title: PhosphateStress_stressed_rep3

status: Public on Mar 31 2012

type: RNA

city: Freiburg

first: Gregor

middle: Josef

last: Gierga

department: Institut of Biology III -Genetics

country: Germany

institute: University of Freiburg

hyb_protocol: The microarrays were hybridized with 3ug of labelled and fragmented RNA. We followed the ElectraSenseTM 4X2K/12K Microarrays: Hybridization and Electrochemical Detection (PTL021) protocol. In detail: Microarrays were pre-hybridized with nuclease-free water for 10 min at 65°C in a hybridization oven with slow rotation. Next, the water in the hybridization chamber was replaced by careful pipetting (all pipetting steps were executed carefully) with Pre-hybridization Solution (6XSSPE, 0.05% Tween-20, 20mM EDTA final concentration, 5X Denhardt's solution, 0.05% SDS, 100 ng/ul Salmon sperm DNA, in aqueous solution) and incubated for 30 min at 45°C in the incubator with slow rotation. In the meantime, the Hybridization Solution was prepared, consisting of 3ug of labelled and fragmented RNA, 6XSSPE, 0.05% Tween-20, 20 mM EDTA (f.c.), 25% DI Formamide, 100 ng/ul Salmon sperm DNA and 0.04% SDS in aqueous solution. The Hybridization Solution was denatured at 95°C for 3 min, then cooled for 1 min on ice and quickly spun down for collecting of the condensate. The Hybridization Solution replaced the Pre-hybridization Solution and was incubated with the microarray for 16 h at 45 °C with gentle rotating. The washing steps after hybridization were the following. The Hybridization solution was removed of the hybridization chamber. Pre-heated (45°C) 3X SSPET Wash Solution (3XSSPE, 0.05% Tween-20) was used to rinse the chamber once and a new aliquot was used to fill the hybridization chamber for incubation with the microarray for 5 min at 45°C. Then, the 3X SSPET Wash solution was removed and 0.5X SSPET Wash solution (0.5XSSPE, 0.05% Tween-20) used first to rinse the chamber and then, with new solution, to fill the chamber and incubate for 1 min at room temperature. Next, PBST Wash Solution (2xPBS, 0.1% Tween-20) was used to rinse the chamber once and then to fill the chamber and incubate the microarray at room temperature for at least 2 min. The PBST Wash Solution was retained in the chamber until Post-hybridization Labelling Procedure started (maximum of 10 min). First the ElectraSenseTM detection kit was warmed-up to room temperature, then the PBST Wash Solution was removed from the hybridization chamber. ElectraSenseTM Blocking Buffer was added to the hybridization chamber and was incubated with the array for 15 min at room temperature. Then ElectraSenseTM blocking buffer was removed and ElectraSenseTM Biotin Labelling Solution was added to the chamber and the microarray was incubated for 30 min at room temperature. Next ElectrSenseTM Biotin Labelling Solution was removed and ElectraSenseTM Biotin Wash Solution was used to rinse the chamber once and new ElectraSenseTM Biotin Wash Solution was taken to fill the chamber and incubate the microarray for 5 min at room temperature. The last step was, rinsing and incubation of the microarray with ElectraSenseTM Biotin Wash Solution was repeated two more times for a total of three washes. The ElectraSenseTM Biotin Wash Solution was retained in the hybridization chamber until preparation of the microarray for electrochemical detection (max. 10 min). Prior to continuing with the next steps, ElectraSenseTM TMB Substrate Solution was pre-warmed to room temperature. ElectraSenseTM Biotin Wash Solution was removed from the hybridization chamber. The chamber was rinsed once with ElectraSenseTM TMB Rinse Solution and removed immediately. The chamber was directly filled with ElectraSenseTM Substrate Solution. The array was immediately scanned (during the next minute) with the ElectraSenseTM Reader using ElectraSenseTM Application Software.

scan_protocol: The Scan Process with the ElectraSenseTM Reader is an automated process. The ElectraSenseTM Reader measures the electron flux generated by the oxidation of TMB (3,3',5,5'-tetramethylbenzidene) for each individual spot. The provided ElectraSenseTM Application Software finally creates a microarray image in grey scale for visualization purposes additionally to a list with values for each feature.

data_processing: Data processing was done with Genespring GX 10.0.2 software. The signal intensities of all experiments were quantile normalized.

label: biotin

molecule: total RNA

organism: Synechococcus sp. WH 7803

label_protocol: 4 ug of DNase treated total RNA was labelled directly with Kreatech ULSTM labelling kit for CombiMatrix arrays with Biotin-ULS according to the manufacturer's protocol, which can be found on http://www.kreatech.com. The RNA fragmentation after labelling was performed as advised using the Ambion aRNA fragmentation reactions following the manufacturer's instructions.

growth_protocol: Bacteria were cultivated in artificial sea water using cell culture flasks. The standard growth conditions were 23°C and 30 μmol quanta m−2s−1 . Experiments were performed with exponentially growing cultures.

extract_protocol: The cells were harvested by rapid filtering and the filter with the cells were transfered into RNA resuspension buffer (10 mM sodium acetate, 200 mM sucrose and 5 mM EDTA) quick-frozen in liquid nitrogen and immediately stored at -80°C until extraction. The frozen cell pellets were thawed under addition of 3 vol Z6 RNA extraction buffer for 60 min at room temperature with gentle shaking. Acidic phenol was added (0.5 vol) and the cells were incubated for 15 min at 60°C water bath with occasional shaking by hand. This step was followed by phase extraction with 0.5 vol of chloroform:isoamylalcohol (24:1). After shaking the phases were separated by centrifugation for 5 min. The aqueous phase was extracted then first with 1 vol phenol:chloroform:isoamylalcohol (25:24:1) and then with 1 vol chloroform:isoamylalcohol (24:1). Finally, the aqueous phase was transferred into a fresh tube, and the RNA was precipitated with 1 vol isopropanol at - 20 °C overnight. After centrifugation at 13,000 g for 30 min and 4 °C the pellet was washed with 70 % ethanol, centrifuged at 13,000g for 5 min and 4 °C. The liquid was removed and the pellet dried for about 10 min and dissolved in water.

treatment_protocol: For every growth condition, the experiment started with the dilution of an exponentially growing culture to a titre of 1 times 107 cells per ml. Regarding High Light stress, the culture was moved from 30 μmol quanta m−2s−1 to 280 μmol quanta m−2s−1 for one hour. Cold stress was achieved by moving the culture flask to a water tank with 10 °C cold running water for two hours. To expose the culture to iron stress or phosphate stress, the cells were spun twice for 10 minutes at room temperature at 10000 g. Each time, the media was removed and the cells were resuspended in the corresponding depleted media. For iron stress, media without FeCl3 • 6H2O and in the case of phosphate stress, media without NaH2PO4 • H2O was prepared, representing the sole iron or phosphate source in the media. RNA from iron starved cells was extracted 12 h after initiating stress conditions. Cyanobacteria growing without added phosphate were harvested after 24 h.

tag: stress condition

value: PhosphateStress

tag: group

value: stressed


title: PhosphateStress_stressed_rep2


title: IronStress_stressed_rep3

value: IronStress


title: PhosphateStress_Control_rep3

value: control


title: IronStress_stressed_rep2


title: PhosphateStress_Control_rep2


title: PhosphateStress_stressed_rep1


title: IronStress_stressed_rep1


title: PhosphateStress_Control_rep1


title: HighLight_Control_rep3

value: HighLight


title: HighLight_Control_rep2


title: IronStress_Control_rep3


title: HighLight_Control_rep1


title: IronStress_Control_rep1


title: ColdStress_stressed_rep3

value: ColdStress


title: HighLight_stressed_rep3


title: ColdStress_Control_rep1


title: ColdStress_Control_rep2


title: ColdStress_stressed_rep2


title: ColdStress_Control_rep3


title: IronStress_Control_rep2


title: HighLight_stressed_rep1


title: Pool_slide3_normal

city: Tampere

first: Eeva

middle: M

last: Laurila

address: Biokatu 6-8

department: Institute of Biomedical Technology

country: Finland

institute: University of Tampere

description: Pool 3

hyb_protocol: Hybridization was done using Agilent miRNA Labeling Reagent and Hybridization Kit, according to manufacturer's protocol. Shortly, samples were denatured and hybridization to Human 8x15K miRNA Microarrays (v1) was allowed to occur at 55°C for 20 hours in a rotating Agilent hybridization oven (speed 20 rpm). Slides were washed in GE Wash Buffer 1 (5min RT) and GE Wash Buffer 2 (5min 37°C) and scanned immediately.

scan_protocol: Arrays were scanned by using Agilent DNA microarray scanner and default one color scan setting for 8x15k array slides.

data_processing: The miRNA array images were transformed to spot intensity data with Agilent Feature Extraction Software (version 9.5.1.1) using default parameters (miRNA-v1_95_May07 protocol, 016436_D_20070426 grid). Control spots, spots which were flagged as saturated, non-uniformity outliers, population outliers were excluded.

organism: Homo sapiens

source_name: Pool of four normal pancreatic RNA samples

label_protocol: Cy3 labeling was done using Agilent miRNA Labeling Reagent and Hybridization Kit, according to manufacturer's protocol. Shortly, 100 ng of total RNA was dephosphorylated, denatured, and labeled with pCp-Cy3 dye. Labeled RNA was purified using the Micro BioSpin 6 columns.

growth_protocol: All cell lines were cultured according to cell line providers' instructions.

extract_protocol: Standard Trizol extraction of total RNA was performed. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer.

tag: disease state

value: normal pancreas

tag: normal pancreas pool for between-slide normalization


title: Clontech_normal

description: Clontech pancreas RNA

source_name: Normal pancreatic RNA

tag: normal pancreas vendor

value: Clontech


title: Pool_slide1_normal

description: Pool 1


title: HighLight_stressed_rep2


title: ColdStress_stressed_rep1


title: Pool_slide2_normal

description: Pool 2


title: Biochain-5_normal

description: Biochain-5 pancreas RNA


title: Biochain-1_normal

description: Biochain-1 pancreas RNA


title: Ambion_normal

description: Ambion pancreas RNA

value: Ambion


title: SW1990_cancer

source_name: Pancreatic cancer

value: pancreatic cancer

tag: cell line

value: pancreatic cancer cell line SW1990


title: HupT4_cancer

value: pancreatic cancer cell line HupT4


title: MIAPaCa-2_cancer

value: pancreatic cancer cell line MIAPaCa-2


title: SU.86.86_cancer

value: pancreatic cancer cell line SU.86.86


title: HupT3_cancer

value: pancreatic cancer cell line HupT3


title: Hs766T_cancer

value: pancreatic cancer cell line Hs766T


title: Capan-2_cancer

value: pancreatic cancer cell line Capan-2


title: AsPC-1_cancer

value: pancreatic cancer cell line AsPC-1


title: HPAC_cancer

description: HPAC

value: pancreatic cancer cell line HPAC


title: Panc-1_cancer

value: pancreatic cancer cell line Panc-1


title: Capan-1_cancer

value: pancreatic cancer cell line Capan-1


title: HPAF-II_cancer

description: HPAF-II

value: pancreatic cancer cell line HPAF-II


title: P2-51_R3

city: College Station

first: Luis

middle: Humberto

last: Reyes

state: Texas

address: 3122 TAMU

department: Chemical Engineering

country: USA

institute: Texas A&M University

description: Biological replicate 3 of 3.

