title: lateralProstate_treatmentICI_662

city: RTP

first: Johannes

middle: M

last: Freudenberg

state: NC

address: 111 TW Alexander Dr

department: Biostatistics Branch

institute: NIEHS

description: lateral prostate,T+E2+ICI

hyb_protocol: Rat Genome 230 2.0 Array GeneChips were hybridized with 15 ug of fragmented aRNA. The hybridization, staining, and washing were carried out using the Affymetrix GeneChip Hybridization Wash and Stain Kit (P/N 900720) following the manufacturer’s protocols. The arrays were hybridized for 16 hr at 45oC using an Affymetrix Hybridization Oven 640 (P/N 800139).  FS450_0001 protocol was used for staining and washing the GeneChips using the Affymetrix Fluidics Station 450 (P/N 00-0079).

scan_protocol: The GeneChips were scanned with Affymetrix GeneChip Scanner 3000 7G using GCOS software and Affymetrix preset settings.

data_processing: Data was processed by performing background correction, quantile normalization, and calculation of expression set summaries using the Robust Multichip Average (RMA) protocol (Irizarry et al. (2003); Biostatistics 4: pages 249-264) as implemented in the affy packge from Bioconductor (http://www.bioconductor.org). Gene-specific probesets were constructed using the Entrez Gene – centric custom CDF, version 10 (Dai et al. (2005); Nucl Acids Res 33: e175).  Log-scale data was further normalized by 1) setting the per-sample median to 6.5 and 2) subtracting the per-gene median.

organism: Rattus norvegicus

source_name: lateral prostate,T+E2+ICI

label_protocol: Total RNA samples of 1 μg or greater were amplified one round, and the amplified RNA (aRNA) was biotinylated using Ambion Biotin-Enhanced Message Amp II kit (#1791, Ambion, Austin, Texas), following the manufacturer’s protocols.

growth_protocol: Male NBL rats (5-6 weeks old) were purchased from Charles River Laboratories (Kingston, NY, USA), kept under standard conditions, and treated as previously reported.

extract_protocol: RNA was extracted by TRIZO reagent from the frozen lateral prostate.

treatment_protocol: Rats in the T+E2, T+E2+Br, T+E2+ICI treatment groups received sc implants of two pieces of 2-cm long silastic capsules containing T (Sigma, St Louis, MO) and one piece of 1-cm long capsules packed with E2 (Sigma).  One group T+ E2-implanted rats received ICI sub-cutaneously in the flank twice per week at a dose of 3 mg/kg. Br pellets implanted sub-cutaneously in the flank and were changed once (after 2 months) during the 16-week protocol to effect a daily release of 4 mg/kg body wt per day.


title: CDK9 Knock Down4

status: Public on May 09 2010

type: RNA

city: Nashville

first: Yan

last: Guo

state: TN

address: 639 Preston Research Bld

country: USA

institute: Vanderbilt Cancer Center

hyb_protocol: Following fragmentation, the RNA was loaded on to the Affymetrix HuGene-1_0-st-v1 GeneChip as directed (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G

data_processing: The primary microarray data was normalized using RMA method in Affymetrix Expression Console 1.1 and annotated using latest annotation file based on genome version hg19.  The analysis was done in R using LIMMA package.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: CDK9 Knock Down

label_protocol: The RNA was labeled with GeneChipR One-Cycle Target Labeling and Control Reagents.

growth_protocol: The cell lines were grown in DMEM + 7.5% FBS

extract_protocol: Total RNA was isolated from the cell lines using Qiagen RNeasy Mini kit as directed (Qiagen, Valencia, CA). The quality and quantity of the RNA was determined using the Agilent RNA 6000 NanoLabChip kit and Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: U2OS cells were transfected with siRNA against NT (non-targeting) or CDK9 at 10 nM using Hi-Perfect (Qiagen) and harvested 72 hours after transfection.

tag: cell line

tag: tissue type

value: osteosarcoma


title: lateralProstate_treatmentICI_672

description: lateral prostate,T+E2+ICI

tag: agent


title: Nonspecific siRNA3

source_name: Nonspecific siRNA


title: CDK9 Knock Down2


title: Nonspecific siRNA2


title: CDK9 Knock Down1


title: lateralProstate_treatmentE2_631

description: lateral prostate,T+E2

source_name: lateral prostate,T+E2


title: lateralProstate_treatmentBr_522

description: lateral prostate,T+E2+Br

source_name: lateral prostate,T+E2+Br


title: lateralProstate_treatmentE2_622

description: lateral prostate,T+E2


title: lateralProstate_treatmentICI_651

description: lateral prostate,T+E2+ICI


title: lateralProstate_treatmentBr_521

description: lateral prostate,T+E2+Br


title: lateralProstate_treatmentBr_711

description: lateral prostate,T+E2+Br


title: lateralProstate_treatmentE2_641

description: lateral prostate,T+E2


title: lateralProstate_treatmentICI_652

description: lateral prostate,T+E2+ICI


title: lateralProstate_treatmentControl_612

description: lateral prostate,control

source_name: lateral prostate,control

value: Control


title: lateralProstate_treatmentE2_632

description: lateral prostate,T+E2


title: lateralProstate_treatmentControl_591

description: lateral prostate,control


title: lateralProstate_treatmentBr_511

description: lateral prostate,T+E2+Br


title: lateralProstate_treatmentControl_592

description: lateral prostate,control


title: lateralProstate_treatmentControl_531

description: lateral prostate,control


title: MM line transfected with shERK2, rep2

status: Public on May 08 2010

city: Burlington

first: Arti

last: Shukla

state: VT

address: 89 Beaumont Avenue

department: Pathology

institute: University of Vermont

description: Gene expression data in ERK2-inhibited epithelioid mesothelioma cell line.

hyb_protocol: Biotin-labeled cDNA fragments were hybridized to the probe array at 45oC for 16 h.

scan_protocol: The probe array were scanned (Affymetrix GeneArray Scanner, GS3000) to quantify the fluorescence intensity associated with each oligonucleotide probe.

data_processing: A human U133A 2.0 array was scanned twice, the images overlaid, and the average intensities of each probe cell compiled. Microarray data were analyzed using GeneSifter software (VizX Labs, Seattle, WA) by the RMA method. Data were log transformed.

label: Biotin

source_name: Stable transfection with shERK2 SureSilencing plasmid

label_protocol: RNA was synthesized to ds cDNA which was then converted to amplified ss cDNA using a Nugen Ovation V2 system. ss cDNA was Biotinylated using TdT end label.

growth_protocol: All cells were incubated at 37oC and 5% CO2 and grown to approximately 80-90% confluency in DMEM/F12 medium at a 1:1 ratio containing 10% fetal bovine serum (FBS), 0.1 ug/ml hydrocortisone, 2.5 ug/ml insulin, 2.5 ug/ml transferrin and 2.5 ng/ml sodium selenite and penicillin-streptomycin (50 U/ml penicillin G, 50 ug/ml streptomycin sulfate).

extract_protocol: Total RNA was extracted from cells using an RNeasy Plus Mini kit according to the manufacturer's protocol (Qiagen, Valencia, CA). RNA was dissolved in RNAse-free water and quantified using the NanoDrop spectrophotometer.

treatment_protocol: In order to achieve inhibition of ERK1 or ERK2, mesothelioma cells (HMESO) were stably transfected with either shControl, shERK1 or shERK2 plasmid from SABiosciences using Lipofectamine 2000. After selection in G418 (400ug/ml) medium for 14 days, limited dilution was performed to get pure clones of more than 70% inhibited ERK1 or ERK2.

value: HMESO

tag: cell type

value: epithelioid malignant mesothelioma (MM)

tag: transfection

tag: property

value: ERK2>70% inhibited


title: MM line transfected with shERK1, rep2

description: Gene expression data in ERK1-inhibited epithelioid mesothelioma cell line.

source_name: Stable transfection with shERK1 SureSilencing plasmid

value: ERK1>70% inhibited


title: MM line transfected with shERK2, rep1


title: MM line transfected with shERK2, rep3


title: MM line transfected with shERK1, rep3


title: CDK9 Knock Down3


title: MM line transfected with shCon, rep3

description: Gene expression data in epithelioid mesothelioma cell line transfected with shCon plasmid.

source_name: Stable transfection with shCon SureSilencing plasmid

value: shControl


title: MM line transfected with shCon, rep1


title: Malignant mesothelioma tumor cell line, rep2

description:
Gene expression data in epithelioid mesothelioma cell line.

Reale et al. (Cancer Res., 1987, 47, 3199-205): PMID 3555770

source_name: malignant mesothelioma tumor cell line, untransfected

value: untransfected


title: MM line transfected with shERK1, rep1


title: MM line transfected with shCon, rep2


title: Malignant mesothelioma tumor cell line, rep3


title: Mesothelial cell line, rep3

description:
Gene expression data in immortalized mesothelial cell line.

Dickson et al. (Mol Cell Biol., 2000, 20, 1436-1447): PMID 10648628

source_name: mesothelial cell line, untransfected

value: mesothelial cells

value: hTERT immortalized


title: Malignant mesothelioma tumor cell line, rep1


title: Mesothelial cell line, rep2


title: Mesothelial cell line, rep1


title: PHF11myc_2

status: Public on May 07 2010

city: Westmead

first: Graham

last: Jones

state: NSW

address: Darcy Road

department: Immunology

country: Australia

institute: Westmead Millennium Institute

description:
replicate 2
The probe set for PHF11 on this Illumina chip is at the 3' end of the cDNA that is NOT present on the PHF11myc construct. Therefore, no increase in PHF11 due to to over-expression of PHF11myc was seen.

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: PHF11myc over-expressing Jurkat T-cells

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

extract_protocol: Total RNA was extracted using the Ambion RNAqueous kit. Quality control was performed with Agilent Bioanalyser.

value: PHF11myc over-expressing Jurkat T-cells


title: PAV, Cyclic Stretch conditions with 5HT plus Fluox added, biological rep 2

city: Philadelphia

first: Marina

last: Bakay

state: PA

address: 3615 Civic Center Boulevard

department: Pediatrics

institute: Children's Hospital of Philadelphia

description: Gene expression data from Porcine Aortic Valve (PAV)

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

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

data_processing: All microarrays were entered into a single normalized project using Partek Genomic Suite (GS) software (Parterk Inc, St. Louis, Missouri). The raw data were normalized using GCRMA across the 24 CEL files. Quality control assessment was performed with Partek GS. Four experimental groups (six arrays per group) were created for gene expression comparisons: 1) Static conditions with no agents added; 2) Cyclic stretch conditions with no agents added; 3) Static conditions with 5HT plus Fluox added; 4) Cyclic stretch conditions with 5HT plus Fluox added.

organism: Sus scrofa

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

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

treatment_protocol: The three leaflets were excised from each porcine aortic valve and a rectangular section of tissue 15x10 mm was isolated from the central region of each valve cusp. These samples were randomized and assigned to one of four groups. Leaflet samples from static control and 5HT plus Fluox groups were statically incubated in DMEM, supplemented with 10% fetal bovine serum (FBS) , 50 mg/l ascorbic acid, 3.7 g/l sodium bicarbonate, 1% nonessential amino acid solution, and 1% antimycotic-antibiotic solution, at 37ºC for duration of experiments (24 hours) without or with mentioned above reagents. Leaflets section from the cyclic stretched groups had loops sutured to 10mm ends and were suspended in DMED supplemented as described above, without or with mentioned above reagents, in a tensile stretch bioreactor (Engelmayr et al, Biomaterials 2003; Balachandran et al, Annals of Biomed Engineering 2006). After the bioreactor incubation was done the samples were removed and immediately washed three times in ice-cold sterile PBS.

tag: tissue

value: Porcine aortic valve

tag: treatment

tag: sample type

value: Domestic pigs

tag: age

value: between 12-24 months


title: CON_1

description:
replicate 1
The probe set for PHF11 on this Illumina chip is at the 3' end of the cDNA that is NOT present on the PHF11myc construct. Therefore, no increase in PHF11 due to to over-expression of PHF11myc was seen.

