
Sample name: MP5
C_E2

source_name: MCF7 cells, 72h no treatment, 6h E2 treatment, rep 1

value: 72h no treatment

value: 6h E2 treatment


title: A103-POST-Placebo

description: SAMPLE 283


title: MCF7_DAC72h_EtOh6h_4

description:
Sample name: MP12
A_EtOH

source_name: MCF7 cells, 72h 1μM DAC treatment, 6h EtOh treatment, rep 4


title: MCF7_DAC72h_EtOh6h_3

description:
Sample name: MP11
A_EtOH

source_name: MCF7 cells, 72h 1μM DAC treatment, 6h EtOh treatment, rep 3


title: Giant Laf-rep3

description: Pyrus communis - 'Giant Laf' - 2010 expt - 1 week before full bloom - receptacle - rep3

source_name: Giant Laf

value: Giant Laf


title: Giant Laf-rep2

description: Pyrus communis - 'Giant Laf' - 2010 expt - 1 week before full bloom - receptacle - rep2


title: MCF7_control72h_E26h_3

description:
Sample name: MP7
C_E2

source_name: MCF7 cells, 72h no treatment, 6h E2 treatment, rep 3


title: MCF7_control72h_E26h_4

description:
Sample name: MP8
C_E2

source_name: MCF7 cells, 72h no treatment, 6h E2 treatment, rep 4


title: 74N normal testis

description: Hybridized to 10K SNP

source_name: normal testis

tag: comment

value: normal testis


title: MCF7_DAC72h_EtOh6h_1

description:
Sample name: MP9
A_EtOH

source_name: MCF7 cells, 72h 1μM DAC treatment, 6h EtOh treatment, rep 1


title: MCF7_control72h_EtOh6h_3

description:
Sample name: MP3
C_EtOH

source_name: MCF7 cells, 72h no treatment, 6h EtOh treatment, rep 3


title: A100-POST-Low dose

description: SAMPLE 280

source_name: POST-Low dose

value: low-dose (0.5mg/kg) of prednisolone

tag: tissue


title: Giant Laf-rep1

description: Pyrus communis - 'Giant Laf' - 2010 expt - 1 week before full bloom - receptacle - rep1


title: MCF7_control72h_E26h_2

description:
Sample name: MP6
C_E2

source_name: MCF7 cells, 72h no treatment, 6h E2 treatment, rep 2


title: A100-PRE-Low dose

description: SAMPLE 279

source_name: PRE-Low dose


title: MCF7_control72h_EtOh6h_2

description:
Sample name: MP2
C_EtOH

source_name: MCF7 cells, 72h no treatment, 6h EtOh treatment, rep 2


title: MCF7_control72h_EtOh6h_4

description:
Sample name: MP4
C_EtOH

source_name: MCF7 cells, 72h no treatment, 6h EtOh treatment, rep 4


title: 1329-02

city: Gotenburg

first: Marta

last: Persson

address: Box 425

institute: Sahlgrenska Cancer Center

hyb_protocol: Oligoarray control targets (Cot-1 DNA and Blocking agent) and hybridization buffer (Agilent oligo aCGH/ChIP-on-Chip Hybridization Kit) were added, the samples were denatured and applied to microarrays (Agilent Human Genome CGH Microarray 44K and 244K 60-mer oligonucleotide arrays) as recommended by the manufacturer. The arrays were enclosed in a rotating hybridization oven at 65°C for 40 h. After hybridization, the slides were sequentially washed and dried.

scan_protocol: The arrays were scanned on an Agilent  Microarray Confocal Scanner (G2567AA) and the images were quantified with Agilent Feature Extraction Software (v.7.5) using the intensity-dependent linear normalization method.

data_processing: Data analysis was carried out using Nexus Copy Number software v.4.1 (BioDiscovery Inc., El Segundo, CA, USA), which uses the Rank segmentation algorithm to define non-random regions of CNAs across the genome. Sex chromosomes were excluded from the analysis. The significance threshold for segmentation was set to p=1.0E-7 and the thresholds of log2 ratio values for gain and loss were 0.4 and −0.3, respectively; the thresholds for high copy number gain/amplification and homozygous deletion were 1.0 and −1.0, respectively.

source_name: Mucoepidermoid carcinoma

label_protocol: 3.0 µg of genomic tumor DNA and sex-matched reference DNA (pooled peripheral blood cells from 5 normal female and male genomes) were digested with AluI and Rsa1 (Promega, Madisaon, WI) and labeled with Cy3-dUTP and Cy5-dUTP (Perkin-Elmer Life and Analytical Sciences Inc., Wellesley, MA, USA).

extract_protocol: Genomic DNA was isolated from FFPE tissue using the standard phenol-chloroform method and from fresh frozen tissue using the QIAamp DNA Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer instructions.

treatment_protocol: Fresh frozen tumor material from 15 MECs and paraffin embedded tumor material from 13 MECs were retrieved from the department of Pathology at Haartman Institute in Helsinki, the department of pathology at Sahlgrenska University Hospital in Gothenburg and the department of Oral Pathology at Guy's Hospital in London. The tumors were classified as low grade and high grade according to the histologic classification of salivary gland tumours by WHO.