hyb_protocol: Samples were for hybridization by adding lyophilized 10X Blocking Agent (supplied with the Agilent Oligo aCGH Hybridization Kit) following the manufacturer's protocol. The samples were hybridized in Agilent's E. coli Gene Expression Microarray, 8x15K.

scan_protocol: The arrays were scanned using the GenePix 4100A Microarray Scanner.

data_processing: The image analysis was performed using GenePix Pro 6.0 Software (Molecular Devices). Data were normalized with MIDAS (LOWESS method), with clustering analysis in MeV (CAST).

organism: Escherichia coli K-12

source_name: wild-type

label_protocol: Cy3- and Cy5-dUTP dyes (GE Healthcare) were used to label 0.5 µg of cDNA samples by following the manufacturer’s protocol.

growth_protocol: E. coli K-12 strain BW25113 was evolved in chemostats. The cells were grown in M9 minimal media (5 g/L glucose) with increasing concentrations of n-butanol.

extract_protocol: RNA was extracted using the RNeasy Mini Kit (QIAGEN). The SuperScript indirect cDNA labeling system (Invitrogen) was used to generate cDNA.

tag: strain

tag: wt or mutant

value: WT @ 0.8%But

tag: growth medium

value: liquid culture


title: P2-08_R3

description: Biological replicate 3 of 3.


title: PF2-12_R2

description: Biological replicate 2 of 3.


title: DanG_cancer

description: DanG

value: pancreatic cancer cell line DanG


title: Hs700T_cancer

value: pancreatic cancer cell line Hs700T


title: PF2-04_R3

description: Biological replicate 3 of 3.


title: CFPAC-1_cancer

value: pancreatic cancer

value: pancreatic cancer cell line CFPAC-1


title: PF2-08_R3

description: Biological replicate 3 of 3.


title: PF2-12_R3

description: Biological replicate 3 of 3.


title: P2-58_R3

description: Biological replicate 3 of 3.


title: BxPC-3_cancer

value: pancreatic cancer cell line BxPC-3


title: P2-66_R3

description: Biological replicate 3 of 3.


title: Retinoblastoma RB03

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

description: Biological replicate 3

hyb_protocol: Fragmented Cy3-labeled cRNA (850ng) of the control sample were mixed with equal amounts of Cy5-labeled cRNA of the gastric tumor sample, and the mixtures were hybridized onto 44K whole human genome DNA microarrays (Agilent Technologies) for 17 hrs at 65°C with constant rotation (10 rpm)

scan_protocol: Scanned on Agilent scanner G2565AA

data_processing: Agilent Feature Extraction Software (v 9.5) was used for feature extraction. Lowess Normalization using GeneSpring GX v11.0.2 from Agilent.

source_name: retinoblastoma tumor

label_protocol: Low RNA input linear amplification kit from Agilent was used and labeling was done based on manufacturer's instructions. cRNA from normal tissues were labeled with Cy3 and cRNA from tumor tissues were labeled with Cy5

extract_protocol: Fresh enucleated or orbital exenterated retinoblastoma tumor tissues collected in RNA stabilizing reagent

tag: tissue

value: retinoblastoma tumor

source_name: Normal retina from corneal eye donors

value: normal retina


title: P2-77_R3

description: Biological replicate 3 of 3.


title: PF2-04_R2

description: Biological replicate 2 of 3.


title: Retinoblastoma RB04

description: Biological replicate 4


title: PF2-08_R2

description: Biological replicate 2 of 3.


title: P2-51_R2

description: Biological replicate 2 of 3.


title: P2-58_R2

description: Biological replicate 2 of 3.


title: P2-66_R2

description: Biological replicate 2 of 3.


title: P2-77_R2

description: Biological replicate 2 of 3.


title: PF2-08_R1

description: Biological replicate 1 of 3.


title: PF2-04_R1

description: Biological replicate 1 of 3.


title: PF2-12_R1

description: Biological replicate 1 of 3.


title: P2-77_R1

description: Biological replicate 1 of 3.


title: P2-66_R1

description: Biological replicate 1 of 3.


title: P2-08_R2

description: Biological replicate 2 of 3.


title: P2-58_R1

description: Biological replicate 1 of 3.


title: P2-51_R1

description: Biological replicate 1 of 3.


title: P2-08_R1

description: Biological replicate 1 of 3.


title: HepG2 sh-p53 AICAR 24h_2

city: Rehovot

first: Ido

last: Goldstein

address: POB 26

country: Israel

institute: The Weizmann Institute of Science

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials :  Heat cocktails at 99C for 5 minutes, then 45C for 5 minutes, centrifuge at max speed for 1 minute, transfer 80μl of hyb solution loaded on each array, hybridize 17 hours at 45C at 60rpm, Fluidics washing FS450_0007 using Affymetrix wash solution.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data was processed applying the RMA algorithm and using the Partek software

source_name: HepG2 sh-p53 AICAR 24h

label_protocol: 200ng TotalRNA were used. cDNA samples were generated and labeled using Affymetrix 1-cycle expression kit (#900493)

growth_protocol: Cells were plated in biological duplicates on 6-well plates (700,000 cells per well)

extract_protocol: RNA was extracted using the TRI reagent method

treatment_protocol: Cells were treated with the following compounds: DMSO (as a control), Nutlin (10uM), AICAR (0.5mM) for 24 hours

tag: cell type

value: hepatoma cells

tag: genotype/variation

value: HepG2sh-p53 (small-hairpin RNA targeting p53)

tag: p53 stimulator

value: AICAR (0.5mM)


title: HepG2 sh-p53 Nutlin 24h_2

source_name: HepG2 sh-p53 Nutlin 24h

value: Nutlin (10uM)


title: HepG2 sh-con Nutlin 24h_2

source_name: HepG2 sh-con Nutlin 24h

value: HepG2sh-con (non-relevant control small-hairpin RNA)


title: HepG2 sh-p53 AICAR 24h_1


title: HepG2 sh-con AICAR 24h_1

source_name: HepG2 sh-con AICAR 24h


title: HepG2 sh-con AICAR 24h_2


title: HepG2 sh-p53 DMSO 24h_2

source_name: HepG2 sh-p53 DMSO 24h

value: DMSO (control)


title: HepG2 sh-con DMSO 24h_1

source_name: HepG2 sh-con DMSO 24h


title: HepG2 sh-p53 DMSO 24h_1


title: HepG2 sh-con Nutlin 24h_1


title: HepG2 sh-p53 Nutlin 24h_1


title: HepG2 sh-con DMSO 24h_2


title: NSC, biological rep2

city: Minato-ku

first: Hideto

last: Koso

state: Tokyo

address: 4-6-1 Shirokanedai

country: Japan

institute: Institute of Medical Science, The University of Tokyo

hyb_protocol: Post SPIA Modification generates sense target cDNA that was fragmented, biotin labeled and hybridized to Affymetrix Mouse Gene 1.0 ST arrays for 18 hours at 45C with rotation at 60 rpm.

scan_protocol: Arrays were then washed and stained using the FS450_0007 fluidics protocol and scanned using an Affymetrix 3000 7G scanner.

data_processing: The scanned images were inspected for hybridization efficiency and CEL files generated from GCOS (GeneChip Operating Software) were imported into Expression Console (EC) 1.1 software for array QC. RMA normalization was performed on the samples to generate the quality control (QC) metrics that we routinely use to determine data quality.

organism: Mus musculus

source_name: Normal NSCs

label_protocol: 100ng of total RNA was reverse transcribed to produce cDNA/mRNA hybrid molecule, which was subsequently used as a template to create double stranded cDNA with a unique DNA/RNA heteroduplex on one end.

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

value: normal Neural stem cells (NSCs)

tag: tissue genotype/variation

value: WT

tag: host strain background

value: CB17/ICR-Prkdcscid/IcrCrl (Sever combined immunodeficiency mice:SCID mice)


title: Subcutaneous tissue, biological rep2

source_name: Subcutaneous tissue

value: Subcutaneous tissue


title: Subcutaneous tissue, biological rep1


title: Tumor (line 1), biological rep2

source_name: Tumor


title: Tumor (line 123), biological rep2


title: Tumor (line 31), biological rep1

value: p53 mutant


title: Immortalized cell line, biological rep5

source_name: Immortalize NSCs

value: immortalized Neural stem cells (NSCs)


title: Tumor (line 31), biological rep3


title: Tumor (line 59), biological rep1


title: Tumor (line 123), biological rep3


title: Tumor (line 59), biological rep2


title: Immortalized cell line, biological rep8


title: Immortalized cell line, biological rep7


title: Immortalized cell line, biological rep9


title: Subcutaneous tissue, biological rep3


title: Tumor (line 59), biological rep3


title: Tumor (line 123), biological rep1


title: Immortalized cell line, biological rep6


title: Tumor (line 31), biological rep2


title: Immortalized cell line, biological rep1


title: Immortalized cell line, biological rep10


title: Tumor (line 1), biological rep3


title: Immortalized cell line, biological rep4


title: Tumor (line 1), biological rep1


title: Immortalized cell line, biological rep2


title: Mutant fully-grown oocytes (GV-stage) sample#1

city: Bar Harbor

first: You-Qiang

last: Su

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: Transcriptional silent oocytes

hyb_protocol: Fragmented and biotin-labeled cDNA from each sample were then hybridized to Affymetrix GeneChip® Mouse Gene 1.0 ST arrays for 16 h at 45°C.  Post-hybridization staining and washing were performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix

scan_protocol: The arrays were scanned with a GeneChip™3000 laser confocal slide scanner (Affymetrix) and the images were quantified using Gene Chip Operating Software version 1.2 (GCOS, Affymetrix).

data_processing: After the post-hybridization staining and washing, the arrays were scanned with a GeneChip™3000 laser confocal slide scanner (Affymetrix) and the images were quantified using Gene Chip Operating Software version 1.2 (GCOS, Affymetrix).   Average signal intensities for each probe set within arrays were calculated by and exported from Affymetrix’s Expression Console (Version 1.1) software using the RMA method which incorporates convolution background correction, summarization based on a multi-array model fit robustly using the median polish algorithm, and sketch-quantile normalization. For this experiment, one pairwise comparison was used to statistically resolve gene expression differences between Type levels using the R/maanova analysis package40 (Wu et al. 2003).  Specifically, differentially expressed genes will be detected by using Fs, a modified F-statistic incorporating shrinkage estimate of variance components from within the R/maanova package40-41.  Statistical significance levels of the pairwise comparison wase calculated by permutation analysis (1000 permutations) and adjusted for multiple testing using the false discovery rate (FDR), q-value, method42.  Differentially expressed genes are declared at an FDR q-value threshold of 0.05.

source_name: Fully-grown oocytes isolated from 23-d eCG-primed Mutant mice

label_protocol: RNA samples were  subjected to cDNA synthesis and amplification using the Nugen Ovation Pico WTA System (NuGEN Technologies, Inc, San Carlos, CA). The resulting cDNAs were then fragmented and biotin-labeled using the Encore™ Biotin Module (NuGEN Technologies, Inc).

