title: 06-14-05_Miller_U133Plus2_0_A8P3d07EST

description:
Pool of 3 samples:
Donor: CD073004/CD062102/CD062802
Age: 25/45/31
Sex: M/M/F
Day: d7/d7/d7


title: 06-14-05_Miller_U133Plus2_0_A6P1d07EST

status: Public on Jul 10 2009

type: RNA

city: Bethesda

first: Jeffery

middle: Lynn

last: Miller

state: MD

address: 10 Center Drive

department: Molecular Medicine Branch

country: USA

institute: NIH/NIDDK

description:
Pool of 3 samples:
Donor: CD092404/CD071604/CD040403
Age: 37/21/50
Sex: M/F/F
Day: d7/d7/d7

hyb_protocol: standard affymetrix protocol

scan_protocol: standard affymetrix protocol

data_processing: MAS 5.0

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: CD34+ cell in EST condition on day 7

label_protocol: standard affymetrix protocol

growth_protocol: After obtaining informed consent, human CD34+ cells were isolated in high purity from the peripheral blood of normal human volunteers. The cells were cultured at a concentration of 104 -105 cells/mL in medium supplemented with 4 U/mL EPO (Amgen, Thousand Oaks, CA), 50ng/ml SCF, and 1.25ng/ml TGFbeta1 (R&D systems) as described previously (PMID: 15367428). Cells were enumerated using an electronic cell counter (Coulter, Hialeah, FL). Adult and fetal hemoglobin was analysed by HPLC.

extract_protocol: Cells harvested and homogenate prepared on 10.20.04 -11.10.04. Stored at -80C. RNA prepared between Dec, 2004 - Jan, 2005. RNA was extracted using QIAshredder and Rneasy Minikit.

treatment_protocol: EST [Erythropoietin (EPO) =4U/ml, Stem Cell Factor (SCF)=50ng/ml, and Transforming growth factor beta-1 (TGFbeta-1)=1.25ng/ml]

tag: cell type

value: CD34+ hematopoietic progenitor cells

tag: developmental stage

value: proerythroblast

tag: tissue type

value: primary cells from donated blood


title: Shfc215|HCC1428

type: genomic

city: Stanford

first: Jonathan

last: Pollack

state: CA

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55453.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1560, 4480; Software: type: feature extraction; Performer: Melanie,,Bocanegra Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-09-02; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 510; Parameter Laser on time = 45613; Parameter Laser Power = 3.51; Parameter Scan Time = 13:34:12; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.17; Performer: Melanie,,Bocanegra Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-09-02; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 550; Parameter Scan Power = 100; Parameter Laser on time = 45658; Parameter Laser Power = 3.50; Parameter Scan Time = 13:34:12; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.17; Performer: Melanie,,Bocanegra

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

molecule: genomic DNA

source_name: Normal human female genomic DNA

label_protocol: not provided

extract_protocol: not provided

tag: Normal human female genomic DNA

source_name: Breast Tumor Cell Line HCC1428 genomic DNA


title: Human MM cell line treated, biological rep1

status: Public on Jul 09 2009

city: Philadelphia

first: JIANMING

last: PEI

state: PA

address: 333 Cottman Ave.

department: Population Science

institute: Fox Chase Cancer Center

description: Gene expression data from Human MM cell line onconase treated

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

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

data_processing: Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.4 with All Probe Sets Scaling of 500.

source_name: Human MM cell line onconase treated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Affymetrix Eukaryote One-Cycle Target Labelling Assay).

growth_protocol: Cells were propagated in 10 cm dishes (Falcon) in RPMI medium containing 10% FBS.

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

treatment_protocol: At ~50 to 80% confluence, all MM cell lines were incubated with Onconase (5 µg/ml, Alfacell) for 24 h in the presence of growth medium containing 10% fetal bovine serum.

tag: cell line

value: Human malignant mesothelioma (MM)


title: Human MM cell line, biological rep3

description: Gene expression data from Human MM cell line not treated

source_name: Human MM cell line not treated


title: Human MM cell line treated, biological rep2


title: HOTAIR4

city: Cambridge

first: Mitchell

last: Guttman

state: MA

address: 7 Cambridge Center

institute: Broad Institute

description: siRNAs targeting specific lincRNAs or non-targeting siRNAs used as controls

hyb_protocol: Standard Affymetrix protocols for Human U133 Plus 2.0 Array

data_processing: RMA

label: Biotin

source_name: Primary Foot Fibroblasts, siRNA-transfected

growth_protocol: Primary human fibroblasts conditions (Rinn et al. 2007)

extract_protocol: Trizol

tag: tissue

value: foot

value: primary fibroblasts

tag: sirna

value: siHOTAIR

tag: replicate


title: Human MM cell line treated, biological rep3


title: Human MM cell line, biological rep1


title: B1_06hr

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

hyb_protocol: Thereafter, 5ug of the Cy3 target cRNAs were hybridised to the JCVI Trypanosoma brucei microarrays (version 3) for 18 hours at 60 0C

scan_protocol: Post washing, arrays were scanned using an excitation wavelength of 532 nm and Cy3 detection filter in an Agilent microarray scanner (G2505B); microarray images were quantified using QuantArray software ver. 3 (Genomic Solutions).

data_processing: All array data analyses were performed in the R environment using Bioconductor packages (www.r-project.org; www.bioconductor.org).  Briefly, array scans were background subtracted prior to QC analysis.  Sub-standard arrays were removed from the analysis.  The remainder were normalised within each array using printtiploess, and subsequently normalised across arrays using quantile normalisation.  Data from control features were removed, and on-array duplicates averaged prior to linear model fitting and comparison of samples.  Subsequently, empirical Bayesian analysis was applied (including p value adjustment for multiple testing, which controls for false discovery rate). The Bioconductor package limma was used (Smyth (2005) In:'Bioinformatics and Computational Biology Solutions using R and Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds), Springer, New York, 2005).  Gene lists, with accompanying statistical data, were generated for each comparison.  Filtering of the data, whether by raw p value, adjusted p value, or fold-change was as described within the text.  Gene ontology (GO) enrichment analyses were carried out on appropriate subsets of the data, applying a hypergeometric test (available in the GOstats Bioconductor package).

organism: Trypanosoma brucei

source_name: in vitro culture

label_protocol: For target preparation, a primer containing poly dT and the T7 polymerase promoter was annealed to 500ng of  polyA+ RNA and reverse transcriptase used to synthesize the first and second strands of cDNA. Next, cRNA was synthesized from the double stranded cDNA using T7 RNA polymerase as specified by the manufacturer (low input linear amplification protocol; Agilent), this incorporating cyanine 3 (Cy3)

growth_protocol: T. brucei AnTat1.1 were used for all assays. For sample generation parasites were grown in cyclophosphamide treated mice and purified from host blood in PSG at 37oC via DEAE cellulose. Harvested parasites were then centrifuged at 2000 rpm in a clinical centrifuge, resuspended in pre-warmed (37oC) HMI-9 medium at approximately 1x108/ml and settled for 60 minutes. Time 0h time points were prepared by harvesting 2ml of culture (2x107 parasites), the remaining 8ml being added to 32ml of SDM-79 medium containing 6mM cis aconitate and 10mM glycerol. 10ml aliquots were then taken at 1h, 6h, 18h, with an additional 1ml being harvested to prepare air dried smears, which were fixed in methanol at -20oC. At 18h a further 10ml of SDM79 was added to the remaining fluid (4-5ml) and 10ml of this harvested at 48h for RNA preparation.  Pleomorphic slender cells were grown for 3 days in cyclophosphamide treated mice, then purified from host blood as for pleomorphic stumpy cells. The harvested parasites were then centrifuged at 2000 rpm in a clinical centrifuge and resuspended in HMI-9 medium, as above. Matching the treatment of stumpy forms, the slender cells were harvested after 1h in HMI-9 and RNA prepared.

extract_protocol: 10ml of cell suspension (~1x107 parasites) was centrifuged at 2000 rpm in a clinical centrifuge for 10 minutes, washed once for 1 minute with PSG and then the cell pellet lysed in 350µl RLT buffer containing b-mercaptoethoanol, as specificied in the “RNAeasy” RNA preparation protocol (QIAgen).  RNA preparation was then completed according to the manufacturer’s protcol, including the DNAse treatment step.  Prior to use in microarray hybridizations, RNA samples were quality controlled using a Thermo Scientific NanoDropTM 1000 Spectrophotometerto assess the quantity and then quality analysed on an Agilent RNA 6000 Nano chip (lab-on-a-chip), using a 2100 Agilent Bioanalyser.

tag: stage of the parasite

value: Stumpy

tag: time (h)

tag: biolgical replicate


title: STXBP3

scan_protocol: Standard Affymetrix protocols for Human U133 Plus 2.0 Array


title: IRX2

label_protocol: Standard Affymetrix protocols for Human U133 Plus 2.0 Array


title: IRX3


title: STXBP1


title: Human MM cell line, biological rep2


title: SCR2/3

value: Non-targetting siRNA Control


title: MTX1


title: STXBP2


title: FOXF1B

source_name: Primary Lung Fibroblasts, siRNA-transfected

value: lung


title: HOTAIR1


title: ZFP161C


title: SCR1


title: MTX2


title: MTX3


title: FOXF1A


title: TNS1B


title: SCRB


title: ZFP161B


title: IRX1


title: TNS1A


title: SCRA


title: hAorticValve_Case10

city: Quebec

first: Yohan

last: Bossé

state: Quebec

address: 2725, chemin Sainte-Foy

country: Canada

institute: Laval University

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol (see complete protocol descriptions: http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

scan_protocol: Chips were scanned using a GeneChip Scanner 3000 G7 (Affymetrix) enabled for high-resolution scanning. Images were extracted with the GeneChip Operating Software (Affymetrix GCOS v1.4).