tag: fusion status

value: Pos

tag: grade

value: High Grade

source_name: Normal tissue

tag: sample type

value: reference

value: F


title: Bambusa_oldhamii_100b

city: Taipei

first: Ai-Yu

last: Wang

address: No. 1, Sec. 4, Roosevelt Road

department: Department of Biochemical Science and Technology

institute: National Taiwan University

hyb_protocol: The GPL15916 microarray slides were incubated in prehybridization buffer (5 x SSC, 0.1% SDS, 1% BSA) at 42°C for 1 h. Then, the prehybridized slides were washed in deionized water and dipped in 2-propanol before they were allowed to air dry. In all, 20 μl of 2 x hybridization buffer (50% formamide, 10 x SSC, 0.2% SDS) was added and the entire sample was loaded onto the slide. A cover glass was placed on the array and the unit was placed in a sealed, humidiﬁed hybridization chamber in a 42°C water bath for 16–20 h. Following hybridization, slides were washed in 2 x SSC/ 0.1% SDS, 1 x SSC/ 0.1% SDS, and 0.2 x SSC for 4 min each followed by a 1 min wash in 0.05 x SSC. Slides were then placed in 2-propanol and spin dried.

scan_protocol: Hybridized arrays were scanned at 10 μm resolution on a GenePix 4000A scanner (Axon Instruments Inc., Union City, CA, USA) at variable PMT voltage settings to obtain maximal signal intensities with <0.1% probe saturation.

data_processing: The scanned images were analyzed by GenePix Pro 6.0 software (Axon Instruments Inc., Union City, CA, USA). The ratios of the sample intensity to the reference red/green intensity for all targets were determined, and ratio normalizations were performed to normalize the center of ratio distribution to 1.0.

organism: Bambusa oldhamii

source_name: the middle region of etiolated shoots

label_protocol: 40 μg reference RNA was labeled with Cy5 using Superscript II Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA). The samples were incubated at 42°C for 60 min.

extract_protocol: Total RNA was extracted from bamboo samples using the RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instructions.

tag: bamboo sample

value: etiolated shoots that had not yet emerged from the ground

tag: tissue part

value: middle region

tag: average shoot height

source_name: the middle region of green shoots

label_protocol: 20 μg of sample RNA was labeled with Cy3 using Superscript II Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA). The samples were incubated at 42°C for 60 min.

value: green shoots.


title: Bambusa_oldhamii_wa

source_name: the culm base of etiolated shoots

value: culm region


title: Bambusa_oldhamii_100a

source_name: the culm base of green shoots


title: MCF7_control72h_EtOh6h_1

description:
Sample name: MP1
C_EtOH

source_name: MCF7 cells, 72h no treatment, 6h EtOh treatment, rep 1


title: Bambusa_oldhamii_wc

source_name: the top region of etiolated shoots

value: top region


title: A098-FU-Low dose

description: SAMPLE 275

source_name: FU-Low dose

tag: disease status

value: Vietnamese dengue patients

tag: treated with

tag: sample collection time

value: follow up; 1 month after illness-onset

value: blood

tag: patient id


title: A099-POST-High dose

description: SAMPLE 277

source_name: POST-High dose

value: high-dose (2mg/kg) of prednisolone

value: post-treatment


title: 1788-00

value: Neg

tag: gender


title: Bambusa_oldhamii_100c

source_name: the top region of green shoots


title: A007-POST-Low dose

description: SAMPLE 274


title: A099-PRE-High dose

description: SAMPLE 276

source_name: PRE-High dose

value: pre-treatment


title: worker/queen_brain_L4

city: Alfenas

first: Joseana

last: Vieira

state: Minas Gerais

address: Rua Gabriel Monteiro da Silva, 700

country: Brazil

institute: Unifal-MG

description: Analysis used RNA from brain of workers at fourth instar larvae as a control to compare with RNA provenient from brain of queens at fourth instar larvae.

hyb_protocol: For hybridization, probes [in 40µL of hybridization solution (0.98mL of formamide, 0.98mL SSC 20X, 39.2µLSDS 10%)] were pre-heated at 55°C during at 3 min and placed on microarrays under lifter-slip cover glasses (22x60, 31.25µL). Microarrays slides were placed in single slide hybridization chambers which were incubated in a water bath for hybridization for 22h, at 42°C. Washing procedure included twice the following steps: SSC 2X, SDS 0,1%; SSC 0,5X, SDS 0,01%; SSC 2X; SSC 0,1X; deionized water, shaking manually for 30s and for the last incubated in isopropanol before centrifuging for 3min at 2000rpm.

scan_protocol: Slides were scanned by using Axon GenePix 4000B at default parameters. For images quantitation we used ScanAlyze 2.35 (http://rana.lbl.gov/EisenSoftware.htm) with default parameters.

data_processing:
Background correction was performed in a manner we could avoid the correction of negative or zero intensities (offset correction) by adding to the background-corrected intensities a positive constant (=50). It restrains spurious variation in log-ratios, particularly at low intensity spots. The “print-tip loess” normalization was used to correct for within-array dye and spatial effects and single channel normalization was used to facilitate comparison between arrays. After normalization we determined a log2 ratio (Queen´s sample intensity/Worker´s sample intensity), for each probe on each array. The fold-change in expression and its standard error for each gene were calculated by fitting a linear regression to the normalized expression data. A Bayesian smoothing procedure was used to shrink the estimated standard errors, with which we calculated the moderated t-statistic for each gene.
The data in the sample data table were combined from two replicates by average.

organism: Apis mellifera

source_name: brain of Apis mellifera worker at fourth instar larvae

label_protocol: RNA amplification (from 1μg of total RNA) and probe synthesis (from 10μg of amplified RNA) were done with and according to Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion).

growth_protocol: Bees were obtained from the Experimental Apiary of the University of São Paulo at Ribeirão Preto.

extract_protocol: Total RNA was extracted using GenElute™ Mammalian Total RNA Kit (Sigma) solution (Invitrogen) following Invitrogen’s protocol and purified using RNeasy Mini Kit (QIAGEN).

