title: Mycelium 96h replicate 09 mat+ fpr1-

description: Biological replicate 1 of 4. Mycelium mat+ fpr1-after 96h of growth

tag: genotype

value: mat+  fpr1-

tag: growth condition

value: harvested after 96 hours of growth in constant light, on M2 media covered with a sheet of cellophane

tag: mating type

value: mat+

tag: biosource 1

value: mat+fpr1-S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: name biosource 1

tag: biosource 2

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: name biosource 2

tag: biosource 3

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

tag: name biosource 3

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.

value: common reference


title: Mycelium 96h replicate 54 mat-

status: Public on Dec 22 2011

type: RNA

city: Orsay

first: Frederique

last: Bidard

address: Bâtiment 400

department: SIGNAL TRANSDUCTION, REPRODUCTION & DEGENERATIVE PROCESSES

country: France

institute: Institut de Génétique et Microbiologie UMR 8621

description: Biological replicate 4 of 4. Mycelium mat- wt after 96h of growth

hyb_protocol: Hybridization experiments were done following the two-color microarray-based gene expression analysis instructions (version 5.0, February 2007) as described by the manufacturer (Agilent). 825 ng of each of the Cy3- and Cy5-labeled targets were mixed and incubated on an Agilent microarray slide for 17 hours at 65°C, in a rotating oven at 10 rpm for a 4x44K array format, using an Agilent in situ hybridization kit. The slides were washed in Agilent’s Gene Expression Wash Buffers following manufacturer’s instructions, then, any traces of solution were removed by centrifugation at 800 rpm for 1 min.

scan_protocol: Microarrays were scanned using the Agilent DNA microarray Scanner model G2567AA at 5 microns resolution using the extended dynamic range (XDR) feature.

data_processing: Spot and background intensities were extracted with the Feature Extraction (FE, v9.5.3) software (Agilent) using the GE2-v4_95_Feb07 default protocol. Preliminary array quality was assessed through the use of Agilent control features as well as spike-in controls (Agilent 2-Color Spike-in Kit for RNA experiment). Subsequent flagging was done according to the GenePix Pro software (Molecular Devices Syunnyvale, CA, USA) nomenclature, including four levels of flags (good (100), bad (-100), not found (-50), moderate (0)). FE software raw data from arrays issued of GPL10115 platform were processed with the MAnGO software with no background subtraction and the Printtip loess normalization method (Smyth G.K. and Speed T., 2003, Methods). FE software normalized data (Local background was subtracted and LOWESS normalization) from arrays issued of GPL10116 platform were processed with the MAnGO. Moderate t-test with adjustment of p-values was computed to measure the significance with each expression difference.

molecule: total RNA

organism: Podospora anserina

source_name: mycelium, mat-

label_protocol: Labelling experiments were done following the two-color microarray-based gene expression analysis instructions (version 5.0, February 2007) as described by the manufacturer (Agilent). One microgram aliquots of total RNA were amplified and Cy-labelled with the Agilent’s Low RNA input fluorescent linear amplification (LRILAK) PLUS kit (Agilent) along with Agilent's Two-Color RNA Spike-in Kit. The labelling efficiency and the product integrity were checked by using a NanoDrop ND-1000 spectrophotometer and the Bionalyzer 2100 system (Agilent)

growth_protocol: P. anserina strains used in this study are derived from the S strain of either mat+ or mat- mating type. Growth was carried out on a minimal synthetic medium at 27°C (Esser K.,1974; pp. 531-51 in Handbook of Genetics)

extract_protocol: Strains were grown on cellophane sheet (cat#1650193, BioRad, Marne la Coquette, France) or cheesecloth (Sefar Nitex 03-48/31, Dominique Dutscher, Brumath, France) placed on Petri-dishes. In order to collect sufficient amounts of biological materials (20 to 100 mg), 1 to 5 Petri-dishes were simultaneously inoculated. Biological material was scraped from cellophane sheets or cheesecloth and flash frozen with buffer RLT (Qiagen, Courtaboeuf, France) in liquid nitrogen. The biological material was grinded with a Mikro-Dismembrator (Sartorius, Aubagne, France) in nitrogen freezed vessels. After removing cell debris by centrifugation, nucleic acids were passed through a Qiashreddrer (Qiagen) for sharing DNA and total RNA was purified on RNeasy Plant Mini Kit columns (Qiagen), with an additional DNase treatment. The quality and quantity of the total RNA was determined by using a NanoDrop ND-1000 spectrophotometer and the Bionalyzer 2100 system (Agilent).

tag: tissue

value: mycelium

value: mat-

source_name: Common reference

value: mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: biosource 4

tag: name biosource 4

tag: sample type


title: NA_CD3__CB_4

type: genomic

city: NEDLANDS

first: David

last: Martino

state: Western Australia

address: Perth Childrens Hospital, 15 Hospital Avenue

country: Australia

institute: Telethon Kids Institute

description: neonatal CD4+

hyb_protocol: Infinium Methylation Assay according to manufacturers protocol (Illumina)

scan_protocol: iScan system

data_processing: Genome studio v2010.3 with Methylation Module v1.8.5 under default settings

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: gDNA from CD4+ cells

label_protocol: Cy5 and Cy3

growth_protocol: cells cultured for 24 hours in AIM-V media + 2Mercapto ethanol (serum free)

extract_protocol: DNA and RNA co purified from source according to Qiagen all prep kit protocol

treatment_protocol: Anti-CD3 (0.5ug/mL) + rhIL2 (20Units) or UNTREATED

tag: cell type

value: neonatal CD4+

tag: gender

value: mixed

tag: age

tag: disease state

value: NORM

tag: treatment

tag: pool id

value: J


title: Whole_Forebrain_2 [ChIP-chip 244K array, 2 of 2]

city: Brest

first: Gaelle

last: Friocourt

address: 46 rue Félix Le Dantec, CS51819

department: Molecular Genetics

institute: Inserm U613

hyb_protocol: 5 µg of labelled DNA was hybridized to mouse promoter 244K ChIP-Chip microarrays set (Agilent Technologies) for 40 hours, at 65°C, at 20 rpm.

scan_protocol: Hybridization images were obtained using an Agilent DNA microarray scanner (G2505B). Scan Region : Agilent HD (61 x 21,6 mm) / Resolution : 5 µm / TIFF : 16 bit / Red PMT : 100% / Green PMT : 100%. Intensity data were extracted using Feature Extraction software (FE v9,5,1) (Agilent Technologies).

data_processing: Intensity data on each array were normalized with the Lowess method. To identify regions of significant Arx association, the enrichment of each probe on the array was calculated as the ratio of the intensities of Arx-immunoprcipitated DNA (y-axis) to control Input chromatin (x-axis). One first important assumption is that points corresponding to non positive probes are distributed symmetrically around the axis x=y. A threshold spline curve was then defined by considering only the probes below this axis. Reporting this curve above the axis allowed discrimination between positive and negative probes. For each probe, a P-Value was obtained using a normalised distance between it and the axis x=y.

label: Alexa Fluor 647

organism: Mus musculus

source_name: Embryonic brains [IP DNA]

label_protocol: Immunoprecipitated chromatin and total Input DNA were amplified using GenomePlex Complete Whole Genome Amplification kit (Sigma).Then, two micrograms of IP and Input DNA were labelled with Alexa Fluor 647 or Alexa Fluor 555 respectively, by use of the BioPrime Plus Array CGH Indirect Genomic Labbeling System (Invitrogen).

growth_protocol: CELLS : N2a cells were grown in Dulbecco's Modified Eagle Medium (DMEM) high glucose (PAA) which was supplemented with 10% fetal bovine serum gold (PAA), 2 mM L-glutamine (Lonza), 0,1 mM non essential amino-acids (Gibco) and 2 mM penicillin/streptomycin (PAA). Cells were grown at 37°C with 5% CO2. BRAINS :  Swiss outbred (RJOrl:SWISS) mice (Janvier, France) were used in all the studies. Mouse brains were extracted from day 15,5 embryos in cold PBS. Following brain isolation, the whole forebrain (ventral telecenphalon, thalamus, cerebral cortex and olfactory bulbs) were frozen in liquid nitrogen.

extract_protocol: DNA of cells and embryonic brains was fragmented by sonication. Immunoprecipitation was perfomed using anti-Arx antibody (ARX C-14; Santa-Cruz; Catalog sc-48843; Lot A2108). Immune complexes were captured by addition of dynabeads protein G. Following washes with gradient stringent buffers, protein-DNA complexes were eluted. Reverse cross-link was performed then, immunoprecipitated DNA and Input DNA were isolated via phenol-chloroform extraction followed by ethanol precipitation.

treatment_protocol: CELLS : Cells were transfected with an expression vector expressing Arx using Lipofectamine 2000 according to the guideline of the manufacturer (Invitrogen). Two days after transfection, cells were fixed in 1% formaldéhyde, followed by the addition of glycine. BRAINS : Embryonic brains disaggregation and homogenization were performed in liquid nitrogen using a pestle and a mortar. Samples were fixed in a solution containing PBS, formaldehyde and protease inhibitor cocktail. Reaction was stopped by the addition of glycine.

tag: strain

value: Swiss outbred (RJOrl:SWISS)

value: brain

tag: developmental stage

tag: chip antibody

value: anti-Arx antibody (ARX C-14)

tag: chip antibody vendor

value: Santa-Cruz

tag: chip antibody lot#

tag: chip antibody catalog#

label: Alexa Fluor 555

source_name: Embryonic brains [Input DNA]


title: NA_CD3__CB_6

description: neonatal CD4+

value: male

value: L


title: FA_CD3_1Y_5

description: 12m CD4+

value: FOOD ALLERGY

value: H


title: Mycelium 96h replicate 84 mat-

description: Biological replicate 1 of 4. Mycelium mat- wt after 96h of growth

tag: genotype

tag: growth condition

value: harvested after 96 hours of growth in constant light, on M2 media covered with a sheet of cellophane

tag: mating type

tag: biosource 1

tag: name biosource 1

tag: biosource 2

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: name biosource 2

tag: biosource 3

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

tag: name biosource 3

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.


title: Whole_Forebrain_1 [ChIP-chip 244K array, 2 of 2]

tag: tissue


title: Mycelium 96h replicate 13 mat+ fpr1-

description: Biological replicate 4 of 4. Mycelium mat+ fpr1-after 96h of growth

source_name: mycelium, fpr1-

value: mycelium

value: mat+  fpr1-

value: mat+

value: mat+fpr1-S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: biosource 4

tag: name biosource 4

tag: sample type

value: common reference


title: Mycelium 96h replicate 98 mat+

description: Biological replicate 3 of 4. Mycelium mat+ wt after 96h of growth

source_name: mycelium, mat+

value: mat+ S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.


title: FA_CD3__CB_6

description: neonatal CD4+

tag: cell type

value: neonatal CD4+

tag: gender

value: mixed

tag: age

tag: disease state

tag: treatment

tag: pool id

value: I


title: FA_CD3_1Y_4

description: 12m CD4+

value: G


title: Cells_Transfected_by_ARX_2 [ChIP-chip 244K array, 2 of 2]

source_name: Neuroblastoma cells [IP DNA]

tag: cell line

value: N2a neuroblastoma cells

tag: chip antibody

value: anti-Arx antibody (ARX C-14)

tag: chip antibody vendor

value: Santa-Cruz

tag: chip antibody lot#

tag: chip antibody catalog#

source_name: Neuroblastoma cells [Input DNA]


title: FA_CD3__CB_5

description: neonatal CD4+

value: male

value: FOOD ALLERGY

value: H


title: Mycelium 96h replicate 99 mat+

description: Biological replicate 4 of 4. Mycelium mat+ wt after 96h of growth

tag: genotype

tag: growth condition

value: harvested after 96 hours of growth in constant light, on M2 media covered with a sheet of cellophane

tag: mating type

tag: biosource 1

tag: name biosource 1

tag: biosource 2

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: name biosource 2

tag: biosource 3

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.