data_processing: Expression values were extracted using the Robust Multichip Average method (Irizarry RA, Hobbs B, Collin F, et al. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-64)

source_name: Calcified aortic valve

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (see complete protocol descriptions: http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

extract_protocol: RNA was extracted using the RNeasy Lipid Tissue Kit (QIAGEN). The RNA extraction protocol was performed according to manufacturer’s instructions using 100 mg of tissue.

tag: gender

value: male

tag: age


title: TNS1C


title: GY Leaf 2 month/GY Root 7 month

city: Tucson

first: David

middle: R

last: Gang

state: AZ

address: 1657 E Helen Street

department: Plant Sciences

institute: The University of Arizona

description: After samples were collected from the greenhouse, they were stored in a -80 freezer until processing.

hyb_protocol: We followed Agilent's protocols using Agilent reagents and hybridization chamber for blocking, hybridization and washing.

scan_protocol: Hardware: GenePix 4000B Software: GenePix Pro 6.0

data_processing: Agilent Feature Extract program processed the TIF image and generated the processed data in log with 10 as base.

organism: Zingiber officinale

source_name: GY Leaf 2 month

label_protocol: We used aaUTP to make aRNA using Amino Allyl MessageAmp™ II aRNA Amplification, then dye coupled for 2 h.

extract_protocol: Qiagen RNeasy Plant kit

tag: variety

value: Zingiber Officinale GY (Yellow Ginger)

value: 2 months old

value: leaf sample

source_name: GY Root 7 month

value: 7 months old

value: root sample


title: hAorticValve_Case9


title: hAorticValve_Case8


title: SCRC


title: GY Leaf 2 month/GY Leaf 7 month

source_name: GY Leaf 7 month


title: hAorticValve_Case7


title: hAorticValve_Case6


title: GY Rhizome 2 month/GY Rhizome 4 month

source_name: GY Rhizome 2 month

value: rhizome sample

source_name: GY Rhizome 4 month

value: 4 months old


title: TYA Rhizome 7 month/FMO Rhizome 7 month

organism: Curcuma longa

source_name: TYA Rhizome 7 month

value: Curcuma Longa TYA (Thin Yellow Aromatic)

source_name: FMO Rhizome 7 month

value: Curcuma Longa FMO (Fat Mild Orange)


title: hAorticValve_Ctrl10

source_name: Normal aortic valve


title: hAorticValve_Ctrl9


title: GY Root 2 month/GY Rhizome 2 month

source_name: GY Root 2 month


title: TYA Rhizome 7 month/TYA Leaf 7 month

source_name: TYA Leaf 7 month


title: FMO Rhizome 7 month/TYA Root 7 month

source_name: TYA Root 7 month


title: TYA Root 7 month/TYA Root 7 month


title: TYA Root 7 month/FMO Leaf 7 month

source_name: FMO Leaf 7 month


title: TYA Leaf 7 month/FMO Leaf 7 month


title: hAorticValve_Ctrl6


title: hAorticValve_Ctrl8


title: FMO Leaf 7 month/FMO Root 7 month

source_name: FMO Root 7 month


title: hAorticValve_Case5

tag: Gender


title: hAorticValve_Case3


title: TYA Root 7 month/TYA Leaf 7 month


title: FMO Leaf 7 month/FMO Rhizome 7 month


title: hAorticValve_Ctrl5


title: hAorticValve_Ctrl4


title: hAorticValve_Case2


title: FMO Root 7 month/ FMO Rhizome 7 month


title: hAorticValve_Ctrl2


title: hAorticValve_Ctrl7


title: TYA Rhizome 7 month/TYA Rhizome 3 month

source_name: TYA Rhizome 3 month

value: 3 months old


title: TYA Rhizome 5 month/TYA Rhizome 3 month

source_name: TYA Rhizome 5 month

value: 5 months old


title: TYA Rhizome 7 month/TYA Rhizome 5 month


title: TYA Leaf 7 month/ FMO Root 7 month

source_name: TYA leaf 7 month


title: hAorticValve_Case1

source_name: Calcified aortic valve


title: TYA Rhizome 3 month/FMO Rhizome 5 month

source_name: FMO Rhizome 5 month


title: hAorticValve_Ctrl1


title: FMO Rhizome 7 month/TYA Rhizome 5 month


title: hAorticValve_Ctrl3


title: FMO Rhizome 5 month/TYA Rhizome 7 month


title: TYA Rhizome 5 month/FMO Rhizome 3 month

source_name: FMO Rhizome 3 month


title: FMO Rhizome 3 month/FMO Rhizome 5 month


title: FMO Rhizome 5 month/FMO Rhizome 7 month


title: GY Rhizome 2 month/GY Rhizome 3 month

source_name: GY Rhizome 3 month


title: GY Rhizome 7 month/GY Rhizome 3 month

source_name: GY Rhizome 7 month


title: FMO Rhizome 3 month/FMO Rhizome 7 month


title: hAorticValve_Case4


title: TYA Rhizome 3 month/FMO Rhizome 3 month


title: GY Leaf 7 month/GY Root 7 month

source_name: GY Leaf 7 month

source_name: GY Root 7 month


title: GY Root 7 month/GY Rhizome 7 month


title: FMO Rhizome 7 month/TYA Rhizome 7 month

source_name: FMO Rhizome 7 month

source_name: TYA Rhizome 7 month


title: GY Leaf 7 month/GY Root 2 month

source_name: GY Root 2 month


title: Total RNA from Foot FB_304601

description: Total RNA

hyb_protocol: Nimblegen ChIP hybridization protocol (http://www.nimblegen.com)

scan_protocol: Arrays were scanned using AXON 5uM scanner

data_processing:
Intensities were computed using the Nimblescan software package. No normalization was used (see paper for the analysis).
NimbleGen-supplied raw files are in gff format; pair files not generated.

source_name: Primary Foot Fibroblasts

label_protocol: Nimblegen ChIP labeling protocol (http://www.nimblegen.com)

value: Foot FB

tag: fraction


title: GY Root 2 month/GY Rhizome 7 month


title: Foot Cells H3K27me3 RIP_304561

description: Modified Histone RIP was performed and hybridized relative to a paired IGG RIP control

data_processing:
Ratios were computed for the RIP and IGG samples using the Nimblescan software package. No normalization was performed on the data except that the ratios were median scaled to 0.
NimbleGen-supplied raw files are in gff format; pair files not generated.

source_name: Foot Cells H3K27me3 RIP

growth_protocol: Rinn et al. 2007

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen). The RNA was treated with DNaseI (Roche) before 2ug of each was used to generate cDNA with the Superscript III kit (Invitrogen). Poly-T was used to prime the cDNA synthesis. The cDNA was purified with phenol chloroform isoamyl alcohol and precipitated before being sent to Nimblegen to be analyzed for gene expression.

treatment_protocol: RIP was performed as described in Rinn et al. 2007

value: Primary Foot Fibroblasts

tag: antibody

value: COREST

tag: rip

value: Modified Histone RIP

source_name: Foot Cells IGG RIP

value: IgG

value: IGG RIP control


title: Total RNA from Foot FB_304613

description: Total RNA


title: Nuclear Fraction HeLa_308292

description: Total RNA

source_name: HeLa Cells

value: HeLa

value: nuclear


title: GY Rhizome 3 month/GY Rhizome 4 month

value: Zingiber Officinale GY (Yellow Ginger)

tag: developmental stage

source_name: GY Rhizome 4 month


title: GY Root 7 month/GY Root 2 month

value: 7 months old

value: 2 months old


title: Foot Cells H3K4me2 RIP_302601

source_name: Foot Cells H3K4me2 RIP


title: GY Rhizome 4 month/GY Rhizome 7 month

value: rhizome sample


title: iPS_rep3

city: Dalian

first: Lan

last: Kang

address: 9 West Section, Lvshun South Road

department: Institute of Cancer Stem Cell

country: China

institute: Dalian Medical University

description: no

hyb_protocol: Hybridization, Wash and Stain Kit(Affymetrix, Inc.)

scan_protocol: GeneChip® Scanner 3000 7G3000 (Affymetrix, Inc.)

data_processing: GCOS 1.4 software provided by Affymetrix

organism: Mus musculus

source_name: inducible pluripotent stem cell derived from mouse embryonic fibroblast

label_protocol: WT Terminal Labeling Kit (Affymetrix, Inc.)

extract_protocol:
following manufacturer’s recommendation using Trizol reagent (Invitrogen)
WT cDNA Synthesis and Amplification Kit(Affymetrix, Inc.)

tag: cell type

value: inducible pluripotent stem cell


title: WCE HeLa_308292

description: Total RNA

value: cytoplasmic


title: Total RNA from HeLa_304619

description: Total RNA


title: Total RNA from Lung FB_304601

description: Total RNA

source_name: Primary Lung Fibroblasts

value: Lung FB


title: Total RNA from Lung FB_304619

description: Total RNA


title: Patient 3, Lin-CD49f+EpCAM+ (Luminal progenitor)

city: Parkville

first: Jane

middle: E

last: Visvader

state: Victoria

address: 1G Royal Parade

department: Victorian Breast Cancer Research Consortium

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

description: no additional information

hyb_protocol: Labeled cRNA (1.5 μg) was prepared for hybridization to Illumina HumanWG-6 V3 (R1) BeadChips.