treatment_protocol: workers and queens were reared under natural conditions.

tag: developmental stages

value: fourth instar larvae

tag: bee type

value: worker

value: brain

source_name: brain of Apis mellifera queen at fourth instar larvae

value: queen


title: A202-P6

description: Sample 4

source_name: Genomic DNA from tumor A202 cells

tag: strain background

value: C57BL/6J x SJL/J

tag: genotype/variation

value: P0-GGFβ3 transgenic

tag: cell type

value: malignant peripheral nerve sheath tumor (MPNST) cells

source_name: Non-neoplastic Schwann cells

tag: strain

value: wild-type

value: Non-neoplastic Schwann cells


title: A099-FU-High dose

description: SAMPLE 278

source_name: FU-High dose

tag: tissue


title: A007-PRE-Low dose

description: SAMPLE 273

source_name: PRE-Low dose

value: low-dose (0.5mg/kg) of prednisolone


title: Rat Muscle 1D 21%

city: Urbana

first: Mark

middle: Robert

last: Band

state: IL

address: 1201 W. Gregory Dr

department: Biotechnology

institute: University of Illinois

hyb_protocol: Agilent hybridization protocol

scan_protocol: Axon 4000B GenePix 6.1

data_processing: Lowess background corrected using the Bioconductor program Limma.

organism: Rattus norvegicus

source_name: Rat Muscle 21% oxygen

label_protocol: Agilent Low input  labeling kit

extract_protocol: RNA isolated with Trizol

value: muscle


title: A100-FU-Low dose

description: SAMPLE 281

value: Vietnamese dengue patients

value: follow up; 1 month after illness-onset


title: Rat Muscle 1A 21%


title: A002-FU-Placebo

description: SAMPLE 271

source_name: FU-Placebo

value: placebo

value: blood


title: 1057-97

source_name: Mucoepidermoid carcinoma

tag: fusion status

value: Pos

tag: grade

value: Low Grade

source_name: Normal tissue

value: reference

value: F


title: Rat Muscle 3A 21%


title: 131-93

value: High Grade

tag: sample type

value: M


title: CG1049

value: Neg


title: 1-93


title: Rat Brain 1A_21%

source_name: Rat Brain 21% oxygen

value: brain


title: Rat Muscle 1D 6%

source_name: Rat Muscle 6% oxygen


title: CG874


title: Rat Brain 1C 21%


title: CG606


title: 1169-90


title: A002-POST-Placebo

description: SAMPLE 270

source_name: POST-Placebo

value: post-treatment


title: Rat Muscle 1B 6%


title: A549 PST 2

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

hyb_protocol: RNA was fragmented by metallic cleavage using manufacturar's protocol. Array lanes were blocked using ssDNA and subsequently samples were hybridized at 65oC for 17h. Array was washed with wash buffer with and without DNA. Finally array was dried.

scan_protocol: Arrays were scanned on Illumina iScan system.

data_processing: Initial data was extracted by gene-expression module of GenomeStudio version 2010.2. Data was analyzed by Genespring GX12.0 software.

source_name: A549 +PST

label_protocol: The product cDNA is converted into cRNA by T7 polymerase and labelled with Cy3 (labelled on cytosine) using Agilent kit.

growth_protocol: A549, KB and MCF-7 cells were collected when they attains 70% of cell growth. Removed the growth medium by aspiration and washed cells once with 2 ml of phosphate buffered saline. Washed the cells again with 1 ml of PBS-EDTA.  Trypsinized cells for 3-5 minutes in 0.5 ml of 0.25%  trypsin at 37°C. Diluted the cells with 1 ml of growth medium to inactivate the trypsin. Transferred 1.5 ml of the cell suspension to a 15 ml falcon tube and centrifuged at 2500 rpm for 10 min. Supernatent was discarded and pellet was transferred to fresh T25 tissue culture flask and added 5 ml fresh growth medium. Placed the cells in a 37°C incubator at 5% CO2 and monitored cell-density daily.

extract_protocol: Total RNA was extracted by Trizol method. RNA was cleaned up using RNeasy MinElute Cleanup Kit (Qiagen) and reverse transcribed.

treatment_protocol: Cells were treated with PST001 polysaccharide along with a control.

tag: cell line

value: Lung Cancer


title: A061-PRE-High dose

description: SAMPLE 269

value: high-dose (2mg/kg) of prednisolone

value: pre-treatment


title: CG1053


title: A046-FU-Low dose

description: SAMPLE 268

source_name: FU-Low dose

value: low-dose (0.5mg/kg) of prednisolone


title: Rat Brain 1D_21%


title: Rat Brain 1D 6%

source_name: Rat Brain 6% oxygen


title: Rat Brain 1A


title: Rat Brain 1B


title: CG579


title: A046-POST-Low dose

description: SAMPLE 267

source_name: POST-Low dose

value: Vietnamese dengue patients


title: A549 PST 1


title: A549 Control 1

source_name: A549 Control


title: A549 Control 2


title: MCF-7 PST 2

source_name: MCF-7 +PST

value: Breast Cancer


title: A032-FU-Low dose

description: SAMPLE 265

value: follow up; 1 month after illness-onset


title: MCF-7 PST 1


title: MCF-7 Control 2

source_name: MCF-7 Control


title: 538-93


title: A029-POST-High dose

description: SAMPLE 263

source_name: POST-High dose

value: blood


title: A149-PRE-High dose

description: SAMPLE 262

source_name: PRE-High dose


title: MCF-7 Control 1


title: KB PST 2

source_name: KB +PST

value: KB

value: Nasopharyngeal tumor


title: KB control 2

source_name: KB control


title: A147-FU-Low dose

description: SAMPLE 261


title: A029-FU-High dose

description: SAMPLE 264

source_name: FU-High dose


title: A034-PRE-Low dose

description: SAMPLE 266

source_name: PRE-Low dose


title: KB PST 1


title: A004-PRE-Low dose

description: SAMPLE 272


title: BMDM_LPS-2

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

hyb_protocol: Samples were hybridized to Agilent mouse 8X60k array (Agilent Technologies).