title: Mycelium 96h replicate 81 mat+

description: Biological replicate 1 of 4. Mycelium mat+ wt after 96h of growth

tag: tissue

value: mycelium

value: mat+

tag: name biosource 3

tag: biosource 4

tag: name biosource 4

tag: sample type


title: FA_CON_1Y_2

description: 12m CD4+

tag: cell type

tag: gender

tag: age

tag: disease state

tag: treatment

value: CON

tag: pool id

value: B


title: FA_CD3__CB_4

description: neonatal CD4+

value: neonatal CD4+

value: mixed


title: NA_CD3_1Y_3

description: 12m CD4+

value: NORM

value: F


title: Cells_Transfected_by_ARX_1 [ChIP-chip 244K array, 2 of 2]

tag: cell line

value: N2a neuroblastoma cells

tag: chip antibody

value: anti-Arx antibody (ARX C-14)

tag: chip antibody vendor

tag: chip antibody lot#

tag: chip antibody catalog#


title: 963_RT

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

hyb_protocol: 5ug of Cy5-labeled sample was combined with 5ug of Cy3-labeled male reference, and samples were hybridized and washed by following Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol v6.2 on on Agilent SurePrint G3 Human Catalog CGH 8x60K (Design ID 021924)

scan_protocol: Scanned at a 3um scan resolution and 20 bit tiff file setting on the Agilent DNA Microarray Scanner G2505C

data_processing:
Quantified signal intensities and pre-processed data with Agilent Feature Extraction 10.5.1.1
We have loaded the FE files directley into Nexus Copy Number Software (Biodiscovery Inc.) for analysis.

label_protocol: 500ng gDNA labeled by following NimbleGen Arrays User’s Guide: CGH Analysis v5.0, which included a 98C heat fragmentation step and labeling with Cy-labeled random nanomers (TriLink Biotechnologies) and Klenow 3'-5'exo-(New England Biolabs).

extract_protocol: Genomic DNA extracted with Promega Wizard Genomic DNA Extraction Kit

tag: tumor foci

value: Right Transitional

source_name: male reference DNA (Promega Corp)

tag: reference

value: male reference DNA (Promega Corp)


title: Cells_Transfected_by_ARX_3 [ChIP-chip 244K array, 2 of 2]

value: Santa-Cruz


title: NA_CON__CB_1

description: neonatal CD4+

value: female

value: D


title: 963_LT

value: Left Transitional


title: Mycelium 96h replicate 85 mat-

description: Biological replicate 2 of 4. Mycelium mat- wt after 96h of growth

tag: tissue

tag: genotype

value: mat-

tag: growth condition

value: harvested after 96 hours of growth in constant light, on M2 media covered with a sheet of cellophane

tag: mating type

tag: biosource 1

tag: name biosource 1

tag: biosource 2

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: name biosource 2

tag: biosource 3

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

tag: name biosource 3

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.

value: common reference


title: NA_CD3_1Y_2

description: 12m CD4+

tag: cell type

tag: gender

value: mixed

tag: age

tag: disease state

tag: treatment

tag: pool id

value: E


title: Mycelium 96h replicate 82 mat+

description: Biological replicate 2 of 4. Mycelium mat+ wt after 96h of growth

value: mycelium

value: mat+

value: mat+ S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: biosource 4

tag: name biosource 4

tag: sample type


title: FA_CON_CB_3

description: neonatal CD4+

value: neonatal CD4+

value: male

value: FOOD ALLERGY

value: CON

value: C


title: 963_L_LN

tag: tumor foci

value: Left Lymph Node

tag: reference

value: male reference DNA (Promega Corp)


title: N2a cells transfected by Arx 7

hyb_protocol: 825 ng of cyanine-labeled, linearly amplified cRNA were hybridized at 65°C at 10 rpm for 17 hours, with 10X Blocking Agent, 25X Fragmentation Buffer, Nuclease free water and 2X GEx Hybridization Buffer HI-RPM (Agilent Technologies). Samples were hybridized on Mouse Gene Expression 4x44K V2 microarray (Agilent Technologies).

scan_protocol: Hybridization images were obtained using an Agilent DNA microarray scanner (G2505B). Profile : Agilent HD_GX_2color / Scan Region : Agilent HD (61 x 21,6 mm) / Resolution : 5 µm / TIFF : 20 bit / RPMT : 100% / GPMT : 100%. Intensity data were extracted using Feature Extraction software (FE v9,5,1) (Agilent Technologies).

data_processing: The Lowess method was used to normalize data expression (using in-house R script).

source_name: Neuroblastoma cells

label_protocol: RNA was labelled using the Low Input Quick Amp Labelling kit (Agilent Technologies). The fluorescent labelled cRNA probes were purified using the RNeasy Mini kit (Qiagen).

growth_protocol: N2a cells were grown in Dulbecco's Modified Eagle Medium (DMEM) high glucose (PAA) which was supplemented with 10% fetal bovine serum gold (PAA), 2 mM L-glutamine (Lonza), 0,1 mM non essential amino-acids (Gibco) and 2 mM penicillin/streptomycin (PAA). Cells were grown at 37°C with 5% CO2.

extract_protocol: Two days after transfection, RNA from N2a cells was isolated using the Total RNA Isolation Nucleospin RNA II kit following the manufacturer's instructions (Macherey-Nagel).

treatment_protocol: Cells were transfected with an expression vector expressing Arx using Lipofectamine 2000 according to the guideline of the manufacturer (Invitrogen)

tag: tissue

value: Brain

tag: cell line

value: N2a neuroblastoma cells

tag: genotype/variation

value: Arx expression


title: NA_CD3__CB_3

description: neonatal CD4+

value: NORM

value: F


title: N2a cells transfected by Arx 8


title: 963_LP

value: Left Posterior


title: liver of db/db mice 4

city: Delhi

first: Malabika

last: Datta

address: Mall Road

country: India

institute: Institute of Genomics and Integrative Biology

description:
db/db mice are an excellent model of obesity and type 2 diabetes and exhibit insulin resistance as early as 10–12 days of age and at  8–12 wk, they exhibit glucose intolerance in response to an oral glucose challenge and a reduced hypoglycemic response to a bolus injection of insulin  compared with nondiabetic control db/+ mice.
The mouse miRNA Microarray (V1) microarrays (G4472A) from Agilent Technologies was used for the experiment. It consisted of probes for 566 mouse miRNAs and 10 mouse viral miRNA.

hyb_protocol: The hybridization mixture [10X GE blocking agent (4.5 ul), 2X Hi-RPM hybridization buffer (22.5ul)] along with labelled miRNA sample was heated for 5 min at 100 °C and immediately cooled to 0 °C. Each 45 mL sample was hybridized onto a microarray at 55 °C for 20 h. Slides were washed 5 min in GE wash buffer 1 at RT and again for 5 min in GE wash buffer 2 at 37 °C, followed by an acetonitrile wash for 1 min at RT to dry the slides completely.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565BA) at 100 and 5% XDR settings. Agilent Feature Extraction software version 9.3.5 was used to extract the raw data.

data_processing: The raw data were global median normalized and log transformed and analyzed by Significance Analysis of Microarray (SAM). SAM calculates a score for each gene as a change of expression relative to the standard deviation of all measurements and therefore identifies genes that are significantly associated with an outcome variable such as the disease stage. In SAM tests, a false Discovery Rate (FDR) of less than 5% was selected and parameters were set as default.

source_name: Liver

label_protocol: miRNA labeling was performed as described in Agilent miRNA microarray protocol version 2.0 using Agilent miRNA labeling kit. 100 ng of total RNA was dephosphorylated with calf intestine alkaline phosphatase for 30min at 37°C. Denaturation was performed by adding DMSO and incubating at 100°C for 7 min and immediately transferred to ice water bath. Ligation was performed with pCp-Cy3 at 16 °C for 2 h. The labeled samples were dried completely in a vaccum concentrator and resuspended in 18 ul of nuclease free water.

extract_protocol: Frozen liver tissues were minced and homogenized and total RNA was extracted using Trizol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. RNA was quantified using Nanodrop spectrophotometer and RNA quality and integrity was analyzed in Bioanalyser.

value: liver

tag: strain

value: db/db


title: NA_CD3__CB_2

description: neonatal CD4+

value: mixed

value: E


title: NA_CD3_1Y_1

description: 12m CD4+

value: female

value: D


title: N2a cells transfected by Arx 5


title: NA_CD3__CB_1

description: neonatal CD4+

value: neonatal CD4+


title: N2a cells transfected by Arx 6


title: doubleKO Dex - C

city: La Jolla

first: Ruth

middle: T

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

country: USA

institute: Salk Institute

description: Cry1/2 double KO MEFs treated with Dex, biological replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using cubic spline in Illumina GenomeStudio and also using the VAMPIRE Bayesian model with a 2-sided Bonferroni-corrected threshold of 0.05.

label: biotin

source_name: doubleKO Dex

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

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

tag: dev stage

value: E15.5 embryos

value: primary MEFs


title: siSTAT3-2

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to a ver. 3 of the Illumina Human-Ht-12 BeadChip (48K) according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

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:
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48803 probes on the Human-Ht12 beadChip ver. 3 were used.
Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization. To export to a data matrix, Sample Gene Profile option of this software was used.

label: Biotin

source_name: SKOV3ip1Ovarian Cancer Cell

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

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

value: SKOV3ip1 Ovarian Cancer Cell line

tag: protocol

value: STAT3 knock down


title: doubleKO EtOH - C

description: Cry1/2 double KO MEFs treated with EtOH, biological replicate 3

source_name: doubleKO EtOH


title: FA_CD3_1Y_6

description: 12m CD4+

tag: cell type

value: FOOD ALLERGY

value: I


title: 963_RP

value: Right Posterior

value: male reference DNA (Promega Corp)


title: FA_CD3_1Y_1

description: 12m CD4+

tag: gender

value: A


title: liver of db/db mice 3


title: doubleKO Dex - A

description: Cry1/2 double KO MEFs treated with Dex, biological replicate 1


title: FA_CD3_1Y_2

description: 12m CD4+

value: male

tag: age

value: B


title: doubleKO Dex - B

description: Cry1/2 double KO MEFs treated with Dex, biological replicate 2


title: siSTAT3-3


title: N2a cells transfected by Arx 4

value: Brain

value: N2a neuroblastoma cells

value: Arx expression


title: FA_CD3__CB_3

description: neonatal CD4+

tag: disease state

value: C


title: liver of db/db mice 1

value: liver

value: db/db


title: FA_CD3_1Y_3

description: 12m CD4+

tag: treatment


title: FA_CD3__CB_2

description: neonatal CD4+

value: neonatal CD4+

tag: pool id


title: FA_CD3__CB_1

description: neonatal CD4+

value: mixed


title: siCon2

value: SKOV3ip1 Ovarian Cancer Cell line

value: control


title: N2a cells transfected by Arx 3


title: doubleKO EtOH - A

description: Cry1/2 double KO MEFs treated with EtOH, biological replicate 1

value: E15.5 embryos

value: primary MEFs


title: liver of control db/+ mice 4

value: db/+


title: N2a cells transfected by FLAG 8


title: doubleKO EtOH - B

description: Cry1/2 double KO MEFs treated with EtOH, biological replicate 2


title: siSTAT3-1

value: STAT3 knock down


title: N2a cells transfected by Arx 1


title: N2a cells transfected by Arx 2


title: N2a cells transfected by FLAG 7


title: siCon1


title: liver of control db/+ mice


title: control Dex - C

description: normal heterozgous MEFs treated with Dex, biological replicate 3

source_name: control Dex


title: control Dex - A

description: normal heterozgous MEFs treated with Dex, biological replicate 1


title: liver of control db/+ mice 3

description: db/db mice are an ecxellent model of obesity and type 2 diabetes and exhibit insulin resistance as early as 10–12 days of age and at  8–12 wk, they exhibit glucose intolerance in response to an oral glucose challenge and a reduced hypoglycemic response to a bolus injection of insulin  compared with nondiabetic control db/+ mice.


title: control EtOH - C

description: normal heterozgous MEFs treated with EtOH, biological replicate 3

source_name: control EtOH


title: livers of control db/+ mice

description:
db/db  (C57BL/KsJ) mice are an excellent model of obesity and type 2 diabetes. They exhibit insulin resistance as early as 10–12 days of age  and at 8–12 wk, diabetic db/db mice exhibit glucose intolerance in response to an oral glucose challenge  and a reduced hypoglycemic response to a bolus injection of insulin compared with nondiabetic control db/+ mice.
The mouse miRNA Microarray (V1) microarrays (G4472A) from Agilent Technologies was used for the experiment. It consisted of probes for 566 mouse miRNAs and 10 mouse viral miRNA.


title: N2a cells transfected by FLAG 5


title: siESR1_3_MCF7

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48803 probes on the Human-Ht12 beadChip ver. 3 were used.