source_name: control Jurkat T-cells

value: control Jurkat T-cells


title: PAV, Cyclic Stretch conditions with no agents added, biological rep 4


title: PAV, Cyclic Stretch conditions with 5HT plus Fluox added, biological rep 1


title: PAV, Cyclic Stretch conditions with 5HT plus Fluox added, biological rep 3


title: PAV, Cyclic Stretch conditions with 5HT plus Fluox added, biological rep 4


title: PHF11myc_1


title: CON_2


title: PAV, Cyclic Stretch conditions with 5HT plus Fluox added, biological rep 5


title: PAV, Cyclic Stretch conditions with no agents added, biological rep 2


title: PAV, Cyclic Stretch conditions with 5HT plus Fluox added, biological rep 6


title: PAV, Cyclic Stretch conditions with no agents added, biological rep 3


title: PAV, Static conditions with 5HT plus Fluox added, biological rep 5


title: PAV, Static conditions with no agents added, biological rep 5

value: Static conditions with no agents added


title: PAV, Static conditions with 5HT plus Fluox added, biological rep 1


title: PAV, Static conditions with 5HT plus Fluox added, biological rep 3


title: PAV, Static conditions with no agents added, biological rep 6


title: PAV, Cyclic Stretch conditions with no agents added, biological rep 5


title: PAV, Static conditions with 5HT plus Fluox added, biological rep 4


title: PAV, Static conditions with no agents added, biological rep 4


title: PAV, Cyclic Stretch conditions with no agents added, biological rep 6


title: PAV, Static conditions with 5HT plus Fluox added, biological rep 2


title: PAV, Static conditions with no agents added, biological rep 1


title: PAV, Static conditions with no agents added, biological rep 2


title: PAV, Static conditions with 5HT plus Fluox added, biological rep 6


title: PAV, Cyclic Stretch conditions with no agents added, biological rep 1


title: Spermatogenesis in S. senegalensis: Mid vs. Late 2

city: Barcelona

first: Josep

middle: V

last: Planas

address: Av. Diagonal 643

department: Fisiologia i Immunologia (Biologia)

country: Spain

institute: Universitat de Barcelona

description: Biological replicate 2 of 3

hyb_protocol: Hybridizations were carried out for 17 h at 60°C using Agilent's gaskets G2534-60002, G2534A hybridization chambers, and DNA Hybridization Oven G2545A, according to the manufacturer's instructions

scan_protocol: Microarray raw data were obtained using Agilent's DNA Microarray Scanner G2505B and Feature Extraction software (v10.1)

data_processing: Raw data were obtained using Agilent's DNA Microarray Scanner G2505B and Feature Extraction software (v10.1). The raw fluorescence intensity data were processed using the Polyphemus software, developed at Oryzon Genomics, which includes spatial data compensation, non-significant expressed data filtering, and data normalization. Data normalization was carried out by an improved version of the nonlinear Q-splines normalization method, enhanced with robust regression techniques.

organism: Solea senegalensis

source_name: Mid spermatogenic testis

label_protocol: Total RNA (0.5 μg) from each sample was amplified and labelled with fluorescent cyanine dyes, Cy3 or Cy5, using the Eberwein mRNA amplification procedure employing the MessageAmp™ aRNA amplification kit from Ambion (Applied Biosystems) following the manufacturer's instructions with minor modifications

extract_protocol: Total RNA was extracted from mid spermatogenic testes using the RNeasy extraction kit (Qiagen) and treated with DNAse following the manufacturer’s instructions

value: testis pieces

tag: developmental stage

value: mid spermatogenesis

source_name: Late spermatogenic testis

extract_protocol: Total RNA was extracted from late spermatogenic testes using the RNeasy extraction kit (Qiagen) and treated with DNAse following the manufacturer’s instructions

value: late spermatogenesis


title: Spermatogenesis in S. senegalensis: Mid vs. Late 3

description: Biological replicate 3 of 3


title: Spermatogenesis in S. senegalensis: Early vs. Late 1

description: Biological replicate 1 of 2

source_name: early spermatogenic testis

extract_protocol: Total RNA was extracted from early spermatogenic testes using the RNeasy extraction kit (Qiagen) and treated with DNAse following the manufacturer’s instructions

value: early spermatogenesis

source_name: late spermatogenic testis


title: Spermatogenesis in S. senegalensis: Functional mature vs. Late 2

description: Biological replicate 2 of 2

source_name: Mature spermatogenic testis

extract_protocol: Total RNA was extracted from testes at the functional maturation stage using the RNeasy extraction kit (Qiagen) and treated with DNAse following the manufacturer’s instructions

value: mature spermatogenesis


title: Spermatogenesis in S. senegalensis: Early vs. Late 2

description: Biological replicate 2 of 2


title: PAV, Static conditions with no agents added, biological rep 3


title: Spermatogenesis in S. senegalensis: Functional mature vs. Late 1

description: Biological replicate 1 of 2


title: Spermatogenesis in S. senegalensis: Mid vs. Late 1

description: Biological replicate 1 of 3


title: Recurrent bladder tumor BT060.2

status: Public on May 06 2010

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

description: To export to gene expression data based on unique gene, we use Sample Gene Profile option of Illumina BeadStudio software.  Therefore, a total of 5553 probe data which have duplicated gene aggregated unique genes from the whole 48701 probes on the Human-6 beadChip ver. 2.

hyb_protocol: Labeled, amplified material (1,500 ng per array) was hybridized to a ver. 2 of the Illumina Human-6 BeadChip (48K) according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA). Array signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the BeadChip manual.

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

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

source_name: Recurrent non-muscle invasive tumor

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina’s recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina® TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using RiboGreen were measured (Quant-iTTM RiboGreen® RNA assay kit; Invitrogen-Molecular Probes, ON, Canada) by the Victor3 spectrophotometer (PerkinElmer, CT) and cRNA quality was checked on a 1% agarose gel.

extract_protocol: Total RNA was isolated from tissues with TRIzol (Life Technologies, NY) reagent according to the manufacturer’s protocol. RNA quality and integrity were confirmed by electrophoresis on agarose gel stained with ethidium bromide and examined under ultraviolet light.