scan_protocol: The acquisition of array image was undertaken by using Agilent Scan Control and Agilent Feature Extraction 10.7 software.

data_processing: Raw data were analyzed using Partek Genomics Suite 6.4 and normalized by using RMA algorithm. Thresholds for selecting significant genes were set at >= 2-fold and FDR corrected p<0.05. Genes which met both criteria were considered as having significant changes.

source_name: bone marrow derived macrophages

label_protocol: RNA was amplified into cRNA and labeled with Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technologies).

growth_protocol: Bone marrow cells were plated on dish for 7 days in the presence of M-CSF or plated on endothelial monolayer for 7 days with HSC media.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Invitrogen). Integrity of the RNA was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Also, CA, USA) and purity/concentration was determined using a NanoDrop 8000 Spectrophotometer (Thermo Scientific, Wilminton, DE, USA).

treatment_protocol: BMDM were induced by LPS or IL4 for 24 hours.

tag: treatment

value: LPS

value: B6.Cg-Tg(CAG-DsRed*MST)1Nagy/J (Jackson stock #006051)


title: CC-1

source_name: bone marrow colony cells

value: endothelial cells


title: CC-2


title: A147-POST-Low dose

description: SAMPLE 260

label_protocol: RNA was amplified and labeled with biotin using Illumina TotalPrep 96 RNA amplification kit.

tag: disease status


title: BMDM_LPS-1


title: BMDM_IL4-1


title: A146-POST-High dose

description: SAMPLE 257

tag: treated with


title: A147-PRE-Low dose

description: SAMPLE 259

tag: sample collection time


title: CD25+ KP MCi

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

description: CD25+ KP MCi

hyb_protocol: 15 µg of each biotinylated cRNA preparation were fragmented and placed in a hybridization cocktail containing four biotinylated hybridization controls (BioB, BioC, BioD, and Cre). Samples were hybridized to individual Human TReg Chips for 16 hours at 42°C using a Lucidea Slidepro (Amersham Biosciences). After hybridisation the microarrays were washed as recommended by the manufacturer’s instructions (CodeLink Expression Bioarray System, Amersham Biosciences) and stained with Cy5-streptavidin (Amersham Biosciences).

scan_protocol: Fluorescent array images were collected for Cy5 with an arrayWorX fluorescent scanner (Applied Precision, USA) and image intensity data were extracted and analyzed with Imagene analysis software (v5.5.2, Biodiscovery).

data_processing: Spots of poor quality (flag=3) or signal intensities lower than the background intensity were excluded from further analysis. After background correction, data normalization was carried out as proposed by MWG. Briefly, signal intensities were normalized by dividing each signal by exp(median of ln[signal intensities of housekeeping genes]).

source_name: Blood

label_protocol: Quality and integrity of the total RNA isolated from 1-2x10^5 CD4+CD25+ and CD4+CD25- T cells was controlled by running all samples on an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany). Samples were prepared by applying a double-linear amplification method according to the Eberwine protocol and modified by Affymetrix. Briefly, the first round of RNA-amplification was performed without biotinylated nucleotides using the Promega P1300 RiboMax Kit for T7 amplification (Promega, Mannheim, Germany). After clean-up of the precipitated aRNA synthesis of second round, first-strand cDNA was done using random hexamers (Pharmacia, Freiburg, Germany). Subsequent second-strand cDNA was prepared like in the first round but integrating an additional RNAse H incubation step to digest the aRNA before annealing of the T7T23V primer. The second round of RNA amplification was performed as an in vitro transcription assay in the presence of biotinylated UTP using the GeneChip® Expression 3’-Amplification Reagents Kit for IVT Labeling (Affymetrix, Santa Clara, CA). The concentration of the obtained biotin-labelled cRNA was determined by UV absorbance and its quality as means of product length distribution was again checked using the Agilent Bioanalyzer.

growth_protocol: ex vivo

extract_protocol: Cells were lysed in RLT-buffer containing 1% beta-Mercaptoethanol. RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from freshly drawn blood by Ficoll density gradient centrifugation. For isolation of CD4+CD25+ regulatory and CD4+CD25- naive T cells, PBMCs were further separated using the regulatory human T cell isolation kit and an AutoMACS separation unit (Miltenyi Biotec).

tag: disease state

value: inactive Crohn's disease

value: CD4+CD25+ T cells


title: CD25+ HD MCi

description: CD25+ HD MCi


title: CD25+ aje A10

description: CD25+ aje A10

value: normal


title: CD25+ CP MCa

description: CD25+ CP MCa

value: active Crohn's disease


title: CD25+ SN MCi

description: CD25+ SN MCi


title: CD25+ WR MCa

description: CD25+ WR MCa


title: CD25+ UW MCa

description: CD25+ UW MCa


title: CD25+ aje A12

description: CD25+ aje A12


title: BMDM_IL4-2


title: CD25+ chu B1

description: CD25+ chu B1


title: BMDM-1

value: control media


title: CD25+ ikr C1

description: CD25+ ikr C1


title: CD25+ chu B2

description: CD25+ chu B2


title: BMDM-2


title: Rat Muscle 1A 6%

source_name: Rat Muscle 6% oxygen

value: muscle


title: A146-FU-High dose

city: Ho Chi Minh

first: Nguyen

address: 764 Vo Van Kiet

institute: Oxford University Clinical Research Unit

description: SAMPLE 258

data_processing: The array intensity values were extracted using GenomeStudio software (v.1.6.0, Illumina Inc., USA) and processed with GeneSpring (v.11.5, Agilent Technologies Inc., USA). First measurements having intensity values less than 5.0 were corrected to 5.0, and then all signals were normalized to the 80th percentile by dividing each value by the 80th percentile value; only genes that were confidently detected in at least 60% of samples in one of the three treatment groups were used for the analysis.