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: MCF7 Breast Cacner Cell

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's TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

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


title: siLuc1_3_MCF7


title: control Dex - B

description: normal heterozgous MEFs treated with Dex, biological replicate 2


title: N2a cells transfected by FLAG 6


title: control EtOH - B

description: normal heterozgous MEFs treated with EtOH, biological replicate 2


title: PTG infected Mouse 1

city: Knoxville

first: Rachel

last: Hill

state: TN

address: 1401 W. Cumberland Ave

department: Microbiology

institute: University of Tennessee Knoxville

hyb_protocol: Five micrograms of fragmented cRNA was hybridized to the GeneChip Mouse Gene 1.0 st array and scanned at UT Affymetrix core facility

scan_protocol: Arrays were immediately scanned using the Affymetrix 7G scanner

data_processing: The raw data from arrays were normalized with with Robust Multichip Algorithm (GC RMA) using Partek® Genomics SuiteTM software. A two way analysis of variance (ANOVA) was used to detect genes with statistically significant expression levels between T. gondii infected mice and the uninfected controls.

source_name: Female outbred

label_protocol: RNA samples were processed according to the Affymetrix protocol for One-Cycle DNA synthesis using a Message Amp II-Biotin Enhanced Kit

growth_protocol: Mice were infected intraperitoneally with 500 tachyzoites of either GT1, PTG or CTG. On day 5 mice were sacrificed and peritoneal lavage was collected in 5ml PBS. Peritoneal lavage was centrifuged and supernatant removed. Pellet was resuspended in 1 ml RNAlater, incubated at 4° for 1 hr, then stored in -70° until use.

extract_protocol: Samples stored in RNAlater were centrifuged at 12,000 rpm for 10 min. Supernatant removed. RNA was isolated using the RNeasy Plus Mini Kit (Qiagen), according to the manufacturer’s instructions.

tag: mouse strain

value: female

value: 6-8 weeks

value: Peritoneal lavage

tag: toxplasma gondii strain

value: PTG


title: bio4-1 mutant, watered with 200µM biotin, leaves, rep3

city: Seibersdorf

first: Günter

last: Brader

address: AIT

department: Health & Environment Department

country: Austria

institute: Austrian Institute of Technology

description: bio4-1 mutant, watered once a week with 200µM biotin, 1l per tray with 28 plants, leaves were harvested and pooled from five plants , rep3

hyb_protocol: Hybridisation was performed according to the Affymetrix GeneChip Technical Analysis Manual at the NASC's International Affymetrix Service

scan_protocol: GeneChips were scanned using the Agilent 2500A GeneArray Scanner at the NASC's International Affymetrix Service

data_processing: The data were analyzed with the R-package using AffylmGUI; Robust multiarray average (RMA) normalization has been performed.

organism: Arabidopsis thaliana

label_protocol: Biotinylated cRNA were prepared using Affymetrix Enzo Kit from 3 ug total RNA and performed at the NASC's International Affymetrix Service

growth_protocol: The seeds were stored at +4ºC, and were kept in the dark in water at +4ºC for 2 days before move to growth room. Seeds were then germinated on MS/2 (Sigma-Aldrich, St. Louis, MO) plates and one-week-old seedlings transferred  to soil (1:1 peat: vermiculite; Finnpeat B2, Kekkilä Oyj, Tuusula, Finland). The plants were grown in a growth room with a temperature of 23ºC (day)/19 ºC (night) and a relative humidity of  50-60%. The photoperiod was 12 h of light and 12 h of dark. The light intensity was 220-280 µmol s-2 m-2 .

extract_protocol: Qiagen's RNeasy Plant mini kit's protocol according to the instructions of the manufacturer with additional precipitation step for the final eluate (1/10 vol 3 M NaAc pH 5.2 and 1 vol isopropanol added, incubation at -20 C for 2 h, centrifuge 13000 rpm 30 min, wash with 70% EtOH, drying, resuspension in DEPC treated MQ water. RNA integrity was checked with Agilent Bioanalyzer 2100 using Agilent RNA 6000 Pico Gene chips.

treatment_protocol: After transfer to soil plants were watered once a week either with 1L water for a tray containing 28 pot with 1 plant each or with 1L 200µM d-biotin. Samples were collected from rosette leaves of five week old plants and each sample was pooled from 5 individuals.

tag: ecotype

value: leaves

value: bio4-1 mutant

value: 5 week old plants


title: Uninfected Mouse 2


title: control EtOH - A

description: normal heterozgous MEFs treated with EtOH, biological replicate 1


title: N2a cells transfected by FLAG 4

value: Brain

value: N2a neuroblastoma cells


title: siESR1_1_MCF7


title: CTG infected Mouse 3

value: CTG


title: N2a cells transfected by FLAG 3


title: PTG infected Mouse 2


title: N2a cells transfected by FLAG 2


title: bio4-1 mutant, watered with 200µM biotin, leaves, rep1

description: bio4-1 mutant, watered once a week with 200µM biotin, 1l per tray with 28 plants, leaves were harvested and pooled from five plants , rep1


title: siLuc1_1_MCF7


title: Uninfected Mouse 1


title: liver of db/db mice 2

description:
db/db mice are an excellent model of obesity and type 2 diabetes and exhibit insulin resistance as early as 10–12 days of age and at  8–12 wk, they exhibit glucose intolerance in response to an oral glucose challenge and a reduced hypoglycemic response to a bolus injection of insulin  compared with nondiabetic control db/+ mice.
The mouse miRNA Microarray (V1) microarrays (G4472A) from Agilent Technologies was used for the experiment. It consisted of probes for 566 mouse miRNAs and 10 mouse viral miRNA.

value: liver

value: db/db


title: shNR2E3_3_MCF7


title: bio4-1 mutant, leaves, rep3

description: bio4-1 mutant, watered once a week with 1l water per tray with 28 plants, leaves were harvested and pooled from five plants , rep3

source_name: bio4-1 mutant, leaves


title: bio4-1 mutant, leaves, rep2

description: bio4-1 mutant, watered once a week with 1l water per tray with 28 plants, leaves were harvested and pooled from five plants , rep2


title: shNR2E3_2_MCF7


title: N2a cells transfected by FLAG 1

value: control


title: siLuc1_2_MCF7


title: bio4-1 mutant, watered with 200µM biotin, leaves, rep2

description: bio4-1 mutant, watered once a week with 200µM biotin, 1l per tray with 28 plants, leaves were harvested and pooled from five plants , rep2


title: bio4-1 mutant, leaves, rep1

description: bio4-1 mutant, watered once a week with 1l water per tray with 28 plants, leaves were harvested and pooled from five plants , rep1


title: Wild type leaves rep 3

description: Col-0 wild type, watered once a week with 1l water per tray with 28 plants, leaves were harvested and pooled from five plants , rep 3

source_name: Col-0 wild type leaves

value: wild type


title: shNR2E3_1_MCF7


title: GT1 infected Mouse 3


title: shCon3_MCF7


title: GT1 infected Mouse 2


title: CTG infected Mouse 1


title: shCon1_MCF7


title: Wild type leaves rep 2

description: Col-0 wild type, watered once a week with 1l water per tray with 28 plants, leaves were harvested and pooled from five plants , rep 2


title: Wild type leaves rep 1

description: Col-0 wild type, watered once a week with 1l water per tray with 28 plants, leaves were harvested and pooled from five plants , rep 1


title: shCon2_MCF7


title: siESR1_2_MCF7


title: GT1 infected Mouse 1


title: CTG infected Mouse 2


title: Normal_BM_8

status: Public on Dec 21 2011

city: Angers

first: Philippe

last: Guardiola

state: Maine et Loire

address: 4 rue Larrey

institute: Angers University Hospital

hyb_protocol: Hybridization on Illumina HumanHT-12 v3 Expression BeadChips and staining were performed according to Illumina’s protocol.

scan_protocol: Detection of cRNAs on microarrays using an I-Scan system were performed according to Illumina’s protocol.

data_processing: GenomeStudio 2010.3 software (Illumina Inc., San Diego, USA) and its Gene Expression Analysis Module (version 1.8.0) were used for signal extraction and normalization. The Invariant Rank normalization method was applied to the primary probe data. Processed probe data were then filtered according to the following criteria: minimal signal intensity fold change of 1.50 across all samples; minimal probe signal intensity absolute change of 150 across all samples; and maximal value for probe signal intensity of 50 000 across all samples.

source_name: normal bone marrow cells

label_protocol: The Illumina Total Prep RNA Amplification Kit (Applied Biosystems / Ambion, Austin, USA) was used to generate biotinylated, amplified cRNA according to the  manufacturer recommendations.

extract_protocol: Total RNAs were extracted from 10e7 thawed cells using RNEasy® Mini Kits (Qiagen Incorporation, Valencia, USA). Total RNA quantification was performed using the Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific Incorporation, Waltham, USA) according to manufacturer recommendations. Integrity of the extracted RNAs was assessed with the Bioanalyzer 2100 and the RNA6000 Nano kit (Agilent Technologies Incorporation, Santa Clara, USA).

treatment_protocol: Blasts and mononuclear cells were purified by Ficoll-Hypaque density gradient centrifugation from bone marrow or peripheral blood samples (Nygaard, Oslo, Norway). Isolated cell samples were then immediately cryopreserved.

value: normal bone marrow cells

tag: aml subtype

tag: cell source

value: Bone Marrow

tag: time point

value: Not Applicable


title: Normal_BM_6


title: Normal_BM_7


title: Pool4_Normal-BMs

source_name: normal bone marrow cells_Pool4

value: pool of normal bone marrow cells


title: Normal_BM_2


title: Pool2_Normal-BMs_dup

source_name: normal bone marrow cells_Pool2


title: UPN97_NK-AML_BM

source_name: NK-AML_Bone Marrow

value: Human acute myeloid leukemic cells

value: NK-AML

value: Diagnosis


title: Pool2_Normal-BMs


title: siCon3

tag: cell line

value: SKOV3ip1 Ovarian Cancer Cell line


title: Normal_BM_4


title: Pool1_Normal-BMs

source_name: normal bone marrow cells_Pool1


title: Pool3_Normal-BMs

source_name: normal bone marrow cells_Pool3


title: Normal_BM_3


title: Pool5_Normal-BMs

source_name: normal bone marrow cells_Pool5


title: Pool5_Normal-BMs_dup


title: Pool4_Normal-BMs_dup


title: UPN89_NK-AML_BM


title: Normal_BM_5


title: UPN83_NK-AML_BM


title: Normal_BM_1


title: Pool3_Normal-BMs_dup


title: UPN77_NK-AML_BM


title: UPN72_NK-AML_BM


title: Pool1_Normal-BMs_dup


title: UPN78_NK-AML_PB

source_name: NK-AML_Peripheral Blood

value: Peripheral Blood


title: UPN75_NK-AML_BM


title: UPN74_NK-AML_BM


title: UPN73_NK-AML_PB


title: UPN70_NK-AML_PB


title: UPN71_NK-AML_BM


title: UPN64_NK-AML_BM


title: UPN25_NK-AML_BM


title: UPN16_NK-AML_BM


title: UPN66_NK-AML_BM


title: ΔsigTΔsigU x ΔsigTSigU++- rep1

city: Sao Paulo

first: Rogerio

last: Lourenco

state: Sao Paulo

address: Av. Prof. Lineu Prestes, 748

department: Bioquimica

country: Brazil

institute: Universidade de Sao Paulo

hyb_protocol: Agilent protocol  Agilent protocol  Agilent protocol  Agilent protocol

scan_protocol: Agilent protocol  Agilent protocol

data_processing: Data were extracted and normalized using Agilent Feature Extraction Software 9.0. Agilent output files were then opened using Excel and the log10 values extracted with no additional processing or filtering

organism: Caulobacter vibrioides NA1000

source_name: ΔsigTΔsigU

label_protocol: standard Cy3-dCTP and Cy5-dCTP incorporations

growth_protocol: Overnight cultures were diluted in fresh minimal medium supplemented with glucose to OD= 0.1