scan_protocol: After washing, we coupled the chips with Cy3 and scanned them in an Illumina BeadArray Reader.

data_processing: Un-normalized summary probe profiles were output from BeadStudio and analysed using the lumi and limma packages of the Bioconductor open-source software project (http://www.bioconductor.org). The raw intensities were normexp background corrected with offset 16, quantile normalized, then log2-transformed.

source_name: FACS sorted mammary cell subpopulation

label_protocol: We labeled up to 500 ng with the Total Prep RNA amplification kit (Ambion).

extract_protocol: RNA from sorted cell populations were prepared with the RNeasy Micro kit (Qiagen). RNA quality was ascertained using the Agilent Bioanalyser 2100 with the NanoChip protocol.

tag: patient

value: 21 years old

value: female

value: FACS sorted mammary cells

tag: cell subpopulation

value: Lin-CD49f+EpCAM+ (Luminal progenitor)

tag: beadchip barcode

tag: beadchip section

value: F


title: Total RNA from HeLa_304613

description: Total RNA

tag: cell line


title: HeLa Cells H3K4me2 RIP_304621

source_name: HeLa Cells H3K4me2 RIP

value: HeLa Cells

value: COREST

value: Modified Histone RIP

source_name: HeLa Cells IGG RIP


title: Lung Cells H3K27me3 RIP_302687

source_name: Lung Cells H3K27me3 RIP

value: Primary Lung Fibroblasts

source_name: Lung Cells IGG RIP

value: IgG

value: IGG RIP control


title: Lung Cells H3K4me2 RIP_302688

source_name: Lung Cells H3K4me2 RIP


title: HeLa Cells H3K27me3 RIP_303881

source_name: HeLa Cells H3K27me3 RIP


title: HeLa Cells COREST RIP_304614

description: COREST RIP was performed and hybridized relative to a paired IGG RIP control

source_name: HeLa Cells COREST RIP

value: COREST RIP

source_name: HeLa IGG RIP


title: HeLa Cells COREST RIP_304615


title: R1_rep2

description: no

source_name: mouse embryonic stem cell line R1

value: mouse embryonic stem cell line R1


title: Lung Cells COREST RIP_302609

source_name: Lung Cells COREST RIP

source_name: Lung IGG RIP


title: Patient 3, Lin-CD49f-EpCAM- (Stromal)

description: no additional information

value: Lin-CD49f-EpCAM- (Stromal)

value: D


title: GY Rhizome 7 month/GY Rhizome 2 month

source_name: GY Rhizome 7 month

value: Zingiber Officinale GY (Yellow Ginger)

value: 7 months old

tag: tissue

value: rhizome sample

source_name: GY Rhizome 2 month

value: 2 months old


title: GY Rhizome 3 month/GY Rhizome 6 month

source_name: GY Rhizome 3 month

value: 3 months old

source_name: GY Rhizome 6 month

value: 6 months old


title: Patient 3, Lin-CD49fhiEpCAM- (MaSC-enriched)

description: no additional information

value: 21 years old

value: female

value: FACS sorted mammary cells

value: Lin-CD49fhiEpCAM- (MaSC-enriched)

value: C


title: GY Leaf 2 month/GY Root 2 month

source_name: GY Leaf 2 month

value: leaf sample

source_name: GY Root 2 month

value: root sample


title: R1_rep1

description: no


title: GY Rhizome 6 month/GY Rhizome 7 month


title: Patient 2, Lin-CD49f-EpCAM- (Stromal)

description: no additional information

source_name: FACS sorted mammary cell subpopulation

value: 57 years old

value: F


title: Patient 2, Lin-CD49f-EpCAM+ (Mature luminal)

description: no additional information

value: Lin-CD49f-EpCAM+ (Mature luminal)

value: A


title: GY Rhizome 6 month/GY Rhizome 2 month

value: Zingiber Officinale GY (Yellow Ginger)


title: MEF_rep3

description: no

source_name: mouse embryonic fibroblast cultured in vitro at passage less than 3 which were used to derive iPS cells

value: mouse embryonic fibroblast


title: GY Rhizome 4 month/GY Rhizome 6 month

source_name: GY Rhizome 4 month

value: 4 months old


title: Lung Cells COREST RIP_304616

value: Primary Lung Fibroblasts

value: COREST

value: COREST RIP

value: IgG

value: IGG RIP control


title: MEF_rep2

description: no


title: R1_rep3

description: no

value: mouse embryonic stem cell line R1


title: Foot Cells COREST RIP_308151

source_name: Foot Cells COREST RIP

value: Primary Foot Fibroblasts

source_name: Foot IGG RIP


title: Patient 1, Lin-CD49f+EpCAM+ (Luminal progenitor)

description: no additional information

value: 39 years old

value: female

value: FACS sorted mammary cells

value: Lin-CD49f+EpCAM+ (Luminal progenitor)

value: D


title: MEF_rep1

description: no


title: Patient 3, Lin-CD49f-EpCAM+ (Mature luminal)

description: no additional information

value: 21 years old

value: Lin-CD49f-EpCAM+ (Mature luminal)

value: E


title: HeLa Cells PRC2 RIP with Suz12 Antibody_dyeswap_308374

description: PRC2 RIP was performed and hybridized relative to a paired IGG RIP control

source_name: HeLa PRC2 RIP

value: HeLa Cells

value: PRC2 RIP


title: Patient 1, Lin-CD49f-EpCAM+ (Mature luminal)

description: no additional information

value: C


title: GY Rhizome 7 month/GY Leaf 7 month

value: Zingiber Officinale GY (Yellow Ginger)

value: 7 months old

value: rhizome sample

source_name: GY Leaf 7 month

value: leaf sample


title: GY Leaf 2 month/GY Root 7 month replicate 2

value: 2 months old

source_name: GY Root 7 month

value: root sample


title: Patient 2, Lin-CD49fhiEpCAM- (MaSC-enriched)

description: no additional information

value: 57 years old

value: Lin-CD49fhiEpCAM- (MaSC-enriched)


title: HeLa Cells PRC2 RIP with Suz12 Antibody_dyeswap_308340

source_name: HeLa IGG RIP

value: IgG

value: IGG RIP control


title: GY Rhizome 7 month/GY Leaf 2 month


title: iPS_rep1

description: no

source_name: inducible pluripotent stem cell derived from mouse embryonic fibroblast

value: inducible pluripotent stem cell


title: iPS-rep2

description: no


title: Lung Cells PRC2 RIP with Ezh2 and Suz12 Antibodies_noproteins_111208

description:
PRC2 RIP was performed and hybridized relative to a paired IGG RIP control.
This co-hybridization was run on an array platform which had no protein coding genes present (just lincRNAs).

source_name: Lung PRC2 RIP

value: Primary Lung Fibroblasts

value: Ezh2 and Suz14

source_name: Lung IGG RIP


title: GY Rhizome 2 month/GY Leaf 7 month

source_name: GY Rhizome 2 month


title: Lung Cells PRC2 RIP with Ezh2 and Suz12 Antibodies_304617

value: Ezh2 and Suz12


title: GY Rhizome 2 month/GY Leaf 2 month


title: M.tb  at 6h, 4X MIC, biological rep1

status: Public on Jul 08 2009

city: San Antonio

first: Deepak

last: Kaushal

state: TX

address: 8715 W Military Dr

department: HPI

institute: Texas Biomedical Research Institute

description: Comparisons of THZ treated  (4X MIC) (ch1) vs non-treated cultures at 6h (ch2)

hyb_protocol: The Tuberculosis Genome Oligo Set consisting of 70mer probes representing 4,269 Mtb (H37Rv and CDC1551) genes, plus 26 controls were obtained from “TB Vaccine Testing and Research Materials” Contract, Colorado State University. Experiments were performed according to standard Mycobacteria Research Laboratories (MRL) at Colorado State University protocols (http://www.cvmbs.colostate.edu/mip/tb/pdf/arrays.pdf).

scan_protocol: Scanned on an Agilent G2565AA scanner. Biological duplicate hybridizations were performed using PDS samples derived from THZ treated and vehicle treated control samples of M. tuberculosis. Spots with i) imperfect spot morphology; ii) a signal to noise ratio < 1.5 in more than 50% of instances; iii) saturated intensity for >65% of the pixels in at least one channel; and iv) co-efficient of variance >20% within the quadruplicates on one slide, were excluded from analysis.

data_processing: Data were analyzed using S+ scripts within Spotfire DecisionSite for Microarray Analysis (TIBCO-Spotfire Inc.) to determine statistically significant expression changes, adjusting for intensity bias using Locally Weighted Scatter-plot Smoothing (LOWESS) normalization (Mehra et al., 2009).

organism: Mycobacterium tuberculosis

source_name: M. tuberculosis culture at 6h, treated with 4XMIC

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: A portion of a recently frozen stock was inoculated into 5 ml of complete Middlebrook 7H9 broth (7H9) supplemented with 10% albumin dextrose catalase, v/v, and 0.05% Tween-80, v/v (Sigma, St. Louis, MO), and incubated at 37oC for 5 days. Then the culture was transferred into 50 ml of 7H9 media and incubated at 37oC with 50 rpm shaking until growth reached log phase.

extract_protocol: RNA was isolated using the Trizol bead beater method, DNase treated, and purified (RNeasy; Qiagen) and its quantity assessed using a NanoDrop spectrophotometer.