tag: biological source

value: recurrent non-muscle invasive tumor


title: Recurrent bladder tumor BT095.1


title: Recurrent bladder tumor BT083.1


title: Recurrent bladder tumor BT071.1


title: Recurrent bladder tumor BT047.4


title: Recurrent bladder tumor BT053.1


title: Recurrent bladder tumor BT047.1


title: Recurrent bladder tumor BT047.3


title: Recurrent bladder tumor BT067.1


title: Recurrent bladder tumor BT060.1


title: Recurrent bladder tumor BT069.1


title: Recurrent bladder tumor BT063.1


title: Recurrent bladder tumor BT041.1


title: Recurrent bladder tumor BT057.2


title: Recurrent bladder tumor BT062.1


title: Recurrent bladder tumor BT067.2


title: Recurrent bladder tumor BT036.2


title: Recurrent bladder tumor BT067.3


title: Recurrent bladder tumor BT047.2


title: Recurrent bladder tumor BT062.2


title: Recurrent bladder tumor BT042.1


title: Recurrent bladder tumor BT036.1


title: Primary bladder cancer BT165

source_name: Primary bladder cancer

value: primary bladder cancer

tag: SEX

value: M

tag: AGE

tag: invasiveness

value: non-muscle invasive

tag: intravesical therapy

value: No

tag: systemic chemo

tag: grade

value: low

tag: recurrence

tag: progression

tag: overall survival

value: survival

tag: cancer specific survival

tag: survival month


title: Primary bladder cancer BT164

value: F

value: muscle invasive

value: Yes


title: Primary bladder cancer BT166

value: high


title: Primary bladder cancer BT162


title: Recurrent bladder tumor BT034.1


title: Primary bladder cancer BT160


title: Primary bladder cancer BT159

value: death


title: Primary bladder cancer BT157


title: Primary bladder cancer BT158


title: Primary bladder cancer BT144


title: Primary bladder cancer BT145


title: Primary bladder cancer BT153


title: Primary bladder cancer BT154


title: Primary bladder cancer BT155


title: Primary bladder cancer BT156


title: Primary bladder cancer BT150


title: Primary bladder cancer BT149


title: Primary bladder cancer BT147


title: Primary bladder cancer BT163


title: Primary bladder cancer BT129


title: Primary bladder cancer BT143


title: Primary bladder cancer BT130


title: Primary bladder cancer BT161


title: Primary bladder cancer BT127


title: Primary bladder cancer BT128


title: Primary bladder cancer BT125


title: Primary bladder cancer BT126


title: Primary bladder cancer BT124


title: Primary bladder cancer BT118


title: Primary bladder cancer BT122


title: Primary bladder cancer BT135


title: Primary bladder cancer BT121


title: Primary bladder cancer BT131


title: Primary bladder cancer BT120


title: Primary bladder cancer BT123


title: Primary bladder cancer BT110


title: Primary bladder cancer BT102


title: Primary bladder cancer BT108


title: Primary bladder cancer BT117


title: Primary bladder cancer BT115


title: Primary bladder cancer BT091


title: Primary bladder cancer BT098


title: Primary bladder cancer BT095


title: Primary bladder cancer BT099


title: Primary bladder cancer BT096


title: Primary bladder cancer BT101


title: Primary bladder cancer BT106


title: Primary bladder cancer BT103


title: Primary bladder cancer BT100


title: Primary bladder cancer BT093


title: Primary bladder cancer BT092


title: Primary bladder cancer BT105


title: Primary bladder cancer BT086


title: Primary bladder cancer BT090


title: Primary bladder cancer BT097


title: Primary bladder cancer BT076


title: Primary bladder cancer BT081


title: Primary bladder cancer BT080


title: Primary bladder cancer BT077


title: Primary bladder cancer BT089


title: Primary bladder cancer BT088


title: Primary bladder cancer BT074


title: Primary bladder cancer BT071


title: Primary bladder cancer BT069


title: Primary bladder cancer BT073


title: Primary bladder cancer BT070


title: Primary bladder cancer BT066


title: Primary bladder cancer BT057


title: Primary bladder cancer BT068


title: Primary bladder cancer BT044


title: Primary bladder cancer BT048


title: Primary bladder cancer BT065


title: Primary bladder cancer BT056


title: Primary bladder cancer BT049


title: Primary bladder cancer BT050


title: Primary bladder cancer BT040


title: Primary bladder cancer BT045


title: Primary bladder cancer BT043


title: Primary bladder cancer BT041


title: Primary bladder cancer BT054


title: Primary bladder cancer BT072


title: Primary bladder cancer BT058


title: Primary bladder cancer BT060


title: Primary bladder cancer BT052


title: Primary bladder cancer BT061


title: Primary bladder cancer BT037


title: Primary bladder cancer BT033


title: Primary bladder cancer BT032


title: Primary bladder cancer BT142


title: Primary bladder cancer BT136


title: Primary bladder cancer BT064


title: Primary bladder cancer BT035


title: Primary bladder cancer BT036


title: Primary bladder cancer BT031


title: Primary bladder cancer BT029


title: Primary bladder cancer BT030


title: Primary bladder cancer BT027


title: Primary bladder cancer BT026


title: Primary bladder cancer BT025


title: Primary bladder cancer BT021


title: Primary bladder cancer BT024


title: Primary bladder cancer BT016


title: Primary bladder cancer BT022


title: Primary bladder cancer BT020


title: Primary bladder cancer BT014


title: Primary bladder cancer BT018


title: Primary bladder cancer BT012


title: Primary bladder cancer BT019


title: Primary bladder cancer BT009


title: Primary bladder cancer BT111


title: Primary bladder cancer BT011


title: Primary bladder cancer BT005


title: Primary bladder cancer BT008


title: Primary bladder cancer BT003


title: Primary bladder cancer BT010


title: Primary bladder cancer BT006


title: Primary bladder cancer BT002


title: Primary bladder cancer BT013


title: Surrounding BS302

source_name: Bladder mucosae surrounding cancer

value: bladder mucosae surrounding cancer


title: Surrounding BS301


title: Surrounding BS169


title: Surrounding BS170


title: Surrounding BS303


title: Surrounding BS168


title: Surrounding BS150


title: Surrounding BS142


title: Surrounding BS135


title: Surrounding BS134


title: Surrounding BS131


title: Surrounding BS125


title: Surrounding BS119


title: Surrounding BS126


title: Surrounding BS123


title: Surrounding BS130


title: Surrounding BS115


title: Surrounding BS117


title: Surrounding BS108


title: Surrounding BS101


title: Surrounding BS109


title: Surrounding BS095


title: Surrounding BS104


title: Surrounding BS093


title: Surrounding BS091


title: Surrounding BS107


title: Surrounding BS100


title: Surrounding BS087


title: Surrounding BS113


title: Surrounding BS089


title: Surrounding BS097


title: Surrounding BS106


title: Surrounding BS111


title: Surrounding BS084


title: Surrounding BS129


title: Surrounding BS068


title: Surrounding BS086


title: Surrounding BS083


title: Surrounding BS073


title: Surrounding BS075


title: Surrounding BS081


title: Surrounding BS080


title: Surrounding BS085


title: Surrounding BS065


title: Surrounding BS054


title: Surrounding BS059


title: Surrounding BS063


title: Surrounding BS039


title: Surrounding BS045


title: Surrounding BS040


title: Surrounding BS047


title: Surrounding BS048


title: Surrounding BS052


title: Surrounding BS038


title: Surrounding BS051


title: Surrounding BS017


title: Control C030

source_name: Normal bladder mucosae

value: normal bladder mucosae


title: Surrounding BS044


title: Control C040


title: Control C045


title: Control C051


title: PaeTBCF10839_wildtype_LB_rep2

city: Hannover

first: Burkhard

last: Tuemmler

address: Carl-Neuberg-Str. 1

country: Germany

institute: Medizinische Hochschule Hannover

hyb_protocol: MES hybridization buffer (100 mM MES [morpholineethanesulfonic acid], 1 M NaCl, 20 mM EDTA, 0.01% Tween), 50 pM B2 control oligonucleotide (Affymetrix), 0.1 mg/ml herring sperm DNA (Promega), 0.5 mg/ml BSA (Invitrogen), and 7% (wt/vol) dimethyl sulfoxide (DMSO) were added to the labeled cDNA and loaded onto a P. aeruginosa PAO1 GeneChip (Affymetrix). After incubation for 16 h at 50°C at 60 rpm in an Affymetrix hybridization oven, the GeneChips were put into the Affymetrix fluidics station for washing. First the GeneChips were washed 20 times with nonstringent buffer (6x SSPE [1.08 M NaCl, 60 mM NaH2PO4, 1 mM EDTA; pH 7.7] and 0.01% [vol/vol] Tween 20) at 25°C and then they were washed 60 times with stringent buffer (100 mM MES, 0.1 M NaCl, 0.01% [vol/vol] Tween 20) at 50°C. Then a streptavidin solution mix, consisting of 10 µg/ml streptavidin, 2 mg/ml bovine serum albumin (BSA), 100 mM MES, 0.1 M NaCl, and 0.01% (vol/vol) Tween 20, was applied for 10 min at 25°C to stain bound cDNA. After washing for 40 times with nonstringent buffer at 30°C, the GeneChip was subjected to a secondary stain (5 µg/ml biotin-antistreptavidin antibody [Vector Laboratories, Burlingame, CA.], 100 µg/ml normal goat immunoglobulin G, 2 mg/ml BSA, 100 M MES, 0.1 M NaCl, 0.01% [vol/vol] Tween 20) for 10 min at 25°C and to a third stain (10 µg/ml streptavidin-phycoerythrin [Molecular Probes], 2 mg/ml BSA, 100 M MES, 0.1 M NaCl, 0.01% [vol/vol] Tween 20) for 10 min at 25°C. Finally excess label was removed by 60 washings with nonstringent buffer at 30°C.

scan_protocol: GeneChips were scanned at 570 nm with 3 µm resolution by the HP Affymetrix GeneChip scanner (Affymetrix Microarray Suite 5.0)

data_processing: Data analysis was performed using the Affymetrix Microarray Suite software 5.0 with Affymetrix default parameters. The average microarray hybridization signal intensity was scaled to 150 and  MAS5.0 was used as transformation algorithm.  Experiments were carried out in duplicate. Two GeneChips for each mutant and wild type were compared by the four-comparison survival method (Chen et al., 2000). The data were imported into a Microsoft Access database capable of searching for genes, which were found in all four pairings defined by the Affymetrix Microarray Suite Software as having significant changes in their signal intensities. The arithmetic average and the standard deviation (SD) were calculated. Finally, a Bonferroni correction for multiple testing was applied as a rigorous criterion for significantly changed signal intensities (Salunkhe et al, 2002). Data were combined with the latest annotation (10 April 2010) from the web site of the P. aeruginosa PAO1 sequence and the community annotation project provided at http://www.pseudomonas.com.

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa TBCF10839 wild type, cultivated in LB

label_protocol: The fragmentation product was end labeled with the Enzo BioArray terminal labeling kit with biotin-ddUTP (Affymetrix, Santa Clara, CA.).

growth_protocol: P. aeruginosa strains were routinely grown overnight as shaken cultures (230 rpm) in Luria broth (LB) medium at 37°C. Five mL LB broth were inoculated with a toothpick of frozen bacterial stock solution and incubated for 16-48 h. Aliquots of these precultures served as inoculates for the main cultures. Stationary phase-grown cultures (3 x 10e10 cells) were resuspended in fresh Luria broth and kept in a dialysis tube (14-kDa cutoff, 25 mm) with an effective length of 6 cm for the exchange of fluids. Then the dialysis tube was resuspended in a 1-liter Erlenmeyer flask containing 600 ml of LB. The flasks were incubated at 37°C and 200 rpm on a rotary shaker for 2 h.

extract_protocol: RNA isolation: Bacterial cells were harvested by centrifugation at 3800 X g for 2 min at 4 oC. Total RNA from approximately 3 x 1010 cells was extracted with a modified hot phenol method (Tao et al., 1999). Bacteria were quickly resuspended in 0.5 ml of distilled water and lysed in 7.5 ml of preheated (65 oC) phenol/lysis-buffer mix 5 ml phenol (pH 5.5); 2.5 ml 2 % SDS, 30 mM Na-acetate, 3 mM EDTA, pH 5.5 with vigorous shaking for 10 min. The cell lysate was centrifuged at 3,800 X g for 20 min and the supernatant was extracted with 3 ml of phenol:chloroform:isoamyl alcohol (25:24:1, v/v) and then subsequently with 3 ml of  chloroform:isoamyl alcohol (24:1, v/v). To pellet the nucleic acids, 0.1 volume of 3 M Na-acetate (pH 5.2) and 2.5 volumes of ethanol were added, incubated at –20oC  overnight and centrifuged for 30 min at 3,800 X g. The pellet was washed with 5 ml 70 % ethanol and resuspended in 175 µl diethyl pyrocarbonate-treated water. DNA was digested by the addition of 40 units of DNaseI (Roche) and 20 units of SUPERaseIn (Ambion, Cambridgeshire, UK) in DNaseI buffer (50 mM Na-acetate, 10 mM MgCl2, 2 mM CaCl2, pH 6.5) for 30 min at 37 oC in a total volume of 200 µl. Then the RNA was purified with the use of RNeasy columns (Qiagen, Hilden, Germany) according to the manufacturer’s instructions and the yield of total cellular RNA was quantified by measuring the light absorption at 260 nm. RNA with a size below 200 bp (e.g., tRNAs, 5S rRNA) is below the cutoff of the column and therefore could not be recovered. All the steps were carried out at 4 oC or RNA was also incubated on ice intermittently during the whole RNA isolation procedure. RNA samples were separated electrophoretically in 1.2 % agarose with 2 % formaldehyde as the denaturing reagent and 1x MOPS (20 mM 4-morpholinepropanesulfonic acid, 10 mM Na-Acetate, 1 mM EDTA, pH 7.0) buffer was used as the running buffer. The agarose gels were stained with ethidium bromide to check the purity and integrity of RNA preparation, with the 16S and 23S ribosomal bands as reference.    cDNA generation, fragmentation and labelling: To reduce variations in the abundance of specific mRNAs due to slight differences in growth conditions and RNA preparation, we pooled equal amounts of RNA from three cultures to get a final amount of 10 µg. The subsequent steps of cDNA generation and biotin-ddUTP terminal labeling were performed as described in the manufacturer's instructions for the P. aeruginosa GeneChip. Ten micrograms of total RNA was mixed with random primers (Invitrogen, Darmstadt, Germany) and control in vitro transcripts of 10 non-Pseudomonas gene sequences (kindly provided by S. Lory and coworkers) and incubated for 10 min at 70°C followed by 10 min at 25°C. Then cDNA reaction mix was added, which consisted of 5x first strand buffer (10 mM dithiothreitol, 0.5 mM deoxynucleoside triphosphates [dNTPs], 25 U/µl SuperScript II [all from Invitrogen], and 0.5 U/µl SUPERaseIn [Ambion]). This was followed by incubation for 10 min at 25°C, 60 min at 37°C, 60 min at 42°C, and 10 min at 70°C. RNA was hydrolyzed by adding 1 N NaOH and incubation for 30 min at 65°C; 1 N HCl neutralized the reaction. The cDNA was purified with the QIAquick column (QIAGEN) and quantified by A260. cDNA was fragmented in One Phor-All buffer with 0.5 U of DNase I  per µg of cDNA for 10 min at 37°C and subsequent inactivation for 10 min at 98°C. To check if the majority of cDNA fragments were in a 50- to 200-bp range, 5 µl was loaded on a 2% (wt/vol) agarose gel stained with SYBR Green.

treatment_protocol: No treatment.  Reference sample.

tag: strain

value: TBCF10839 wild type

tag: genotype

value: wild type

tag: growth protocol

value: cultivated in LB

tag: growth phase

value: stationary phase

tag: stress


title: PaeTBCF10839_nadK1::Tn5_H2O2_rep2

source_name: Pseudomonas aeruginosa TBCF10839 nadK1::Tn5, cultivated in the presence of H2O2

treatment_protocol: For exposure of bacteria to hydrogen peroxide, stationary phase-grown cultures (3 x 1010 cells) were resuspended in fresh Luria broth and kept in a dialysis tube (14-kDa cutoff, 25 mm) with an effective length of 6 cm for the exchange of fluids. Then the dialysis tube was resuspended in a 1-liter Erlenmeyer flask containing 600 ml of LB with 10 mM hydrogen peroxide (Sigma-Aldrich, Steinheim, Germany) to generate oxidative stress. The flasks were incubated at 37°C and 200 rpm on a rotary shaker for 2 h.

value: TBCF10839 mutant

value: nadk1 mutant

tag: transposon (mini-tn5) knock out

value: gene PA1572 (nadK1)

value: cultivated in the presence of H2O2


title: Surrounding BS041

tag: biological source


title: Undifferentiated embryonic stem cells, H9, 2

city: Los Angeles

first: Denis

last: Evseenko

state: CA

address: 1450 Biggy St

department: Orthopaedic Surgery

institute: University of Southern  California

description: Gene expression data from ubdifferentiated hESC H9

scan_protocol: The acquisition of each array image was undertaken by using Affymetrix GeneChip Command Console 1.1 (AGCC)

data_processing: raw data were analyzed using DNA-Chip Analyzer (D-Chip) with the .CEL files obtained from AGCC. Thresholds for selecting significant genes were set at a relative difference >= 2-fold, absolute difference >100 signal intensity units and p<0.05.

source_name: Human Embryonic Stem Cells (hESC H9)

label_protocol: Biotinylated cRNA were prepared by using MessageAmp™ Premier RNA Amplification Kit (Ambion) according to the instructions

growth_protocol: Mesoderm induction using activin a, BMP4, FGF2 and VEGF in Stemline II media

extract_protocol: mRNA extraction from undiffentiated hESC and CD326negCD56+ mesodermal progenitors weas carried out using Rneasy Qiagen micro kit

treatment_protocol: CD326negCD56+progenitors were sorted by FACS at day 3.5 of culture

tag: cell line

value: Human Embryonic Stem Cells (hESC H9)

tag: cell population

value: Undifferentiated cells


title: Control C029


title: PaeTBCF10839_nadK1::Tn5_H2O2_rep1


title: Control C044


title: Control C072


title: PaeTBCF10839_nadK1::Tn5_PMN_rep1

source_name: Pseudomonas aeruginosa TBCF10839 nadK1::Tn5, cultivated in the presence of polymorphonuclear neutrophils

treatment_protocol: To examine the effect of exoproducts of PMNs on P. aeruginosa strains, stationary phase-grown bacterial cultures (1 x 10e10 cells) were pelleted and resuspended in 2 ml of RPMI 1640 medium (Invitrogen, Darmstadt, Germany), placed into a dialysis bag (300 kDa) and incubated in presence of 1x 10e7 PMNs in 15 ml RPMI 1640 medium containing 10 % (v/v) human AB blood serum, at 200 rpm on a rotary shaker for 2 h (37°C).

value: PMN exoproducts


title: PaeTBCF10839_nadK1::Tn5_PMN_rep2

value: cultivated in the presence of polymorphonuclear neutrophils


title: Control C017


title: Undifferentiated embryonic stem cells, H9, 3


title: PaeTBCF10839_wildtype_H2O2_rep2

source_name: Pseudomonas aeruginosa TBCF10839 wild type, cultivated in the presence of H2O2


title: Zebrafish embryo: PCP Low dose Replicate 1 versus PCP Control Replicate 3

city: Liverpool

first: Ashley

last: Sawle

address: Crown Street

department: Biosciences

country: United Kingdom

institute: University of Liverpool

hyb_protocol: Labelled aRNA (1 μg) from each sample was hybridized to the array in 1x Nexterion Hyb buffer (Schott) for 16-18 hours at 42°C.