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

treatment_protocol: Exponentially growing cells were exposed to 150 mM sucrose for 30 min (mutant x parental cells) or harvested without any treatment (sigU overexpressing x double mutant cells)

tag: genotype/variation

value: sigTsigU double mutant

source_name: ΔsigT- sigU overexpression

value: sigU overexpression in sigT mutant


title: UPN62_NK-AML_BM


title: UPN54_NK-AML_PB


title: UPN46_NK-AML_BM


title: ΔsigU x WT- rep2

source_name: WT- sucrose

tag: stress

value: sucrose stress

source_name: ΔsigU- sucrose

value: sigU mutant


title: UPN44_NK-AML_PB


title: UPN32_NK-AML_PB


title: UPN38_NK-AML_BM


title: ΔsigTΔsigU x ΔsigTSigU++- rep3


title: ΔsigTΔsigU x ΔsigTSigU++- rep2


title: UPN28_NK-AML_BM


title: UPN20_NK-AML_BM


title: ΔsigU x WT- rep3


title: UPN12_NK-AML_BM


title: UPN41_NK-AML_BM


title: ΔsigU x WT- rep1


title: UPN8_NK-AML_BM


title: ΔphyR x WT- rep3

source_name: ΔphyR- sucrose

value: phyR mutant


title: UPN84_inv(16)-AML_PB

source_name: inv(16)-AML_Peripheral Blood


title: ΔsigT x WT- rep1

source_name: ΔsigT- sucrose

value: sigT mutant


title: ΔsigT x WT- rep2


title: UPN56_inv(16)-AML_BM

source_name: inv(16)-AML_Bone Marrow


title: ΔsigT x WT- rep3


title: RA.CABG.AF.RA39 [V2]

city: Darlinghurst

first: Mark

last: Cowley

state: NSW

address: 384 Victoria St.

department: Genome Informatics & Clinical Genomics

institute: Garvan Institute of Medical Research

description: miRNA derived from Heart tissue, from a patient with CABG (averaged sample)

hyb_protocol: Samples were hybridised following manufacturers protocols. Arrays were hybridized in 3 separate batches

scan_protocol: Samples were scanned on a G2505C Agilent Scanner, using the miRNA_107_Sep09 xml array design file.

data_processing: The n=11 raw TXT files were RMA normalised. These data were then combined with arrays corresponding to GPL10850 and quantile normalised across all n=39 arrays. Control probes and those not detected on any of the arrays were filtered out. A slide-of-origin batch effect was removed by fitting a linear model to the array barcode. The residuals from the model fit represent the batch-removed log-base-2, normalised expression levels of each microRNA. Technical replicates were then averaged, to produce n=34 samples, from the n=39 arrays.

label_protocol: samples were labelled with Cy3 following manufacturers protocols. Samples were labelled in 3 separate batches

extract_protocol: Total RNA was extracted using Trizol® reagent (Invitrogen).

treatment_protocol: Tissue was extracted from patients either undergoing mitral valve surgery or coronary artery bypass graft surgery, or from donor hearts. Tissue removed at surgery was placed immediately in ice cold saline and was removed into RNA later wihtin 10 min of excision. RNA later was removed after ovenight treatment and the samples stored at -80degrees C.

tag: class

tag: af or sr

value: AF (atrial fibrillation)

tag: atrium

value: RA

tag: disease

value: CABG

tag: patientid

tag: batch

tag: hybridisation date (first array)

tag: hybridisation date (second array)


title: UPN81_inv(16)-AML_PB

tag: cell type


title: ΔphyK x WT- rep3

value: wild type

source_name: ΔphyK- sucrose

value: phyK mutant


title: ΔphyK x WT- rep1


title: RA.CABG.SR.RA45 [V2]

description: miRNA derived from Heart tissue, from a patient with CABG

value: SR (sinus rhythm)


title: LA.VHD.AF.LA58 [V2]

description: miRNA derived from Heart tissue, from a patient with VHD (averaged sample)

value: LA

value: VHD


title: LA.VHD.SR.LA88 [V2]


title: UPN47_inv(16)-AML_PB

value: Human acute myeloid leukemic cells

value: Diagnosis


title: UPN80_inv(16)-AML_BM

value: Bone Marrow


title: UPN1_NK-AML_PB

value: NK-AML

value: Peripheral Blood


title: UPN35_inv(16)-AML_BM


title: UPN24_inv(16)-AML_BM


title: LA.VHD.AF.LA56 [V2]


title: ΔphyR x WT- rep1

value: sucrose stress


title: ΔphyK x WT- rep2


title: UPN45_inv(16)-AML_BM


title: UPN17_inv(16)-AML_PB


title: UPN27_inv(16)-AML_BM


title: Human Placenta - rep6

city: Brisbane

first: Nic

last: Waddell

address: St Lucia

institute: Queensland Centre for Medical Genomics

description: RNA from Ambion

hyb_protocol: Hybridized to the Agilent Human miRNA array (AMADID 016436) for 20 hrs at 55°C

scan_protocol: The slides were scanned using the Agilent Scanner G2505B US22502591 (Agilent Technologies)

data_processing: Data was extracted using the Feature Extraction software v9.5.3.1 (Agilent Technologies).

source_name: placenta, Ambion

label_protocol: 100 ng of input material which was labeled according to Agilent Human miRNA array protocol

extract_protocol: RNA was purchased from Ambion

tag: tissue

value: placenta


title: Human Placenta - rep5

description: RNA from Ambion


title: Human Placenta - rep4

description: RNA from Ambion


title: UPN15_inv(16)-AML_PB


title: Human Placenta - rep3

description: RNA from Ambion


title: UPN11_NK-AML_BM


title: UPN49_inv(16)-AML_BM


title: UPN18_inv(16)-AML_PB


title: Human Placenta - rep1

description: RNA from Ambion


title: Human Placenta - rep2

description: RNA from Ambion


title: LA.VHD.AF.LA35 [V2]


title: UPN2_inv(16)-AML_BM


title: UPN10_inv(16)-AML_BM


title: UPN92_t(8;21)-AML_BM

source_name: t(8;21)-AML_Bone Marrow


title: UPN69_t(8;21)-AML_PB

source_name: t(8;21)-AML_Peripheral Blood


title: UPN68_t(8;21)-AML_BM


title: UPN63_t(8;21)-AML_PB


title: UPN55_t(8;21)-AML_BM


title: UPN61_t(8;21)-AML_PB


title: UPN30_t(8;21)-AML_PB


title: UPN33_t(8;21)-AML_BM


title: Sunflower meal, fish 4

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Arrays were scanned with Agilent scanner at a resolution of 5 microns

data_processing: Microarray data were extracted using Feature Extraction Software v9.6.1, gMedianSignal and gBGMedianSignal were used for further analyses. The spots were filtered by criterion (I/B)>8, where I is the median signal and B the background intensity.

organism: Salmo salar

source_name: Intestine of salmon fed with saponins

label_protocol: Amplified and labeled according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol

growth_protocol: Atlantic salmon post smolts with mean weight of 270 g were reared in fiberglass tanks containing running seawater. Water temperature varied between 9 and 13 °C.  A 24 h lighting regime was employed.

extract_protocol: Total RNA was extracted with Invitrogen Trizol and purified with Pure Link

treatment_protocol: The feeding trial continued for 80 days.

value: intestine

tag: diet

value: Sunflower meal

source_name: Intestine of control salmon

value: control


title: UPN14_t(8;21)-AML_PB

tag: aml subtype


title: UPN51_t(8;21)-AML_BM_diag

tag: cell source


title: UPN4_t(8;21)-AML_PB

tag: time point


title: ESC_Sample2

city: Louisville

first: DONG-MYUNG

last: SHIN

state: KY

address: 500 South, Floyd Street

department: Stem Cell Institute at James Graham Brown Cancer Center

institute: University of Louisville

description: Gene expression data from PCR amplified cDNA library representign FACS sorted twenty cells

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip 3’ Mouse Genome 430 2.0 array (Affymetrix),according to manufacture mannual (GeneChip 3'IVT Expression Kit User Mannual, Affymetrix)

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 1.0 (Affymetrix)

data_processing: The CEL files for 9 cell samples (3 VSEL, 3 HSC, and 3 ESC-D3) were imported into Partek software Version 6.5 (Partek Inc) and normalized using Robust Multi-Array (RMA) normalization. A one-way ANOVA was set up for the different cell types with contrasts comparing VSEL versus HSC, ESC versus HSC, and VSEL versus ESC.

source_name: T7-primed cDNA libraries was synthesized using FACS sorted twenty ESC-D3

label_protocol: The gel-eluted T7-primed cDNA libraries were biotin-labeled using the GeneChip 3’ in vitro transcription (IVT) kit (Affymetrix), starting from ‘‘In vitro Transcription to Synthesize Labeled aRNA”.

growth_protocol: Bone marrow mononuclear cells (BMMNCs) were prepared from 4 weeks old mice and VSELs (Sca-1+Lin–CD45–) and HSCs (Sca-1+Lin–CD45+) was isolated by multiparameter live-cell sorting (MoFlo, Dako). Murine ESC-D3 cells (ATCC) were grown in a 0.1% gelatin-coated dish with ESC specific meida supplemented with 10 ng/ml of recombinant mouse LIF (Chemicon-Millipore).

extract_protocol: RNA was directly eluted from twenty cells by lysis buffer (0.5 % NP-40) according to the previous reports (Nat. Protoc. Vol2, p739-752, 2007).

treatment_protocol: FACS-sorted Sca-1+Lin–CD45– VSELs, Sca-1+Lin–CD45+ HSCs, or trypsinized ESC-D3 cells were distributed into each well of a 384-well plate (Thermo Scientific) containing 4.5 ul of lysis buffer per well using a MoFlo cell sorter

tag: cell line

tag: strain

tag: age

value: embryo before implantation


title: HSC_Sample2

source_name: T7-primed cDNA libraries was synthesized using FACS sorted twenty HSCs

value: HSC

value: 4 weeks after birth


title: Sunflower meal, fish 1


title: ESC_Sample3


title: Sunflower meal, fish 2


title: HSC_Sample1


title: UPN93_t(8;21)-AML_PB


title: Sunflower meal, fish 3


title: HSC_Sample3


title: UPN91_APL_BM

source_name: APL_Bone Marrow

value: APL


title: Rapeseed meal, fish 3

value: Rapeseed meal


title: UPN3_t(8;21)-AML_BM


title: Rapeseed meal, fish 2


title: UPN86_APL_BM


title: Rapeseed meal, fish 4


title: VSEL_Sample2

source_name: T7-primed cDNA libraries was synthesized using FACS sorted twenty VSELs

value: VSEL


title: UPN85_APL_PB

source_name: APL_Peripheral Blood


title: Rapeseed meal, fish 1


title: Pea protein concentrate, fish 4

value: Pea protein concentrate


title: Pea protein concentrate, fish 3


title: VSEL_Sample1


title: Pea protein concentrate, fish 2


title: UPN58_APL_BM

value: Human acute myeloid leukemic cells


title: Horse bean meal, fish 4

value: Horse bean meal


title: Pea protein concentrate, fish 1


title: ESC_Sample1


title: 4 lung CL4 (naive)

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

description: 4 lung CL4 (naive)

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 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 150.

source_name: lung CL4 (naive)