treatment_protocol: THZ (Sigma) was added to the culture at a final concentration of 4XMIC, and the culture was then incubated at 37oC

tag: strain

source_name: M. tuberculosis culture at 6h, untreated


title: Patient 1, Lin-CD49fhiEpCAM- (MaSC-enriched)

description: no additional information

value: 39 years old

value: female

value: FACS sorted mammary cells

value: A


title: Patient 1, Lin-CD49f-EpCAM- (Stromal)

description: no additional information

value: Lin-CD49f-EpCAM- (Stromal)

value: B


title: Foot Cells PRC2 RIP with Ezh2 and Suz12 Antibodies_noproteins_112508

source_name: Foot PRC2 RIP

value: Primary Foot Fibroblasts

value: Ezh2 and Suz15

value: PRC2 RIP


title: HeLa Cells PRC2 RIP with Ezh2 and Suz12 Antibodies_304618

value: HeLa Cells


title: M.tb  at 6h, 1X MIC, biological rep2

description: Comparisons of THZ treated (1X MIC) (ch1) vs non-treated cultures at 6h (ch2)

source_name: M. tuberculosis culture at 6h, treated with 1XMIC

treatment_protocol: THZ (Sigma) was added to the culture at a final concentration of 1XMIC  and the culture was then incubated at 37oC


title: M.tb  at 4h, 4X MIC, biological rep2

description: Comparisons of THZ treated (4X MIC) (ch1) vs non-treated cultures at 4h (ch2)

source_name: M. tuberculosis culture at 4h, treated with 4XMIC

source_name: M. tuberculosis culture at 4h, untreated


title: HeLa Cells H3K27me3 RIP_303700

source_name: HeLa Cells H3K27me3 RIP

value: COREST

value: Modified Histone RIP

source_name: HeLa Cells IGG RIP


title: Foot Cells PRC2 RIP with Ezh2 and Suz12 Antibodies_304711

source_name: Foot IGG RIP

value: IgG

value: IGG RIP control


title: HeLa Cells PRC2 RIP with Suz12 Antibody_302599

source_name: HeLa PRC2 RIP


title: Lung Cells PRC2 RIP with Ezh2 and Suz12 Antibodies_noproteins_110708

value: Primary Lung Fibroblasts

value: Ezh2 and Suz13


title: HeLa Cells PRC2 RIP with Ezh2 and Suz12 Antibodies_noproteins_112508

value: Ezh2 and Suz12


title: M.tb  at 4h, 4X MIC, biological rep1


title: M.tb  at 6h, 4X MIC, biological rep2

description: Comparisons of THZ treated (4X MIC) (ch1) vs non-treated cultures at 6h (ch2)


title: M.tb  at 1h, 1X MIC, biological rep2

description: Comparisons of THZ treated(1X MIC) (ch1) vs non-treated cultures at 1h (ch2)

source_name: M. tuberculosis culture at 1h, treated with 1XMIC

source_name: M. tuberculosis culture at 1h, untreated


title: M.tb  at 1h, 4X MIC, biological rep2

description: Comparisons of THZ treated (4X MIC) (ch1) vs non-treated cultures at 1h (ch2)

source_name: M. tuberculosis culture at 1h, treated with 4XMIC


title: M.tb  at 1h, 4X MIC, biological rep1


title: M.tb  at 1h, 1X MIC, biological rep1

description: Comparisons of  THZ treated(1X MIC) (ch1) vs non-treated cultures at 1h (ch2)


title: M.tb  at 0h, biological rep2

description: Comparisons of non-treated cultures at 0h.

source_name: M. tuberculosis culture at 0h, untreated

treatment_protocol: untreated (Control) samples were treated with the appropriate solvent vehicle.


title: M.tb  at 0h, biological rep1


title: M.tb  at 4h, 1X MIC, biological rep1

description: Comparisons of THZ treated (1X MIC) (ch1) vs non-treated cultures at 4h (ch2)

source_name: M. tuberculosis culture at 4h, treated with 1XMIC


title: miRNA_T00327099_SAMPLE002

type: other

city: Radnor

first: Hongtao

last: Fan

address: 145 King of Prussia Rd

department: RDI

institute: Centocor

description: no additional information

hyb_protocol: Each sample was then hybridized to the Bioarray slides for 14 hours at 42oC (Ambion).

scan_protocol: The arrays were washed and scanned using an Agilent 2505B confocol laser microarray scanner (Agilent) data was obtained using the Expression Analysis software (Codelink, version 4.2)

data_processing: Probes flagged by the Expression Analysis software were first removed and background median values were subtracted from the spot mean. Spot intensity values below zero were set to 0.5 and the data was then quantile normalized. A background cutoff of 6 (log2 normalized) was identified by plotting the correlations of replicate probes across all samples versus the median of median intensities.

molecule: other

source_name: LUNG tissue

label_protocol: The small RNA samples were subject to poly(A) polymerase reaction wherein amine modified uridines were incorporated (Ambion). The tailed samples were then fluorescently labeled using the amine-reactive Cy3 (Invitrogen). The fluorescently labeled RNAs were purified using a glass-fiber filter and eluted (Ambion).

extract_protocol: Total RNA was isolated using Trizol. miRNA was isolated from 4 ug of total RNA using the mirVana isolation kit (Ambion). All samples were then fractionated by polyacrylamide gel electrophoresis (Flash-Page Ambion) and small RNAs (< 40nt) were recovered by ethanol precipitation with linear acrylamide.

tag: histology

value: LUNG

tag: stage

value: IIIb

tag: t (extent of the primary tumor)

tag: n  (extent of spread to the lymph nodes )

tag: m  (presence of metastasis )

tag: sex

value: F


title: M.tb  at 2h, 4X MIC, biological rep1

description: Comparisons of THZ treated (4X MIC) (ch1) vs non-treated cultures at 2h (ch2)

source_name: M. tuberculosis culture at 2h, treated with 4XMIC

source_name: M. tuberculosis culture at 2h, untreated


title: miRNA_T00327073_SAMPLE002

description: no additional information

source_name: SCC tissue

value: SCC

tag: death

value: Ib

tag: differentiation

value: poor

tag: age

value: M


title: miRNA_T00327073_SAMPLE001

description: no additional information

value: mod


title: miRNA_T00327098_SAMPLE002

description: no additional information

value: IIb


title: M.tb  at 2h, 1X MIC, biological rep2

description: Comparisons of THZ treated (1X MIC) (ch1) vs non-treated cultures at 2h (ch2)

source_name: M. tuberculosis culture at 2h, treated with 1XMIC


title: miRNA_T00327098_SAMPLE001

description: no additional information


title: miRNA_T00327099_SAMPLE001

description: no additional information


title: M.tb  at 2h, 1X MIC, biological rep1


title: miRNA_T00327072_SAMPLE002

description: no additional information

value: Ia


title: M.tb  at 2h, 4X MIC, biological rep2


title: miRNA_T00327072_SAMPLE001

description: no additional information


title: miRNA_T00327071_SAMPLE002

description: no additional information


title: miRNA_T00327071_SAMPLE001

description: no additional information

value: IIIa


title: M.tb  at 6h, 1X MIC, biological rep1

description: Comparisons of THZ treated (1X MIC) (ch1) (ch1) vs non-treated cultures at 6h (ch2)

source_name: M. tuberculosis culture at 6h, treated with 1XMIC

source_name: M. tuberculosis culture at 6h, untreated


title: miRNA_T00327097_SAMPLE002

description: no additional information


title: miRNA_T00327097_SAMPLE001

description: no additional information


title: miRNA_T00327053_SAMPLE002

description: no additional information


title: miRNA_T00327054_SAMPLE002

description: no additional information


title: miRNA_T00327052_SAMPLE002

description: no additional information


title: miRNA_T00327053_SAMPLE001

description: no additional information


title: miRNA_T00327052_SAMPLE001

description: no additional information

value: well-mod


title: miRNA_T00327015_SAMPLE002

description: no additional information


title: miRNA_T00327016_SAMPLE002

description: no additional information


title: miRNA_T00327054_SAMPLE001

description: no additional information


title: miRNA_T00327014_SAMPLE002

description: no additional information


title: miRNA_T00327014_SAMPLE001

description: no additional information


title: miRNA_T00327010_SAMPLE002

description: no additional information

value: mod-poor


title: miRNA_T00327015_SAMPLE001

description: no additional information


title: miRNA_T00327010_SAMPLE001

description: no additional information


title: miRNA_T00327009_SAMPLE001

description: no additional information


title: M.tb  at 4h, 1X MIC, biological rep2

source_name: M. tuberculosis culture at 4h, untreated


title: miRNA_T00327008_SAMPLE001

description: no additional information


title: miRNA_T00327008_SAMPLE002

description: no additional information


title: miRNA_T00326985_SAMPLE001

description: no additional information


title: miRNA_T00326985_SAMPLE002

description: no additional information


title: miRNA_T00327009_SAMPLE002

description: no additional information


title: miRNA_T00326984_SAMPLE002

description: no additional information


title: miRNA_T00326984_SAMPLE001

description: no additional information


title: miRNA_T00326983_SAMPLE001

description: no additional information


title: miRNA_T00326983_SAMPLE002

description: no additional information


title: miRNA_T00326972_SAMPLE001

description: no additional information


title: miRNA_T00326971_SAMPLE002

description: no additional information


title: miRNA_T00326925_SAMPLE001

description: no additional information


title: miRNA_T00326970_SAMPLE001

description: no additional information


title: miRNA_T00326970_SAMPLE002

description: no additional information


title: miRNA_T00326925_SAMPLE002

description: no additional information


title: miRNA_T00326926_SAMPLE001

description: no additional information


title: miRNA_T00326926_SAMPLE002

description: no additional information


title: 13689286 - 4nx2n seed 1 vs Ler seed 1

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: What are other genes involved in haiku pathway?