growth_protocol: 21-day old (For Experiment 1) female Marf1+/+ (WT) and Marf1 Mutant mice were primed with eCG (5IU/mouse, EMD Biosciences, Inc., Calbiochem, La Jolla, CA) for 46 hours to stimulate follicle development.  Cumulus-oocyte complexes (COCs) were released by puncturing large antral follicles on ovarian surface with a pair of 26 gauge needles.  Released COCs were collected and washed for three times by passing through 3 dishes of medium.  Cumulus cells were then stripped from the oocyte by passing COCs several times through a hand-drawn small fine glass pipette with an inner diameter slightly narrower than the oocyte.  The resulting denuded fully-grown oocytes (FGOs) were then collected into a 1.5 ml eppendorf centrifuge tube and re-suspended in 350 µl of RLT buffer (Qiagen, Valencia, CA).  After brief vortexing, the oocyte lysate was snap frozen in liquid nitrogen and temporarily stored at -80°C until RNA isolation.  Growing oocytes (Experiment2) were isolated from 12-d old mice by digesting the whole ovaries with 4 mg/ml of collagenase, type I (Worthington Biochemical Corporation, Lakewood, NJ) and 0.02 mg/ml of deoxyribonuclease I in culture medium. The dissociated oocyte-granulosa cells complexes were then transferred into Ca2+, Mg2+-free PBS containing 1 mg/ml of collagenase and digested for about 20 min to remove the granulosa cells. Growing oocytes (GOs) were then collected into a 1.5 ml eppendorf centrifuge tube and re-suspended in 350 µl of RLT buffer (Qiagen, Valencia, CA).  After brief vortexing, the oocyte lysate was snap frozen in liquid nitrogen and temporarily stored at -80°C until RNA isolation.  Three sets of Marf1+/+ (WT) and Marf1 Mutant FGO and GO samples were collected and employed in microarray study.   Medium used for oocyte isolation was MEM-α (Invitrogen Corporation, Grand Island, NY) supplemented with 3 mg/ml of crystallized lyophilized bovine serum albumin (Sigma, St. Louis, MO), 75 mg/liter of penicillin G (Sigma) and 50 mg/liter streptomycin sulfate (Sigma).  Milrinone (Sigma), a selective inhibitor of oocyte-specific phosphodiesterase (PDE3), was added into the medium at the concentration of 5 µM to prevent the GV-stage oocytes from undergoing maturation during the process of COC and FGO.

extract_protocol: Total RNA was extracted from oocytes using the PicoPure RNA isolation kit according to the manufacturer's instruction. The quality and quantity of RNA were measured by the Bioanalyzer 2100 and RNA 6000 Pico LabChip assay (Agilent Technologies Inc, Palo Alto, CA) in combination with Quant-iT™ RiboGreen Reagent according to supplied protocols (Invitrogen, Carlsbad, CA).

treatment_protocol: no additional treatments were carried out

tag: cell

value: isolated oocytes

tag: genotype


title: Mutant fully-grown oocytes (GV-stage) sample#2

description: Transcriptional silent oocytes


title: Mutant fully-grown oocytes (GV-stage) sample#3

description: Transcriptional silent oocytes


title: Wildtype fully-frown oocytes (GV-stage) sample#1

description: Transcriptional silent oocytes

source_name: Fully-grown oocytes isolated from 23-d eCG-primed WT mice

value: Wildtype


title: surgically resected, primary breast tumor OXF5469

city: Auckland

first: Cris

last: Print

address: Grafton Campus, Park Rd

country: New Zealand

institute: Auckland University

description: primary breast tumour analysed using Affymetrix microarray

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133A and U133B Affymetrix GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were normalised with the RMA algorithym using default settings appart from no background correction.

source_name: primary excised breast tumour

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

value: primary breast tumor

value: breast cancer


title: surgically resected, primary breast tumor OXF5514


title: Immortalized cell line, biological rep3


title: E. coli O157:H7 EDL933 in LB at 37oC for 7 hrs incubation with honey

city: Gyeongsan-Si

first: Jintae

last: Lee

state: Gyeongsangbuk-Do

address: 214-1 Daedong

department: Chemical engineering

country: South Korea

institute: Yeungnam University

description: RNA extracted from E. coli EDL933 cells grown on glass wool for 7 hrs in LB at 37ºC plus honey

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Escherichia coli

source_name: rna extracted from e. coli o157: H7 EDL933 cells grown (7 hrs incubation) in LB at 37ºC with 0.5% honey

label_protocol:
Following affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: E. coli O157:H7 EDL933 was inoculated in 250 ml of LB in 1000 ml shake flasks with overnight cultures that were diluted 1:100. Cells were shaken with 10 g of glass wool at 100 rpm and 37°C for 7 hrs.  Cells were immediately chilled with dry ice and 95% ethanol (to prevent RNA degradation) for 30 sec before centrifugation in 50 ml centrifuge tubes at 13,000 g for 2 min; cell pellets were frozen immediately with dry ice and stored -80°C.  RNA was isolated using Qiagen RNeasy mini Kit (Cat# 74104) with Qiagen RNase-free DNase I (Cat# 79254).

tag: agent

value: 0.5% honey


title: VMH of WT-1 mice

city: Dallas

first: Ki Woo

last: Kim

address: 5323 Harry Hines Blvd.

department: Internal Medicine and Pharmacology

institute: UT-Southwestern

description:
W5
Replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Partek Genomic Suite V6.5

source_name: Wild type_VMH

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: No treatment done, but samples were taken in WT and VMH-specific FoxO1 KO mice.

tag: strain background

value: Mixed

value: wild type

value: ventromedial hypothalamus (VMH)


title: E. coli O157:H7 EDL933 in LB at 37oC for 7 hrs incubation

description: RNA extracted from E. coli EDL933 cells grown on glass wool for 7 hrs in LB at 37ºC

source_name: rna extracted from e. coli o157: H7 EDL933 cells grown (7 hrs incubation) in LB at 37ºC

value: control


title: VMH of KO3 mice

description:
K12
Replicate 3

source_name: FoxO1 KO_VMH

value: VMH-specific FoxO1 Knockout


title: surgically resected, primary breast tumor OXF5510

tag: disease state


title: surgically resected, primary breast tumor OXF5463


title: VMH of WT-3 mice

description:
W11
Replicate 3


title: Wildtype fully-frown oocytes (GV-stage) sample#3

description: Transcriptional silent oocytes


title: surgically resected, primary breast tumor OXF5534


title: surgically resected, primary breast tumor OXF5489


title: surgically resected, primary breast tumor OXF5465


title: surgically resected, primary breast tumor OXF5467


title: surgically resected, primary breast tumor OXF5512


title: surgically resected, primary breast tumor OXF5468


title: VMH of KO1 mice

description:
K4
Replicate 1


title: surgically resected, primary breast tumor OXF5522


title: surgically resected, primary breast tumor OXF5470


title: surgically resected, primary breast tumor OXF5464


title: VMH of KO2 mice

description:
K6
Replicate 2


title: VMH of WT-2 mice

description:
W8
Replicate 2


title: surgically resected, primary breast tumor OXF5505


title: NSC, biological rep1


title: surgically resected, primary breast tumor OXF5466


title: Wildtype fully-frown oocytes (GV-stage) sample#2

description: Transcriptional silent oocytes


title: surgically resected, primary breast tumor OXF5445


title: surgically resected, primary breast tumor OXF5462


title: surgically resected, primary breast tumor OXF5460


title: surgically resected, primary breast tumor OXF5451


title: surgically resected, primary breast tumor OXF5449


title: surgically resected, primary breast tumor OXF5455


title: surgically resected, primary breast tumor OXF5457


title: surgically resected, primary breast tumor OXF5461


title: surgically resected, primary breast tumor OXF5459


title: surgically resected, primary breast tumor BC0050

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133plus2 Affymetrix GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

tag: tumour histological grade

tag: estrogen receptor status

value: ER+

tag: progesterone receptor status

value: PgR+

tag: lymph node metastasis

value: LN+


title: surgically resected, primary breast tumor OXF5447


title: surgically resected, primary breast tumor OXF5453


title: surgically resected, primary breast tumor OXF5443


title: surgically resected, primary breast tumor OXF5452


title: surgically resected, primary breast tumor OXF5458


title: surgically resected, primary breast tumor BC0031R


title: surgically resected, primary breast tumor BC0043


title: surgically resected, primary breast tumor BC0047


title: surgically resected, primary breast tumor OXF5446


title: surgically resected, primary breast tumor OXF5454


title: surgically resected, primary breast tumor BC0045


title: surgically resected, primary breast tumor OXF5441


title: surgically resected, primary breast tumor OXF5442


title: surgically resected, primary breast tumor BC0030

value: LN-


title: surgically resected, primary breast tumor OXF5450


title: surgically resected, primary breast tumor OXF5448


title: surgically resected, primary breast tumor OXF5444


title: surgically resected, primary breast tumor OXF5456


title: surgically resected, primary breast tumor BC0049


title: surgically resected, primary breast tumor BC0029


title: surgically resected, primary breast tumor BC0023R


title: surgically resected, primary breast tumor OXF5440


title: surgically resected, primary breast tumor OXF5439


title: surgically resected, primary breast tumor OXF5436


title: surgically resected, primary breast tumor OXF5437


title: surgically resected, primary breast tumor OXF5438


title: surgically resected, primary breast tumor OXF5435


title: surgically resected, primary breast tumor BC0025


title: surgically resected, primary breast tumor OXF5432


title: surgically resected, primary breast tumor BC0022


title: surgically resected, primary breast tumor BC0020


title: surgically resected, primary breast tumor BC0021


title: surgically resected, primary breast tumor BC0026

value: PgR-


title: surgically resected, primary breast tumor NUH_BT97_A

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


title: surgically resected, primary breast tumor BC0018


title: surgically resected, primary breast tumor BC0019


title: surgically resected, primary breast tumor NUH_BT95_A


title: surgically resected, primary breast tumor NUH_BT96_A


title: surgically resected, primary breast tumor OXF5433


title: surgically resected, primary breast tumor OXF5431


title: surgically resected, primary breast tumor OXF5430


title: surgically resected, primary breast tumor NUH_BT94_A


title: surgically resected, primary breast tumor BC0017


title: surgically resected, primary breast tumor OXF5434


title: surgically resected, primary breast tumor NUH_BT99_A


title: surgically resected, primary breast tumor BC0016


title: surgically resected, primary breast tumor NUH_BT92_A


title: surgically resected, primary breast tumor BC0015

value: ER-


title: surgically resected, primary breast tumor NUH_BT90_A


title: surgically resected, primary breast tumor NUH_BT91_A


title: surgically resected, primary breast tumor NUH_BT93_A


title: surgically resected, primary breast tumor BC0013


title: surgically resected, primary breast tumor BC0012


title: surgically resected, primary breast tumor OXF5429


title: surgically resected, primary breast tumor NUH_BT89_A


title: surgically resected, primary breast tumor NUH_BT86_A


title: surgically resected, primary breast tumor BC0011R


title: surgically resected, primary breast tumor NUH_BT88_A


title: surgically resected, primary breast tumor NUH_BT85_A


title: surgically resected, primary breast tumor BC0010


title: surgically resected, primary breast tumor NUH_BT87_A


title: surgically resected, primary breast tumor NUH_BT83_A


title: surgically resected, primary breast tumor BC0006


title: surgically resected, primary breast tumor NUH_BT78_A


title: surgically resected, primary breast tumor BC0009R


title: surgically resected, primary breast tumor NUH_BT84_A


title: surgically resected, primary breast tumor NUH_BT82_A


title: surgically resected, primary breast tumor NUH_BT8_A


title: Influenza virus, RG LP (W/PB1)2

city: Tsukuba

first: Yuko

last: Uchida

institute: National Institute of Animal Health

description:
LP (W/PB1)2
Gene expression of chicken lung at 24 hours post infection of influenza virus