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

extract_protocol: Rneasy

value: CD8+ T

value: lung, lymphocytes


title: Horse bean meal, fish 2


title: UPN65_APL_BM

value: Bone Marrow

value: Diagnosis


title: VSEL_Sample3


title: 5 BLN SPC-HAxCL4

description: 5 BLN SPC-HAxCL4

source_name: BLN SPC-HAxCL4

value: bronchial lymphnodes, lymphocytes


title: Corn gluten, fish 4

value: intestine

value: Corn gluten


title: 6 lung SPC-HAxCL4

description: 6 lung SPC-HAxCL4

source_name: lung SPC-HAxCL4


title: Corn gluten, fish 2

value: control


title: Horse bean meal, fish 1


title: 3 BLN CL4 (naive)

description: 3 BLN CL4 (naive)

source_name: BLN CL4 (naive)


title: Horse bean meal, fish 3


title: UPN50_APL_PB

value: Peripheral Blood


title: ΔphyR x WT- rep2

source_name: WT- sucrose

tag: genotype/variation

value: wild type

tag: stress

value: sucrose stress

source_name: ΔphyR- sucrose

value: phyR mutant


title: Corn gluten, fish 3


title: UPN57_APL_BM

value: APL


title: UPN53_APL_BM


title: 2 BLN CL4 activated

description: 2 BLN CL4 activated

source_name: BLN CL4 activated


title: UPN40_APL_BM


title: IMW005 lactate batch -1 (MA151)

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

description: ethanol-limited chemostatsteady state at time point 350h

hyb_protocol: Acquisition and quantification of the Affymetrix yeast S98 array images as well as primary data analysis were performed using the Affymetrix GeneChip Operating Software (GCOS) 2.1.

scan_protocol: Scanning of the Affymetrix Genechip® microarrays was performed with The Affymetrix scanner 3000 following Affymetrix instructions

data_processing: Data were processed with the GeneChip® Operating Software version 1.2 (GCOS 1.2) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity was scaled to 150.

organism: Saccharomyces cerevisiae

source_name: 20 g.l aerobic lactate batch

label_protocol: cDNA synthesis, cRNA synthesis and labelling, as well as array hybridization were performed as described (De Nicola et al 2007 AEM,73, 7680-7692 )

growth_protocol: Aerobic batch cultures for transcriptome analysis were carried out at 30oC in 2 litre laboratory fermentors (Applikon, Schiedam, The Netherlands) with a working volume of 1 litre. Synthetic medium [1] was supplemented with 20 g·l-1 lactic acid (Fluka 09578) as sole carbon source. The pH of this medium was set to 5.0 before autoclaving (120oC). Antifoam Emulsion C (Sigma, St. Louis, USA) was autoclaved separately (120 ºC) as a 20% (w/v) solution and added to a final concentration of 0.2 g·l-1. The culture pH was maintained at 5.0 by automatic addition of 2 M KOH and 2 M H2SO4. Cultures were stirred at 800 rpm and sparged with 500 ml air·min-1. The precultures were grown on ethanol as described above. Six hours before inoculation of the batch cultures, 25 mM lactate was added to the preculture to induce lactate metabolism.   [1] Verduyn C, Postma E, Scheffers WA, Van Dijken JP: Effect of benzoic acid on metabolic fluxes in yeasts: A continuous culture study on the regulation of respiration and alcoholic fermentation. Yeast 1992, 8(7):501-517.

extract_protocol: The RNA to be used for the microarrays was extracted using the hot-phenol method

treatment_protocol: Yeast cells were collected by rapid filtration (Belinchón et al 2004) and stored at  -70 oC until use

tag: growth condition


title: Corn gluten, fish 1


title: IMW004 lactate batch -2 (MA155)

description: ethanol-limited chemostatsteady state at time point 200h


title: IMW005 lactate batch -2 (MA1514)

value: ethanol-limited chemostatsteady state at time point 350h


title: UPN29_APL_PB


title: IMW004 lactate batch -1 (MA153)

value: ethanol-limited chemostatsteady state at time point 200h


title: UPN22_APL_BM

value: Human acute myeloid leukemic cells


title: UPN5_APL_BM


title: CEN.PK113-7D lactate batch -2 (MA156)

description: ethanol-limited chemostatsteady state at time point 75h


title: UPN39_APL_BM


title: CEN.PK113-7D lactate batch -1 (MA152)

value: ethanol-limited chemostatsteady state at time point 75h


title: UPN34_APL_BM


title: Preadipocytes_ControlRPMImedia_R6

city: Sharnbrook

first: Fei Ling

last: Lim

state: Bedfordshire

address: Colworth Science Park

country: United Kingdom

institute: Unilever

hyb_protocol: The Agilent Hybridisation Kit (catalogue number 5188-5242) was used in conjunction with Agilent human whole genome Oligo Arrays (catalogue number G4112F).  2μg of the labelled sample RNA were used for hybridisation according to the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol. The hybridisation was performed for 17 h at 65 ºC with 10 rpm rotation. Slides were then washed for 1 min at 22 ºC in Wash Solution 1 (catalogue number 5188-5325), followed by 1 min in Wash Solution 2 that was pre-warmed to 37 ºC (catalogue number 5188-5326) as described in the manufacturer’s manual. Slides were then washed in acetonitrile (Fisher cat# A/0630/PB15) for 1 min followed by 30s in Agilent Stabilisation and Drying Solution (catalogue number 5185-5979).

scan_protocol: The slides were scanned with the Agilent G2565BA Microarray Scanner System.

data_processing: For data extraction and quality control, the Agilent G2567AA Feature Extraction Software (v.9.1) was used.

source_name: Preadipocytes, control RPMI media, rep R6

label_protocol: 300ng RNA and 3µl (1:5000 dilution) Agilent One-Color RNA Spike-In RNA were labelled with reagents supplied in the Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color according to Manufacturer’s instructions as follows:  Primers were annealed to template by mixing 1.2 µl T7 Promoter Primer, 200ng RNA and 2µl spike in control (in a volume of 11.5µl), denatured at 65ºC for 10min followed by incubation at 4ºC for 5min. First Strand Buffer (to 1X), DTT (to 10mM), dNTP (to 0.5mM), MMLV (1µl) and RNaseOut (0.5 µl) were then added to make up the cDNA synthesis reaction (20µl), which was incubated for 2h at 40 ºC. After 15 min denaturation at 65ºC, the reaction was made up to 80µl with the addition of Cyanine 3-CTP (to 0.3mM), Transcription Buffer (to 1X), DTT (to 10mM), NTP (8µl), PEG (to 4%), RNaseOUT (0.5µl), Inorganic Phosphatase (0.6µl), and T7 RNA Polymerase (0.8µl) and incubated for 2h at 40 ºC to synthesise the fluorescent labelled cRNA.  The labelled cRNA was purified with the RNeasy Mini Kit (Qiagen Ltd, Crawley, UK) according to Manufacturer’s protocol.

growth_protocol: SGBS pre-adipocytes were grown to confluence and plated out in a 12-well plate at 20,000 cells per well (per ml).  Once confluent, the cells were treated with conditioned medium.  The U937 cells were grown to confluence, then plated out in 12-well plates at 200000 cells per well (per ml).  Once 20-30% confluent, PMA (30 nM) was added to the medium to induce differentiation, the cells were differentiatied for seven days at which point conditioned medium was collected.

extract_protocol: Total RNA was extracted using the Qiagen Rneasy kit (Qiagen), and the integrity of the RNA determined by the Agilent 2100 bioanalyser using the RNA 6000 LabChip kit.

treatment_protocol: The pre-adipocytes were treated with 150 µl of macrophage-conditioned medium per ml of media for 24 h.  Control pre-adipocytes were treated with unconditioned medium (control) or with RPMI 1640 medium alone to contol for differences in the medium used to culture the U937 cells

value: SGBS cells

tag: treatment

value: Control RPMI

tag: biological replicate


title: Preadipocytes_ControlRPMImedia_R3

source_name: Preadipocytes, control RPMI media, rep R3


title: Preadipocytes_ControlRPMImedia_R4

source_name: Preadipocytes, control RPMI media, rep R4


title: Preadipocytes_ControlRPMImedia_R5

source_name: Preadipocytes, control RPMI media, rep R5


title: 10b rep2

description: see Cloonan et al. MicroRNAs and their isomiRs function cooperatively to target common biological pathways.

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data were preprocessed by Bioconductor lumi package (version 2.2.1), along with other data from the same chips that are not described in this paper. It was background adjusted, vst transformed and rsn normalized. Probes that did not have a detection p-value < 0.01 in all of the mock-transfected replicates were excluded from further analysis.

source_name: HEK293T cells

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

tag: transfection

value: biotinylated miR-10b

tag: pull down

value: streptavidin


title: mock rep1

value: mock transfection


title: 10b rep1


title: 10b-iso rep1

value: biotinylated miR-10b-iso


title: 10b-iso rep3


title: IPH-926

data_processing: RMA summarization

source_name: IPH-926 human lobular breast cancer cells

growth_protocol: ex vivo

extract_protocol: RNeasy

treatment_protocol: temperature: 37 C

value: human lobular breast cancer cells

tag: genetic modification

value: p53 status:off, CDH1_241ins4 validated in D059, ABCB1 validated in C302


title: mock rep3


title: mock rep2


title: 10b-iso rep2


title: 10a rep3

value: biotinylated miR-10a


title: 10a rep2


title: Preadipocytes_ControlRPMImedia_R2

source_name: Preadipocytes, control RPMI media, rep R2

tag: cell type


title: UPN42_t(8;21)-AML_BM

source_name: t(8;21)-AML_Bone Marrow

value: Bone Marrow

value: Diagnosis


title: KLECB2B7

city: Helsinki

first: Paive

last: Ojala

state: (Haartmaninkatu 8)

department: Biomedicum Helsinki

country: Finland

institute: University of Helsinki

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix hgu133plus2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix hgu133plus2 chips were scanned using the Affymetrix Scanner 3000 7G and the MAS 5.1 software as per the manufacturers protocol http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf

data_processing: Data was preprocessed and normalised using the Bioconductor 'affy' package, specifically the robust multiarray ('rma') algorithm.

source_name: lymphatic endothelial cells

label_protocol: 1 ug of total RNA was used to generate first strand cDNA using T7-linked oligo(dT)primer and the custom SuperScript dscDNA synthesis kit (invitrogen). After second-strand syntheis, in vitro transcription was carried with biotinylated UTP and CTP using One-Cycle Target Labeling kit (Affymetrix) and the GeneChip Sample Cleanup Module (Affymetrix).

growth_protocol: Human lymphatic endothelial cells (LECs) were cultured in Endothelial Cell Growth Medium MV (C-22020, PromoCell, Heidelberg, Germany) and supplied by 5% human serum.

extract_protocol: TRIzol solution (Invitrogen) extraction followed by RNeasy Mini kit (Qiagen) purification. Assessed RNA integrity and quantity using RNA 6000 Nano chips (Agilent).

treatment_protocol: Confluent monolayers of K-LECs or uninfected control LEC cells were trypsinized, resuspended in the EC culture medium and seeded into 0.5% agarose pre-coated, round-bottom 96-well plate with 4000 cells per well. After 16 h to 24 h incubation at 37°C, the suspended cells formed spheroids, which were harvested and embedded into the fibrin gel for the corresponding experiments. Three days after embedding the spheroids were harvested for RNA extraction.

tag: agent

value: KSHV

value: LEC spheroids


title: LECB2B7

value: control


title: 10a-iso rep2

value: biotinylated miR-10a-iso


title: 10a-iso rep3


title: Preadipocytes_ControlMedia_C3

source_name: Preadipocytes, control media, rep C3

value: Control


title: Preadipocytes_ControlMedia_C2

source_name: Preadipocytes, control media, rep C2


title: LECB4B7


title: 10a rep1


title: Preadipocytes_ControlMedia_C5

source_name: Preadipocytes, control media, rep C5


title: 10a-iso rep1

description: see Cloonan et al. MicroRNAs and their isomiRs function cooperatively to target common biological pathways. MicroRNAs and their isomiRs function cooperatively to target common biological pathways.


title: KLECB4


title: Preadipocytes_ControlMedia_C1

source_name: Preadipocytes, control media, rep C1


title: Preadipcytes_MacrophageConditionedRPMIMedia_T5-2

source_name: Preadipcytes, macrophage conditioned RPMI media, rep T5

tag: treated with

value: U937 cells

value: Conditioned RPMI

tag: technical replicate


title: CorticalBone_Control_rep2

city: Uppsala

first: Anders

last: Isaksson

address: Akademiska sjukhuset ing61 3tr

country: Sweden

institute: Uppsala University

hyb_protocol: Hybridization was performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).