hyb_protocol: Ler seed 1 Cy5 / 4nx2n seed 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,460V,laser power 35%, Cy5:635nm,pmt voltage 460V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: Ler seed 1

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: seed - Media=Soil 	 hygrometry=60%	 Temperature=21°C/17°C	 Light=16h of light/8h of dark

extract_protocol: Ler seed 1:10ug.

treatment_protocol: no treatment

tag: ecotype

value: landsberg erecta

tag: genotype/variation

value: wildtype

tag: developmental stage

value: (boyes et al. plant cell 2001):boyes:6.00

source_name: 4nx2n seed 1

extract_protocol: 4nx2n seed 1:5ug.

value: mutant (ler)


title: 13689285 - Ler seed 1 vs 4nx2n seed 1

hyb_protocol: 4nx2n seed 1 Cy5 / Ler seed 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: miRNA_T00326972_SAMPLE002

description: no additional information


title: miRNA_T00326924_SAMPLE002

description: no additional information


title: miRNA_T00326924_SAMPLE001

description: no additional information


title: 13688916 - iku 1 seed 2 vs Ler seed 2

hyb_protocol: Ler seed 2 Cy5 / iku 1 seed 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Ler seed 2

extract_protocol: Ler seed 2:10ug.

source_name: iku 1 seed 2

extract_protocol: iku 1 seed 2:5ug.

value: mutant (iku1)


title: 13688917 - Ler seed 2 vs iku 1 seed 2

hyb_protocol: iku 1 seed 2 Cy5 / Ler seed 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: miRNA_T00326923_SAMPLE001

description: no additional information


title: 13689651 - iku 1 seed 1 vs Ler seed 1

hyb_protocol: Ler seed 1 Cy5 / iku 1 seed 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: iku 1 seed 1

extract_protocol: iku 1 seed 1:5ug.


title: miRNA_T00326971_SAMPLE001

description: no additional information


title: miRNA_T00326923_SAMPLE002

description: no additional information


title: miRNA_T00326922_SAMPLE001

description: no additional information


title: 13689649 - Ler seed 1 vs iku 1 seed 1

hyb_protocol: iku 1 seed 1 Cy5 / Ler seed 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: miRNA_T00326921_SAMPLE002

description: no additional information


title: 13689498 - iku 2 seed 2 vs Ler seed 2

hyb_protocol: Ler seed 2 Cy5 / iku 2 seed 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: iku 2 seed 2

extract_protocol: iku 2 seed 2:10ug.

value: mutant (iku2)


title: HeLa Cells PRC2 RIP with EZH2 Antibody_303715

source_name: HeLa PRC2 RIP

value: HeLa Cells

tag: antibody

tag: rip

value: PRC2 RIP

source_name: HeLa IGG RIP

value: IgG

value: IGG RIP control


title: Patient 2, Lin-CD49f+EpCAM+ (Luminal progenitor)

description: no additional information

source_name: FACS sorted mammary cell subpopulation

tag: patient

value: 57 years old

tag: gender

value: female

tag: cell type

value: FACS sorted mammary cells

tag: cell subpopulation

value: Lin-CD49f+EpCAM+ (Luminal progenitor)

tag: beadchip barcode

tag: beadchip section

value: B


title: 13689497 - Ler seed 2 vs iku 2 seed 2

hyb_protocol: iku 2 seed 2 Cy5 / Ler seed 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: miRNA_T00326881_SAMPLE002

description: no additional information

tag: histology

value: SCC

tag: stage

value: IIIb

tag: t (extent of the primary tumor)

tag: n  (extent of spread to the lymph nodes )

value: well-mod

value: M


title: miRNA_T00326881_SAMPLE001

description: no additional information

tag: death

value: IIIa

tag: m  (presence of metastasis )

tag: differentiation

value: mod

tag: sex

value: F


title: miRNA_T00326921_SAMPLE001

description: no additional information

value: Ia

tag: age


title: 13689652 - Ler seed 2 vs 4nx2n seed 2

hyb_protocol: 4nx2n seed 2 Cy5 / Ler seed 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 4nx2n seed 2

extract_protocol: 4nx2n seed 2:5ug.

tag: ecotype

value: landsberg erecta

tag: genotype/variation

value: mutant (ler)

tag: developmental stage

value: (boyes et al. plant cell 2001):boyes:6.00

value: wildtype


title: miRNA_T00326880_SAMPLE001

description: no additional information

value: IIb

value: mod-poor


title: miRNA_T00326863_SAMPLE001

description: no additional information


title: miRNA_T00327016_SAMPLE001

description: no additional information

value: poor


title: miRNA_T00326861_SAMPLE002

description: no additional information


title: miRNA_T00326862_SAMPLE002

description: no additional information

value: Ib


title: 13689284 - iku 2 seed 1 vs Ler seed 1

hyb_protocol: Ler seed 1 Cy5 / iku 2 seed 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: iku 2 seed 1

extract_protocol: iku 2 seed 1:10ug.

value: mutant (iku2)


title: 13689287 - 4nx2n seed 2 vs Ler seed 2

hyb_protocol: Ler seed 2 Cy5 / 4nx2n seed 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: miRNA_T00326862_SAMPLE001

description: no additional information

value: SCC


title: 13689283 - Ler seed 1 vs iku 2 seed 1

hyb_protocol: iku 2 seed 1 Cy5 / Ler seed 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13697369 - iku 2 seed3dap 1 vs Ler seed3dap 1

hyb_protocol: Ler seed3dap 1 Cy5 / iku 2 seed3dap 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,500V,laser power 35%, Cy5:635nm,pmt voltage 500V,laser power 30%

source_name: Ler seed3dap 1

extract_protocol: Ler seed3dap 1:4.19ug.

tag: harvest date

source_name: iku 2 seed3dap 1

extract_protocol: iku 2 seed3dap 1:1.67ug.


title: 13697376 - iku 2 seed3dap 2 vs Ler seed3dap 2

hyb_protocol: Ler seed3dap 2 Cy5 / iku 2 seed3dap 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Ler seed3dap 2

extract_protocol: Ler seed3dap 2:4ug.

source_name: iku 2 seed3dap 2

extract_protocol: iku 2 seed3dap 2:4.26ug.


title: 13697368 - Ler seed3dap 1 vs iku 2 seed3dap 1

hyb_protocol: iku 2 seed3dap 1 Cy5 / Ler seed3dap 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13697375 - Ler seed3dap 2 vs iku 2 seed3dap 2

hyb_protocol: iku 2 seed3dap 2 Cy5 / Ler seed3dap 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13697366 - iku 1 seed3dap 2 vs Ler seed3dap 2

hyb_protocol: Ler seed3dap 2 Cy5 / iku 1 seed3dap 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: iku 1 seed3dap 2

extract_protocol: iku 1 seed3dap 2:4.31ug.

value: mutant (iku1)


title: miRNA_T00326861_SAMPLE001

description: no additional information

hyb_protocol: Each sample was then hybridized to the Bioarray slides for 14 hours at 42oC (Ambion).

source_name: SCC tissue

value: well-mod


title: miRNA_T00326880_SAMPLE002

description: no additional information

source_name: SCC-Ad tissue


title: miRNA_T00326853_SAMPLE002

description: no additional information


title: miRNA_T00326852_SAMPLE002

description: no additional information

value: M


title: 13697365 - Ler seed3dap 2 vs iku 1 seed3dap 2

hyb_protocol: iku 1 seed3dap 2 Cy5 / Ler seed3dap 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: miRNA_T00326851_SAMPLE001

description: no additional information


title: miRNA_T00326851_SAMPLE002

description: no additional information


title: miRNA_T00326842_SAMPLE002

description: no additional information

value: IIIa


title: miRNA_T00326842_SAMPLE001

description: no additional information

value: well


title: miRNA_T00326840_SAMPLE001

description: no additional information


title: 13697364 - iku 1 seed3dap 1 vs Ler seed3dap 1

hyb_protocol: Ler seed3dap 1 Cy5 / iku 1 seed3dap 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: iku 1 seed3dap 1

extract_protocol: iku 1 seed3dap 1:3.95ug.


title: 13697308 - Ler seed3dap 1 vs iku 1 seed3dap 1

hyb_protocol: iku 1 seed3dap 1 Cy5 / Ler seed3dap 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: miRNA_T00326835_SAMPLE002

description: no additional information


title: miRNA_T00326834_SAMPLE002

description: no additional information

value: mod


title: PRB12554 MixC

status: Public on Jul 07 2009

city: South San Francisco

first: Alex

last: Abbas

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

description: PRB12554 MixC

hyb_protocol: cRNA was hybridized on GeneChip HGU133 plus v2.