scan_protocol: Slides were scanned with an Axon Genepix 4000A Scanner using Genepix 3.0 software (Molecular Devices, Union City, USA). The scanned images were quantified using BlueFuse 3.3 software (Bluegnome, Cambridge, U.K.).

data_processing: Statistical analysis of microarray data was carried out within the R software environment. Data was normalised, using the marray package (Dudoit and Yang 2002), firstly with a print-tip-group intensity LOESS normalisation and secondly by a between array global scale normalisation using median absolute deviation (MAD) (Yang et al. 2002).

organism: Danio rerio

source_name: Zebrafish embryo, 72 hpf, Exposed

label_protocol: 0.35 µg of total RNA was amplified using TargetAmp™ 1-Round Aminoallyl-aRNA Amplification Kits (Epicentre® Biotechnologies, Madison, U.S.A.) following the manufacturers instructions and post-labeled using either Cy3 or Cy5 dyes (GE Healthcare, Piscataway, USA).

growth_protocol: Fish were maintained in 10 litre tanks from Aquatic Ecosystems at a stocking level of not more than 10 fish per tank, with 5-7 males per tank, and 3-5 females. Water temprerature was maintained at 28±1 °C. Light regime 14 hours light:10 hours dark. Fish were artemia in the mornings and flake food in the evenings.

extract_protocol: Total RNA was extracted using RNeasy mini-kits (Ambion) following the manufacturers instructions.

treatment_protocol: Eggs were collected half an hour after the aquarium lights were switched on. Replicated exposures of 30 selected fertilized eggs were carried out at 26 °C, 12:12 light:dark cycle, in 15 ml of test solution in 80 mm borosilicate petri dishes with lids, starting approximately 1.5 h post-fertilisation (hpf).

tag: tissue

value: embryo

tag: developmental stage

value: 72 hpf

tag: toxicant

value: PCP

tag: concentration

tag: exposure date

source_name: Zebrafish embryo, 72 hpf, Control

tag: dose

value: 0 mM


title: Undifferentiated embryonic stem cells, H9, 1


title: Control C010

value: normal bladder mucosae


title: PaeTBCF10839_wildtype_LB_rep1

value: TBCF10839 wild type


title: Zebrafish embryo: CdCl2 Low dose Replicate 3 versus PCP Low dose Replicate 8


title: PaeTBCF10839_wildtype_PMN_rep1

source_name: Pseudomonas aeruginosa TBCF10839 wild type, cultivated in polymorphonuclear neutrophils

value: wild type


title: PaeTBCF10839_wildtype_H2O2_rep1


title: Zebrafish embryo: CdCl2 High dose Replicate 7 versus PCP High dose Replicate 8


title: Zebrafish embryo: DCA Control Replicate 6 versus DCP Control Replicate 6

value: DCA

value: DCP


title: Zebrafish embryo: PCP Control Replicate 6 versus DCA Control Replicate 8


title: Zebrafish embryo: DCA Low dose Replicate 6 versus DCP Low dose Replicate 6


title: Zebrafish embryo: DCA High dose Replicate 6 versus DCP High dose Replicate 7


title: Zebrafish embryo: PCP High dose Replicate 7 versus DCA High dose Replicate 7


title: Zebrafish embryo: PCP Low dose Replicate 7 versus DCA Low dose Replicate 7


title: Zebrafish embryo: DCP Low dose Replicate 7 versus CdCl2 Low dose Replicate 8


title: Zebrafish embryo: PCP High dose Replicate 3 versus PCP Control Replicate 3


title: Zebrafish embryo: PCP Low dose Replicate 4 versus PCP High dose Replicate 6


title: Zebrafish embryo: CdCl2 Control Replicate 6 versus PCP Control Replicate 7


title: Zebrafish embryo: DCP High dose Replicate 8 versus CdCl2 High dose Replicate 8


title: Zebrafish embryo: PCP Control Replicate 4 versus PCP High dose Replicate 4


title: Loop Design replicate 31

city: Cambridge

first: Bernardo

last: Lemos

state: MA

address: 16 Divinity Avenue, Room 2105

institute: Harvard University

hyb_protocol: Followed Genisphere's 3DNA

scan_protocol: Scanned on a Axon scanner. Images were quantified using Genepix

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

organism: Drosophila melanogaster

label_protocol: Labelled with Genisphere's 3DNA

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: age

value: 3 days

value: whole flies

tag: gender

value: Male


title: Loop Design replicate 32


title: Loop Design replicate 27


title: Zebrafish embryo: CdCl2 High dose Replicate 2 versus CdCl2 Control Replicate 3


title: Loop Design replicate 25


title: Loop Design replicate 24


title: Loop Design replicate 29


title: Zebrafish embryo: PCP Control Replicate 2 versus PCP Low dose Replicate 2


title: Zebrafish embryo: DCP Control Replicate 4 versus CdCl2 Control Replicate 8


title: Loop Design replicate 26


title: Loop Design replicate 28


title: Loop Design replicate 30


title: Loop Design replicate 23


title: Loop Design replicate 22


title: Zebrafish embryo: CdCl2 Low dose Replicate 6 versus CdCl2 High dose Replicate 6


title: Loop Design replicate 21


title: PaeTBCF10839_wildtype_PMN_rep2

tag: strain

value: stationary phase


title: Loop Design replicate 17

tag: genotype


title: Zebrafish embryo: CdCl2 Control Replicate 2 versus CdCl2 Low dose Replicate 4


title: Zebrafish embryo: CdCl2 Low dose Replicate 2 versus CdCl2 Control Replicate 1


title: Zebrafish embryo: CdCl2 High dose Replicate 5 versus CdCl2 Low dose Replicate 5


title: Zebrafish embryo: DCP Control Replicate 5 versus DCP High dose Replicate 4


title: Zebrafish embryo: DCP Low dose Replicate 5 versus DCP High dose Replicate 6


title: Loop Design replicate 20


title: Zebrafish embryo: CdCl2 Control Replicate 4 versus CdCl2 High dose Replicate 3


title: Loop Design replicate 19


title: Loop Design replicate 18


title: Loop Design replicate 16


title: Zebrafish embryo: DCP High dose Replicate 2 versus DCP Control Replicate 3


title: Zebrafish embryo: DCA Low dose Replicate 5 versus DCA High dose Replicate 4


title: Loop Design replicate 14


title: Loop Design replicate 15


title: Loop Design replicate 10


title: Zebrafish embryo: DCA High dose Replicate 3 versus DCA Low dose Replicate 4


title: Zebrafish embryo: DCP High dose Replicate 5 versus DCP Low dose Replicate 4


title: Loop Design replicate 8


title: Loop Design replicate 13


title: Loop Design replicate 12


title: Zebrafish embryo: DCA Control Replicate 5 versus DCA High dose Replicate 2


title: Zebrafish embryo: DCA High dose Replicate 1 versus DCA Control Replicate 4


title: Zebrafish embryo: DCA Control Replicate 3 versus DCA Low dose Replicate 2


title: Loop Design replicate 11


title: Loop Design replicate 7


title: Zebrafish embryo: DCP Control Replicate 2 versus DCP Low dose Replicate 3


title: Loop Design replicate 5


title: Glioblastoma tissue pool

city: Seattle

first: Biaoyang

last: Lin

state: WA

address: 550 17th Ave, James Tower suite 550

department: Swedish Neuroscience Institute

institute: Swedish Medical Center

description: The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634. Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library. The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.

molecule: polyA RNA

source_name: Five GBM tissue pool

extract_protocol: Qiagen RNA extraction kit

value: glioblastoma tissue


title: Loop Design replicate 6


title: Loop Design replicate 9


title: Zebrafish embryo: DCP Low dose Replicate 2 versus DCP Control Replicate 1


title: Zebrafish embryo: DCA Low dose Replicate 1 versus DCA Control Replicate 2


title: DK1622 (wt), 2h ind., Exp.3

city: Marburg

first: Penelope

last: Higgs

address: Karl-von-Frisch-Str.

department: Ecophysiology

institute: Max Planck Institute for Terrestrial Microbiology

description: no additional information

hyb_protocol: Standard protocol see Müller, F.-D. & J. S. Jakobsen, (2008) Expression analysis. In: Myxobacteria. Multicellularity and Differentiation. D. E. Whitworth (ed). Washington, DC.: ASM Press, pp. 479 - 489.

scan_protocol: GenePix 6.0

data_processing: spot finding algorithm GenePix 6.0; ratio-normalized (mean ratio of medians = 1)

organism: Myxococcus xanthus

source_name: veg. cells DK1622 (wt) [reference]

tag: growth stage

value: mid log vegetative cells DK1622 (wt)

source_name: ind. cells DK1622 (wt) 2h [test]

tag: agent

value: glycerol

tag: time


title: Normal brain tissues pool

data_processing: The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.

source_name: Five brain tissue pool

value: normal brain


title: DK1622 (wt), 0.5h ind., Exp.3

description: no additional information

label_protocol: Standard protocol see Müller, F.-D. & J. S. Jakobsen, (2008) Expression analysis. In: Myxobacteria. Multicellularity and Differentiation. D. E. Whitworth (ed). Washington, DC.: ASM Press, pp. 479 - 489.

source_name: ind. cells DK1622 (wt) 0.5h [test]


title: DK1622 (wt), 4h ind., Exp.3

description: no additional information

extract_protocol: Standard protocol see Müller, F.-D. & J. S. Jakobsen, (2008) Expression analysis. In: Myxobacteria. Multicellularity and Differentiation. D. E. Whitworth (ed). Washington, DC.: ASM Press, pp. 479 - 489.

source_name: ind. cells DK1622 (wt) 4h [test]


title: Loop Design replicate 3


title: Loop Design replicate 4


title: DK1622 (wt), 1h ind., Exp.3

description: no additional information

source_name: ind. cells DK1622 (wt) 1h [test]


title: Hippocampus_2h_rep3

city: Milan

first: Daniela

last: Toniolo

address: Via Olgettina, 58

department: Dibit

country: Italy

institute: San Raffaele Scientific Institute

description: gene expression data from hippocampus of trained mice collected 2 h after the training

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45°C on GeneChip MOE 430A 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

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

organism: Mus musculus

source_name: Hippocampus of trained mice collected 2 h after trace fear conditioning

label_protocol: Biotinilated cRNA  was generated from 10 ug total RNA using the BioArray HighYield RNA Transcript Labeling kit (Enzo Life Sciences, Farmingdale, NY)

extract_protocol: Hippocampal total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA). RNA purification and DNAse digestion were performed using the RNeasy kit, according to manufacturer’s instructions (Qiagen, Valencia CA)

treatment_protocol: Trace fear conditioning test was performed as described in D'adamo et al (2002). Deletion of the mental retardation gene Gdi1 impairs associative memory and alters social behavior in mice. Hum Mol Genet, 11, 2567-2580. Hippocampi were collected at 0.5h,  2 h and 6 h after the end of the test.