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

scan_protocol: Scanning was performed by Axon GenePix 4000B, 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: Gallus gallus

source_name: Influenza virus, RG LP (W/PB1)2

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA.  Control1, Control2, HP1 and HP2 were labelled with NimbleGen 60mer Hybriweel protocol, biotin-labeled method by in vitro transcription. For the other samples,  complemental strand was synthesized from Cy3-random 9 mer using with double strand cDNA as a template.

growth_protocol: Chickens were kept in the biosafety level three facility for 24hour.

extract_protocol: Chicken lung soaked into RNAlater(Ambion) was homogenaized with TRIzol (Invitrogen).   Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).  These processes were carried out in Nihon Gene research laboratories.

treatment_protocol: Chikens were inoculated with 100ul of PBS or H5N1 influenza virus intranasally.

value: Lung

tag: infected with

value: recombinant H5N1 subtype influenza virus


title: surgically resected, primary breast tumor NUH_BT76_A


title: Influenza virus, RG LP (W/PB1)1

description:
LP (W/PB1)1
Gene expression of chicken lung at 24 hours post infection of influenza virus

source_name: Influenza virus, RG LP (W/PB1)1


title: surgically resected, primary breast tumor BC0003


title: Influenza virus, RG LP (W/PA)2

description:
LP (W/PA)2
Gene expression of chicken lung at 24 hours post infection of influenza virus

source_name: Influenza virus, RG LP (W/PA)2


title: surgically resected, primary breast tumor BC0002R2


title: Influenza virus, RG LP (W/PA)1

description:
LP (W/PA)1
Gene expression of chicken lung at 24 hours post infection of influenza virus

source_name: Influenza virus, RG LP (W/PA)1


title: surgically resected, primary breast tumor BC0005R


title: surgically resected, primary breast tumor NUH_BT74_A


title: surgically resected, primary breast tumor BC0008


title: surgically resected, primary breast tumor NUH_BT77_A


title: Influenza virus, RG LP2

description:
LP2
Gene expression of chicken lung at 24 hours post infection of influenza virus

source_name: Influenza virus, RG LP2


title: surgically resected, primary breast tumor BC0001


title: surgically resected, primary breast tumor NUH_BT73_A


title: Influenza virus, RG LP1

description:
LP1
Gene expression of chicken lung at 24 hours post infection of influenza virus

source_name: Influenza virus, RG LP1


title: surgically resected, primary breast tumor AL0087


title: surgically resected, primary breast tumor NUH_BT71_A


title: surgically resected, primary breast tumor NUH_BT72_A


title: surgically resected, primary breast tumor NUH_BT7_A


title: surgically resected, primary breast tumor AL0088


title: Influenza virus, RG WB2

description:
WB2
Gene expression of chicken lung at 24 hours post infection of influenza virus

source_name: Influenza virus, RG WB2


title: Influenza virus, RG LP (W/MNS)1

description:
LP (W/MNS)1
Gene expression of chicken lung at 24 hours post infection of influenza virus

source_name: Influenza virus, RG LP (W/MNS)1


title: surgically resected, primary breast tumor NUH_BT66_A


title: surgically resected, primary breast tumor AL0078


title: Influenza virus, RG WB1

description:
WB1
Gene expression of chicken lung at 24 hours post infection of influenza virus

source_name: Influenza virus, RG WB1


title: surgically resected, primary breast tumor AL0077


title: surgically resected, primary breast tumor AL0075


title: surgically resected, primary breast tumor NUH_BT63_A


title: surgically resected, primary breast tumor AL0079


title: surgically resected, primary breast tumor AL0073


title: surgically resected, primary breast tumor NUH_BT64_A


title: surgically resected, primary breast tumor NUH_BT70_A


title: surgically resected, primary breast tumor AL0086


title: surgically resected, primary breast tumor AL0074


title: surgically resected, primary breast tumor NUH_BT67_A


title: surgically resected, primary breast tumor NUH_BT68_A


title: surgically resected, primary breast tumor NUH_BT62_A


title: Influenza virus, RG Ck/Yamaguchi/7/2004_2

description:
rHP2
Gene expression of chicken lung at 24 hours post infection of influenza virus

source_name: Influenza virus, RG Ck/Yamaguchi/7/2004


title: Influenza virus, RG LP (W/MNS)2

description:
LP (W/MNS)2
Gene expression of chicken lung at 24 hours post infection of influenza virus

source_name: Influenza virus, RG LP (W/MNS)2


title: surgically resected, primary breast tumor NUH_BT65_A


title: Influenza virus, Ck/Yamaguchi/7/2004_1

description:
HP1
Gene expression of chicken lung at 24 hours post infection of influenza virus

source_name: Influenza virus, Ck/Yamaguchi/7/2004

value: original H5N1 subtype influenza virus


title: PBS control_2

description:
Control2
Gene expression of chicken lung at 24 hours post inoculation of PBS

source_name: PBS

value: PBS control


title: Influenza virus, RG Ck/Yamaguchi/7/2004_1

description:
rHP1
Gene expression of chicken lung at 24 hours post infection of influenza virus


title: surgically resected, primary breast tumor AL0072

description: primary breast tumour analysed using Affymetrix microarray

source_name: primary excised breast tumour

value: primary breast tumor

value: breast cancer


title: surgically resected, primary breast tumor NUH_BT60_A


title: Influenza virus, Ck/Yamaguchi/7/2004_2

description:
HP2
Gene expression of chicken lung at 24 hours post infection of influenza virus


title: PBS control_1

description:
Control1
Gene expression of chicken lung at 24 hours post inoculation of PBS


title: surgically resected, primary breast tumor NUH_BT61_A


title: surgically resected, primary breast tumor AL0070


title: Retinoblastoma RB01

description: Biological replicate 1

source_name: retinoblastoma tumor

value: retinoblastoma tumor

source_name: Normal retina from corneal eye donors

value: normal retina


title: surgically resected, primary breast tumor NUH_BT6_A


title: surgically resected, primary breast tumor AL0068


title: surgically resected, primary breast tumor AL0071


title: surgically resected, primary breast tumor NUH_BT59_A


title: surgically resected, primary breast tumor AL0069


title: Retinoblastoma RB02

description: Biological replicate 2


title: surgically resected, primary breast tumor NUH_BT58_A


title: surgically resected, primary breast tumor NUH_BT56_A


title: surgically resected, primary breast tumor AL0067


title: surgically resected, primary breast tumor NUH_BT51_A


title: surgically resected, primary breast tumor AL0065


title: surgically resected, primary breast tumor NUH_BT55_A


title: surgically resected, primary breast tumor NUH_BT52_A


title: surgically resected, primary breast tumor NUH_BT54_A


title: surgically resected, primary breast tumor AL0063


title: surgically resected, primary breast tumor AL0061


title: surgically resected, primary breast tumor AL0060


title: surgically resected, primary breast tumor AL0062


title: surgically resected, primary breast tumor AL0058


title: surgically resected, primary breast tumor NUH_BT50_A


title: surgically resected, primary breast tumor NUH_BT53_A


title: surgically resected, primary breast tumor AL0057


title: surgically resected, primary breast tumor NUH_BT5_A


title: surgically resected, primary breast tumor AL0056


title: HuH-7 gDNA

type: genomic

city: Tokyo

first: satoshi

last: matsumura

address: 1-5-45 Yushima, Bunkyo-ku

department: Dept. of Mol. Cytogenet.

institute: Inst. of Med. Sci., Tokyo Med. & Dent. Univ.

hyb_protocol: according to the manufacturer's instructions (Agilent microarray analysis of methylated DNA immunoprecipitation protocol version 1.0, Agilent Technologies)

data_processing: Data from scanned images (tiff) were extracted using Feature Extraction Software, version 9.0 (Agilent Technologies)

molecule: genomic DNA

growth_protocol: DMEM containing 10% FBS

extract_protocol: genomic DNA was extracted using common method prior to MeDIP method

tag: cell line

tag: antibody

value: none, input DNA

value: MeDIP


title: C20 gDNA

scan_protocol: according to the manufacturer's instructions (Agilent microarray analysis of methylated DNA immunoprecipitation protocol version 1.0, Agilent Technologies)

tag: tissue

value: normal liver tissue


title: surgically resected, primary breast tumor AL0053


title: surgically resected, primary breast tumor AL0054

value: ER+


title: surgically resected, primary breast tumor AL0052


title: surgically resected, primary breast tumor AL0050

value: PgR+


title: surgically resected, primary breast tumor NUH_BT47_A


title: surgically resected, primary breast tumor NUH_BT46_A


title: surgically resected, primary breast tumor NUH_BT49_A


title: Hep3B gDNA

label_protocol: according to the manufacturer's instructions (Agilent microarray analysis of methylated DNA immunoprecipitation protocol version 1.0, Agilent Technologies)


title: surgically resected, primary breast tumor NUH_BT48_A


title: surgically resected, primary breast tumor AL0051


title: surgically resected, primary breast tumor NUH_BT45_A


title: HepG2 gDNA


title: surgically resected, primary breast tumor AL0048


title: surgically resected, primary breast tumor NUH_BT42_A


title: C40 mRNA rep 2

hyb_protocol: according to the manufacturer's instructions (Microarray-based gene expression analysis protocol ver. 5.0.1, Agilent Technologies)

data_processing: data extraction were done with Feature Extraction Software, version 9.0 (Agilent Technologies)

extract_protocol: TRIsure

treatment_protocol: Total RNAs extracted from Hep3B, HepG2, and HuH-7 cell lines and from these cell lines treated with 10 μM 5-aza-dCyd for 5 days


title: surgically resected, primary breast tumor NUH_BT43_A


title: C40 mRNA rep 1

scan_protocol: according to the manufacturer's instructions (Microarray-based gene expression analysis protocol ver. 5.0.1, Agilent Technologies)


title: surgically resected, primary breast tumor NUH_BT40_A


title: surgically resected, primary breast tumor AL0049

value: LN+


title: C20 mRNA rep 1

label_protocol: according to the manufacturer's instructions (Microarray-based gene expression analysis protocol ver. 5.0.1, Agilent Technologies)


title: surgically resected, primary breast tumor AL0047

value: LN-


title: HuH-7 5-aza-dcyd mRNA rep 1

source_name: HuH-7 5-aza-dcyd

tag: treatment

value: 10 uM 5-aza-dCyd for 5 days


title: C20 mRNA rep 2


title: HuH-7 mRNA rep 2


title: surgically resected, primary breast tumor AL0046

value: ER-

value: PgR-


title: surgically resected, primary breast tumor AL0045


title: HuH-7 mRNA rep 1


title: surgically resected, primary breast tumor AL0044


title: surgically resected, primary breast tumor NUH_BT41_A


title: HepG2 mRNA rep 2


title: Hyper Gravity

first: Akira

last: Higashibata

state: Ibaraki

department: Department of Space Biology and Microgravity Sciences

institute: Japan Aerospace Exploration Agency

description:
Sample name: Hyper Gravity
G030040_05abs_hyper_gravity
Gene expression data from worms (mixed stage) grownunder hyper gravity condition (10G)

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

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

data_processing: The data were analyzed with GeneChip Operating Software version 1.0 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Caenorhabditis elegans

source_name: C.elegans N2 Hyper Gravity

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: C.elegans N2 were grown at 20C for 10 days in CeMM (liquid media).

