title: Sarcoma tumor PT146MRC

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT144MRC

status: Public on Jul 06 2010

type: genomic

city: New York

first: Barry

middle: Stephen

last: Taylor

state: NY

address: 1275 York Avenue, Box #460

country: USA

institute: Memorial Sloan-Kettering Cancer Center

description: Hybridized to 250K_Sty

hyb_protocol: Per manufacturer's instructions

scan_protocol: After hybridization, arrays were washed with Affymetrix fluidics station and scanned with the Gene Chip Scanner 3000 7G and Affymetrix Genotyping Tools Version 2.0

data_processing:
Signal instensities were were quantified and normalized with the Affymetrix Chromosomal Copy Number Analysis Tool (CNAT 4.0, 1.5.6_v3.1) and copy number was converted to tumor-to-normal log2 ratios using the algorithm described in Taylor BS, et al PLoS ONE 2008; 3(9):e3179. Cell line signal intensities were normalized to a baseline array with median intensity and quantile normalization in GenePattern based on the dChipSNP algorithm. SNP-level inteisities were obtained for these using the model-based PM/MM method. Data from each were compared to data from 1800 normal datasets, and the 5 normal samples with noise profiles most similar to each cell line were used to determine log2 ratios at each SNP locus.
The normalized tumor/normal ratio data described above are presented in the Sample data tables of the Tumor sample (normal Samples therefore do not have data tables).  The matrix of ratio data is also available as a text file on the Series record.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: tumor DNA

label_protocol: PCR projects, after pooling, concentration, and fragmentation with Dnase I were labeled and denatured as per manufacturer's instructions with Bioprime Array CHG labeling kit (Invitrogen) using Cy3/Cy5.

extract_protocol: Genomic DNA was extracted from cyromoled-macrodissected tumor samples and from blood or normal adjacent tissue and digested with the StyI restriction enzyme

tag: tissue

value: Soft-tissue sarcoma

tag: disease status

tag: sample id


title: Sarcoma tumor PT149MRC

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT145MRC

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT142MRC

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT140MRC

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT141MRC

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT138MRC

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT136MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT137MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT160PL

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT157MRC

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT132MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT172PL

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT134MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT131MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT133MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT147MRC

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT124MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT135MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT126MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT125MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT139MRC

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT128MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT123MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT116MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT130MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT121MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT115MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT129MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT104MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT114MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT102MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT101MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT111MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT122MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT118MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT103MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT108MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT117MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT106MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT96LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT107MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT113MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT100MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT119MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT150MRC

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT112MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT105MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT110MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT109MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT98LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT93LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT95LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT92LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT94LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT99LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT120MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT91LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT127MF

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT97LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT88LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT85LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT83LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT84LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT87LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT90LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT75LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT80LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT89LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT81LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT77LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT79LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT73LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT74LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT78LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT72GT

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT86LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT70GT

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT82LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT76LMS

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT63GT

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT61GT

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT59GT

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT64GT

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT69GT

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT62GT

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT71GT

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT60GT

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT66GT

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT67GT

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT56GT

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT57GT

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT65GT

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT54GT

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT52GT

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT51GT

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT37DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT50DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT42DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT40DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT48DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT39DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT43DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT35DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT58GT

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT41DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT55GT

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT44DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT38DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT49DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT68GT

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT33DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT53GT

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT46DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT32DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT47DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT31DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT36DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT25DD

description: Hybridized to 250K_Sty


title: Biofilm_South_Saskatchewan_River_Sulfamethazine_rep3

type: mixed

city: Montreal

first: Etienne

last: Yergeau

state: Qc

address: 6100 Royalmount Ave

department: Environmental Microbiology

country: Canada

institute: NRC-BRI

hyb_protocol: The whole cDNA labelling reaction was dried and resuspended in 45µL DIG Easy Hyb hybridization buffer (Roche Diagnostics, Laval, QC, Canada) and mixed with 500ng of labelled composite DNA (in 45 µL of DIG buffer). This mixture was denatured at 95°C for 2 min and hybridized to the microarray slides for 16h at 50°C on a Slide Booster apparatus (Advalytix-Beckman Coulter, Munich, Germany). The slides were washed three times in 0.1X SSC and 0.1% SDS for 5 min at 42°C, rinsed three times in 0.1X SSC and dried with filtered nitrogen.

scan_protocol: The slides were scanned in a ScanArray Lite (Perkin Elmer, Boston, MA) at a 10 µm resolution. The resulting image files were gridded and quantified using ScanArray Express.