value: male

value: 8-10 weeks

value: hippocampus


title: Hippocampus_6h_rep2

description: gene expression data from hippocampus of trained mice collected 6 h after the training

source_name: Hippocampus of trained mice collected 6h after trace fear conditioning


title: Hippocampus_6h_rep1


title: Loop Design replicate 1


title: Loop Design replicate 2


title: Zebrafish embryo: PCP High dose Replicate 5 versus PCP Low dose Replicate 3

value: embryo

value: 72 hpf

value: PCP


title: Hippocampus_6h_rep3


title: CSES1 maternal

type: genomic

first: Tamar

last: Dvash

address: 695 Charles E. Young Drive South

department: Human Genetics

institute: University of California Los Angeles

description: Hybridized to 250K_Sty

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: standard Affymetrix protocol

molecule: genomic DNA

source_name: granulosa cells

label_protocol: standard Affymetrix protocol

extract_protocol: lysis with detergents follwed by salt and ethanol precipitation

tag: cell type

value: somatic cells


title: DK1622 (wt), 4h ind., Exp.2

description: no additional information


title: Hippocampus_2h_rep2


title: DK1622 (wt), 2h ind., Exp.2

description: no additional information


title: DK1622 (wt), 1h ind., Exp.2

description: no additional information


title: DK1622 (wt), 4h ind., Exp.1

description: no additional information


title: DK1622 (wt), 0.5h ind., Exp.2

description: no additional information


title: CSES8

description: Hybridized to 250K_Sty

source_name: human embryonic stem cells

value: embryonic stem cells


title: CSES8 maternal

description: Hybridized to 250K_Sty


title: Hippoacampus_0.5h_rep2

description: gene expression data from hippocampus of trained mice collected 0.5 h after the training

source_name: Hippocampus of trained mice collected 0.5 h after trace fear conditioning


title: Hippocampus_2h_rep1


title: CAM_Wound_rep3

city: Birmingham

first: Philipp

last: Antczak

state: West-Midlands

address: Edgbaston Park Road

department: Bioscience

institute: University of Birmingham

hyb_protocol: Affymetrix Standard protocol

scan_protocol: Affymetrix Standard protocol

data_processing: R/Bioconductor, RMA

organism: Gallus gallus

source_name: Wound Tissue CAM

label_protocol: Affymetrix Standard protocol

extract_protocol: Rneasy mini kit extraction protocol

value: chorioallantoic membrane

tag: wound injury

value: yes


title: CAM_Wound_rep2


title: CAM_Wound_rep1


title: SLE human bone marrow-derived mesenchymal stem cell  1

city: Nanjing

first: Yu

last: Tang

state: Jiangsu Province

address: 321 Zhongshan Road

department: Department of Rheumatology and  Immunology

country: China

institute: The Affiliated Drum Tower Hospital of Nanjing University Medical School

description: mensenchymal stem cells derived from bone marrow of SLE patient, cultured in vitro and harvested at passage 3

hyb_protocol: Oligoarray control targets and hybridization buffer  were added, and samples were applied to microarrays. After hybridization ,the slides were washed.

scan_protocol: Arrays were scanned with a confocal LuxScan 10 KA scanner (CapitalBio)

data_processing: Data of obtained images were extracted with LuxScan 3.0 software (CapitalBio). Genes with the signal intensity more than 800 (Cy3 or Cy5) were regarded as the expressed ones. In every two channel slides, the intensity ratio of the Cy3 to Cy5 (test/reference) of each spot was calculated after normalization with LOWESS regression. Statistical data and differential analysis files were generated by using SAM software 3.0 (Stanford University, Stanford, CA, USA). The significant changed genes were selected based on P-value < 0.05 and > 2-fold as criteria.

source_name: SLE human bone marrow-derived mensenchymal stem cell

label_protocol: Total RNA was first reverse transcribed into first-stranded complementary 1st-strand cDNA using a T7-Oligo (dT) promoter Primer kit (Promega,USA) and CbcScript. Rnase H was then added together with Escherichia coli DNA polymerase I and Ecoli DNAligase, followed by a short incubation with T4-DNA polymerase in order to achieve synthesis of the second-strand cDNA. The purified double-stranded cDNA served as the template for the invitro transcription reaction to synthesize the cRNA in the presence of T7 Enzyme Mix. The cRNA was then cleaned by the RNA Clean-up Kit (MN). At last, 2μg cRNA was reverse-transcribed using CbcScript Ⅱ and Random Primer, and subsequently purified by NucleoSpin Extract II Kit (MN). The cDNA of BMMSCs from SLE patients and controls were added with Cy3-dCTP (GE Healthcare Cat. No. PA 55021/ PA) and the cDNA of human Reference were added with Cy5-dCTP in the present with Klenow enzyme.

growth_protocol: Cells were cultured in low glucose Dulbecco Modiﬁed Eagle Medium (L-DMEM)  supplemented with 10% heat inactivated fetal bovine serum (FBS) at 37°C with 5% CO2

extract_protocol: BMMSCs from SLE patients and controls were placed in TRIzol  and processed for RNA extraction using the RNeasy kit according to the instructions of the manufacturer

treatment_protocol: The medium was changed  every three days.

value: bone marrow

value: mensenchymal stem cell

source_name: universal human reference RNA

value: composed of total RNA isolated from cell lines representing different human tissues

value: various


title: SLE human bone marrow-derived mesenchymal stem cell  4


title: Normal human bone marrow-derived mesenchymal stem cell  4

description: mensenchymal stem cells derived from bone marrow of normal donors, cultured in vitro and harvested at passage 3

source_name: Normal human bone marrow-derived mensenchymal stem cell


title: CSES1

description: Hybridized to 250K_Sty

tag: cell line


title: SLE human bone marrow-derived mesenchymal stem cell  3


title: DK1622 (wt), 2h ind., Exp.1

description: no additional information

value: mid log vegetative cells DK1622 (wt)


title: SLE human bone marrow-derived mesenchymal stem cell  2


title: Hippoacampus_0.5h_rep3


title: Hippoacampus_0.5h_rep1


title: Normal human bone marrow-derived mesenchymal stem cell  2


title: Normal human bone marrow-derived mesenchymal stem cell  3


title: DK1622 (wt), 1h ind., Exp.1

description: no additional information

value: glycerol


title: DK1622 (wt), 0.5h ind., Exp.1

description: no additional information


title: CAM_Control_rep2

source_name: Control Tissue CAM

value: no


title: CAM_Control_rep3


title: Hippocampus_naive_rep3

description: gene expression data from Naive mice

source_name: Hippocampus of naive mice

value: male


title: Hippocampus_naive_rep2

description: gene expression data from Naive mice

value: 8-10 weeks


title: Normal human bone marrow-derived mesenchymal stem cell  1


title: CAM_Control_rep1


title: NaCl8.6g_AcR_F4_24h

status: Public on May 05 2010

city: Raleigh

first: Stan

last: Martin

address: 1404 Crete Dr.

institute: Science Apps, L3C

hyb_protocol: Nimblegen internal protocols were followed

data_processing: Data was normalized using the Loess normalization analytical process in the JMP Genomics 4.0 Package from SAS Institute

organism: Zymomonas mobilis

source_name: AcR, NaCl, F4, 24h

growth_protocol: Z. mobilis ZM4 was obtained from the American Type Culture Collection (ATCC31821) and cultured in RM medium at 30°C.

extract_protocol: RNA was isolated from samples which were harvested by centrifugation. The TRIzol reagent (Invitrogen, Carlsbad, CA) was used to extract total cellular RNA.

treatment_protocol: Cultured in media containing sodium chloride at 8.6 grams/liter.

value: AcR

tag: phenotype

value: sodium acetate-tolerant

tag: treatment

value: sodium chloride

tag: treatment time

tag: fermentor


title: Hippocampus_naive_rep1

description: gene expression data from Naive mice

tag: tissue

value: hippocampus


title: NaCl8.6g_AcR_F2_5h

scan_protocol: Nimblegen internal protocols were followed

source_name: AcR, NaCl, F2, 5h


title: NaCl8.6g_ZM4_F1_5h

source_name: ZM4, NaCl, F1, 5h

label_protocol: Nimblegen internal protocols were followed

value: wild-type


title: NaCl8.6g_ZM4_F1_24h

source_name: ZM4, NaCl, F1, 24h


title: NaCl8.6g_AcR_F4_5h

source_name: AcR, NaCl, F4, 5h


title: NaAc12g_AcR_F5_24h

source_name: AcR, NaAc, F5, 24h

treatment_protocol: Cultured in media containing sodium acetate at 12 grams/liter.

value: sodium acetate


title: NaCl8.6g_AcR_F2_24h

source_name: AcR, NaCl, F2, 24h


title: NaAc12g_AcR_F6_24h

source_name: AcR, NaAc, F6, 24h


title: NaAc12g_ZM4_F3_24h

source_name: ZM4, NaAc, F3, 24h


title: NaCl8.6g_ZM4_F3_24h

source_name: ZM4, NaCl, F3, 24h


title: NaAc12g_AcR_F6_6.5h

source_name: AcR, NaAc, F6, 6.5h


title: NaCl8.6g_ZM4_F3_5h

source_name: ZM4, NaCl, F3, 5h


title: NaAc12g_AcR_F5_6.5h

source_name: AcR, NaAc, F5, 6.5h


title: NaAc12g_ZM4_F1_6.5h

source_name: ZM4, NaAc, F1, 6.5h


title: NaAc12g_ZM4_F3_6.5h

source_name: ZM4, NaAc, F3, 6.5h


title: NaAc12g_AcR_F6_4h

source_name: AcR, NaAc, F6, 4h


title: NaAc12g_AcR_F5_4h

source_name: AcR, NaAc, F5, 4h


title: NaAc12g_ZM4_F1_4h

source_name: ZM4, NaAc, F1, 4h


title: NaAc12g_ZM4_F3_4h

source_name: ZM4, NaAc, F3, 4h


title: NaAc12g_ZM4_F1_24h

source_name: ZM4, NaAc, F1, 24h


title: Mouse androgenetic (AG)-derived cells_MeDIP-chip

city: Sendai

first: Hitoshi

last: Hiura

address: 2-1 Seiryo-cho, Aoba-ku

department: Obstetrics and Gynecology

country: Japan

institute: Tohoku University Graduate School of Medicine

description: MeDIP-on-chip in AG-derived cells using monoclonal anti-methylcytidie (MCA2201) antibody.

hyb_protocol: Labelled DNA mixed with Cot-1 DNA (Invitrogen) and Agilent blocking solution was hybridized to microarray at 65ºC for 40 hours with constant rotation (18-19 rpm). Arrays were washed as per Agilent protocol.

scan_protocol: Arrays scanned with a GenePix 4000B scanner (Agilent Technologies) per Agilent protocol.

data_processing: The scanned data was processed using Feature Extraction Ver.9.1 (Agilent Technologies), and the IP (Cy5) and WG (Cy3) signal values were obtained. These two values were normalized using background subtraction, and signal log ratio [log2(IP/WG)], VALUE and P[Xbar] were obtained using ChIP Analytics 1.3 software (Agilent Technologies). Xbar is a signal value for a probe that takes account of signals for neighboring probes (within 1 kb), and P[Xbar] is a probability how the Xbar value is deviated from a normal distribution of Xbar values of the entire genome of a sample.

source_name: MeDIP in AG-derived cells

label_protocol: For MeDIP tilling microarray analysis, amplified immunoprecipitated-DNA was labeled with Cy5 (GE Healthcare) using a BioPrime Array CGH Genomic Labeling System (Invitrogen).

growth_protocol: Cells were cultured with TS medium (RPMI 1640 (Gibco) supplemented with 20% fetal bovine serum (Gibco), 1 mM sodium pyruvate (Gibco), 100 μM β-mercaptoethanol (Sigma), 2 mM l-glutamine (Gibco), 100 U/ml penicillin and 100 μg/ml streptomycin (Gibco)). All cell cultures were maintained at 37ºC with 5% CO2.

extract_protocol: DNA was extracted using Phenol extraction and ethanol precipitation, followed by RNase A (Invitrogen) treatment and PEG precipitation. Ten μg of genomic DNA was sheared by sonication (Sonics & Materials) to a length of about 200-1000 bp. After heat denaturation at 95ºC for 10 min, DNA was incubated with 10 μg of antibody against 5-methylcytidine (AbD Serotec, MCA2201) in 1 x block solution [1 x PBS (-), pH 8.0, 0.5% (w/v) BSA] at 4ºC overnight with rotation. Immuno-complexes were collected with 100 μl of Dynabeads Protein G (Invitrogen), washed with 1 x RIPA buffer [50 mM Hepes-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, pH 8.0, 1% (w/v) NP-40, 0.7% (w/v) Na-deoxycholate] seven times, and then were recovered by Proteinase K treatment, followed by phenol extraction and ethanol precipitation. DNA was dissolved in 50 μl of 1 x elution buffer [50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% (w/v) SDS]. Immunoprecipitated DNA was checked with Q-PCR to ensure that it was enriched for methylated DNA. This DNA was amplified by GenomePlex Complete Whole Genome Amplification kit (Sigma–Aldrich).

value: AG-derived cells from b6d2f1 (c57bl/6 x dba/2) embryos (Ogawa H et al., 2009. Placenta. 30:448-56).

tag: antibody

value: monoclonal anti-methylcytidie (MCA2201)

source_name: Sonicated input-DNA in AG-derived cells

label_protocol: For MeDIP tilling microarray analysis, amplified input-DNA was labeled with Cy3 (GE Healthcare) using a BioPrime Array CGH Genomic Labeling System (Invitrogen).

extract_protocol: DNA was extracted using Phenol extraction and ethanol precipitation, followed by RNase A (Invitrogen) treatment and PEG precipitation. Ten μg of genomic DNA was sheared by sonication (Sonics & Materials) to a length of about 200-1000 bp. After heat denaturation at 95ºC for 10 min, DNA was incubated at 4ºC. Input DNA was amplified by GenomePlex Complete Whole Genome Amplification kit (Sigma–Aldrich).