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

treatment_protocol: All worms were frozen by liquid nitrogen before extracting RNA.

tag: strain

value: Bristol N2

tag: genotype/variation

value: wild type

tag: Stage

value: mixed

tag: stress


title: surgically resected, primary breast tumor NUH_BT38_A

value: primary breast tumor


title: HepG2 5-aza-dcyd mRNA rep 2

source_name: HepG2 5-aza-dcyd


title: surgically resected, primary breast tumor NUH_BT4_A

value: breast cancer


title: Ground Control (Tsukuba space center)

description:
Sample name: Laboratry Control
G030040_02abs_Tsukuba_control
Gene expression data from ground control worms (Tsukuba space center) (mixed stage)

source_name: C.elegans N2 ground control (lab)


title: Clino Rotation

description:
Sample name: Clino Rotation
G030040_04abs_clinorotation
Gene expression data from clino-rotated worms (mixed stage)

source_name: C.elegans N2 Clinorotation

value: random gravity vector


title: surgically resected, primary breast tumor NUH_BT39_A


title: surgically resected, primary breast tumor AL0043


title: HepG2 mRNA rep 1


title: Ground Control (operation site)

description:
Sample name: Ground Control
G030040_01abs_ground_control
Gene expression data from ground control worms (operation site) (mixed stage)

source_name: C.elegans N2 ground control


title: surgically resected, primary breast tumor NUH_BT35_A


title: HepG2 5-aza-dcyd mRNA rep 1


title: Hep3B 5-aza-dcyd mRNA rep 2

source_name: Hep3B 5-aza-dcyd


title: Space Flight

description:
Sample name: Space Flight
G030040_03abs_space_flight
Gene expression data from space flown worms (mixed stage)

source_name: C.elegans N2 space flight

value: micro gravity


title: surgically resected, primary breast tumor AL0041


title: surgically resected, primary breast tumor NUH_BT36_A


title: surgically resected, primary breast tumor NUH_BT37_A


title: Hep3B 5-aza-dcyd mRNA rep 1


title: surgically resected, primary breast tumor AL0042


title: Hep3B mRNA rep 2


title: surgically resected, primary breast tumor AL0039


title: surgically resected, primary breast tumor AL0038


title: Vector-only control_11-day-old seedling

city: Taipei

first: Mao-Sen

last: Liu

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

country: Taiwan

institute: Institute of Plant and Microbial Biology, Academia Sinica, Taiwan

description:
11D p1380
Gene expression data from 11-day-old seedling of p1380 transgenic broccoli grown under long day condition

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16.5 hr at 45C on GeneChip Arabidopsis  ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 7G

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

organism: Brassica oleracea var. italica

source_name: 11-day-old seedlings of broccoli harboring pCAMBIA1380 vector

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

growth_protocol: Seedlings were grown on 0.8 % agar plates with half-strength of MS and 1.5 % sucrose under long day condition (16h light/ 8h dark) at 21 centigrade.

treatment_protocol: Seedlings of p1380 vector-only broccoli and antisenseBoEMF2.1 broccoli grown on MS plates under long day condition (16h/8h) for 11 days.

tag: cultivar

value: Elegance

value: wild type background harboring pCAMBIA1380 vector

value: whole seedlings

tag: age


title: Hep3B mRNA rep 1


title: surgically resected, primary breast tumor AL0040

value: ER+


title: surgically resected, primary breast tumor NUH_BT34_A


title: surgically resected, primary breast tumor NUH_BT33_A


title: surgically resected, primary breast tumor NUH_BT23_A


title: asBoEMF2.1_11-day-old seedling

description:
11D asBoEMF2
Gene expression data from 11-day-old seedling of anitsenseBoEMF2.1 transgenic broccoli grown under long day condition

source_name: 11-day-old seedlings of broccoli harboring 35S::antisenseBoEMF2.1

value: wild type background harboring 35S::BoEMF2.1


title: surgically resected, primary breast tumor AL0037

value: PgR+

value: LN+


title: seedling at 14 day_mock treatment_biological replica 1

city: Potsdam

first: Jos

last: Schippers

address: Am Muehlenberg 1

department: Plant Signaling

institute: MPIMP-golm

hyb_protocol: Hybridizations against Arabidopsis ATH1 Genome Array (GeneChip System®, Affymetrix) chips were performed at 45 °C for 16 h, in the Affymetrix GeneChip Workstation (hybridization oven 640, Fluidics Station 450), using 10 µg of Biotin-labeled aRNA, according to the manufacturer's protocol.

scan_protocol: GeneChips were scanned by use of the Affymetrix GeneChip Workstation Scanner 3000.

data_processing: Expression values are calculated based on the difference of the PM signal and MM signal at each of the probe pairs using the Affymetrix GeneChip Operating System (GCOS).  Present, Marginal or Absent (P/M/A) calls were computed with the affy package. This software employs statistical algorithms to calculate qualitative and quantitative expression values for each transcript. It also generates a statistical p-value, which suggests the level of confidence in each of the qualitative measurements.

organism: Arabidopsis thaliana

source_name: Seedling_Long Day 16/8 h_½ MS medium_14 day

label_protocol: RNA was labelled with the MessageAMP II biotin enhanced (Ambion) kit according to the manufactures protocol

growth_protocol: T3 seeds were stratified on plate for 72 h in the dark at 4°C and then transferred to 22°C with a 16-h light (100 μE m−2 s−1)/8-h dark period.

extract_protocol: Total RNA was extracted with the Plant RNAeasy kit (Qiagen)

tag: ecotype

tag: agent

value: ethanol

value: seedling


title: seedling at 14 day_2 h EST treatment_biological replica 3

treatment_protocol: For estradiol (EST) treatment, 14 day-old seedlings were selected and synchronized in ½ MS liquid medium in long-day condition for one night. Subsequently, fresh medium with 10 μM EST was added to the seedlings in a 12-well plate and the same amount of inducer-free medium to control samples as a mock treatment. After 2 hours seedlings were harvested and directly frozen in liquid nitrogen.

value: 10 uM estradiol


title: surgically resected, primary breast tumor NUH_BT22_A

tag: disease state


title: surgically resected, primary breast tumor AL0034

tag: tumour histological grade

tag: estrogen receptor status

value: ER-

value: PgR-

value: LN-


title: surgically resected, primary breast tumor AL0035

tag: progesterone receptor status

tag: lymph node metastasis

value: primary breast tumor


title: surgically resected, primary breast tumor NUH_BT31_A

value: breast cancer


title: seedling at 14 day_mock treatment_biological replica 2


title: surgically resected, primary breast tumor NUH_BT29_A


title: surgically resected, primary breast tumor NUH_BT3_A


title: seedling at 14 day_mock treatment_biological replica 3


title: seedling at 14 day_2 h EST treatment_biological replica 2


title: surgically resected, primary breast tumor AL0036


title: seedling at 14 day_2 h EST treatment_biological replica 1


title: surgically resected, primary breast tumor AL0033


title: surgically resected, primary breast tumor AL0032


title: surgically resected, primary breast tumor NUH_BT18_A


title: surgically resected, primary breast tumor NUH_BT17_A


title: surgically resected, primary breast tumor NUH_BT19_A


title: surgically resected, primary breast tumor NUH_BT20_A


title: surgically resected, primary breast tumor AL0030


title: surgically resected, primary breast tumor NUH_BT16_A


title: surgically resected, primary breast tumor AL0031


title: surgically resected, primary breast tumor NUH_BT2_A


title: surgically resected, primary breast tumor AL0029


title: surgically resected, primary breast tumor NUH_BT15_A


title: surgically resected, primary breast tumor AL0026


title: surgically resected, primary breast tumor AL0028


title: surgically resected, primary breast tumor NUH_BT14_A


title: surgically resected, primary breast tumor AL0025


title: Caudal Arteries Notch3-/-, biological rep3

city: Paris

first: Anne

last: Joutel

address: 10 avenue de Verdun

country: France

institute: INSERM

description:
Gene expression data from caudal arteries of Notch3-/- mice (P28)
AJ_N3KO_4

hyb_protocol: Following fragmentation, 10µg of cRNA were hybridized for 16 hr at 45°C on GeneChip® Mouse Genome 430 2.0  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G

data_processing: CEL files were generated using Affymetrix GeneChip® Operating Software v1.4 and further analyzed using Robust Multi-array Average (RMA) algorithms in R/Bioconductor

source_name: Caudal Arteries from Notch3-/- Mice (P28)

label_protocol: Biotinylated cRNA were prepared from 2.5 µg total RNA using the one-cycle target labeling assay in Affymetrix GeneChip® Expression Analysis, Technical Manual P/N 701021 Rev5

growth_protocol: Mice were maintained in a temperature-controlled room with a 12-h light/dark cycle and access to food and water ad libitum.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions followed by a clean-up on RNeasy Qiagen's columns. RNA quality was checked using Bioanalyzer (Agilent).

value: Caudal Artery

tag: genotype

value: 4 weeks (P28)


title: Caudal Arteries Notch3+/+, biological rep2

description:
Gene expression data from caudal arteries of Notch3+/+ mice (P28)
AJ_N3WT_3

source_name: Caudal Arteries from Notch3+/+ Mice (P28)


title: Caudal Arteries Notch3-/-, biological rep1

description:
Gene expression data from caudal arteries of Notch3-/- mice (P28)
AJ_N3KO_1


title: Caudal Arteries Notch3+/+, biological rep3

description:
Gene expression data from caudal arteries of Notch3+/+ mice (P28)
AJ_N3WT_4


title: Caudal Arteries Notch3-/-, biological rep2

description:
Gene expression data from caudal arteries of Notch3-/- mice (P28)
AJ_N3KO_2


title: Kinin B1 receptor knockout with selective rescue in fat, biological rep3

city: Boston

first: Marcelo

middle: A.

last: Mori

state: MA

address: 1 Joslin Place

institute: Joslin Diabetes Center

hyb_protocol: 6µg of biotinylated cRNA were hybridized for 16hr at 45C to the Affymetrix Mouse Genome 430 2.0 array.  Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 450.