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

source_name: PRB12554 MixC

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

extract_protocol: RNeasy Mini Kit (Qiagen)

tag: MixC

tag: mixed cells


title: Lung Cells COREST RIP_302612

hyb_protocol: Nimblegen ChIP hybridization protocol (http://www.nimblegen.com)

source_name: Lung Cells COREST RIP

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen). The RNA was treated with DNaseI (Roche) before 2ug of each was used to generate cDNA with the Superscript III kit (Invitrogen). Poly-T was used to prime the cDNA synthesis. The cDNA was purified with phenol chloroform isoamyl alcohol and precipitated before being sent to Nimblegen to be analyzed for gene expression.

tag: cell line

value: Primary Lung Fibroblasts

tag: antibody

value: COREST

tag: rip

value: COREST RIP

source_name: Lung IGG RIP

value: IgG

value: IGG RIP control


title: PRB12556 MixD

description: PRB12556 MixD

source_name: PRB12556 MixD

tag: MixD


title: PRB12553 MixC

description: PRB12553 MixC

source_name: PRB12553 MixC


title: PRB12551 MixB

description: PRB12551 MixB

source_name: PRB12551 MixB

tag: MixB


title: Bt_DE17

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

description: Anterior limb muscle collected from male beef cattle, submerged in RNALater and stored at -20°C until extraction.

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

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5 and normalized using R2.6.1 statistical software

label: Cyanine 3

organism: Bos taurus

source_name: Male beef cattle, TREATED WITH DEXAMETHAZONE via feed 0.75 mg/head for 43 days and WITH 17β-ESTRADIOL intramuscolarly 20mg/head for three times

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

extract_protocol: Extracted according to QiAgen RNeasy MiniKit protocol for tissues samples

tag: Anterior limb muscle (biceps branchii)


title: PRB12557 MixD

description: PRB12557 MixD

source_name: PRB12557 MixD


title: PRB12550 MixB

description: PRB12550 MixB

source_name: PRB12550 MixB


title: Bt_DE16


title: Bt_DE14


title: Bt_D4

source_name: Male beef cattle, TREATED WITH DEXAMETHAZONE via feed 0.75 mg/head for 43 days


title: PRB12546 MixA

description: PRB12546 MixA

source_name: PRB12546 MixA

tag: MixA


title: PRB12544 THP-1

description: PRB12544 THP-1

tag: purified cells


title: PRB12549 MixB

description: PRB12549 MixB

source_name: PRB12549 MixB


title: PRB12552 MixC

description: PRB12552 MixC

source_name: PRB12552 MixC


title: PRB12543 THP-1

description: PRB12543 THP-1


title: Bt_DE13


title: Bt_D5


title: PRB12547 MixA

description: PRB12547 MixA

source_name: PRB12547 MixA


title: Bt_D3


title: PRB12555 MixD

description: PRB12555 MixD

source_name: PRB12555 MixD


title: Bt_D2


title: PRB12548 MixA

description: PRB12548 MixA

source_name: PRB12548 MixA


title: Bt_DE18


title: Bt_D6


title: Bt_DE15


title: PRB12545 THP-1

description: PRB12545 THP-1


title: PRB12541 Raji

description: PRB12541 Raji

source_name: PRB12541 Raji

tag: Raji


title: Bt_Ctrl_759M

source_name: Male beef cattle, UNTREATED CONTROL


title: Bt_Ctrl_011M


title: Bt_Ctrl_K12


title: PRB12536 Jurkat

description: PRB12536 Jurkat

source_name: PRB12536 Jurkat

tag: Jurkat


title: PRB12539 IM-9

description: PRB12539 IM-9


title: PRB12542 Raji

description: PRB12542 Raji

source_name: PRB12542 Raji


title: Bt_Ctrl_K9


title: Bt_Ctrl_K11


title: P1 lung, polysomal RNA, biological replicate 1

city: Toronto

first: Gail

last: Otulakowski

state: ON

address: 555 University Ave

department: Physiology & Experimental Medicine

institute: Hospital for Sick Children Research Institute

description: polysome-associated RNA from postnatal saccular lung

hyb_protocol: 15 ug of labeled cRNA were used for hybridization to Affymetrix RAE2302 chips using protocol EukGE-WS2v4

scan_protocol: Scanned using Affymetrix GeneChip Scanner 3000

data_processing: scaling target signal 150 using GCOS 1.4

organism: Rattus norvegicus

source_name: RNA from large polysomes from P1 rat lung

label_protocol: Biotinylated cRNA were prepared from 5 ug RNA using Enzo IVT kit for in vitro transcription

growth_protocol: fetuses and newborn rats from timed pregnant gestation.  Fetuses delivered by Cesarean section.  Newborns vaginally delivered.

extract_protocol: Total RNA by Trizol extraction according to the manufacturer's instructions.  Polysomal RNA from sucrose density gradient fractions where n> 7 ribosomes/mRNA, extracted by guanidine-HCl, phenol/CHCl3 extracted, and ethanol precipitated.  All further purified with Qiagen RNeasy according to the manufacturer's instructions.

treatment_protocol: lungs excised and snap-frozen in liquid nitrogen

tag: Strain

value: Wistar


title: P1 lung, total RNA, biological replicate 3

description: steady-state expression data from postnatal saccular lung

source_name: total RNA from P1 rat lung


title: Bt_Ctrl_075M


title: Bt_Ctrl_K8


title: PRB12538 IM-9

description: PRB12538 IM-9


title: Vibrio parahaemolyticus 0.66% vs. 2% NaCl shift growth

city: Beijing

first: Ruifu

last: Yang

address: No.20, DOngdajie, Fengtai

institute: Institute of Microbiology and Epidemiology

description:
Vibrio parahaemolyticus strain LAMVP1 (tdh-PCR+, GS-PCR+ and KP+) used in this study is a pandemic O3:K6 strain isolated from a diarrhoea patient in Thailand in 1996. According to the DNA microarray-based comparative genomic hybridization (data not shown), its genomic content is almost identical to that of another pandemic O3:K6 strain RIMD2210633, whose genomic sequence has been determined (Erdenebaatar et al., 2003).
A modified V-5 (MV-5) minimal medium, consisting of 2% or 0.66% NaCl, 40mM D-Mannitol, 10mM (NH4)2SO4, 100mM K2HPO4, 0.75mM MgSO4, 0.05mM CaCl2, 0.025mM ZnCl2, and 0.025mM FeSO4 (pH 8.0), was used for bacterial cultivation. Strain LAMVP1 was grown at 37°C to an OD600 of 1.0, and then 50-fold diluted into fresh MV-5 medium. For the ‘shift growth’ design, bacteria were grown in MV-5 containing 2% NaCl to an OD600 of 1.2, and cells were then harvested by centrifugation at 3,000×g for 5 min and then the culture supernatant was removed; the remaining cell pellets were re-suspended in fresh MV-5 containing 2% (reference condition) or 0.66% (test condition) NaCl, and cells were allowed to grow at 37 °C for 1h and further harvested for RNA isolation.
Gene expression profiles were compared between reference and test condition. RNA samples were isolated from four individual bacterial cultures, as biological replicates, for each strain. The dual-fluorescently (Cy3 or Cy5 dye) labeled cDNA probes, for which the incorporated dye was reversed, were synthesized from the RNA samples, and then hybridized to four separated microarray slides, respectively.

hyb_protocol: For two-sample (reference vs. test) microarray hybridization, four independent bacterial cultures from each condition were prepared as biological replicates for RNA isolation. Accordingly, for each time point, four dual-fluorescence-labeled cDNA probes were prepared to hybridize with four slides, respectively. Pairwise comparisons were made using dye swaps to avoid labeling bias. For hybridization, the slides were incubated in 50 µl of prehybridization buffer (5X SSC, 0.1% SDS and 0.1% BSA) at 42°C for at least 1 hr. The slides were washed twice in water for 1 min and once in 95% ethanol for 1 min, and then blown to dry with hot air. Dual-fluorescence labeled dried probes were resuspended in 35 µl of hybridization solution (50% deionized formamide, 5×SSC, 0.1% SDS, 5×Denhardt’s solution, and 0.5 µg/µl of sheared salmon sperm DNA). The mixture was denatured at 98°C for 5 min, and then was applied to the microarray slide followed by covering a 24×50 mm glass coverslip. The slides were hybridized in a moisture chamber at 42°C for 18 to 20 hr in a hybridization incubator (Robbins Scintific). After hybridization, the slides were washed in 1×SSC with 0.06% SDS for 2 min, then in 0.06×SSC for 2 min and finally in ethanol for 1 min. The slides were blown dry for scanning.

scan_protocol: The hybridized slides were scanned at a resolution of 10 µm by using a GenePix Personal 4100A Microarray Scanner (Axon Instruments). The scanning images were processed and the data were further analyzed by using GenePix Pro 5.0 software (Axon Instruments) combined with Microsoft Excel software.

data_processing: The scanning images were processed and the data were further analyzed by using GenePix Pro 5.0 software (Axon Instruments) combined with Microsoft Excel software. Spots were analyzed by adaptive quantitation, and the local background was subsequently subtracted. Spots with background-corrected signal intensity (median) in both channels less than two folds of background intensity (median) were rejected from further analysis. Data normalization was performed on the remaining spots by total intensity normalization methods. The normalized log2 ratio of reference/test signal for each spot was recorded. Genes with less than four data points were considered unreliable, and their data points were discarded as well. The averaged log2 ratio for each remaining gene on the four replicate slides was ultimately calculated. Significant changes of gene transcription level were identified with SAM software using one class mode. After the SAM analysis, only genes with at least 2-fold changes in expression were collected for further analysis.