title: 1070_yellow_Rep1

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

hyb_protocol: Hegde et al. 2000. Approximately 80ug of total RNA from the reference stage (100-200mg cotyledon) was labeled by reverse transcription with a Cy-dUTP dye and compared to 80ug of total RNA from each of the five experimental stages (25-50mg, 75-100mg, 400-500mg, yellow, dry seed), labeled with the opposite dye. The cDNA arrays were prehybridized, hybridized, and washed as described by Vodkin et al., 2004. Duplicate dye swaps were set up as well.

scan_protocol: The slides were scanned using a ScanArray Express Microarray Scanner (Perkin Elmer Life Sciences, Boston, MA). The spots were found and their fluorescence intensity level quantitated using the ScanArray Express Microarray Analysis System.

data_processing: Spots with high background or low signal were flagged. Cy3-Cy5 were normalized at the slide level. Replicate slides were normalized at the slide level. Mean spot intensity was used. The p-value was calculated by GeneSpring using a one-sample, two-tailed t-test with the hypothetical mean set to 1.

organism: Glycine max

source_name: 100-200mg cotyledon

label_protocol: Direct incorporation using Cy3-dUTP or Cy5-dUTP

growth_protocol: Multiple Glycine max cv. Williams plants were grown in the greenhouse.

extract_protocol: McCarty D. 1986. Phenol chloroform, lithium chloride total RNA extraction method

treatment_protocol: Immature seeds were harvested over the course of several weeks. The seeds were shelled, pooled together, and then sorted by weight range. The seeds were dissected to separate the seed coat from the cotyledon. The tissue was frozen in liquid nitrogen and stored at -80° until it was lyophilized. Dry seeds were harvested at maturity and stored at room temperature. Approximately 80 beans, from multiple plants, are represented by the cotyledon RNA used in this study.

tag: cultivar

value: Williams 43

source_name: 200-300mg yellow cotyledon


title: 1070_yellow_Rep2


title: 1070_25-50mg_Rep4

source_name: 25-50mg cotyledon


title: 1070_25-50mg_Rep3


title: 1070_25-50mg_Rep1


title: 1070_25-50mg_Rep2


title: 1070_75-100mg_Rep3

source_name: 75-100mg cotyledon


title: Mouse parthenogenetic (PG)-derived cells_MeDIP-chip

description: MeDIP-on-chip in PG-derived cells using monoclonal anti-methylcytidie (MCA2201) antibody.

source_name: MeDIP in PG-derived cells

value: PG-derived cells from b6d2f1 (c57bl/6 x dba/2) embryos (Ogawa H et al., 2009. Placenta. 30:448-56).

source_name: Sonicated input-DNA in PG-derived cells


title: Mouse sperm_MeDIP-chip

description: MeDIP-on-chip in sperm using monoclonal anti-methylcytidie (MCA2201) antibody.

source_name: MeDIP in sperm

tag: age

value: sperm

source_name: Sonicated input-DNA in sperm


title: 1070_dry_Rep2

source_name: dry whole seed


title: 1070_75-100mg_Rep1


title: 1070_dry_Rep1


title: 1070_400-500mg_Rep4

source_name: 400-500mg cotyledon


title: 1070_75-100mg_Rep2


title: 1070_400-500mg_Rep2


title: 1070_400-500mg_Rep1


title: 2183_dry_Rep1


title: 2183_dry_Rep2


title: 2183_25-50mg_Rep3


title: 2183_yellow_Rep1


title: 2183_yellow_Rep2


title: 1070_75-100mg_Rep4


title: 2183_25-50mg_Rep4


title: 2183_75-100mg_Rep4


title: 1070_400-500mg_Rep3


title: 2183_25-50mg_Rep1


title: common reference array 2

city: Berlin

first: Soroush

last: Sharbati

address: Oertzenweg 19b

department: Institute of Veterinary Biochemistry

institute: Freie Universitaet Berlin

hyb_protocol: Hybridization for 16 hours at 42°C has been carried out overnight according to manufacturs instructions. Then, the biochip was washed automatically and a program for signal enhancement was processed with the Geniom Real Time Analyzer

scan_protocol: The resulting detection pictures were evaluated using the Geniom Wizard Software.

data_processing: For each array, the median signal intensity was extracted from the raw data file such that for each miRNA seven intensity values have been calculated corresponding to each replicate copy of miRBase on the array. Following background subtraction the seven replicate intensity values of each miRNA were summarized by their median value. To normalize the data across different arrays, quantile normalizatio was applied.

source_name: Porcine common reference

label_protocol: Sample labeling with biotin has been carried out either by using the miRVANA™ miRNA Labeling Kit (Applied Biosystems Inc, Foster City, California USA) or by microfluidic-based enzymatic on-chip labeling of miRNAs (MPEA).

extract_protocol: Intestinal samples (~ 2 cm circle segments) were taken from duodenum, proximal and distal jejunum, ileum, ascending and transverse colon of four 31 days old healthy piglets (EUROC x Pietrain) as described earlier (Scholven et al. 2009). The piglets were weaned at the age of 28 days. Samples were quick-frozen in liquid nitrogen and stored at -80 °C. In order to obtain representative measurements in each intestinal locus, three cross sections of approximately 2 mm out of the 2 cm segment of frozen intestine were examined. These 3 sections were pooled and total RNA was isolated from samples using an automated homogenizer (FastPrep Instrument, MP Biomedicals, Heidelberg, Germany) and the mirVana miRNA Isolation Kit (Applied Biosystems, Darmstadt, Germany), according to the manufacturer’s protocol. The RNA quality and quantity of all samples were proven using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Kits (Agilent, Waldbronn, Germany) and the Nanodrop 1000 Spectrophotometer (Thermo Scientific, MA, USA).

value: pool of intestinal sample from porcine duodenum, proximal and distal jejunum, ileum, ascending and transverse colon


title: 2183_75-100mg_Rep2


title: 2183_75-100mg_Rep1


title: ileum array 2

source_name: Porcine ileum

value: porcine ileum


title: ascending colon array 2

source_name: Porcine ascending colon

value: porcine ascending colon


title: transverse colon array 2

source_name: Porcine transverse colon

value: porcine transverse colon


title: 2183_25-50mg_Rep2


title: proximal jejunum array 2

source_name: Porcine proximal jejunum

value: porcine proximal jejunum


title: distal jejunum array 2

source_name: Porcine distal jejunum

value: porcine distal jejunum


title: 2183_75-100mg_Rep3


title: duodenum array 2

source_name: Porcine duodenum

value: porcine duodenum


title: 2183_400-500mg_Rep4

source_name: 100-200mg cotyledon


title: 2183_400-500mg_Rep1


title: 2183_400-500mg_Rep3


title: MCF-7 transfected with pcDNA3.2, rep.2

city: Washington

first: Sidney

middle: W

last: Fu

state: DC

address: 2300 Eye St. NW, Ross 402C

department: Medicine

institute: George Washington University

hyb_protocol: 15ug of fragmented cRNA hybridized for 16 hours at 45C with constant rotation

scan_protocol: Scanned with GeneChip Scanner 3000 7G

data_processing: Chips were normalized using RMA summarization algorithm

source_name: MCF-7 breast cancer cell, transfected, pcDNA3.2

label_protocol: Affymetrix biotin labeling protocol

extract_protocol: Trizol reagent (Invitrogen) and RNeasy kit (Qiagen) was used to isolate and purify total RNA

tag: expression

value: Control


title: MCF-7 transfected with pcDNA3.2-BP1, rep.2

source_name: MCF-7 breast cancer cell, transfected, pcDNA3.2-BP1


title: MCF-7 transfected with pcDNA3.2-BP1, rep.1


title: 2183_400-500mg_Rep2


title: 1088_dry_Rep2


title: MCF-7 transfected with pcDNA3.2, rep.1


title: NGP aCGH

city: Helsinki

first: Maija

middle: K

last: Wolf

address: Biomedicum Helsinki 2U, Tukholmankatu 8,

country: Finland

institute: Institute for Molecular Medicine Finland (FIMM)

description: Male genomic DNA reference (Promega, Cat. # G1471).

hyb_protocol: After labelling, tumour DNA and reference DNA samples were pooled, cleaned and hybridization cocktails were prepared according to the protocol. Hybridization and washes were also performed according to the protocol.

scan_protocol: Arrays were scanned using the G2565 scanner from Agilent Technologies. Feature Extraction software (version 8.1.1.1, Agilent Technologies) was used in image analysis with settings recommended by the manufacturer (44K_CGH_0605).

data_processing: Agilent Feature Extraction Software (v 8.1.1.1) was used for spot quality filtering and normalization.

source_name: Male genomic DNA reference

label_protocol: Sample processing and hybridization were performed according to the August 2005 (version 2) protocol (Agilent Technologies), with minor modifications. 4 ug of digested tumour DNA and reference DNA were labelled with Cy5-dUTP and Cy3-dUTP, respectively, in a random priming reaction using a BioPrime Array CGH Genomic Labelling Module.

growth_protocol: Cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and 2mM L-glutamine, and Minimum Essential Medium supplemented with 10% FBS, 2mM L-glutamine, 1% non-essential amino acids and 1% sodium pyruvate, respectively.

extract_protocol: Genomic DNAs were obtained from the same samples by swirling a glass rod in the cell lysate, followed by standard phenol-chloroform purification.

treatment_protocol: Untreated.

tag: gender

value: male

source_name: genomic DNA from NGP cell line

value: NGP

value: neuroblastoma


title: IMR-32 aCGH

source_name: genomic DNA from IMR-32 cell line


title: 1088_dry_Rep1


title: 1088_25-50mg_Rep4

source_name: 25-50mg cotyledon


title: 1088_25-50mg_Rep2


title: 1088_75-100mg_Rep3

source_name: 75-100mg cotyledon


title: 1088_75-100mg_Rep4


title: 1088_25-50mg_Rep1


source_name: MeDIP in AG-derived cells

source_name: Sonicated input-DNA in AG-derived cells


title: 1088_yellow_Rep1

source_name: 200-300mg yellow cotyledon


title: 1088_75-100mg_Rep2


source_name: MeDIP in PG-derived cells

source_name: Sonicated input-DNA in PG-derived cells


title: 1088_25-50mg_Rep3


title: 1088_yellow_Rep2


title: 1088_75-100mg_Rep1


title: 1088_400-500mg_Rep4

source_name: 400-500mg cotyledon


title: 1088_400-500mg_Rep3


title: Mouse sperm_MeDIP-chip

source_name: MeDIP in sperm

tag: strain

source_name: Sonicated input-DNA in sperm


title: 1088_400-500mg_Rep1


title: rat hippocampus (combined dorsal and ventral aspects), aged PIO, subject 10

city: Lexington

first: Eric

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

hyb_protocol: Standard Affimetrix

scan_protocol: Standard Affymetrix

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.

label: Standard Affymetrix

label_protocol: Standard Affymetrix

extract_protocol: Total RNA was isolated using the TRIzol reagent and following the manufacturer's RNA isolation protocol (Invitrogen, #15596). One milliliter of TRIzol solution was added to each tube containing the frozen tissue block, and the tissue was homogenized by 10 passages through an 18.5 ga syringe needle. After centrifugation, the RNA was precipitated from the aqueous layer, washed, and dissolved in RNase-free water. RNA concentration and integrity were assessed by spectrophotometry and gel electrophoresis. The RNA samples were stored at 80°C.

tag: model

value: Fischer 344

value: Male

value: 21 to 22 months old


title: rat hippocampus (combined dorsal and ventral aspects), aged PIO, subject 5


title: distal jejunum array 1

source_name: Porcine distal jejunum


title: common reference array 1

source_name: Porcine common reference

value: pool of intestinal porcine duodenum, proximal and distal jejunum, ileum, ascending and transverse colon


title: ascending colon array 1

source_name: Porcine ascending colon


title: ileum array 1

source_name: Porcine ileum


value: AG-derived cells from b6d2f1 (c57bl/6 x dba/2) embryos (Ogawa H et al., 2009. Placenta. 30:448-56).