extract_protocol: RNA was extracted from blood using PAXgene Blood RNA kit (PreAnalytiX, Switzeland) as instructions of manufacturer.

value: high-dose (2mg/kg) of prednisolone

tag: patient id


title: CD25+ ikr C18

description: CD25+ ikr C18


title: A146-PRE-High dose

description: SAMPLE 256

value: pre-treatment


title: CD25+ khu 60

description: CD25+ khu 60


title: CD25+ khu 59

description: CD25+ khu 59


title: CD25+ ikr C2

description: CD25+ ikr C2


title: A143-POST-Placebo

description: SAMPLE 254

source_name: POST-Placebo

value: Vietnamese dengue patients

value: placebo

value: post-treatment


title: A142-FU-Low dose

description: SAMPLE 252

source_name: FU-Low dose

value: low-dose (0.5mg/kg) of prednisolone

value: follow up; 1 month after illness-onset

value: blood


title: CD25+ rog 52

description: CD25+ rog 52


title: CD25+ mpk B28

description: CD25+ mpk B28


title: CD25+ mpk B26

description: CD25+ mpk B26


title: CD25+ mpk B27

description: CD25+ mpk B27


title: CD25+ lgrFCS A38

description: CD25+ lgrFCS A38


title: CD25+ lgrFCS 71

description: CD25+ lgrFCS 71


title: CD25+ rog 53

description: CD25+ rog 53


title: CD25+ rog 54

description: CD25+ rog 54


title: A143-FU-Placebo

description: SAMPLE 255

source_name: FU-Placebo


title: A143-PRE-Placebo

description: SAMPLE 253

source_name: PRE-Placebo


title: CD25+ lgrFCS 72

description: CD25+ lgrFCS 72


title: CD25+ spf 81

description: CD25+ spf 81


title: CD25+ spf 82

description: CD25+ spf 82


title: A142-POST-Low dose

description: SAMPLE 251

source_name: POST-Low dose


title: A024-PRE-Low dose

description: SAMPLE 250


title: KB control 1

value: KB

value: Nasopharyngeal tumor


title: CD25+ spf A34

description: CD25+ spf A34


title: A010-POST-Placebo

description: SAMPLE 246


title: A014-FU-Low dose

description: SAMPLE 248


title: A014-POST-Low dose

description: SAMPLE 247


title: A022-FU-High dose

description: SAMPLE 249


title: A010-PRE-Placebo

description: SAMPLE 245


title: A006-FU-Low dose

description: SAMPLE 244


title: CD25+ suk 69

description: CD25+ suk 69


title: CD25+ ukr C12

description: CD25+ ukr C12


title: CD25+ suk B50

description: CD25+ suk B50


title: CD25+ suk 68

description: CD25+ suk 68


title: CD25+ xyz C6

description: CD25+ xyz C6


title: CD25+ ukr C14

description: CD25+ ukr C14


title: CD25+ xyz C4

description: CD25+ xyz C4


title: A002-PRE-Placebo

description: SAMPLE 242


title: A006-POST-Low dose

description: SAMPLE 243


title: A046-PRE-Low dose

description: SAMPLE 240


title: A044-FU-Placebo

description: SAMPLE 239


title: A075-FU-Low dose

description: SAMPLE 237


title: DG+AICAR-2

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48804 probes on the Human-6 beadChip.

hyb_protocol: Labeled, amplified material (1,500 ng per array) was hybridized to the Illumina Human-6 BeadChip (48K) according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA). Array signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the BeadChip manual.

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. To export to a data matrix, Sample Gene Profile option of this software was used.

source_name: SK4 treated with 2-deoxy-glucose (4mM) and AICAR (2mM) for 12 hrs

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer's protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

tag: tissue type

value: esophageal cancer


title: A001-FU-Placebo

last: Tien

description: SAMPLE 241


title: AICAR-4

source_name: SK4 treated with AICAR (2mM) for 12 hrs


title: MET-2

source_name: SK4 treated with Metformin (5mM) for 12 hrs


title: AICAR-3


title: DG+AICAR-1


title: A073-POST-Placebo

description: SAMPLE 233


title: DG+MET-4

source_name: SK4 treated with 2-deoxy-glucose (4mM) and Metformin (5mM) for 12 hrs


title: DG+MET-1


title: MET-1


title: DG+MET-2


title: DG+MET-3


title: A075-PRE-Low dose

description: SAMPLE 235


title: DG+AICAR-4


title: DG+AICAR-3


title: MET-3


title: A073-FU-Placebo

description: SAMPLE 234


title: AICAR-2


title: MET-4


title: A075-POST-Low dose

description: SAMPLE 236


title: A071-FU-Low dose

description: SAMPLE 231


title: AICAR-1


title: A073-PRE-Placebo

description: SAMPLE 232


title: A076-PRE-High dose

description: SAMPLE 238

source_name: PRE-High dose


title: CD25+ chu B16

description: CD25+ chu B16


title: 2DG-4

source_name: SK4 treated with 2-deoxy-glucose (4mM) for 12 hrs


title: A071-POST-Low dose

description: SAMPLE 230


title: A069-POST-Placebo

description: SAMPLE 227


title: 2DG-1


title: Control-2

source_name: SK4 control, no-treatment group


title: 2DG-3


title: Control-4


title: Control-1


title: A069-FU-Placebo

description: SAMPLE 228


title: 2DG-2


title: A069-PRE-Placebo

description: SAMPLE 226


title: A071-PRE-Low dose

description: SAMPLE 229

source_name: PRE-Low dose


title: 20070918_A.2.RhoL (GTPase) RNAi 05/12/2007

city: Cambridge

first: Michael

last: Baym

state: MA

address: MIT 32-G572 / 32 Vassar St.