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

data_processing: Data were analyzed using Affymetrix GCOS v. 1.3, MAS5.0 algorithm, and globally scaled with the trimmed mean target intensity set to 1500.

source_name: Epididymal fat, knockout+rescue

label_protocol: Biotinylated aRNA synthesis was performed using the MessageAmp III aRNA Amplification Kit (Ambion)

growth_protocol: Animals were maintained on standard mouse chow diet at 22oC on 12 h light-dark cycle allowed ad libitum access to food and tap water.

treatment_protocol: Three-month-old mice were killed and tissues were collected and snap frozen in liquid nitrogen.

tag: gender

value: Male

value: Epididymal fat

value: 3 month-old


title: surgically resected, primary breast tumor AL0024

source_name: primary excised breast tumour

value: ER+

tag: tissue


title: Kinin B1 receptor knockout, biological rep3

source_name: Epididymal fat, knockout


title: Kinin B1 receptor knockout with selective rescue in fat, biological rep2


title: Kinin B1 receptor knockout, biological rep2


title: Kinin B1 receptor knockout with selective rescue in fat, biological rep1


title: surgically resected, primary breast tumor AL0027


title: Kinin B1 receptor knockout, biological rep4


title: surgically resected, primary breast tumor NUH_BT13_A


title: Caudal Arteries Notch3+/+, biological rep1

description:
Gene expression data from caudal arteries of Notch3+/+ mice (P28)
AJ_N3WT_1


title: surgically resected, primary breast tumor NUH_BT12_A


title: HuH-7 5-aza-dcyd mRNA rep 2

tag: cell line

tag: treatment

value: 10 uM 5-aza-dCyd for 5 days


title: surgically resected, primary breast tumor NUH_BT120_A


title: surgically resected, primary breast tumor AL0023

value: PgR+


title: LEC1::GR uninduced 4, membrane B

city: Gatersleben

first: Astrid

last: Junker

address: Corrensstrasse 3

department: Molecular Genetics

institute: Leibniz Institute for Plant Genetics and Crop Plant Research

description: hybridization on membrane B

hyb_protocol: Arrays were prehybridized for 1h at 65°C in Church buffer (0,5M sodium phosphate, pH7,2, 7% SDS, 1% BSA, 1mM EDTA, 10µg/ml sheared salmon sperm DNA) per cm2 of membrane in a rotating thermal oven. Labelled probes were added and hybridization continued for 4 days. Membranes were washed twice in 0,2x SSC, 0,1% SDS for 20 min at 65°C and then placed on a moist Whatman paper, wrapped in Saran wrap and exposed to a Fuji image plate for 10 days in a lead chamber.

scan_protocol: Signals were detected using a FLA 3000 phosphoimager at 50µm resolution and 16 bit grey scale (Fuji). Spot intensities were obtained by aligning the pre-defined spotting pattern using ArrayVision software (GE Healthcare).

data_processing: Four biological replicates were performed and the group of LEC1_EtOH ChIP-chip experiments and the group of LEC1_DEX experiments were normalized independently. First, log-2-hybridization intensities were calculated from Dens - PSL / mm2 values (see raw data file) for each experiment. Then, the median of log-2-hybridization intensities of an experiment was centered to zero. Finally, quantile normalization was applied separately to both groups resulting in normalized log-2-hybridization intensities for each experiment (Bolstad et al., 2003). For quality control within an experiment each intergenic region was spotted twice on the macroarray resulting in two normalized log-2-hybridization intensities per intergenic region. A filter was applied to exclude each intergenic region from an experiment if the absolute difference in normalized log-2-hybridization intensities of both spots of this intergenic region was greater than one. Separately for both groups of experiments, missing normalized log-2-hybridization intensities of an excluded intergenic region were substituted by mean log-2-hybridization intensities of this region in other experiments if this region passed the filter in at least three other experiments. We used an inducible expression system and used DEX for induction and ethanol (as dissolvent for DEX) as a control treatment. The anti-LEC1 antibody was added to chromatin samples of both treatments and the results of the ethanol-treated sample as control values. [log2 ratio of normalized signal intensities of (EtOH/DEX)] data file is available on Series record.

source_name: whole plant

label_protocol: Labelled probes were obtained by combining three parallel random priming reactions using the Megaprime Kit (GE Healthcare, Uppsala, Sweden), 1ng amplified chromatin, and 50µCi [α-33P]dCTP per reaction.

growth_protocol: Two weeks old 35S::LEC1::GR seedlings were treated with Dexamethasone or ethanol for 24 hours before cross-linking and chromatin isolation.

extract_protocol: About 1g seedling material was used for each chromatin preparation. For crosslinking plant material was vacuum infiltrated for 20min at 4°C in PBS (8mM Na2HPO4, 2mM KH2PO4, 150mM NaCl, pH7,5) plus 1% formaldehyde. The reaction was stopped by adding glycine (f.c. 125 mM) and continuing the infiltration for 10 min. All following steps were performed at 4°C and buffers were supplemented with a proteinase inhibitor cocktail (Roche). Seedlings were washed extensively with TBS and finally suspended in 15mM Tris-HCl, 2mM EDTA, 0.5mM spermin, 80mM KCl, 20mM NaCl, 15mM mercaptoethanol, 0.1% Triton X-100, pH7,5 (Dolezel et al., 1992). Seedlings were homogenized with a Potter homogenizer and passed through 50µm filters (Celltrics, Partec) and sedimented by centrifugation for 20min at 3000g. The pellet was resuspended in 50 mM Hepes, 140 mM NaCl, 1 mM EDTA, 1% TritonX-100, 0.1% Na-deoxycholate (DOC), 10% glycerol, pH7,5, incubated for 20min and centrifuged for 12min at 12800g. The pellet was washed several times with the same buffer until the supernatant was colorless. After a final wash with IP buffer (50 mM Tris-HCl, 150 mM NaCl, 1% Triton X-100, pH7.9) the chromatin was suspended in 800µl IP buffer. 400µl aliquots were treated with ultrasound to reduce the average fragment size of chromatin to 500bp. After centrifugation (12 min, 12000 g) the clear supernatant was stored at -80°C. To determine chromatin yield, 50µl aliquots were incubated overnight at 65°C for breaking DNA-protein cross-links, and purified using a PCR purification kit (Qiagen, Hilden, Germany). DNA concentration was determined by UV spectrometry using a NanoDrop 1000 (Peqlab,) photometer. For each immunoprecipitation 10µg chromatin were combined with 2µg of affinity purified anti-LEC1 antibody in 800µl of IP buffer supplemented with 0,1% DOC. After incubation for 2h at 4°C on a rotating wheel the antibody chromatin complex was captured on 50µl of protein A coated magnetic beads (Dynal) by continuing the incubation for 2h. The beads were separated magnetically from the supernatant and washed successively with 1 ml each of the following buffers: IP buffer; 50µM Tris-HCl, 0,5M NaCl, pH7,5; 50µM Tris-HCl, 0,5M LiCl, 0,5% NP 40, pH 7,5; 50µM Tris-HCl, 0,5M LiCl, 1% NP 40, 1mM EDTA, 0,7% DOC, pH 7,5,  and TE buffer (20mM Tris-HCl, 1mM EDTA, pH 7,5). For each wash beads were incubated 5 min at 4°C on a rotating wheel and afterwards magnetically separated from the supernatant. The antibody-TF-DNA complex was eluted from the beads with 1% SDS at 65°C. Eluates from a first elution with 70 µl and a second elution with 30µl were combined, mixed with 7µl 3M NaCl, and incubated overnight at 65°C to reverse the cross-link between TF and DNA. Chromatin fragments were purified using the PCR Purification Kit (Qiagen) and their concentration determined using Picogreen (Invitrogen, Groningen, Holland) and a NanoDrop 3300 (Peqlab) fluorescence spectrophotometer. The control “input” DNA was treated identical. For amplification 1 – 2ng of chromatin fragments were blunted with 5U Klenow polymerase (Fermentas, Vilnius, Lithuania) and ligated with 75pmol adapters using 15U T4 ligase at 16°C for 12h. Adapters were obtained by mixing equal amounts of the oligonucleotides oJW102 (GCGGTGA¬CCCGGG¬AGATC¬TGA¬ATTC) and oJW103 (GAATTCAGATC) (Odom et al., 2004). Ligation reactions were terminated by heat inactivation (65°C, 10min), purified by reverse osmosis (PCR purification Kit, Qiagen, Hilden, Germany), and resuspended in 45µl water. Chromatin fragments were amplified for 40 cycles (95°C for 30s, 60°C for 60s, 72°C for 60s) using oJW102 as sole primer (10µM) in three separate reactions of 20µl (buffer: 10mM Tris-HCl, pH9,0, 50mM KCl, 0.1% (v/v) Triton X-100 containing 200µM dNTPs each and 2mM MgCl2). PCR products were pooled and purified (PCR purification Kit, Qiagen, Hilden, Germany).

treatment_protocol: Dexamethasone was added to a final concentration of 30µM and the isovolume of ethanol was added to control plants.

tag: developmental stage according to boyes et al. (2004)

tag: plant treatment

value: EtOH

tag: antibody

value: anti-LEC1 antibody (non-commercial)

tag: antibody preparation

value: Antibodies specific for the transcription factor LEC1 were raised in rabbits. For antigen production, the whole gene fragment encoding LEC1 (AT1G21970) was cloned into the expression plasmid pET23a (Novagen) creating a C-terminal fusion with a His-tag and a N-terminal T7 tag. The LEC1 protein was produced in Escherichia coli BL21(DE3)Lys cells and purified via affinity chromatography on Ni-agarose (Qiagen). Rabbits were immunized three times (0d, 28d and 38d) with 800µg protein per injection. Immunoglobulins in the sera were enriched by precipitation with 50% saturated ammonium sulfate. The precipitate was dissolved in PBS, dialysed, and stored frozen at -20°C. The anti-LEC1 antibodies were purified via antigen-loaded CNBr-sepharose (Amersham). Protein concentrations were determined by Bradford assays.

tag: treatment time


title: surgically resected, primary breast tumor AL0022

value: LN+


title: LEC1::GR induced 4, membrane B

description: hybridization on membrane B

value: Dexamethasone


title: surgically resected, primary breast tumor NUH_BT119_A


title: LEC1::GR uninduced 3, membrane B

description: hybridization on membrane B


title: LEC1::GR induced 3, membrane B

description: hybridization on membrane B


title: surgically resected, primary breast tumor AL0021

value: ER-

value: PgR-


title: surgically resected, primary breast tumor NUH_BT117_A

value: primary breast tumor


title: surgically resected, primary breast tumor NUH_BT114_A

value: breast cancer


title: surgically resected, primary breast tumor NUH_BT113_A


title: surgically resected, primary breast tumor NUH_BT112_A


title: Wild type, biological rep3

source_name: Epididymal fat, control

tag: strain

tag: genotype/variation

tag: age


title: Kinin B1 receptor knockout, biological rep1


title: Wild type, biological rep4


title: surgically resected, primary breast tumor AL0020

tag: tumour histological grade

value: LN-

tag: disease state


title: surgically resected, primary breast tumor AL0017

tag: estrogen receptor status

tag: progesterone receptor status


title: Wild type, biological rep2


title: LEC1::GR uninduced 2, membrane B

description: hybridization on membrane B


title: LEC1::GR induced 2, membrane B

description: hybridization on membrane B


title: Wild type, biological rep1


title: surgically resected, primary breast tumor NUH_BT111_A


title: surgically resected, primary breast tumor AL0018

tag: lymph node metastasis


title: Tumor #2 with p53R172H/+ mutation

city: Houston

first: Carlos

last: Caulin

state: TX

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

description: Gene expression data from oral tumors from K-p53R172H/+ mice

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized on Mouse430_2 GeneChip following the recommended procedures.

scan_protocol: The arrays were scanned using an Affymetrix Gene Chip Scanner 2500

data_processing: The signal was quantified with Affymetrix Microarray Suite 5.0 and analyzed following the model-based expression method implemented by dChip after normalization using the invariant set method

source_name: Mouse oral tumor from K-p53R172H/+ mice

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

extract_protocol: RNA was purified using RNeasy Mini Kit according to the manufacturer’s instructions (Qiagen).