label: Cy3 or Cy5

organism: Vibrio parahaemolyticus

source_name: LAMVP1, 2%NaCl MV-5 minimal medium, shift growth, 37°C

label_protocol: A cDNA microarray imprinted with 4669 genes representing about 97% of V. parahaemolyticus genome was used for transcriptome analysis. For two-sample (reference versus test) microarray hybridization, four independent bacterial cultures from each condition were prepared as biological replicates for RNA isolation. Accordingly, for each time point, four dual-fluorescence-labeled cDNA probes were prepared to hybridize with four slides, respectively. Pairwise comparisons were made using dye swaps to avoid labeling bias. 20 µg of total RNA was mixed with 3µg random hexamer primers, heated to 70°C for 10 min, and cooled quickly on ice. 1µl of RNasin RNase inhibitor (Promega), 8 µl of 5×reverse transcription buffer, 4 µl of 0.1 M DDT, 1.6 µl of unmodified dNTP mixture (12.5 mM of each dATP, dGTP, and dCTP, plus 7.5 mM dTTP), 2 µl of 4 mM aminoallyl-dUTP (Sigma) and 200 U of SuperScript Ⅲ reverse transcriptase (Invitrogen) were added to a final volume of 40 µl. The reaction occurred at 50°C for 1 hr, after which an additional 200 U of Superscript Ⅲ reverse transcriptase was added. The mixture was then incubated at 50°C for an additional hour. The reaction was stopped by the addition of 20 mM EDTA, and the RNA was degraded by the addition of NaOH to a final concentration of 30 mM, followed by incubation at 65°C for 15 min. The mixture was neutralized by adding HCl to a final concentration of 30 mM. Free amines were removed by using Qiaquick PCR purification columns (Qiagen). The purified cDNA was air dried at 50°C, and then was labeled by the addition of 1/10 of one reaction vial of Cy3 or Cy5 monofunctional dye (Amersham) in 0.05 M sodium bicarbonate (pH9.3) and incubated for 2 hr at room temperature in the dark.

extract_protocol: Before bacterial harvest, double-volume of RNAprotect Bacteria Reagent (Qiagen) was added immediately to each cell culture. Total RNA extraction was performed by using MasterPureTM RNA Purification kits (Epicenter) as mentioned in our previous report . RNA quality was monitored by agarose gel electrophoresis and RNA quantity was measured by spectrophotometer.

tag: strain

value: LAMVP1, reference, 2% Nacl shift

tag: growth

value: middle exponential growth phase

source_name: LAMVP1, 0.66%NaCl, MV-5 minimal medium, shift growth, 37°C

value: LAMVP1, test, 0.66% Nacl shift


title: PRB12540 Raji

description: PRB12540 Raji

source_name: PRB12540 Raji


title: PRB12535 Jurkat

description: PRB12535 Jurkat

source_name: PRB12535 Jurkat


title: PRB12537 IM-9

description: PRB12537 IM-9


title: Bt_Ctrl_K10


title: P1 lung, total RNA, biological replicate 1


title: P1 lung, polysomal RNA, biological replicate 2


title: Vibrio parahaemolyticus 0.66% vs. 2% NaCl continuous growth

description:
Vibrio parahaemolyticus strain LAMVP1 (tdh-PCR+, GS-PCR+ and KP+) used in this study is a pandemic O3:K6 strain isolated from a diarrhoea patient in Thailand in 1996. According to the DNA microarray-based comparative genomic hybridization (data not shown), its genomic content is almost identical to that of another pandemic O3:K6 strain RIMD2210633, whose genomic sequence has been determined (Erdenebaatar et al., 2003).
A modified V-5 (MV-5) minimal medium, consisting of 2% or 0.66% NaCl, 40mM D-Mannitol, 10mM (NH4)2SO4, 100mM K2HPO4, 0.75mM MgSO4, 0.05mM CaCl2, 0.025mM ZnCl2, and 0.025mM FeSO4 (pH 8.0), was used for bacterial cultivation. Strain LAMVP1 was grown at 37°C to an OD600 of 1.0, and then 50-fold diluted into fresh MV-5 medium. For the ‘continuous growth’ design, bacteria were grown in MV-5 containing 2% (reference condition) or 0.66% (test condition) NaCl, and cell cultures with an OD600 of 1.2 at the middle exponential phase were harvested for RNA isolation.
Gene expression profiles were compared between reference and test condition. RNA samples were isolated from four individual bacterial cultures, as biological replicates, for each strain. The dual-fluorescently (Cy3 or Cy5 dye) labeled cDNA probes, for which the incorporated dye was reversed, were synthesized from the RNA samples, and then hybridized to four separated microarray slides, respectively.

source_name: LAMVP1,  2%NaCl MV-5 minimal medium, continuous growth, 37°C

value: LAMVP1, reference

source_name: LAMVP1,  0.66%NaCl, MV-5 minimal medium, continuous growth, 37°C

value: LAMVP1, test


title: P1 lung, total RNA, biological replicate 2


title: Bt_Ctrl_K7

tag: Male beef cattle, UNTREATED CONTROL


title: PRB12534 Jurkat

description: PRB12534 Jurkat

source_name: PRB12534 Jurkat


title: P1 lung, polysomal RNA, biological replicate 3


title: FD22 lung, polysomal RNA, biological replicate 1

description: polysome-associated RNA from prenatal saccular lung

source_name: RNA from large polysomes from FD22 rat lung


title: FD22 lung, polysomal RNA, biological replicate 2


title: FD22 lung, polysomal RNA, biological replicate 3


title: FD22 lung, total RNA, biological replicate 1

description: steady-state expression data from prenatal saccular lung

source_name: total RNA from FD22 rat lung


title: FD19 lung, total RNA, biological replicate 2

description: steady-state expression data from canalicular lung

source_name: total RNA from FD19 rat lung


title: FD22 lung, total RNA, biological replicate 2


title: FD19 lung, polysomal RNA, biological replicate 3

description: polysome-associated RNA from canalicular lung

source_name: RNA from large polysomes from FD19 rat lung


title: FD19 lung, total RNA, biological replicate 3


title: FD19 lung, polysomal RNA, biological replicate 1


title: FD19 lung, polysomal RNA, biological replicate 2


title: Mouse_Lung_Saline_14days_C

city: London

first: Chris

last: Scotton

address: 5 University Street

department: Medicine

institute: University College London

description: Total RNA from homogenized mouse lung, 14 days following intratracheal saline administration, analysed using Affymetrix MOE430A GeneChips.

hyb_protocol: Hybridization was performed according to the Affymetrix guidelines, using a GeneChip Fluidics Station 450.

scan_protocol: Scanning was performed according to the Affymetrix guidelines, using a GeneChip Scanner 3000.

data_processing: Processed data provided here are RMA expression values generated using RMAexpress software, with the default parameters (quartiles normalization and median polishing).

source_name: Homogenized mouse lung, 14 days following intratracheal saline administration

label_protocol: cRNA was synthesized using the BioArray High Efficiency RNA Transcript Labeling kit (Enzo Life Sciences, UK) according to the manufacturer's instructions and fragmented prior to microarray analysis.

extract_protocol: Frozen lung tissue was pulverized under liquid nitrogen using a pestle and mortar, then an aliquot of lung powder was immediately placed in Trizol (Invitrogen).  Total RNA was extracted according to the manufacturer's instructions, and DNase-treated using DNAfree kit (Ambion).  RNA quality was assessed using an Agilent Bioanalyser.  Double-stranded cDNA was synthesized using the Superscript Double-Stranded cDNA synthesis kit (Invitrogen, UK) according to the manufacturerâ€™s instructions, except that a T7-(dT)24 oligonucleotide (5'-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGT24-3') was used.

treatment_protocol: Bleomycin (1mg/kg body weight in 50ul of saline) or saline was administered by oropharyngeal installation as described previously by Lakatos et al., Exp Cell Res, 2006, under light halothane-induced anaesthesia. After 14 days, lungs were dissected, then immediately snap frozen in liquid nitrogen and stored at -80degC prior to use.

tag: genotype

value: wildtype

tag: gender

value: male

tag: age

value: 8-10 weeks

tag: tissue

value: lung

tag: treatment

value: saline


title: PVY_vs_Mock_rep1

city: Madrid

first: Francisco

last: Tenllado

state: Madrid

address: Ramiro de Maeztu, 9

department: Plant Biology

country: Spain

institute: Centro de Investigaciones Biológicas, CSIC

description:
4 week old plants were mock inoculated by rubbing sap from healthy plants
4 week old plants were inoculated by rubbing Potato virus Y (PVY) infected plant sap onto leaves dusted with carborundum powder

hyb_protocol: 300 pmol of dye of each aRNA labeled with either Cy3 or Cy5, were mixed with 20 µg of poly(A) and 20 µg of yeast tRNA (Sigma-Aldrich) in a volume of 7 µL. To this volume, 1 µL of RNA fragmentation buffer was added (RNA fragmentation reagents; Ambion) and after 15 min at 70°C, 1 µL of stop solution. Slides were prehybridized in 6x SSC, 0.5% SDS (w/v), and 1% BSA (w/v) at 42°C for 30 min, followed by five rinses with milliQ water. Excess water was drained with a 2000-rpm spin for 2 min. Formamide, 20x SSC, 50x Denhardt's, and 20% SDS were added to a final concentration of 50% formamide, 6x SSC, 5x Denhardt's, and 0.5% SDS. This mix was boiled for 3 min at 95°C and then added to the prehybridized slide. Hybridization took place overnight at 37°C in a hybridization chamber. Arrays were then washed for 5 min at 37°C in 0.5x SSC and 0.1% SDS, twice for 5 min at room temperature (21°C) with 0.5x SSC and 0.1% SDS, three times with 0.5x SSC at room temperature, and 5 min with 0.1x SSC. The slides were drained with a 2000-rpm spin for 2 min and stored in darkness until they were scanned.