scan_protocol: The arrays were washed using Affymetrix fluidics stations, and scanned using the GeneChip® Scanner 3000 7G.

data_processing: Gene expression data were processed in the freely available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project. The raw data was normalized using the robust multi-array average (RMA) method.

organism: Rattus norvegicus

label_protocol: Sample preparation and processing were performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).

growth_protocol: They were acclimatized for one week and kept in groups of three animals and had free access to water and commercial pellet diet (Lactamin R36, Stockholm, Sweden).

extract_protocol: Bones were snap-frozen in liquid nitrogen and quickly crushed into a fine powder using a mortar and pestle followed by total RNA extraction with TRI Reagent® (Sigma-Aldrich). For cortical bone without marrow, diaphyseal bones were cut into pieces, vortexed in ice-cold PBS three times for 10 s to remove marrow cells followed by snap-freezing in liquid nitrogen, crushing into a fine powder and RNA extraction.

treatment_protocol: The rats were divided into two groups, each with 12 animals. They were fed a standard diet containing 12 IU vitamin A/g pellet (“cont”), or a standard diet supplemented with 1700 IU (“Ex. vitA”) vitamin A/g pellet. The vitamin A was added to the pellets in the form of retinyl palmitate and retinyl acetate. After eight days, the rats were euthanized by exsanguinations from the abdominal aorta under Eqvitesin anesthesia (chloral hydrate 182 mg/kg, pentobarbital 41.7 g/kg).

tag: breed

value: Sprague-Dawley

tag: gender

value: male

value: 8 week

tag: disease status

tag: tissue

value: Humerus, Diaphyseal Cortical Bone


title: CorticalBone+Marrow_Control_rep3

tag: age

value: Humerus, Diaphyseal Cortical Bone including Marrow


title: CorticalBone+Marrow_Control_rep4


title: CorticalBone_Control_rep1


title: CorticalBone+Marrow_Control_rep2


title: CorticalBone+Marrow_Control_rep1


title: CorticalBone_Control_rep3


title: -HAQs + 2AA replicate 2

city: Boston

first: Laurence

middle: G

last: Rahme

state: MA

address: 50 Blosson St, Thier 340

department: Surgery

institute: Massachusetts General Hospital

hyb_protocol: The P. aeruginosa PAO1 GeneChipH Genome array (Affymetrix) was used for hybridization.

scan_protocol: Standard Affymetrix protocol

data_processing: Affymetrix DAT files were processed using the Affymetrix Gene Chip Operating System (GCOS) to create .cel files. The raw intensity .cel files were normalized using GCOS (see CHP file and Data table below). Array quality control metrics generated by the Affymetrix Microarray Suite 5.0 were used to assess hybridization quality. Normalized expression values were analyzed with SAM (Significance Analysis of Microarray) using the permuted unpaired two-class test.

organism: Pseudomonas aeruginosa PA14

source_name: Pseudomonas aeruginosa PA14

label_protocol: Enzo Bioarray kit

growth_protocol: medium: LB, OD600nm of 2, Shaking 200rpm in 37C. 2-AA: 3mM

extract_protocol: Qiagen RNeasy kit

treatment_protocol: 2-AA (3mM) treated culture of pqsA mutant was grown to OD600nm of 2.0 in LB.

tag: strain

tag: genotype/variation

value: non-polar pqsA mutant


title: CorticalBone_Control_rep4


title: Preadipcytes_MacrophageConditionedRPMIMedia_T2

source_name: Preadipcytes, macrophage conditioned RPMI media, rep T2

value: SGBS cells


title: Preadipcytes_MacrophageConditionedRPMIMedia_T5


title: -HAQs + 2AA replicate 3


title: Preadipcytes_MacrophageConditionedRPMIMedia_T6

source_name: Preadipcytes, macrophage conditioned RPMI media, rep T6


title: CorticalBone+Marrow_ExcessVitA_rep3

value: Hypervitaminosis A


title: LECB4


title: CorticalBone_ExcessVitA_rep4


title: -HAQs - 2AA  replicate 3

growth_protocol: medium: LB, OD600nm of 2, Shaking 200rpm in 37C.

treatment_protocol: Culture of pqsA mutant was grown to OD600nm of 2.0 in LB


title: CorticalBone+Marrow_ExcessVitA_rep2


title: CorticalBone+Marrow_ExcessVitA_rep1


title: -HAQs + 2AA replicate 1


title: KLECB4B7


title: Preadipcytes_MacrophageConditionedRPMIMedia_T3

source_name: Preadipcytes, macrophage conditioned RPMI media, rep T3


title: -HAQs - 2AA  replicate 2


title: -HAQs - 2AA  replicate 1


title: CorticalBone+Marrow_ExcessVitA_rep4


title: Preadipcytes_MacrophageConditionedRPMIMedia_T1

source_name: Preadipcytes, macrophage conditioned RPMI media, rep T1


title: CorticalBone_ExcessVitA_rep1


title: CorticalBone_ExcessVitA_rep2


title: MEF WT replicate 2

city: Fitzroy

first: Jörg

last: Heierhorst

state: Victoria

address: 9 Princes Street

institute: St. Vincent's Institute

description: Asciz+/+ rep2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All samples were normalised by quantile normalisation method using lumi package in R statistical software.

source_name: single-passage MEF

label_protocol: Biotinylation using Ambion Total Prep RNA Amplification Kit (Cat. No. IL1791).

growth_protocol: 48 hours Dulbecco's Modified Eagle's Medium 10% fetal bovine serum in 10-cm dish, then transfer to 15-cm dish in same medium

extract_protocol: Total RNA was extracted using Rneasy Mini kit (Qiagen).

tag: genetic background

value: MEF

tag: genotype

value: Asciz+/+


title: topA + 2AA replicate 2

treatment_protocol: 2-AA (3mM) treated culture of topA mutant was grown to OD600nm of 2.0 in LB

value: topA::gent, A mutant from the non-redundent library of PA14 mutants with an insertion in topA gene of a Mariner transposon that carries gentamicin resistance cassette


title: MEF KO replicate 3

description: Asciz-/- rep3

value: Asciz-/-


title: MEF WT replicate 3

description: Asciz+/+ rep3


title: MEF WT replicate 1

description: Asciz+/+ rep1


title: topA + 2AA replicate 1


title: topA mutant OD 2.0 replicate 3

hyb_protocol: The P. aeruginosa PAO1 GeneChipH Genome array (Affymetrix) was used for hybridization,

growth_protocol: Cells were grown  to OD600nm of 2.0 in LB, shaking of 200rpm in flasks at 37C

value: control


title: MEF KO replicate 1

description: Asciz-/- rep1


title: Heart_Sham_8

city: Amsterdam

first: Diederik

last: Kuster

address: van der Boechorststraat 7

institute: VU University Medical Center

hyb_protocol: Labeled cRNA was hybridized to according to the manufacturer’s instructions

scan_protocol: standard Affymetrix protocol

data_processing: Data was analyzed with R. To prevent batch effect, data was first rma per group and then all arrays were quantile normalized.

organism: Sus scrofa

source_name: Swine left ventricle of Sham heart

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

growth_protocol: 2-3 months old swine

extract_protocol: Trizol followed by Qiagen's Rneasy clean-up kit

treatment_protocol: Frozen myocardium was crushed in liquid nitrogen.

tag: group

value: Sham

tag: Sex

value: M

value: Yorkshire x Landrace


title: Heart_Sham_5

value: F


title: topA + 2AA replicate 3


title: topA mutant OD 2.0 replicate 2


title: normal mouse macrophage sorted CD11cint F4/80hi rep 2

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from  normal mouse macrophage sorted CD11cint F4/80hi

hyb_protocol: Samples were hybridized onto Affymetrix GeneChip Arrays (Affymetrix) according to manufacturer's recommendations

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with GCOS 1.4 and EC 1.1 using Affymetrix default analysis and normalization method.

label_protocol: The cDNA was prepared and labeled according to standard manufacturer protocols (Affymetrix)

growth_protocol: Rag2–/– mice were injected i.p. with 1.5 x 105 CD4+ CD45RBhigh + 1.5 x 105 CD4+ CD45RBlow T cells (non-colitic CD45RBhigh+low mice), isolated from the spleens of wild type C57BL/6 mice.

extract_protocol: total RNA was isolated using TRIzol reagent (Invitrogen), according to the manufacturer’s instructions. RNA quantity /quality were assessed using the Agilent 2100 Bioanalyzer. RNA was reverse transcribed into cDNA (SuperScript III; Invitrogen)

treatment_protocol: After removing extra-intestinal fat tissue and blood vessels, colons were flushed of their luminal content with HBSS, opened longitudinally, and cut into 2 cm pieces and incubated with HBSS containing 0.015% DTT (15 min, 37°C in a shaking water bath). Epithelial cells and mucus were removed by extensive washes in HBSS, 5% FCS, 25 mM Hepes, before colons were cut into smaller 2mm2 pieces and digested in complete Iscoves media containing Liberase TL (167 µg/mL) and DNAse I (30 µg/mL) (Roche # 05401020001 and #10104150001) for 60 min at 37°C in a shaking water bath. The digested cell suspension was then passed through 100- and 40-µm cell strainers and resuspended in 1.077 g/cm3 iso-osmotic NycoPrep medium (Accurate Chemical & Scientific Corp.). After centrifugation at 1,600 g for 15 min, the low-density fraction was collected. Cells were then stained with Fc block [CD16/32 (2.4G2)] and antibodies to CD11c(HL-3), MHC-II (AF6-120.1), F4/80 mAb (BM8), CD11b (M1/70), CD103 (M290), as well as antibodies to B cell and T cell lineages (referred here after as “lin”): CD19 (RA3-6B2), CD3 (145-2C11), TCRβ (H57-597), TCRγδ (eBioGL3) all from eBioscience. After pre-gating on live, MHC-IIhigh lin- cells, the indicated dendritic cell and macrophage subsets were sorted using a BD Biosciences FACSVantage or FACSAria machine.


title: normal mouse dendritic sorted CD11cint F4/80int rep 1

description: Gene expression data from  normal mouse dendritic sorted CD11cint F4/80int


title: MEF KO replicate 2

description: Asciz-/- rep2


title: 2-AA treated PA14 cells in OD2 replicate 1

treatment_protocol: 2-AA (3mM) treated culture was grown to OD600nm of 2.0 in LB

value: wild type


title: Heart_Sham_4


title: Preadipocytes_ControlMedia_C6

source_name: Preadipocytes, control media, rep C6

tag: treatment

value: Control

tag: biological replicate


title: 2-AA treated PA14 cells in OD2 replicate 2


title: 2-AA treated PA14 cells in OD2 replicate 3


title: topA mutant OD 2.0 replicate 1


title: normal mouse dendritic sorted CD11cint F4/80int rep 2


title: CorticalBone_ExcessVitA_rep3

value: Sprague-Dawley

value: male

value: 8 week


title: Heart_Sham_1


title: Heart_MI_7

source_name: Swine left ventricle of post-MI heart

value: MI


title: Heart_Sham_3


title: normal mouse dendritic sorted CD11chi-F4/80- rep 3

description: Gene expression data from  normal mouse dendritic sorted CD11chi-F4/80-


title: Heart_Sham_6


title: normal mouse dendritic sorted CD11chi-F4/80- rep 2


title: normal mouse macrophage sorted CD11cint F4/80hi rep 3


title: normal mouse dendritic sorted CD11chi-F4/80- rep 1


title: Heart_MI_8


title: Normal_20

type: protein

city: Vienna

first: Parvez

last: Syed

address: Muthgasse 11

institute: Austrian Institution of Technology

hyb_protocol: The microarrays were blocked for 30 min with PBST+3% non-fat milk powder. Microarrays were washed with PBST, twice for 5 min. Serum diluted 1:10 in PBST was applied onto the microarray and incubated for 2 hours.  Microarrays were washed with PBST, twice for 5 min. Antihuman IgG conjugated with Alexa 532 was diluted  1:500 in PBST+3% non-fat milk powder and incubated for 30 min. Microarrays were washed with PBST, twice for 5 min.