department: Mathematics

institute: MIT

description:
20070918_A_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

hyb_protocol: The aRNA mixtures were fragmented in a solution of 40 mM Tris-Acetate pH8.1, 100 mM KOAc, 30 mM MgOAc) at 95°C for 20 minutes, then placed on ice. Hybridization to Combimatrix CustomArrayä microarrays was performed as described by the manufacturer at 45°C for 18 hours under gentle rotation in a Fisher Biotech Hybridization Incubator under gentle rotation. Following hybridization and washing, arrays were blocked in 2XPBS, 0.1% Tween-20, 1% Acetylated BSA (Sigma) for 15 minutes at room temperature (RT), and subsequently incubated with Streptavidin-Alexa Fluor 647 (Molecular Probes) at final concentration of 1 μg/ml in the blocking solution for 30 minutes at RT while protected from light. Two subsequent washing steps were then performed at RT for 5 minutes using 2X PBS, 0.1% Tween-20 followed by 2 rounds of washing using 2X PBS with no detergent.

scan_protocol: Arrays were scanned using the Axon Genepix 4000B scanner.

data_processing: Median expression was extracted, spatial artifacts were removed by iterative surface-fit, features were averaged by probe sequence, and Loess-normalized with span=0.4.

organism: Drosophila melanogaster

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RhoL RNAi

label_protocol: The Ambion MegaScript Kit was used to produce biotin-labeled antisense RNA (aRNA) by combining Biotin-11-UTP (PerkinElmer) and Biotin-CTP (PerkinElmer) with unlabelled UTP and CTP in a molar ratio of 1:3. Biotin-labeled aRNA was purified using the Qiagen RNeasy kit.

growth_protocol: Drosophila S2R+ cells were cultured in Schneider’s media (Sigma), supplemented with 10% Fetal Bovine Serum (SAFC Biosciences), and Penicillin-Streptomycin (Gibco).

extract_protocol: Total RNA was isolated using TRIzol Reagent (Invitrogen) as directed by the manufacturer. Double-stranded cDNA incorporating a T7 RNA Polymerase promoter site was prepared from total RNA using the Roche Applied Sciences Microarray cDNA Synthesis Kit and purified using the Qiagen QIAquick purification kit.

treatment_protocol: RNAi experiments were performed by transfecting S2R+ cells with specific dsRNAs in combination with actin-GAL4 and UAS-GFP plasmids. Alternatively, cells were transfected with actin-GAL4 and UAS-GFP plasmids in addition to plasmids encoding activated forms of Rho-family GTPases, RhoGEFs, or RhoGAPs. All transfections were performed using Effectene Reagent (Qiagen). Following plasmid/RNAi transfection, cells were incubated for 5 days at room temperature. S2R+ cells were transfected in batches of 4-6 over the course of several months.

tag: cell line derivation

value: late stage embryos


title: Control-3


title: 20070918_A.1.RhoGAP1A RNAi 05/12/2007

description:
20070918_A_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RhoGAP1A RNAi


title: 20070907_B.3.sif (RhoGEF) *AUG7_07 sample

description:
20070907_B_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and sif RNAi


title: 20070907_B.4.RacGAP50C (RhoGAP) *AUG7_07 sample

description:
20070907_B_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RacGAP50C RNAi


title: 20070918_A.4.GFP May 12 2007

description:
20070918_A_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP


title: 20070918_A.3.RhoBTB (GTPase) RNAi 05/12/2007

description:
20070918_A_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RhoBTB RNAi


title: 20070907_B.2.pbl (RhoGEF) *AUG 7_07 sample

description:
20070907_B_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and pbl RNAi


title: multiple myeloma_t(11;14)(q13;q32)_M105

city: Kuala Lumpur

first: Ivyna

middle: PN

last: Bong

state: Kuala Lumpur

address: Jalan Pahang

department: Cancer Research Centre

country: Malaysia

institute: Institute for Medical Research

description: Multiple myeloma derived from newly diagnosed patients with translocation in BCL1/JH t(11;14)(q13;q32)

hyb_protocol: Hybridization procedure was performed according to Agilent manufacturer instruction. Test and reference samples were mixed and hybridization buffer (Agilent oligo aCGH hybridization kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After 40 hours of hybridization at 65°C, slides were washed following Wash Procedure B according to Agilent manufacturer recommendations.

scan_protocol: Arrays were scanned on G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and normalization. Microarray data were then analyzed with ADM2 algorithm, bin size 10 and threshold 6.0 by using DNA Analytics Software (v4.0).

source_name: Cytogenetically fixed myeloma cells

label_protocol: 1.5 µg each of genomic DNAs from test and reference sample were fragmented at 95°C for 10 minutes and then labeled with ULS-Cy3 or ULS-Cy5 and followed by removal of non-reacted Cy-ULS by Agilent KREApure column.

extract_protocol: Genomic DNAs were extracted from myeloma cells following standard protocol provided in Qiagen DNA mini kit.