scan_protocol: The slides were scanned with a GenePix 4000B scanner and the images were quantified with GenePix Pro 5.1 software (Molecular Devices).

data_processing: Data processing was carried-out using the LIMMA package (Smyth, 2003) of Bioconductor project. Raw intensities were background-substracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were then normalized by LOWESS algorithm (intra-arrays normalization) followed by adjustment of their quantiles (inter-arrays normalization).

organism: Nicotiana benthamiana

source_name: mock inoculated plants

label_protocol: RNA was amplified with the MessageAmp II aRNA amplification kit (Ambion, Inc, Austin, USA) as described in the instruction manual. Aminoallyl UTP was added to the mix of the T7 RNA polymerase-driven aRNA amplification reaction. The amount of aRNA was quantified with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). aRNA quality was assessed with a 2100 Bioanalyzer (Agilent Technologies).The aminoallyl-labeled aRNA (10 µg) was incubated in 1 M Na2CO3 with 8 nmol of dye monofunctional NHS ester (Cy3/Cy5) RPN 5661 (Amersham Biosciences) at room temperature in the dark for 1 h. 35 µL of 0.1 M sodium acetate, pH 5.2, was added and incubated for 5 min in the dark. The Cy-labeled aRNA was purified with the Megaclear kit (Ambion, Inc, Austin, USA) and measured with the Nanodrop ND-1000 spectrophotometer.

growth_protocol: Grown in soil in growth chamber using 16 h period of light (25±2°C) and 8 h of darkness (22±1°C), light intensity 70-90 mmol m-2 s-2 , 65±2 % humidity

extract_protocol: Three leaves from each of five plants per treatment were harvested and immediately frozen in liquid N2. Total RNA was extracted with Trizol reagent, followed by purification with RNeasy midiprep columns (Qiagen).

treatment_protocol: Samples (pooled systemic leaves) were collected at 6 days post inoculation.

value: leaves

tag: disease state

value: healthy

source_name: plants infected with Potato virus Y (PVY)

value: upper leaves

value: symptomatic


title: PVX+PVY_vs_Mock_rep1

description:
4 week old plants were mock inoculated by rubbing sap from healthy plants
4 week old plants were inoculated by rubbing PVX+PVY infected plant sap onto leaves dusted with carborundum powder

source_name: plants infected with PVX plus PVY


title: Mouse_Lung_Bleomycin_14days_E

description: Total RNA from homogenized mouse lung, 14 days following intratracheal Bleomycin administration, analysed using Affymetrix MOE430A GeneChips.

source_name: Homogenized mouse lung, 14 days following intratracheal Bleomycin administration

extract_protocol: Frozen lung tissue was pulverized under liquid nitrogen using a pestle and mortar, then an aliquot of lung powder was immediately placed in Trizol (Invitrogen).  Total RNA was extracted according to the manufacturer's instructions, and DNase-treated using DNAfree kit (Ambion).  RNA quality was assessed using an Agilent Bioanalyser.  Double-stranded cDNA was synthesized using the Superscript Double-Stranded cDNA synthesis kit (Invitrogen, UK) according to the manufacturer’s instructions, except that a T7-(dT)24 oligonucleotide (5'-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGT24-3') was used.

value: Bleomycin


title: Mouse_Lung_Bleomycin_14days_D


title: Mouse_Lung_Saline_14days_A

extract_protocol: Frozen lung tissue was pulverized under liquid nitrogen using a pestle and mortar, then an aliquot of lung powder was immediately placed in Trizol (Invitrogen).  Total RNA was extracted according to the manufacturer's instructions, and DNase-treated using DNAfree kit (Ambion).  RNA quality was assessed using an Agilent Bioanalyser.  Double-stranded cDNA was synthesized using the Superscript Double-Stranded cDNA synthesis kit (Invitrogen, UK) according to the manufacturer’s instructions, except that a T7-(dT)24 oligonucleotide (5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGT24-3') was used.


title: PVX+PVY_vs_Mock_rep3


title: PVX_vs_Mock_rep2

description:
4 week old plants were mock inoculated by rubbing sap from healthy plants
4 week old plants were inoculated by rubbing Potato virus X (PVX) infected plant sap onto leaves dusted with carborundum powder

source_name: plants infected with Potato virus X (PVX)


title: PVX+PVY_vs_Mock_rep2


title: PVY_vs_Mock_rep2


title: PVX_vs_Mock_rep3


title: Mouse_Lung_Bleomycin_14days_F


title: PVY_vs_Mock_rep3


title: FD22 lung, total RNA, biological replicate 3


title: Mouse_Lung_Saline_14days_B


title: PVX_vs_Mock_rep1


title: Cisplatin 12h1

status: Public on Jul 06 2009

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

institute: Candiolo Cancer Institute, University of Torino

description: Cells  Treated with Cisplatin for 12h

hyb_protocol: 0.85 microgram of biotin-labeled cRNA was hybridized to Illumina Human_RefSeq-8V2 BeadChips at 55 °C overnight. BeadChips were incubated with Cy3 streptavidin and washed according to the manufacturer’s protocol.

scan_protocol: The hybridized BeadChips were scanned by Illumina BeadScan confocal scanner and analyzed by Illumina's BeadStudio version 1.5.1.3

label_protocol: Five hundred ng of total RNA was reverse transcribed and amplified overnight with T7 RNA polymerase and labeled with biotin following the manufacturer’s protocol.

growth_protocol: HT1080 cells were grown in DMEM supplemented with 4mM glutamine, penicillin  streptomicyn, and 10%FBS (complete growth medium)

extract_protocol: RNA extraction was performed using Trizol plus RNA purification kit (Invitrogen). RNA qualitative and quantitative assessment was performed using the Bioanalyzer 2100 (Agilent Tecnologies).

treatment_protocol: Cells were incubated in complete growth medium supplemented with cisplatin or A0, 25µM, for the indicated times.

tag: fibrosarcoma cell line


title: Noninfected monkey brain Rep. 3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description:
- RNA quality control with Agilent Bioanalyzer 2100
- Dye incorporation with NanoDrop ND-1000
Keywords = BSE miRNA

hyb_protocol: - hybridization according to Agilent 60-mer oligo microarray processing protocol v2.1 with the following modifications: 600 nano gram labeled DNA were denatured for 3 min at 70 degree celcius hybridisation at 58 degree celcius SSPE washes as recommended

scan_protocol: - scanned with a G2505B Microarray Scanner (Agilent Technologies) - quantification software: 'Automic Imageprocessing for Microarrays' (for details: http://www.techfak.uni-bielefeld.de/ags/ai/projects/microarray/)

data_processing:
- Normalization of the log2(cy5)-values with quantile normalization
- as statistical software we use 'R'

organism: Macaca mulatta

source_name: non-infected monkeys

label_protocol: 2 µg of the enriched miRNA preparation was polyudenylated using equal amounts of UTP and aminoallyl-UTP (Biozym, Hamburg, Germany) with poly(A) polymerase (Epicentre Biotechnologies, Madison, Wisconsin) for 2 h at 37°C. Polyudenylated miRNAs were recovered by Ethanol/NaAcetat precipitation and labeled with fluorescent dye DY647 (MoBiTec, Göttingen, Germany), respectively, in 100 mM NaCO_3 -buffer, pH 9.5 for 2 h in the dark. After an additional precipitation step, samples were resuspended in RNase-free ddH_2 O and were frozen at -20°C before further use.

extract_protocol: small fraction RNA isolation (mirVana miRNA-isolation kit, Ambion) according to the manufactures standard protocol

tag: Brain section (basis pontis) of non-infected monkeys


title: Cisplatin 3h2

description: Cells  Treated with Cisplatin for 3h

data_processing: analyzed by Illumina's BeadStudio version 1.5.1.3


title: Cisplatin 12h2

description: Cells  Treated with Cisplatin for 12h


title: A0 12h2

description: Cells  Treated with A0 for 12h


title: Noninfected monkey brain Rep. 2


title: Cisplatin 6h2

description: Cells  Treated with Cisplatin for 6h


title: Cisplatin 3h1

description: Cells  Treated with Cisplatin for 3h


title: 24 hrs after the third OVA challenge Lung tissue Group3_3

city: Budapest

first: Gergely

last: Tolgyesi

address: Nagyvarad ter 4

country: Hungary

institute: Semmelweis University Budapest

description: This is the third sample of the four biological replicates, belonging to group3

hyb_protocol: Agilent dual color protocol version 5.5

scan_protocol: Agilent microarray scanner default setting for 4x44k dual color microarray

data_processing:
Data were normalised by Agilent Feature Extraction 7.5
Value is normalized log10Ratio, default Per Spot and Per Chip: Intensity dependent (Lowess) normalization

source_name: Placebo treated control pool (Cy3)

label_protocol:
Agilent dual color microarray protocol version 5.5
Data normalisation by Agilent Feature Extraction 7.5

extract_protocol:
Qiagen RNeasy kit
Quality controlled by Agilent bioanalyzer

tag: Balb/c mice  placebo challenged control lung tissue

molecule: polyA RNA

source_name: OVA challenged mice

tag: Balb/c mice treated and challenged with OVA lung tissue RNA

value: 24 hours after the third OVA allergen challenge (day31), after the AHR measurement


title: Cisplatin 6h1

description: Cells  Treated with Cisplatin for 6h


title: 24 hrs after the third OVA challenge Lung tissue Group3_5

description: This is the fifth sample of the four biological replicates, belonging to group3


title: 24 hrs after the third OVA challenge Lung tissue Group3_2

description: This is the second sample of the four biological replicates, belonging to group3