scan_protocol: The processed microarray images were captured using an Axon Genepix 4000A microarray scanner

data_processing: For microarray data analyses in addition to R, BRB-ArrayTools Version: 3.6.0 - Stable Release

label: Alexa 532

molecule: protein

source_name: Healthy controls

label_protocol: After the hybridization of human sera with the protein microarrays, secondary antibody (anti-human IgG) conjuagted with Alexa532 was used for detecting the sero-reactive proteins on the microarray

extract_protocol: The His-tag recombiant proteins were expressed in E. coli using autoinduction and purified using Ni-NTA agarose. Elution of the purified recombinant proteins was done using 50 mM Imidazole. These proteins were used for the generation of protein microarrays. The serum autoantibody profiling of the sera from breast cancer patients (benign & malignant) and healthy controls was done using the protein micrarrays

tag: disease state

value: Healthy controls


title: Normal_19


title: Normal_17


title: Heart_Sham_2


title: PA14 control of 2-AA treated cells in OD2 replicate 3

treatment_protocol: Untreated culture grown to OD600nm of 2.0 in LB

tag: agent


title: Normal_14


title: normal mouse macrophage sorted CD11cint F4/80hi rep 1


title: normal mouse macrophage sorted CD11c-F4/80hi rep 1

description: Gene expression data from  normal mouse macrophage sorted CD11c-F4/80hi


title: Normal_16


title: Heart_MI_6


title: Normal_15


title: Normal_18


title: Normal_11


title: Normal_13


title: Normal_12


title: normal mouse macrophage sorted CD11c-F4/80hi rep 2


title: RA.VHD.SR.RA87 [V3]

description: miRNA derived from Heart tissue, from a patient with VHD

data_processing: The n=28 raw TXT files were RMA normalised. These data were then combined with arrays corresponding to GPL8227 and quantile normalised across all n=39 arrays. Control probes and those not detected on any of the arrays were filtered out. A slide-of-origin batch effect was removed by fitting a linear model to the array barcode. The residuals from the model fit represent the batch-removed log-base-2, normalised expression levels of each microRNA. Technical replicates were then averaged, to produce n=34 samples, from the n=39 arrays.

tag: class

tag: af or sr

value: SR (sinus rhythm)

tag: atrium

value: RA

tag: disease

value: VHD

tag: patientid

tag: batch

tag: hybridisation date (first array)


title: RA.VHD.AF.RA90 [V3]

value: AF (atrial fibrillation)


title: RA.CABG.AF.RA81 [V3]

value: CABG


title: Normal_8

tag: age


title: Normal_10


title: Normal_7


title: RA.VHD.SR.RA79 [V3]


title: Heart_MI_5

tag: breed


title: Normal_5


title: Normal_6


title: Normal_4


title: RA.VHD.SR.RA75 [V3]


title: PA14 control of 2-AA treated cells in OD2 replicate 2

tag: strain

tag: genotype/variation

value: control


title: Normal_9


title: Normal_3


title: Normal_1


title: Normal_2


title: Heart_MI_4

tag: group


title: Benign_16


title: RA.CABG.SR.RA71 [V3]


title: RA.VHD.SR.RA74 [V3]


title: B12:LJ110 pTM30pdhr MMAcetat

description: B12:LJ110  pTM30pdhr MMAcetat

hyb_protocol: Labeled cRNA was hybridized to Agilent´s E.coli 8x15k microarrays for 16h at 68°C

scan_protocol: Agilent DNA Microarray Scanner with default settings.

data_processing: Expression values were calculated by the software package Feature Extraction 10.5.1.1 using protocol GE1_105_Dec08 (Agilent Technologies; Waldbronn, Germany)

organism: Escherichia coli

source_name: LJ110 pTM30pdhr MMAcetat

label_protocol: 200 ng of total RNA were applied for Cy3-labelling reaction using the MessageAmp II-Bacteria Kit according to supplier´s recommendation (Ambion). As a result of IVT (in vitro transcription) reaction using aminoallyl-dUTP antisense aRNA were generated and subsequently coupled with fluorescent dye Cy3.

growth_protocol: MMAcetat

extract_protocol: RNAeasy

tag: background strain

tag: genetic modification

value: PdhR overexpression strain (LJ110/pTM30PdhRhis)


title: B11:LJ110 pTM30 MMAcetat

description: B11:LJ110  pTM30 MMAcetat

source_name: LJ110 pTM30 MMAcetat

value: empty plasmid (LJ110/pTM30)


title: Heart_MI_2

tag: Sex

value: Yorkshire x Landrace


title: PA14 control of 2-AA treated cells in OD2 replicate 1


title: Heart_MI_3

value: M


title: 1 lung CL4 activated

description: 1 lung CL4 activated

source_name: lung CL4 activated

tag: cell type

value: CD8+ T

tag: tissue

value: lung, lymphocytes


title: B9:LJ110 MMAcetat

description: B9:LJ110 MMAcetat

source_name: LJ110 MMAcetat

value: wild type LJ110


title: B10:LJ110 del pdhr MMAcetat

description: B10:LJ110 del pdhr MMAcetat

source_name: LJ110 del pdhr MMAcetat

value: PdhR knockout mutant (LJ110deltapdhR)


title: B8:LJ110 pTM30pdhr MMPyruvat

description: B8:LJ110  pTM30pdhr MMPyruvat

source_name: LJ110 pTM30pdhr MMPyruvat

growth_protocol: MMPyruvat


title: RA.CABG.SR.RA64 [V3]

hyb_protocol: Samples were hybridised following manufacturers protocols. Arrays were hybridized in 3 separate batches

extract_protocol: Total RNA was extracted using Trizol® reagent (Invitrogen).

tag: class


title: RA.VHD.AF.RA62 [V3]

tag: af or sr


title: Benign_15

tag: disease state


title: Benign_14


title: Malignant_24

source_name: Carcinoma, intraductal, noninvasive

value: Carcinoma, intraductal, noninvasive


title: RA.VHD.AF.RA50 [V3]

tag: atrium

tag: disease


title: Benign_13


title: B7:LJ110 pTM30 MMPyruvat

description: B7:LJ110  pTM30 MMPyruvat

source_name: LJ110 pTM30 MMPyruvat


title: Malignant_23

source_name: Invasive ductal carcinoma

value: Invasive ductal carcinoma


title: Benign_12


title: RA.CABG.AF.RA5 [V3]

tag: patientid

tag: batch


title: Malignant_22

tag: age


title: Heart_MI_1

value: MI

value: F

tag: breed


title: Benign_11


title: Benign_10


title: Malignant_21


title: RA.VHD.SR.RA23 [V3]

value: SR (sinus rhythm)

value: RA

tag: hybridisation date (first array)


title: Malignant_20

source_name: Invasive lobular carcinoma (10-20%)

value: Invasive lobular carcinoma (10-20%)


title: Malignant_19

source_name: intraductal Carcinoma with microinvasion


title: B6:LJ110 del pdhr MMPyruvat

description: B6:LJ110 del pdhr MMPyruvat

source_name: LJ110 del pdhr MMPyruvat


title: RA.VHD.AF.RA19 [V3]

value: AF (atrial fibrillation)

value: VHD


title: Heart_Sham_7

value: Sham


title: B5:LJ110 MMPyruvat

description: B5:LJ110 MMPyruvat

source_name: LJ110 MMPyruvat


title: RA.CABG.SR.RA17 [V3]

value: CABG


title: Malignant_18


title: RA.CABG.SR.RA10 [V3]


title: Malignant_16


title: Malignant_17


title: RA.VHD.SR.RA1 [V3]


title: B4:LJ110 pTM30pdhr LBo

description: B4:LJ110  pTM30pdhr LBo

source_name: LJ110 pTM30pdhr LBo

growth_protocol: LBO

value: PdhR overexpression strain (LJ110/pTM30PdhRhis)


title: Benign_8


title: Malignant_15


title: B3:LJ110 pTM30 LBo

description: B3:LJ110  pTM30 LBo

source_name: LJ110 pTM30 LBo

value: empty plasmid (LJ110/pTM30)


title: LA.VHD.SR.LA74 [V3]

value: LA


title: LA.VHD.AF.LA68 [V3]


title: A11:LJ110 pTM30 MMAcetat

description: A11:LJ110  pTM30 MMAcetat


title: Malignant_14

source_name: Muzinous carcinoma

value: Muzinous carcinoma


title: Benign_7


title: A12:LJ110 pTM30pdhr MMAcetat

description: A12:LJ110  pTM30pdhr MMAcetat


title: LA.VHD.AF.LA65 [V3]


title: B1:LJ110 LBo

description: B1:LJ110 LBo

source_name: LJ110 LBo

value: wild type LJ110


title: Benign_9


title: A10:LJ110 del pdhr MMAcetat

description: A10:LJ110 del pdhr MMAcetat

value: PdhR knockout mutant (LJ110deltapdhR)


title: B2:LJ110 del pdhr LBo

description: B2:LJ110 del pdhr LBo

source_name: LJ110 del pdhr LBo


title: LA.VHD.AF.LA62 [V3]


title: LA.VHD.SR.LA61 [V3]


title: A8:LJ110 pTM30pdhr MMPyruvat

description: A8:LJ110  pTM30pdhr MMPyruvat


title: LA.VHD.AF.LA50 [V3]


title: LA.Healthy.LA2a [V3]

description: miRNA derived from Heart tissue, from a healthy patient

value: Healthy


title: A7:LJ110 pTM30 MMPyruvat

description: A7:LJ110  pTM30 MMPyruvat


title: LA.Healthy.LA1a [V3]


title: Malignant_10

value: Invasive ductal carcinoma


title: Malignant_13


title: Benign_6


title: Malignant_11


title: A9:LJ110 MMAcetat

description: A9:LJ110 MMAcetat


title: Malignant_12

value: Carcinoma, intraductal, noninvasive


title: Benign_4


title: Benign_5


title: LA.Healthy.LA13a [V3]


title: A5:LJ110 MMPyruvat

description: A5:LJ110 MMPyruvat


title: Benign_3


title: LA.Healthy.LA12a [V3]


title: A6:LJ110 del pdhr MMPyruvat

description: A6:LJ110 del pdhr MMPyruvat


title: Pt074B Leukoplakia_Soft palate

city: Genova

first: PAOLA

last: SCARUFFI

state: GE

address: LARGO R. BENZI, 10

country: Italy

institute: "San Martino" Hospital

description:
DNA amplification kit: Nugen
aCGH analysis

hyb_protocol: Labeled DNAs were hybridized to Human Genome CGH 105K array platform (Agilent Technologies)following the "Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0. Briefly, fluorescent-labeled reference and tumor DNAs (4 µg each) were mixed with 25 µg of human Cot-1 DNA (Invitrogen Life Technologies) and control targets (Agilent). Slides were hybridized in SureHyb gasket (Agilent Technologies) placed in rotisserie (20 RPM rotation speed) in hybridization oven at 65°C for 40 hrs. After hybridization, the slides were washed with Oligo aCGH Wash Buffer 1 (Agilent Technologies) at room temperature for 5 min, with Oligo aCGH Wash Buffer 2 (Agilent Technologies) at 37°C for 1 min, with the Stabilization and Drying Solution (Agilent) for 1 minute at room temperature.

scan_protocol: Slides were scanned immediately after washing by the Agilent G2565BA Scanner using two color scan setting for 2x105k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel 1 is set to Red & Green, Red PMT is set to 100%, Green PMT is set to 100%) . Microarray performance was assessed by QC metric tool.

data_processing: The scanned TIFF images were processed by Feature Extraction version 9.5.3.1 (Agilent Technologies). Data files were analyzed byAgilent CGH Analytics Software (version 3.5.14) according to ADM-2 algorithm. The quality of each experiment was assessed by QC metric tool.

source_name: Leukoplakia

label_protocol: DNA was amplified using Ovation WGA System kit (Nugen Technologies) (DNA<50ng). We followed the "Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0 (Agilent Technologies). For each array, amplified test and reference DNAs (2 µg each) were labeled by Bioprime Labeling Kit (Invitrogen, Paisley, UK). Briefly,  amplified DNA was labeled with Cy3-dUTP or Cy5-dUTP (Perkin Elmer) (reference and test samples, respectively) using the Random-Primed Bioprime DNA Labeling kit (Invitrogen Life Technologies). Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore) according to the manufacturer’s protocol. Dye incorporations of post-labeling products were measured by ND-1000 spectrophotometer (NanoDrop Technologies) and the parameters that predicted successful hybridization were a minimum Cy3 incorporation of 0.5 pmol/ul and Cy5 incorporation of 0.3 pmol/ul.