tag: gender

value: Male

tag: age (at diagnosis)

tag: race

value: Malay

tag: cytogenetics analysis

value: No chromosomal abnormality

value: multiple myeloma

value: myeloma cells

source_name: Genomic DNAs pooled from 10 matched healthy individuals, labeled with Cy3

tag: age (average)

value: Peripheral blood

value: healthy


title: A068-FU-Placebo

description: SAMPLE 225

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

source_name: FU-Placebo

value: Vietnamese dengue patients

tag: tissue


title: A068-POST-Placebo

description: SAMPLE 224

source_name: POST-Placebo

value: placebo


title: A068-PRE-Placebo

description: SAMPLE 223

source_name: PRE-Placebo

value: pre-treatment


title: 20070907_B.1.GFP August 7 2007

description:
20070907_B_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: multiple myeloma_t(11;14)(q13;q32)_M55

value: Indian


title: multiple myeloma_t(11;14)(q13;q32)_M101

value: Female

value: Chinese

value: Few chromosome spread, not suitable for cytogenetic analysis


title: 20070907_A.4.Rac 1 (Amplicon #1 Rac1/Rac2) *AUG18_07 sample

description:
20070907_A_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and Rac1 RNAi


title: 20070907_A.3.Rac 2 (no Rac1) *AUG18_07 sample

description:
20070907_A_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and Rac2 RNAi


title: 20070907_A.2.Rac 1 (Amplicon #2 Rac1 only) *AUG18_07 sample

description:
20070907_A_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: Brucella melitensis delta prlR mutant strain OD 600nm 0.3 rep3

city: NAMUR

first: LETESSON

middle: Jean-Jacques

last: marie

address: 61 rue de Bruxelles

country: Belgium

institute: University of Namur

description: This sample is of Brucella melitensis 16M delta prlR mutant. It is the third of three mutant strain biological replicates used in this experiment, each from separate cultures.

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Brucella melitensis bv. 1 str. 16M

source_name: Brucella melitensis delta prlR mutant strain ; OD 600nm : 0.3

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

growth_protocol:
Brucella melitensis 16M wild type strain was grown to early-log phase (O.D.600nm 0.3)  with shaking at 37°C in rich media 2YT (10% yeast extract, 16g l-1 peptone, NaCl 5g l-1) from an initial optical density of 0.05.
Brucella melitensis delta prlR mutant strain was grown to early-log phase (O.D.600nm 0.3)  with shaking at 37°C in rich media 2YT (10% yeast extract, 16g l-1 peptone, NaCl 5g l-1) from an initial optical density of 0.05.

extract_protocol: Total RNA were extracted from wt and ∆prlR (all cultured in triplicate) as following: 45 ml of culture (OD600 of 0.75) were centrifuged at 3500 rpm for 15 min. Bacterial pellets were resuspended in 100 µl SDS 10% and 20 µl proteinase K (20 mg ml-1) and incubated at 37°C with shaking for 1h. Five milliliters of TRIzol® Reagent (Invitrogen) were added and suspensions were vigorously shacked. After 10 min of incubation at 65°C, 1 ml chloroform was added to the suspensions and the mixes were shaked and incubated at room temperature for 5-10 min. Samples were centrifuged at 14.000 rpm for 15 min at 4°C. Then, 2.5 ml propan-2-ol were added to the aqueous phases and samples were stored overnight at -20°C. After centrifugation for 30 min at 14.000 rpm at 4°C, pellets were washed with 75% ethanol RNase free. Supernatants were discarded and pellets were dried 15 min at room temperature. Total RNA samples were resuspended in 100 µl RNase free water, incubated 10 min at 55°C and stored at -80°C. The integrity of the RNA and the absence of DNA were checked by gel electrophoresis.

tag: genotype

value: Deletion mutant prlR

tag: phenotype

value: acapsular


title: 20070824_A.3.Rac 1 (Amplicon #2 Rac1 only)

description:
20070824_A_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

tag: cell line

value: late stage embryos


title: 20070824_A.4.Rac 2 (no Rac1)

description:
20070824_A_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 20070824_A.2.Rac 1 (Amplicon #1 Rac1/Rac2)

description:
20070824_A_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 20070824_A.1.GFP August 17 2007

description:
20070824_A_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: multiple myeloma_t(11;14)(q13;q32)_M96

value: Male

value: Chromosome spread not available. Not suitable for cytogenetics analysis


title: multiple myeloma_t(11;14)(q13;q32)_M39


title: multiple myeloma_t(11;14)(q13;q32)_M41

value: No chromosomal abnormality


title: 20070814_B.3.RacGAP50C (RhoGAP)

description:
20070814_B_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 20070814_B.1.pbl (RhoGEF)

description:
20070814_B_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 20070814_B.2.sif (RhoGEF)

description:
20070814_B_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 20070814_A.4.GFP August 7 2007

description:
20070814_A_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: Brucella melitensis delta prlR mutant strain OD 600nm 0.3 rep2

description: This sample is of Brucella melitensis 16M delta prlR mutant. It is the second of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: multiple myeloma_t(11;14)(q13;q32)_M98

value: Malay

value: multiple myeloma


title: A067-POST-Low dose

description: SAMPLE 221

source_name: POST-Low dose

value: low-dose (0.5mg/kg) of prednisolone

value: post-treatment

value: blood


title: Brucella melitensis delta prlR mutant strain OD 600nm 0.3 rep1

description: This sample is of Brucella melitensis 16M delta prlR mutant. It is the first of three mutant strain biological replicates used in this experiment, each from separate cultures.