value: monoclonal anti-methylcytidie (MCA2201)


title: rat hippocampus (combined dorsal and ventral aspects), aged PIO, subject 8


title: proximal jejunum array 1

source_name: Porcine proximal jejunum


title: 1088_400-500mg_Rep2

value: Williams 43

source_name: 100-200mg cotyledon


title: duodenum array 1

source_name: Porcine duodenum


title: rat hippocampus (combined dorsal and ventral aspects), aged PIO, subject 1


title: rat hippocampus (combined dorsal and ventral aspects), aged PIO, subject 2

value: model:Fischer  344


title: rat hippocampus (combined dorsal and ventral aspects), aged control, subject 8

source_name: rat hippocampus (combined dorsal and ventral apsects), aged control, subject 8


title: rat hippocampus (combined dorsal and ventral aspects), aged control, subject 4


title: rat hippocampus (combined dorsal and ventral aspects), aged control, subject 6


title: rat hippocampus (combined dorsal and ventral aspects), aged control, subject 7


title: rat hippocampus (combined dorsal and ventral aspects), aged control, subject 3


title: rat hippocampus (combined dorsal and ventral aspects), aged control, subject 1


title: transverse colon array 1

source_name: Porcine transverse colon


title: rat hippocampus (combined dorsal and ventral aspects), aged control, subject 2


title: rat hippocampus (combined dorsal and ventral aspects), young PIO, subject 7

value: 7 to 8 months old


title: rat hippocampus (combined dorsal and ventral aspects), young PIO, subject 6


title: rat hippocampus (combined dorsal and ventral aspects), young PIO, subject 5


title: rat hippocampus (combined dorsal and ventral aspects), young PIO, subject 8


title: rat hippocampus (combined dorsal and ventral aspects), young PIO, subject 3


title: rat hippocampus (combined dorsal and ventral aspects), young PIO, subject 4


title: rat hippocampus (combined dorsal and ventral aspects), young PIO, subject 1


title: rat hippocampus (combined dorsal and ventral aspects), young PIO, subject 2


title: rat hippocampus (combined dorsal and ventral aspects), young control, subject 7


title: rat hippocampus (combined dorsal and ventral aspects), young control, subject 6


title: rat hippocampus (combined dorsal and ventral aspects), young control, subject 8


title: rat hippocampus (combined dorsal and ventral aspects), young control, subject 5


title: Human sperm_MeDIP-chip

value: sperm


title: Mouse sperm_MeDIP-chip


title: Mouse parthenogenetic (PG)-derived cells_MeDIP-chip

value: PG-derived cells from b6d2f1 (c57bl/6 x dba/2) embryos (Ogawa H et al., 2009. Placenta. 30:448-56).


title: Mouse androgenetic (AG)-derived cells_MeDIP-chip

source_name: MeDIP in AG-derived cells


title: rat hippocampus (combined dorsal and ventral aspects), aged PIO, subject 4


title: rat hippocampus (combined dorsal and ventral aspects), young control, subject 2


title: rat hippocampus (combined dorsal and ventral aspects), young control, subject 1


title: rat hippocampus (combined dorsal and ventral aspects), young control, subject 4


title: rat hippocampus (combined dorsal and ventral aspects), young control, subject 3


title: Lymph node DCs untreated for 17h

city: SÃO PAULO

first: Helder

middle: I.

last: Nakaya

state: SÃO PAULO

address: AVENIDA PROFESSOR LINEU PRESTES, 580, Block 17

country: Brazil

institute: Universidade de São Paulo

description: Gene expression from mouse lymph node CD11c+ DCs left untreated for 17 h

hyb_protocol: As per Vanderbilt Microarray Shared Resource Standard Protocol

data_processing: For this analysis, we used Affymetrix Mouse Genome 430 2.0 Array (GPL1261), but instead of using Affymetrix’s sequence clusters to define genes, gene sequence clusters were RMA pre-processed and normalized with the UniGene Custom CDF Version 10 available fromhttp://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp to yield a list of 19,508 genes

source_name: Lymph node

growth_protocol: CD11c+ LN DCs were purified using the MACS-column from Miltenyi. Cells were cultured in the presence of 3T3-CD40L cells and left untreated for 17 h

extract_protocol: RNA was extracted using the Qiagen RNeasy Mini Kit protocol according to the manufacturer’s instructions. Samples were treated with DNase

treatment_protocol: Lymph node CD11c+ DCs left untreated for 17h

value: Lymph node CD11c+ DCs

tag: agent

value: control (untreated)


title: Lymph node DCs + Papain for 17h

description: Gene expression from mouse lymph node CD11c+ DCs and treated with Papain for 17h

scan_protocol: As per Vanderbilt Microarray Shared Resource Standard Protocol

growth_protocol: CD11c+ LN DCs were purified using the MACS-column from Miltenyi. Cells were cultured in the presence of 3T3-CD40L cells and treated with papain (25 µg/ml) for 17 h

treatment_protocol: Lymph node CD11c+ DCs treated with Papain for 17h

value: Papain

tag: time


title: Lymph node DCs + LPS for 17h

description: Gene expression from mouse lymph node CD11c+ DCs and treated with LPS for 17h

label_protocol: As per Vanderbilt Microarray Shared Resource Standard Protocol

growth_protocol: CD11c+ LN DCs were purified using the MACS-column from Miltenyi. Cells were cultured in the presence of 3T3-CD40L cells and treated with LPS (1 µg/ml) for 17 h

treatment_protocol: Lymph node CD11c+ DCs treated with LPS for 17h

tag: cell type

value: LPS


title: Lymph node DCs 0h – rep2

description: Gene expression from mouse lymph node CD11c+ DCs, freshly isolated

growth_protocol: CD11c+ LN DCs were purified using the MACS-column from Miltenyi.

treatment_protocol: Freshly isolated lymph node CD11c+ DCs before treatment, replicate 2 (0h)

value: Lymph node CD11c+ DCs (freshly-isolated)

value: control (before treatment)


title: Lymph node DCs 0h – rep1

treatment_protocol: Freshly isolated lymph node CD11c+ DCs before treatment, replicate 1 (0h)


title: Lymph node DCs + Papain for 4h

description: Gene expression from mouse lymph node CD11c+ DCs treated with Papain for 4h

growth_protocol: CD11c+ LN DCs were purified using the MACS-column from Miltenyi. Cells were cultured in the presence of 3T3-CD40L cells and treated with papain (25 µg/ml) for 4h

treatment_protocol: Lymph node CD11c+ DCs treated with Papain for 4h


title: Lymph node DCs untreated for 4h

description: Gene expression from mouse lymph node CD11c+ DCs left untreated for 4h

growth_protocol: CD11c+ LN DCs were purified using the MACS-column from Miltenyi. Cells were cultured in the presence of 3T3-CD40L cells and left untreated for 4h

treatment_protocol: Lymph node CD11c+ DCs left untreated for 4h


title: Lymph node DCs + LPS for 4h

description: Gene expression from mouse lymph node CD11c+ DCs treated with LPS for 4h

growth_protocol: CD11c+ LN DCs were purified using the MACS-column from Miltenyi. Cells were cultured in the presence of 3T3-CD40L cells and treated with LPS (1 µg/ml) for 4h

treatment_protocol: Lymph node CD11c+ DCs treated with LPS for 4h


title: HTCC1062_Iron-Limited_11days_rep3

city: Corvallis

first: Daniel

middle: Patrick

last: Smith

state: OR

address: 220 Nash Hall

department: Microbiology Department

institute: Oregon State University

hyb_protocol: 5.5 µg of labeled aRNA was hybridized to chips at 45˚C, rotating at 60 rpm for 16 hours.

scan_protocol: The samples were scanned with an Affymetrix GeneChip Scanner 3000 7G with autoloader using AGCC software.

data_processing: RMA normalization conducted with Affymetrix ExpressionConsole software package.

organism: Candidatus Pelagibacter ubique HTCC1062

source_name: Iron-Limited Culture, 11 Days

label_protocol: RNA was labeled with biotin labeled nucleotides (perkin-elmer) during the in-vitro transcription reaction.

growth_protocol: Natural seawater media amended with 50 µM pyruvate, 50 µM glucose, 10 µM nitrogen, 1 µM methionine, 1 µM glycine, 1 µM phosphate, and vitamins. Cells were grown at 16°C with intermittent light and sparging with air.

extract_protocol: Total RNA was extracted using RNeasy Kit (Qiagen) and amplified using MessageAmp-II-Bacteria RNA Amplification Kit (Ambion).

treatment_protocol: 40 ml of culture from each biological replicate were harvested via centrifugation (1 hour at 43 000 g, 10°C), then re-suspended in 1 ml of Bacteria Protect (Qiagen) for 15 min. Following RNA stabilization, cells were collected by centrifugation (30 min at 40 000 g, 10°C), the supernatant was removed, and cells were then stored frozen at -80°C prior to extraction.

tag: growth phase

value: Stationary


title: Mono cultures 12 h _ Mixed culture 12 h (3 merged hybs)

city: Ede

first: Sander

last: Sieuwerts

address: Kernhemseweg 2

department: Health

country: Netherlands

institute: NIZO Food Research

description:
Merged data from biological replicates:
Mono cultures in milk grown for 12 h rep2 compared to Mixed culture in milk grown for 12 h rep2 [Array_T.txt]
Mono cultures in milk grown for 12 h rep1 compared to Mixed culture in milk grown for 12 h rep2 [Array_W.txt]
Mono cultures in milk grown for 12 h rep2 compared to Mixed culture in milk grown for 12 h rep1 [Array_X.txt]

hyb_protocol: For each array, 0.3 µg of cDNA labeled with either Cyanine 3 or Cyanine 5 was hybridized using the solutions and following the protocol delivered by Agilent (version 5.5) for 8x15K slides.

scan_protocol: Slides were scanned using an Agilent microarray scanner (G2565BA). Lasers of wavelengths at 532 and 635 nm were used to excite Cyanine3 and Cyanine5 dyes, respectively. Fluorescent images were captured as multi-image-tagged image file format and analyzed with Imagene software (Axon) (BioDiscovery, Marina del Rey, USA).

data_processing: The extent of hybridization was derived from a median value of pixel-by-pixel ratios. S. thermophilus and L. bulgaricus spots were normalized using Lowess separately as a varying ratio between both organisms would impact the determined expression of genes in each species. Differential regulation was determined by false-discovery rate (FDR) from the Cyber-T p-values by means of multiple testing connections. Differential regulation was defined as a two-fold or higher differential expression with a FDR cut-off value of 0.05 or lower.

organism:
Streptococcus thermophilus CNRZ1066
Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365

source_name: Mono cultures grown for 12 h (RNA isolated from S. thermophilus and L. bulgaricus mono cultures was mixed)

label_protocol: Five to seven μg of RNA was used for cDNA synthesis and labelling using the Cyscribe Post-labelling kit (Amersham Biosciences, Amersham, UK) according to the manufacturer's protocol.

growth_protocol: Cells were inoculated at an OD600 of 0.005 and grown in 275 mL reconstituted skim milk at 42°C for 3.5, 5.5, 8 or 12 h, dependent on the sampling time.

extract_protocol: RNA was isolated using a phenol chloroform extraction followed by column-purification. Cells were disrupted by shaking 3 times 45 s in a Fastprep (Qbiogene Inc., France) at 5.5 m/s separated by 1 min on ice.

treatment_protocol: Yoghurt cultures were quenched in 3 volumes 60% glycerol of -40°C and kept at -20°C for 0.5 h. The pH was adjusted to 6.5 – 7.0 with 1 M NaOH. The medium was cleared by adding 4 mL 25% (w/v) trisodium citrate per 100 mL. The sample was gently mixed each 5 min for 0.5 h while keeping it at -20°C. Cells were centrifuged at -20°C and 23,000 G for 16 min. In order to remove residual protein, the cell pellet was resuspended in a solution comprised of 50% (w/v) guanidinethiocyanate (Sigma), 0.5% (w/v) N-laurylsarcosine (Sigma) and 2.5% (v/v) of a 1 M trisodium citrate solution, adjusted to pH 7.0. After centrifugation, the cells were resuspended in 500 µL 1xTE (10xTE contains 10 mM tris pH 8.0 and 1 mM EDTA pH 8.0) and transferred to a screw-cap tube.