extract_protocol: DNA was extracted using ArchivePure DNA (5-Prime) with some modifications: after protein precipitation the DNA was purified by phenol-chloroform extraction and collected by ethanol precipitation using 20 µg of glycogen (20 mg/ml). DNA quality was assessed by agarose gel and ND-1000 spectrophotometer (NanoDrop Technologies).

treatment_protocol: Samples were processed to obtain DAPI stained nuclei suspensions following the method of Otto et al., (Methods Cell Biol., 1994 Academic Press San Diego; 211-217) with modifications. High resolution DNA flow cytometry of these samples was used to obtain DNA content histograms and to evaluate the DNA Index (DI), as previously described in details (Donadini et al., 2010, Cell. Oncol. 32, 373-383). DNA diploid controls were represented by gender-specific human lymphocytes. The mean CV of the corresponding DNA diploid G0-G1 peaks was 1.2±0.2%. The DNA diploid (DI=1) and aneuploid sublines were sorted using a Cyflow Space FCM equipped with a PPCS unit (Partec GmbH) at the purity of about 99%.

tag: main site

value: Soft palate

tag: histology

value: Mild dysplastic leukoplakia

tag: smoke habit

value: Smoker

tag: age (years)

tag: dna index

tag: gender

value: Male

tag: dna amplification kit

value: Nugen

source_name: Human Genomic DNA: male Cat G147A Promega, Madison, WI


title: Pt076A Distal mucosa_Border tongue right

description:
DNA amplification kit: Sigma
aCGH analysis

source_name: Distal mucosa

label_protocol: DNA was amplified using GenomePlex Whole Genome Amplification Kit (Sigma-Aldrich) (DNA= 50ng) or Ovation WGA System kit (Nugen Technologies) (DNA<50ng). We followed the "Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0 (Agilent Technologies). For each array, amplified test and reference DNAs (2 µg each) were labeled by Bioprime Labeling Kit (Invitrogen, Paisley, UK). Briefly,  amplified DNA was labeled with Cy3-dUTP or Cy5-dUTP (Perkin Elmer) (reference and test samples, respectively) using the Random-Primed Bioprime DNA Labeling kit (Invitrogen Life Technologies). Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore) according to the manufacturer’s protocol. Dye incorporations of post-labeling products were measured by ND-1000 spectrophotometer (NanoDrop Technologies) and the parameters that predicted successful hybridization were a minimum Cy3 incorporation of 0.5 pmol/ul and Cy5 incorporation of 0.3 pmol/ul.

value: Border tongue right

value: Non dysplastic

value: Non Smoker

value: Female

value: Sigma

source_name: Human Genomic DNA: female Cat G152A,Promega, Madison, WI


title: Pt062A Distal mucosa_Hard palate

value: Hard palate


title: Pt059A Distal field_Buccal mucosa

source_name: Distal field

value: Buccal mucosa


title: LA.Healthy.LA11a [V3]

scan_protocol: Samples were scanned on a G2505C Agilent Scanner, using the miRNA_107_Sep09 xml array design file.

label_protocol: samples were labelled with Cy3 following manufacturers protocols. Samples were labelled in 3 separate batches

tag: class

value: SR (sinus rhythm)

value: LA


title: A4:LJ110 pTM30pdhr LBo

description: A4:LJ110  pTM30pdhr LBo

tag: background strain

tag: genetic modification

value: PdhR overexpression strain (LJ110/pTM30PdhRhis)


title: Malignant_9

tag: disease state

value: Invasive ductal carcinoma


title: Pt074B Distant field_Soft palate

source_name: Distant field


title: Benign_2


title: Pt043A Distal mucosa_Buccal mucosa, cheek

value: Buccal mucosa, cheek


title: LA.VHD.SR.LA1 [V3]

tag: af or sr

tag: atrium

tag: disease

value: VHD


title: A1:LJ110 LBo

description: A1:LJ110 LBo

value: wild type LJ110


title: Pt061A Distal mucosa_Buccal mucosa, retromolar trigone left

value: Buccal mucosa, retromolar trigone left

value: Smoker


title: A3:LJ110 pTM30 LBo

description: A3:LJ110  pTM30 LBo

value: empty plasmid (LJ110/pTM30)


title: Malignant_8

tag: age


title: Pt042A  Leukoplakia_Buccal mucosa, cheek right

value: Buccal mucosa, cheek right

value: Leukoplakia without dysplasia

value: Male

value: Nugen


title: V583 in THB rep1

city: Norman

first: Scott

middle: M

last: Maddox

state: OK

address: 101 David L. Boren Blvd.

department: Botany and Microbiology

institute: University of Oklahoma

hyb_protocol: Hybridization was at 60 degrees C for 16 h according to Affymetrix protocol ProkGE_WS2v2_450.

scan_protocol: Affymetrix GCOS scanner software and GeneChip Scanner 3000

data_processing: RMA with quartile normalization according to method of Irizarry et al, 2003.  The raw .cel files were processed in RMA using Bioconductor R package: Affy Version: 1.8.1 Date: 2005-09-03, with option Filter. Only Enterococcus faecalis V583 probesets were included in the analysis.  Replicates were averaged for ratio calculations.

organism: Enterococcus faecalis V583

source_name: E. faecalis V583 mid-log

label_protocol: RNA converted to cDNA by random-hexamer primed first strand synthesis with Superscript II and biotinaylated with Roche Enzo kit according to Affymetrix protocol.

growth_protocol: E. faecalis V583 was infected into RAW264.7 cells and bacterial RNA was subsequently extracted and compared to V583 grown in THB + 1% glucose.

extract_protocol: Qiagen RNeasy extraction kit with optional DNase step

treatment_protocol: E. faecalis V583 RNA was extracted at 4, 8, and 12 h post-infection

tag: genotype/variation

value: wild-type


title: V583 in THB rep2


title: Malignant_6

value: Invasive lobular carcinoma (10-20%)


title: Malignant_7

source_name: Invasive ductal carcinoma


title: V583 intra 12hrs rep2

source_name: E. faecalis V583 12 h post-infection


title: Pt041A Leukoplakia_Tongue right

value: Tongue right

value: Mild dysplastic leukoplakia

value: Sigma


title: Malignant_4

source_name: Invasive lobular carcinoma (10-20%)


title: Slice9_reps1-4

city: Duesseldorf

first: Andrea

last: Braeutigam

address: Universitaetsstrasse 1

department: Botany

institute: Heinrich Heine University Duesseldorf

description: Gene expression based on physical location in a leaf

scan_protocol: Arrays were scanned according to manufacturer's standard protocols.

data_processing: Transcripts were normalized to the 75th percentile within each array using the Agilent Gene spring program. For K-means clustering and hierachical clustering, four replicates were averaged.

organism: Zea mays

source_name: third leaf, 18cm length

label_protocol: The cDNA and following antisense cRNA synthesis was performed according the one-color microarray-based gene expression analysis protocol (Agilent).

growth_protocol: Z. mays plants of the ecotype B73 were grown in the greenhouse for 14 to 15 days in clay pots in Floraton soil. Natural light, a shading system and artificial light were used to extend the daylight period to 16 hours at a photon flux density of approximately 500 μmol m-2 s-1. The humidity in the greenhouse was between 75 and 90%. The green house’s ventilation system kept the temperature at 24°C.

extract_protocol: The 3rd leaf was harvested at 18cm length measured from tip to emergence from the stem. Leaves were harvested by placing them atop a custom made leaf guillotine where they were snap frozen. By closing the lid, the leaf is cut into ten pieces of 2cm width, the last of which had not yet emerged.  Twenty plants were pooled for each biological replicate. The mRNA was isolated after the method of Logemann et al. (1987) and from the same plant material the enzyme activities and metabolites were measured of. The isolated RNA was purified with the RNeasy Purification Kit according to the producer’s instruction (Qiagen). The quality was checked with the Agilent 2100 Bioanalyzer using the RNA 6000 Nano Kit. The cDNA and following antisense cRNA synthesis was performed according the one-color microarray-based gene expression analysis protocol (Agilent ). An aliquot of 1.65 µg of this RNA was loaded on one-color microarrays with custom designed oligonucleotide probes (Agilent 025271).

treatment_protocol: No treatment was applied

tag: tissue

value: third leaf

tag: slice (slice1=oldest, slice10=youngest)


title: Pt035A Distal mucosa_Buccal mucosa, cheek

tag: main site

tag: histology

value: Non dysplastic


title: V583 intra 8hrs rep2

source_name: E. faecalis V583 8 h post-infection


title: Pt041A Distal mucosa_Buccal mucosa, cheek right

tag: smoke habit

tag: age (years)


title: V583 intra 12hrs rep1


title: VitD/control 48h rep2

status: Public on Dec 20 2011

city: MADRID

first: Luis

last: LOMBARDIA

state: Madrid

address: Melchor Fernandez Almagro, 3

department: Molecualr Pathology Programme

country: Spain

institute: CNIO (Spanish National Cancer Center)

hyb_protocol: Hybridization conditions were as per Mirus' kit recommendations. Slides were pre-soaked (in buffer with 2X SSC, 0.05% SDS, 0.25% Sodium Borohydride) for 30min at 45ºC and pre-hybridized (in buffer with 5X SSC, 0.1% SDS, 1% BSA) at 42°C for 45min. Arrays were hybridized  overnight at 42°C simultaneously with Cy5- and Cy3-labeled samples previously denatured in 1X hybridization solution (provided in Mirus' kit). After incubation, slides were washed 2 x 5 min. each in 2X SSC, 0.1% SDS at hybridization temperature, 2 x 5 min. each in 1X SSC at hybridization temperature and finally 2 x 1 min each in 0.1X SSC at room temperature. Slides were briefly dip  in dH20 and dried by centrifugation at 500 rcf for 1 minute.

scan_protocol: The slides were scanned at a resolution of 10 µm with Agilent G2565BA Microarray Scanner (Agilent Technologies) and Cy3 and Cy5 fluorescent signals were quantified using Feature Extraction Software (Agilent Technologies).

data_processing: Raw data from microarray images were background subtracted and global Lowess normalized with Feature Extraction Software (Agilent Technologies).

source_name: Control cells 48h

label_protocol: One-step, direct labeling of 500 ng miRNA's extract has been carried out with the Label IT® miRNA Labeling Kit, Cy™3/Cy™5 (Mirus)  by following manufacturer instructions. Extracts from cells treated with 1,25(OH)2D3 or vehicle at each time point were compared in dye swapped hybridizations.

growth_protocol: A human colon cancer cell line, SW480-ADH, was cultured in DMEM plus 10% foetal bovine serum (Invitrogen, Paisley, UK).

extract_protocol: Cellular small RNA fractions were extracted with PureLink miRNA isolation kit (Invitrogen) by following manufacturer instructions. Quality of the RNA was determined with a 2100 Bioanalyzer (Agilent Technologies, Carlsbad, CA) and RNA amount was established by using a NanoDrop spectrophotometer (NanoDrop, Wilmington, DE).

treatment_protocol: Treatments with 1,25(OH)2D3 or isopropanol (vehicle) were performed in medium supplemented with charcoal-treated serum.

tag: cell line

tag: treatment

value: control

tag: time

source_name: VitD treated cells 48h

value: vitamin D


title: V583 intra 8hrs rep1


title: VitD/control 96h rep1

source_name: VitD treated cells 96h

source_name: Control cells 96h


title: VitD/control 96h rep2


title: V583 intra 4hrs rep1

source_name: E. faecalis V583 4 h post-infection


title: V583 intra 4hrs rep2


title: Slice10_reps1-4

hyb_protocol: An aliquot of 1.65 µg of this RNA was loaded on one-color microarrays with custom designed oligonucleotide probes (Agilent 025271)

tag: development

value: base (youngest segment)