value: do not aggregate in 2YT 400mM


title: Brucella melitensis 16M wild-type OD 600nm 0.3 rep2

description: This sample is of wild-type Brucella melitensis 16M. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Brucella melitensis 16M wild-type; OD 600nm : 0.3

value: Wild-type

value: normal


title: Brucella melitensis 16M wild-type OD 600nm 0.3 rep3

description: This sample is of wild-type Brucella melitensis 16M. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Brucella melitensis 16M wild-type ; OD 600nm : 0.3


title: A067-PRE-Low dose

description: SAMPLE 220

source_name: PRE-Low dose

value: Vietnamese dengue patients

value: pre-treatment


title: multiple myeloma_t(11;14)(q13;q32)_M07

description: Multiple myeloma derived from newly diagnosed patients with translocation in BCL1/JH t(11;14)(q13;q32)

value: myeloma cells

value: Peripheral blood

value: healthy


title: A067-FU-Low dose

description: SAMPLE 222

source_name: FU-Low dose

value: follow up; 1 month after illness-onset


title: A044-POST-Placebo

description: SAMPLE 216

value: placebo


title: A054-POST-Low dose

description: SAMPLE 217


title: A054-FU-Low dose

description: SAMPLE 218


title: 20070814_A.2.RhoGEF4

description:
20070814_A_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RhoGEF4 RNAi

value: late stage embryos


title: A064-FU-Placebo

description: SAMPLE 219


title: 20070814_A.3.RhoGEF2

description:
20070814_A_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RhoGEF2 RNAi


title: 20070814_A.1.p190RhoGAP

description:
20070814_A_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and p190RhoGAP RNAi


title: Brucella melitensis 16M wild-type OD 600nm 0.3 rep1

description: This sample is of wild-type Brucella melitensis 16M. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.

value: aggregate in 2YT 400mM


title: 20070801_B.3.MTL (GTPase) RNAi 07/13/2007

description:
20070801_B_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and MTL RNAi


title: 20070801_B.4.GFP July 13 2007

description:
20070801_B_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP


title: 20070801_B.1.CdGAPr (GAP) RNAi 07/13/2007

description:
20070801_B_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and CdGAPr RNAi


title: 20070801_B.2.CG3799 RNAi 07/13/2007

description:
20070801_B_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and CG3799 RNAi


title: 20070801_A.4.CdGAPr (GAP) RNAi 07/13/2007

description:
20070801_A_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 20070801_A.3.CG3799 RNAi 07/13/2007

description:
20070801_A_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: 20070628_B.4.RacF28L (ACTIVATED Rac) 06/25/2007

description:
20070628_B_4
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and plasmid encoding RacF28L (constitutively active)


title: 20070801_A.1.GFP July 13 2007

description:
20070801_A_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: MEF_p53(246/-)_transformed_rep3

city: Singapore

first: Kanaga

last: Sabapathy

state: Singapore

address: 11 Hospital Drive

country: Singapore

institute: National Cancer Centre Singapore

description: 193P 2359-9ER.CEL

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials as per manufactorere's instructions

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Partek software (v.6.5). Quantile normalization uisng GC-RMS method, gene level expression were summarized from the quantile normalized data.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps

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

extract_protocol: Early passage primary MEFs and the coresponding E1A/Ras transformed clones were used.  Total RNA was extracted from all samples using Trizol and further purified by RNeasy RNA extraction kit (Qiagen).  cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Nalgene).

tag: strain background

value: C57BL6/129 hybrid

tag: genotype/variation

tag: cell type

value: Mouse Embryonic Fibroblasts

tag: transformed with

tag: state

value: transformed


title: 20070628_B.2.RhoF30L (ACTIVATED RHO) 06/25/2007

description:
20070628_B_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and plasmid encoding RhoF30L (constitutively active)


title: 20070628_B.3.Cdc42Y32A (ACTIVATED CDC42) 06/25/2007

description:
20070628_B_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and plasmid encoding Cdc42Y32A (constitutively active)


title: 20070628_B.1.GFP June 25 2007

description:
20070628_B_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.


title: MEF_p53(246/-)_transformed_rep2

description: 193P 2336-10ER.CEL


title: A097-FU-High dose

description: SAMPLE 212

source_name: FU-High dose

tag: disease status

tag: treated with

value: high-dose (2mg/kg) of prednisolone

tag: sample collection time

tag: patient id


title: MEF_p53(246/-)_primary_rep3

description: 193P 2359-9.CEL

value: primary


title: A044-PRE-Placebo

description: SAMPLE 215

source_name: PRE-Placebo

value: blood


title: 20070801_A.2.MTL (GTPase) RNAi 07/13/2007

description:
20070801_A_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

tag: cell line derivation


title: MEF_p53(246/-)_transformed_rep1

description: 193P 2336-4ER.CEL


title: MEF_p53(246/-)_primary_rep2

description: 193P 2336-10.CEL


title: A098-POST-Low dose

description: SAMPLE 214

source_name: POST-Low dose

value: low-dose (0.5mg/kg) of prednisolone

value: post-treatment


title: 20070628_A.3.RhoBTB (GTPase) RNAi 05/12/2007

description:
20070628_A_3
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RhoBTB RNAi


title: A097-PRE-High dose

description: SAMPLE 210

source_name: PRE-High dose

value: Vietnamese dengue patients


title: 20070628_A.2.RhoL (GTPase) RNAi 05/12/2007

description:
20070628_A_2
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.

source_name: Drosophila S2R+ cells transfected with act-GAL4, UAS-GFP and RhoL RNAi


title: 20070628_A.1.GFP May 12 2007

description:
20070628_A_1
S2R+ cells have been repeatedly passaged in the Perrimon laboratory for several years.