value: Oral tumor

value: 1 year


title: LEC1::GR induced 1, membrane B

description: hybridization on membrane B


title: Tumor #3 with p53R172H/+ mutation


title: surgically resected, primary breast tumor AL0016

description: primary breast tumour analysed using Affymetrix microarray


title: LEC1::GR uninduced 1, membrane B

description: hybridization on membrane B


title: surgically resected, primary breast tumor AL0019


title: LEC1::GR induced 4, membrane A

description: hybridization on membrane A


title: surgically resected, primary breast tumor AL0015


title: LEC1::GR uninduced 4, membrane A

description: hybridization on membrane A


title: Tumor #2 with p53R172H/- mutation

description: Gene expression data from oral tumors from K-p53R172H/- mice

source_name: Mouse oral tumor from K-p53R172H/- mice


title: LEC1::GR uninduced 3, membrane A

description: hybridization on membrane A


title: Tumor #1 with p53R172H/+ mutation


title: surgically resected, primary breast tumor NUH_BT110_A


title: Tumor #1 with p53R172H/- mutation


title: surgically resected, primary breast tumor AL0013


title: surgically resected, primary breast tumor NUH_BT108_A


title: surgically resected, primary breast tumor AL0011


title: surgically resected, primary breast tumor NUH_BT107_A


title: surgically resected, primary breast tumor AL0014


title: surgically resected, primary breast tumor NUH_BT106_A


title: Tumor #3 with p53R172H/- mutation


title: LEC1::GR induced 3, membrane A

description: hybridization on membrane A


title: surgically resected, primary breast tumor NUH_BT109_A


title: LEC1::GR induced 2, membrane A

description: hybridization on membrane A


title: LEC1::GR uninduced 2, membrane A

description: hybridization on membrane A


title: surgically resected, primary breast tumor AL0008


title: surgically resected, primary breast tumor AL0010


title: LEC1::GR induced 1, membrane A

description: hybridization on membrane A


title: surgically resected, primary breast tumor NUH_BT103_A


title: surgically resected, primary breast tumor NUH_BT104_A


title: Tumor #2 with loss of p53

description: Gene expression data from oral tumors from K-p53-/- mice

source_name: Mouse oral tumor from K-p53-/- mice


title: surgically resected, primary breast tumor AL0009


title: surgically resected, primary breast tumor AL0012


title: surgically resected, primary breast tumor NUH_BT105_A


title: Dicer knockout preadipocytes, biological rep4

source_name: Subcutaneous preadipocytes, Dicer knockout

growth_protocol: Cells were grown in DMEM (Invitrogen) with 10% fetal bovine serum (BenchMark, Gemini) in a humidified 5% CO2 atmosphere at 37 °C. Penicillin/Streptomycin (Invitrogen) and Normocin (Invivogen) was supplemented to the culture medium.

treatment_protocol: Cells were transduced with 750 MOI adenoviruses harboring GFP (Ad5CMVeGFP) or CRE recombinase (Ad5CMVCre-eGFP) (Gene Transfer Vector Core, University of Iowa) in the presence of 4 μg/mL polybrene. Four days after adenovirus infection, Dicer knockout cells or controls were harvested for RNA isolation.

tag: genetic background

tag: genotype

value: Dicer lox/lox

tag: cell type

value: Subcutaneous preadipocytes

tag: cell source

value: Isolated from day 2 newborns

value: Dicer ablation


title: LEC1::GR uninduced 1, membrane A

description: hybridization on membrane A

tag: developmental stage according to boyes et al. (2004)


title: surgically resected, primary breast tumor NUH_BT102_A

tag: tissue


title: Tumor #3 with loss of p53


title: surgically resected, primary breast tumor AL0007


title: surgically resected, primary breast tumor NUH_BT101_A


title: Dicer knockout preadipocytes, biological rep3

tag: treatment


title: surgically resected, primary breast tumor NUH_BT10_A


title: surgically resected, primary breast tumor AL0006

value: ER+

value: PgR+


title: Dicer knockout preadipocytes, biological rep1


title: surgically resected, primary breast tumor NUH_BT100_A


title: surgically resected, primary breast tumor NUH_BT1_A


title: Mature seed 2 [single channel]

status: Public on Mar 30 2012

city: Rondebosch

first: Nicola

last: Illing

state: Western Cape

address: Chemistry Rd

department: Molecular and Cell Biology

country: South Africa

institute: University of Cape Town

description: Biological replicate 2 of 3. Gene expression levels in mature seed.

hyb_protocol: The X. humilis cDNA microarrays were hybridized with Cy3 fluorescently labeled probes of desiccated leaf, hydrated leaf, desiccated root, hydrated root and seed. Three biological replicates were examined for all experimental conditions apart from the hydrated root condition.  In this case, one biological replicate was hybridised to three separate slides. The statistical analysis was based on a total of three replicates per experimental condition (three biological replicates for all conditions except the hydrated root condition which has three technical replicates). The processed microarray slide was prehybridized with 100 ul of hybridization buffer (50% formamide, 50% SSC, 0.2% SDS) for 2 h at 42°C to reduce background. Slides were washed in dH20 and dried by centrifugation at 1000 rpm for 5 minutes. A total of 100 ul denatured probe mix (80 pmol labelled cDNA, 25% formamide, 5X SSC, 0.1% SDS) was injected under the lifterslip (Erie Scientific, USA) covering the array and the slide was incubated horizontally in a Telechem hybridisation chamber (Telechem International Inc, USA) at 42°C for 16 h in the dark. Slides were subsequently transferred to a fresh dish and washed in a series of wash buffers preheated to 55°C beginning with 2X SSC, 0.5% SDS, followed by 0.5.X SSC and finally 0.05X SDS for 5min each with agitation at room temperature. They were dipped in 100% ethanol and dried by centrifugation at 1000 rpm for 5 minutes.

scan_protocol: Axon confocal scanning system (Genepix 4000B) and GenePix Pro 6.0 data acquisition software (Molecular Devices Products, USA) were used according to the manufacturer’s instructions to capture the X. humilis data. Normalisation of the Cy3 fluorescent dye emission intensities across all the slides was achieved by adjusting the level of the photomuliplier gains. The signal intensities for all 7200 spots were quantified and the mean fluorescence values were extracted.

data_processing: A feature-indicator grid was aligned onto the image of each scanned slide to capture fluorescent intensity data from the scanned slides. Each printed cDNA spot was identified and the foreground, background signal intensities as well as other information for each spot were quantified and extracted by the GenePix Pro 6.0 software according to manufacturer’s instructions. Raw expression data captured and extracted after slide scanning were imported into and processed in R version 2.2.1. Spatial correction of the X. humilis data was conducted using the spat.norm function followed by background correction (bkg.norm function) using the “deterministic” approach in smida. The data sets were normalised using affy quantile normalisation using the normalize.quantiles function in the affy package. Normalized log2 expression values for all technical replicates were merged by averaging.

organism: Xerophyta humilis

source_name: mature, dry seeds

label_protocol: RNA samples extracted from X humilis leaf, root and seed were assessed by visualisation on denaturing formamide gels and spectrophotometrically with a Nanodrop ND-1000 (Nanodrop, USA). The ratios of A260 nm/A280 nm and A260 nm/A230 nm were recorded. Fifteen micrograms of total RNA was fluorescently labeled by reverse transcription in the presence of 5-(3-aminoallyl)-dUTP (Sigma-Aldrich, St. Louis) and 500ng oligodT primer using Superscript III (Invitrogen) overnight at 42ºC.  The RNA was hydrolysed with 500 nM NaOH and 250 nM EDTA at 65°C for 15 minutes and the cDNA was purified through QIAquick PCR Purification columns (Qiagen, Germany) according to the manufacturers recommendations with the replacement wash buffer and elution buffer by phosphate wash buffer (5 mM KPO4, pH 8.0, 80% ethanol) and phosphate elution buffer (4 mM M KPO4, pH 8.5), respectively. Cy3 monofunctional dye (Amersham, Germany) was linked to the aminomodified nucleotides of the purified cDNA in 0.2 M sodium carbonate buffer (pH 9.0) for 1 hour at room temperature in a separate coupling step to generate fluorescently labeled cDNA. The labelled cDNA was separated from uncoupled Cy3 by purification through QIAquick PCR Purification columns (Qiagen, Germany) following the manufacturers protocol and measured at 260 nm and 550 nm on a nanodrop to quantitate both cDNA concentration and Cy dye incorporation.

growth_protocol: X. humilis plants collected from Barakalalo National Park, Limpopo, South Africa, were maintained in trays with good drainage under glasshouse conditions at the University of Cape Town.  Plants were watered every second day for two weeks, prior to the commencement of the desiccation treatment.

extract_protocol: For vegetative tissue: X. humilis leaf and root tissue was ground up with liquid nitrogen and thawed in 5M Na-perchlorate, 0.3M Tris-HCl (pH 8.3), 1% [v/v] SDS, 8.5% [w/v] PVPP, 2% [v/v] PEG-6000, 1% [v/v] beta-ME.  The samples were incubated at room temperature with shaking for 30 minutes, and centrifuged at 10,000 x g for 10 minutes at 4oC. The supernatant was subjected to two rounds of phenol:chloroform:isoamylalcohol (PCI) precipitation followed by an overnight isopropanol precipitation at -20oC.  The precipitated RNA was recovered by centrifugation at 10,000 x g for 10 minutes at 4oC, and the pellet resuspended in 1ml dH2O at 65oC for 5 minutes.  The RNA was selectively precipitated overnight at 4oC with 2.5M LiCl and recovered by centrifugation at 12,000 x g at 4oC for 30 minutes. For seed tissue: Approximately 200 mg X. humilis seeds were ground up in liquid nitrogen and together with 700 ul XT buffer (0.2 M sodium borate decahydrate, 30 mM EGTA, 1% SDS, 1% sodium deoxycholate, 2% PVP, 10 mM DTT, 1% IGEPAL, pH 9.0). The powder was decanted to a 15 ml falcon tube, thawed at room temperature and an additional 700 ul XT buffer added.  The liquid was divided into two eppendorf tubes, 56 ul 2M KCL added to each tube, mixed and incubated on ice for 60 min.  The supernatant was recovered by centrifugation at 13 000 rpm for 20 min at 4ºC and the RNA selectively precipitated by the addition of LiCl to a final of 2.5M and incubation at -20ºC overnight.  The RNA was collected by centrifugation at 13 000 rpm for 20 min at 4ºC and the pellets resuspended in 100 ul RNase-free water.  The RNA was subsequently purified following the RNeasy kit protocol (Qiagen, Germany).

treatment_protocol: Three trays of plants were allowed to dry naturally by withholding water until fully desiccated (~5%RWC) for a total of three weeks and an additional three trays of plants were maintained in a hydrated state (~90%RWC) with watering three times a week.  Desiccated leaf and root samples and hydrated leaf and root samples were harvested simultaneously and flash frozen and stored at -80oC. To calculate the RWC three leaves were removed from the plant and weighed to obtain the fresh weight. These leaves were then placed in a beaker of water for 24 hours and weighed to obtain the weight at full turgour. Subsequently the leaves were placed at 105°C for 24 hours and weighed to obtain the dry weight. The RWC was determined by subtracting average dry weight from the average fresh weight, which is divided by the average fresh weight subtracted from the average weight at full turgor, multiplied by 100. Mature seeds were collected over several flowering intervals from genetically diverse populations of X. humilis plants.

value: seed


title: Mature seed 1 [single channel]

description: Biological replicate 1 of 3. Gene expression levels in mature seed.


title: Mature seed 3 [single channel]


title: Tumor #1 with loss of p53


title: Dicer knockout preadipocytes, biological rep2


title: Root at 100%RWC Replicate 3 [single channel]

description: Biological replicate 2 of 3. Gene expression levels in 100%RWC root.

source_name: Single root at 100%RWC harvested from desiccating plants

value: root

tag: %rwc


title: Root at 100%RWC Replicate 2 [single channel]


title: Control preadipocytes, biological rep4

source_name: Subcutaneous preadipocytes, control

value: control


title: surgically resected, primary breast tumor AL0005

value: LN+


title: Leaf at 100%RWC Replicate 1

description: Biological replicate 1 of 5. Gene expression levels in 100%RWC leaf relative to that in Common reference sample.