value: Streptococcus thermophilus CNRZ1066

source_name: Mixed culture grown for 12 h


title: Mono cultures 8 h rep1 _ Mixed culture 8 h rep1

description: Mono cultures in milk grown for 8 h rep1 compared to Mixed culture in milk grown for 8 h rep1

source_name: Mono cultures grown for 8 h (RNA isolated from S. thermophilus and L. bulgaricus mono cultures was mixed)

value: Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365

source_name: Mixed culture grown for 8 h


title: Mixed culture 12 h rep1 _ Mono cultures 12 h rep1

description: Mixed culture in milk grown for 12 h rep1 compared to Mono cultures in milk grown for 12 h rep1


title: HTCC1062_Iron-Limited_11days_rep1


title: HTCC1062_Iron-Limited_11days_rep2


title: Mixed culture 5.5 h rep1 _ Mono cultures 5.5 h rep1

description: Mixed culture in milk grown for 5.5 h rep1 compared to Mono cultures in milk grown for 5.5 h rep1

source_name: Mixed culture grown for 5.5 h

source_name: Mono cultures grown for 5.5 h (RNA isolated from S. thermophilus and L. bulgaricus mono cultures was mixed)


title: Mixed culture 3.5 h _ Mono cultures 3.5 h (3 merged hybs)

description:
Merged data from biological replicates:
Mixed culture in milk grown for 3.5 h rep2 compared to Mono cultures in milk grown for 3.5 h rep2 [Array_Q.txt]
Mixed culture in milk grown for 3.5 h rep1 compared to Mono cultures in milk grown for 3.5 h rep2 [Array_U.txt]
Mixed culture in milk grown for 3.5 h rep2 compared to Mono cultures in milk grown for 3.5 h rep1 [Array_V.txt]

source_name: Mixed culture grown for 3.5 h

source_name: Mono cultures grown for 3.5 h (RNA isolated from S. thermophilus and L. bulgaricus mono cultures was mixed)


title: HTCC1062_Control_11days_rep3

source_name: Control culture, 11 Days


title: Mono cultures 5.5 h rep2 _ Mixed culture 5.5 h rep2

description: Mono cultures in milk grown for 5.5 h rep2 compared to Mixed culture in milk grown for 5.5 h rep2


title: Mixed culture 8 h rep2 _ Mono cultures 8 h rep2

description: Mixed culture in milk grown for 8 h rep2 compared to Mono cultures in milk grown for 8 h rep2


title: Mono cultures 3.5 h rep1 _ Mixed culture 3.5 h rep1

description: Mono cultures in milk grown for 3.5 h rep1 compared to Mixed culture in milk grown for 3.5 h rep1


title: Mixed culture 12 h rep2 _ Mixed culture 8 h rep2

description: Mixed culture in milk grown for 12 h rep2 compared to Mixed culture in milk grown for 8 h rep2


title: HTCC1062_Control_11days_rep2


title: Mixed culture 8 h rep2 _ Mixed culture 5.5 h rep2

description: Mixed culture in milk grown for 8 h rep2 compared to Mixed culture in milk grown for 5.5 h rep2


title: Mouse parthenogenetic (PG)-derived cells_MeDIP-chip

description: MeDIP-on-chip in PG-derived cells using monoclonal anti-methylcytidie (MCA2201) antibody.

source_name: MeDIP in PG-derived cells

source_name: Sonicated input-DNA in PG-derived cells


title: Mouse androgenetic (AG)-derived cells_MeDIP-chip

description: MeDIP-on-chip in AG-derived cells using monoclonal anti-methylcytidie (MCA2201) antibody.

source_name: Sonicated input-DNA in AG-derived cells


title: HTCC1062_Control_11days_rep1


title: HTCC1062_Iron-Limited_2days_rep3

source_name: Iron-Limited Culture, 2 Days


title: HTCC1062_Iron-Limited_2days_rep1


title: HTCC1062_Iron-Limited_2days_rep2


title: Mouse sperm_MeDIP-chip

description: MeDIP-on-chip in sperm using monoclonal anti-methylcytidie (MCA2201) antibody.

source_name: MeDIP in sperm

source_name: Sonicated input-DNA in sperm


title: HTCC1062_Control_2days_rep3

source_name: Control culture, 2 Days

value: Early Stationary


title: Mono cultures 3.5 h rep2 _ Mono cultures 5.5 h rep2

description: Mono cultures in milk grown for 3.5 h rep2 compared to Mono cultures in milk grown for 5.5 h rep2


title: Mono cultures 5.5 h rep2 _ Mono cultures 8 h rep2

description: Mono cultures in milk grown for 5.5 h rep2 compared to Mono cultures in milk grown for 8 h rep2


title: HTCC1062_Control_2days_rep2


title: Mono cultures 8 h rep2 _ Mono cultures 12 h rep2

description: Mono cultures in milk grown for 8 h rep2 compared to Mono cultures in milk grown for 12 h rep2


title: Mixed culture 5.5 h rep2 _ Mixed culture 3.5 h rep2

description: Mixed culture in milk grown for 5.5 h rep2 compared to Mixed culture in milk grown for 3.5 h rep2


title: Mixed culture 5.5 h rep1 _ Mixed culture 8 h rep1

description: Mixed culture in milk grown for 5.5 h rep1 compared to Mixed culture in milk grown for 8 h rep1


title: Mixed culture 8 h rep1 _ Mixed culture 12 h rep1

description: Mixed culture in milk grown for 8 h rep1 compared to Mixed culture in milk grown for 12 h rep1


title: HTCC1062_Iron-Limited_1day_rep3

source_name: Iron-Limited Culture, 1 Day


title: HTCC1062_Control_2days_rep1


title: Mixed culture 3.5 h rep1 _ Mixed culture 5.5 h rep1

description: Mixed culture in milk grown for 3.5 h rep1 compared to Mixed culture in milk grown for 5.5 h rep1


source_name: MeDIP in AG-derived cells

value: AG-derived cells from b6d2f1 (c57bl/6 x dba/2) embryos (Ogawa H et al., 2009. Placenta. 30:448-56).


title: Mono cultures 12 h rep1 _ Mono cultures 8 h rep1

description: Mono cultures in milk grown for 12 h rep1 compared to Mono cultures in milk grown for 8 h rep1

source_name: Mono cultures grown for 12 h (RNA isolated from S. thermophilus and L. bulgaricus mono cultures was mixed)


value: monoclonal anti-methylcytidie (MCA2201)


title: HTCC1062_Iron-Limited_1day_rep2


title: Mono cultures 8 h rep1 _ Mono cultures 5.5 h rep1

description: Mono cultures in milk grown for 8 h rep1 compared to Mono cultures in milk grown for 5.5 h rep1

source_name: Mono cultures grown for 8 h (RNA isolated from S. thermophilus and L. bulgaricus mono cultures was mixed)


title: HTCC1062_Control_1day_rep1

source_name: Control culture, 1 Day

value: Late Exponential


title: HTCC1062_Control_1day_rep3


title: embryo inversion EIn(1)103.8 vs progenitor cis103.8 replicate 3

first: Lisa

last: Meadows

address: Downing Street

department: Department of Genetics

institute: University of Cambridge

hyb_protocol: Hybridisation to amino-modified long oligonucleotide microarrays using a Genomic Solutions hybridisation station with the Biosolutions hybridisation buffer (http://www.flychip.org.uk/protocols/hybridisation/)

scan_protocol: Operating instructions for the Genepix 4000B dual laser scanner (http://www.flychip.org.uk/protocols/imaging/)

data_processing: Spot finding and quantitation via the Dapple package. VSN-normalised experiment/control ratio equivalent to log[2] ratio.

label_protocol: Direct Labelling: Up to 50µg total RNA are mixed with anchored oligo (dT)23 (Sigma). The RNA is reverse transcribed using Superscript III (Invitrogen). Cy3-dCTP or Cy5-dCTP (GE Healthcare) are incorporated during cDNA synthesis. (http://www.flychip.org.uk/protocols/gene_expression)

growth_protocol: Flies maintained at 25 degrees C on standard cornmeal agar then transferred to cages on standard apple juice agar plates with yeast paste at 25C for egg collection

extract_protocol: Medium scale RNA extraction using TRIzol (http://www.flychip.org.uk/protocols/gene_expression/)

treatment_protocol: Embryos laid over a 21hr period at 25C were dechorionated in bleach and transfered to Trizol, approximately 1000 embryos per aliquot

tag: developmental stage

value: embryo

value: whole embryos

value: progenitor cis103.8

value: inversion EIn(1)103.8


title: MPNST_13

status: Public on May 04 2010

city: Glasgow

first: W.

middle: Nicol

last: Keith

state: Lanarkshire

address: Center for Oncology and Applied Pharmacology, University of Glasgow, CRUK Beatson Laboratories, Garscube Estate, Switchback Road

institute: The University of Glasgow

hyb_protocol: 100 μl of purified labelled total RNA was hybridised to Agilent 4x44K whole human genome arrays for 17 hours at 65 °C rotating at 10 rpm and washed as as per manufacturor's instructions for one colour arrays (Agilent Technologies).

scan_protocol: Slides were scanned using DNA microarray scanner model G2539A (Agilent Technologies) and Agilent Scan Control Software. Spot intensity and identity information was extracted using Agilent Feature Extraction Software.

data_processing: Normalised to the 75th percentile with intensities below 0.01 being set to 0.01.

source_name: Malignant Peripheral Nerve Sheath Tumour, Fresh Frozen

label_protocol: 800 ng of total RNA was labelled with Cy3 using the Low RNA Input Linear Amplification Kit (Agilent technologies) as per manufacturor's instructions.

extract_protocol: Frozen tumour tissue was disrupted using a Hybaid Ribolyser at a setting of 5.5 for 5 x 10 second pulses with 30 second pauses in between and RNA was extracted using the RNeasy Lipid kit (Qiagen Inc, Hilden, Germany) as per manufacturers’ instructions.

tag: sex

value: F

tag: grade

tag: histology

tag: chemo/radio therapy given

value: surgery + RT

tag: survival (months)

tag: survival status


title: embryo inversion EIn(1)103.8 vs progenitor cis103.8 replicate 2 dye swap

city: Cambridge

tag: tissue


title: MPNST_16

tag: age

value: Malignant Peripheral Nerve Sheath Tumour

value: no


title: MPNST_15


title: MPNST_14


title: MPNST_12

value: M


title: embryo inversion EIn(1)103.8 vs progenitor cis103.8 replicate 4 dye swap


title: MPNST_9


title: MPNST_11

value: surgery + CT


title: MPNST_8

value: unknown


title: MPNST_5

value: LTF


title: MPNST_7


title: embryo inversion EIn(1)103.8 vs progenitor cis103.8 replicate 1


title: MPNST_4


title: MPNST_3


title: MPNST_2

value: Surgery + CT + RT


title: MPNST_10


title: MPNST_1


title: Liposarcoma_22

source_name: Liposarcoma, Fresh Frozen

value: Pleomorphic


title: Liposarcoma_21

value: Dedifferentiated

value: only surgery


title: Liposarcoma_19

value: Myxoid-round cell

value: Radiotherapy


title: MPNST_6


title: Liposarcoma_17

value: WD, Lipoma-like


title: Liposarcoma_16

value: WD

value: hyperthermic i.p. chemotherapy (Doxorubicin + Cisplatin)


title: Liposarcoma_24


title: Liposarcoma_13


title: Liposarcoma_23

value: F


title: Liposarcoma_20


title: Liposarcoma_15

value: RT


title: Liposarcoma_10

value: Radiotherapy + Chemotherapy (Epidoxorubicin + Ifosfamide)


title: Liposarcoma_12

value: no


title: Liposarcoma_6

value: M


title: Mono cultures 5.5 h rep1 _ Mono cultures 3.5 h rep1

description: Mono cultures in milk grown for 5.5 h rep1 compared to Mono cultures in milk grown for 3.5 h rep1

source_name: Mono cultures grown for 5.5 h (RNA isolated from S. thermophilus and L. bulgaricus mono cultures was mixed)

value: Streptococcus thermophilus CNRZ1066

value: Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365


title: Liposarcoma_7


title: Liposarcoma_5


title: Liposarcoma_18


title: Liposarcoma_14

value: Myxoid


title: Liposarcoma_11


title: Liposarcoma_9

value: unknown


title: Liposarcoma_3


title: Liposarcoma_2

value: Radiotherapy + Chemotherapy (Epdoxorubicin + Ifosfamide)


title: Liposarcoma_8

value: Dedifferentiated


title: Liposarcoma_4

value: LTF


title: Peritoneal_Mesothelioma_20

source_name: Peritoneal Mesothelioma, Fresh Frozen

value: Epithelial tubulopapillary

value: cytoreductive surgery + hyperthermic i.p. chemotherapy (doxorubicin + cisplatin)


title: Peritoneal_Mesothelioma_16

value: Epithelial solid


title: Peritoneal_Mesothelioma_18


title: Liposarcoma_1

value: WD, Lipoma-like


title: Peritoneal_Mesothelioma_17

value: Biphasic


title: Peritoneal_Mesothelioma_9

value: F


title: Peritoneal_Mesothelioma_13

value: Epithelial