hyb_protocol: Microarray slides containing arrayed cDNA clones were pre-hybridized at 42°C for 2 hours in a 100 µl buffer containing 5X SSC, 0.1% SDS and 1% BSA under lifterslips (Erie Scientific, US) in Telechem hybridization chambers (Telechem International Inc., California, US). After pre-hybridization, the slides were washed five times in MilliQ H2O for 30 sec with agitation, dipped in absolute ethanol, before drying by centrifugation at 1000 g for 5 mins. A mixture comprising  1 µg Cy3 labelled experimental probe (i.e synthesized from leaf mRNA from different RWC samples), 1 µg Cy5 labelled common reference probe, 1 µg Mouse COT1-DNA (Life Technologies, Maryland, US), 12 µg Poly(A)-DNA (Pharmacia), 25% formamide, 5X SSC and 0.2% SDS in a 60ul reaction was denatured at 90°C for 3 min.  Each microarray slide was subsequently hybridized to the labelled mixture under lifterslips (Erie Scientific, US)  in the dark for 16 hours at 42°C in Telechem hybridization chambers (Telechem International Inc., California, US). Post-hybridization washes of the microarray slides were carried out as follows: (1) 4 min with agitation at 42°C pre-warmed buffer containing 2X SSC and 0.5% SDS; (2) 4 min with agitation at room temperature in 0.5X SSC; and (3) 4 min with agitation at room temperature in 0.05X SSC. The slides were dipped in absolute ethanol after these washes, and then dried by centrifugation at 1000 g for 5 min.

scan_protocol: Slide scanning and data capturing were carried out using the Axon GenePix 4000 scanner and GenePix Pro 5.0 software (Molecular Devices, California, US) following manufacturer’s instructions. During preview scanning, PMT gain (Photomultiplier tube) settings for both Cy3 and Cy5 channels were adjusted to ensure that the same amount of red and green signals were acquired in each channel. Saturation thresholds were also adjusted to ensure that the majority of the feature signals were below saturation level. The slides were then scanned properly with PMT gain settings optimized from preview scans.

data_processing: A feature-indicator grid was aligned onto the image of each scanned slide to capture fluorescent intensity data from the scanned slides. Each printed cDNA spot was identified and the foreground, background signal intensities as well as other information for each spot were quantified and extracted by the GenePix Pro 5.0 software according to manufacturer’s instructions. Raw expression data captured and extracted after slide scanning were imported into and processed in R version 2.2.1. Spatial bias within each array was normalized by a median based method in package marray using function “maNorm”. Scaling of different arrays was done by Rquantile normalization in package limma, using function “normalizeBetweenArrays”. Normalized log2 ratio values (Cy5/Cy3) for all technical replicates were merged by averaging. Later the normalized log2 ratio values were converted to Cy3/Cy5  (test/reference) log2 ratio values.

source_name: Single leaf at 100%RWC harvested from desiccating plants

label_protocol: One microgram of purified total RNA extracted from each harvested leaf sample was linearly amplified and labelled with Cy3 using Ambion Allyl MessageAmp II aRNA Amplification Kit (Ambion Incorporated, Texas, US) following the manufacturer’s instructions. A common reference sample was constructed by pooling equal amounts of purified total RNA derived from a set of 6 harvested leaf samples at 100%, 80%, 60%, 40%, 20% and 5% RWC respectively (Samples RWC100-rep1, RWC80-rep1, RWC60-rep1, RWC40-rep1, RWC20-rep1 and RWC5-rep1). This pooled total RNA was also linearly amplified and labelled with Cy5 using Ambion Allyl MessageAmp II aRNA Amplification Kit (Ambion Incorporated, Texas, US).

extract_protocol: Total RNA was extracted from each leaf sample using TRI-Reagent (Molecular Research Centre, Inc., US), and purified by using Qiagen RNeasy Mini kit columns (Qiagen, Germany) according to the manufacturer’s instructions. The concentration and purity of the purified total RNA from each sample was quantified on a NanoDrop 1000 spectrophotometer (NanoDrop Technologies, Delaware, US). The integrity of RNA was checked by visualization of 0.5 ug of each sample electrophoresed on a formaldehyde denaturing gel containing 1% agarose, 1X MOPS and 6.75% formaldehyde.

treatment_protocol: A night before the start of the desiccation treatment, plants were watered thoroughly, and covered with plastic bags. The plastic covers were removed the following day and plants were allowed to dry under natural weather conditions by not watering for several days. Several single leaf samples were harvested daily at 10 am, 2 pm or 4 pm, by handpicking from random trays of plants during the course of desiccation. Each harvested leaf was immediately split into two halves by carefully tearing along the midrib. One half was immediately snap frozen in liquid nitrogen and stored at -80°C until being used for RNA extraction. The other half was used to determine the %RWC of that harvested leaf.

tag: actual %rwc

tag: harvest time

source_name: Common Reference: Pool of 6 single leaves (at 6 different RWC figures) harvested from desiccating plants

value: 10am, 2pm, 4pm, 10am, 10am, 10am respectively


title: surgically resected, primary breast tumor NUH_BT09_A


title: Control preadipocytes, biological rep1


title: Control preadipocytes, biological rep2


title: surgically resected, primary breast tumor AL0002


title: Control preadipocytes, biological rep3


title: surgically resected, primary breast tumor AL0001

value: PgR-


title: surgically resected, primary breast tumor AL0004

value: primary breast tumor


title: surgically resected, primary breast tumor AL0003

value: breast cancer


title: Leaf at 100%RWC Replicate 1 [single channel]

description: Biological replicate 1 of 3. Gene expression levels in 100%RWC leaf.

value: leaf


title: Leaf at 100%RWC Replicate 2 [single channel]

description: Biological replicate 2 of 3. Gene expression levels in 100%RWC leaf.


title: Root at 5%RWC Replicate 1 [single channel]

description: Biological replicate 1 of 3. Gene expression levels in 5%RWC root.

source_name: Single root at 5%RWC harvested from desiccating plants


title: Root at 5%RWC Replicate 2 [single channel]

description: Biological replicate 2 of 3. Gene expression levels in 5%RWC root.


title: Leaf at 5%RWC Replicate 2 [single channel]

description: Biological replicate 2 of 3. Gene expression levels in 5%RWC leaf.

source_name: Single leaf at 5%RWC harvested from desiccating plants


title: Leaf at 5%RWC Replicate 1 [single channel]

description: Biological replicate 1 of 3. Gene expression levels in 5%RWC leaf.


title: Leaf at 5%RWC Replicate 3 [single channel]


title: Leaf at 100%RWC Replicate 3 [single channel]


title: Leaf at 5%RWC Replicate 5

description: Biological replicate 5 of 5. Gene expression levels in 5%RWC leaf relative to that in Common reference sample.


title: Leaf at 5%RWC Replicate 4

description: Biological replicate 4 of 5. Gene expression levels in 5%RWC leaf relative to that in Common reference sample.


title: Leaf at 5%RWC Replicate 3

description: Biological replicate 3 of 5. Gene expression levels in 5%RWC leaf relative to that in Common reference sample.


title: Leaf at 5%RWC Replicate 1

description: Biological replicate 1 of 5. Gene expression levels in 5%RWC leaf relative to that in Common reference sample.


title: Leaf at 20%RWC Replicate 5

description: Biological replicate 5 of 5. Gene expression levels in 20%RWC leaf relative to that in Common reference sample.

source_name: Single leaf at 20%RWC harvested from desiccating plants


title: Leaf at 20%RWC Replicate 4

description: Biological replicate 4 of 5. Gene expression levels in 20%RWC leaf relative to that in Common reference sample.


title: Leaf at 5%RWC Replicate 2

description: Biological replicate 2 of 5. Gene expression levels in 5%RWC leaf relative to that in Common reference sample.


title: Leaf at 20%RWC Replicate 3

description: Biological replicate 3 of 5. Gene expression levels in 20%RWC leaf relative to that in Common reference sample.


title: Leaf at 20%RWC Replicate 1

description: Biological replicate 1 of 5. Gene expression levels in 20%RWC leaf relative to that in Common reference sample.


title: Leaf at 20%RWC Replicate 2

description: Biological replicate 2 of 5. Gene expression levels in 20%RWC leaf relative to that in Common reference sample.


title: Leaf at 40%RWC Replicate 5

description: Biological replicate 5 of 5. Gene expression levels in 40%RWC leaf relative to that in Common reference sample.

source_name: Single leaf at 40%RWC harvested from desiccating plants


title: Leaf at 40%RWC Replicate 3

description: Biological replicate 3 of 5. Gene expression levels in 40%RWC leaf relative to that in Common reference sample.


title: Leaf at 40%RWC Replicate 4

description: Biological replicate 4 of 5. Gene expression levels in 40%RWC leaf relative to that in Common reference sample.


title: Leaf at 40%RWC Replicate 2

description: Biological replicate 2 of 5. Gene expression levels in 40%RWC leaf relative to that in Common reference sample.


title: Leaf at 40%RWC Replicate 1

description: Biological replicate 1 of 5. Gene expression levels in 40%RWC leaf relative to that in Common reference sample.


title: Leaf at 80%RWC Replicate 3

description: Biological replicate 3 of 5. Gene expression levels in 80%RWC leaf relative to that in Common reference sample.

source_name: Single leaf at 80%RWC harvested from desiccating plants


title: Leaf at 80%RWC Replicate 4

description: Biological replicate 4 of 5. Gene expression levels in 80%RWC leaf relative to that in Common reference sample.


title: Leaf at 80%RWC Replicate 5

description: Biological replicate 5 of 5. Gene expression levels in 80%RWC leaf relative to that in Common reference sample.


title: Leaf at 80%RWC Replicate 2

description: Biological replicate 2 of 5. Gene expression levels in 80%RWC leaf relative to that in Common reference sample.


title: Leaf at 60%RWC Replicate 2

description: Biological replicate 2 of 5. Gene expression levels in 60%RWC leaf relative to that in Common reference sample.

source_name: Single leaf at 60%RWC harvested from desiccating plants


title: Leaf at 60%RWC Replicate 1

description: Biological replicate 1 of 5. Gene expression levels in 60%RWC leaf relative to that in Common reference sample.


title: Leaf at 60%RWC Replicate 3

description: Biological replicate 3 of 5. Gene expression levels in 60%RWC leaf relative to that in Common reference sample.


title: Leaf at 60%RWC Replicate 5

description: Biological replicate 5 of 5. Gene expression levels in 60%RWC leaf relative to that in Common reference sample.


title: Leaf at 100%RWC Replicate 5

description: Biological replicate 5 of 5. Gene expression levels in 100%RWC leaf relative to that in Common reference sample.


title: Leaf at 60%RWC Replicate 4

description: Biological replicate 4 of 5. Gene expression levels in 60%RWC leaf relative to that in Common reference sample.


title: Root at 5%RWC Replicate 3 [single channel]

description: Biological replicate 2 of 3. Gene expression levels in 5%RWC root.


title: Leaf at 100%RWC Replicate 4

description: Biological replicate 4 of 5. Gene expression levels in 100%RWC leaf relative to that in Common reference sample.


title: Leaf at 100%RWC Replicate 3

description: Biological replicate 3 of 5. Gene expression levels in 100%RWC leaf relative to that in Common reference sample.


title: Leaf at 80%RWC Replicate 1

description: Biological replicate 1 of 5. Gene expression levels in 80%RWC leaf relative to that in Common reference sample.


title: Leaf at 100%RWC Replicate 2

description: Biological replicate 2 of 5. Gene expression levels in 100%RWC leaf relative to that in Common reference sample.