data_processing: Text files containing quantitative data were imported in the R package (v. 2.9.0, The R Foundation for Statistical Computing) and normalized using the “limma” package. The spot intensities were corrected for background using the “backgroundCorrect” function with the “normexp” method. Spot intensities were normalized within each array using the “normalizeWithinArrays” function with the “loess” method. Spot log-ratios were then normalized between arrays using the “normalizeBetweenArrays” function with the “Gquantile” method. The resulting normalized A-matrix (average log-2 expression values) was then exported to Excel where duplicate probes values were averaged. This matrix was used in further statistical analyses.

molecule: total RNA

organism: environmental samples

source_name: Reactor grown biofilm, 0.5 µg/L sulfamethazine

label_protocol: mRNA was enriched using the MicrobExpress kit (Ambion, Austin, TX), amplified using the MessageAmp II kit (Ambion) and labelled with Cy3 dyes (GE Healthcare, Piscataway, NJ) using the Amino Allyl cDNA Labelling Kit (Ambion). The composite DNA sample (see below) was labelled with Cy5 using the BioPrime Array CGH Genomic Labelling kit (Invitrogen, Carlsbad, CA).

growth_protocol: The reactor design for biofilm development has been previously described (Lawrence et al., 2004; Lawrence et al., 2000). Two duplicate experiments were carried out, with reactors being inoculated with either water from the WC (nutrient rich) or the SSR (nutrient poor). Treatments consisted in the addition of various pharmaceutical compounds: 1 µg l-1 erythromycin (ER), 1 µg l-1 gemfibrozil (GM), 0.5 µg l-1 sulfamethazine (SN), 0.5 µg l-1 sulfamethoxazole (SL). Nothing was added to control reactors (CO).

extract_protocol: Total DNA and RNA were simultaneously extracted from 250-500 mg biofilm subsamples using bead beating in a CTAB buffer followed by phenol-chloroform purification (Yergeau et al., 2007; Yergeau and Kowalchuk, 2008). Nucleic acids were resuspended in 100 µl DEPC-water and separated in two 50µl parts. One part was treated with RNAse A to give DNA and the other was treated with DNAse to give RNA.

treatment_protocol: 0.5 µg/L sulfamethazine

tag: geographical region

value: South Saskatchewan River, Saskatoon, SK, Canada

source_name: Total DNA pooled from the 33 biofilm samples from Wascana Creek

value: Wascana Creek, Regina, SK, Canada


title: Biofilm_South_Saskatchewan_River_Sulfamethazine_rep2


title: Sarcoma tumor PT23DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT26DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT28DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT45DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT27DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT34DD

description: Hybridized to 250K_Sty


title: Biofilm_South_Saskatchewan_River_Sulfamethoxazole_rep3

source_name: Reactor grown biofilm, 0.5 µg/L sulfamethoxazole

treatment_protocol: 0.5 µg/L sulfamethoxazole


title: Sarcoma tumor PT30DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT29DD

description: Hybridized to 250K_Sty


title: Biofilm_South_Saskatchewan_River_Gemfibrozil_rep1

source_name: Reactor grown biofilm, 1 µg/L gemfibrozil

treatment_protocol: 1 µg/L gemfibrozil


title: Biofilm_South_Saskatchewan_River_Erythromycin_rep3

source_name: Reactor grown biofilm, 1 µg/L erythromycin

treatment_protocol: 1 µg/L erythromycin


title: Biofilm_South_Saskatchewan_River_Gemfibrozil_rep2


title: Biofilm_South_Saskatchewan_River_Sulfamethoxazole_rep2


title: Biofilm_South_Saskatchewan_River_Control_rep3

source_name: Reactor grown biofilm, control

treatment_protocol: control


title: Biofilm_South_Saskatchewan_River_Control_rep2


title: Biofilm_South_Saskatchewan_River_Control_rep1


title: Sarcoma tumor PT12DD

description: Hybridized to 250K_Sty


title: Biofilm_South_Saskatchewan_River_Gemfibrozil_rep3


title: Biofilm_South_Saskatchewan_River_Erythromycin_rep1


title: Biofilm_South_Saskatchewan_River_Erythromycin_rep2


title: Biofilm_South_Saskatchewan_River_Sulfamethoxazole_rep1


title: Sarcoma tumor PT15DD

description: Hybridized to 250K_Sty


title: Biofilm_Wascana_Creek_Sulfamethazine_rep2


title: Biofilm_Wascana_Creek_Sulfamethazine_rep3


title: Sarcoma tumor PT2DD

description: Hybridized to 250K_Sty


title: Biofilm_South_Saskatchewan_River_Sulfamethazine_rep1


title: Sarcoma tumor PT13DD

description: Hybridized to 250K_Sty


title: tumor T30_Hpa2_Sty

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

description: Hybridized to 250K_Sty

hyb_protocol: DNA was restric digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The array were then washed using Affymetrix fluidics stations, and scanned usingthe Affymetrix GeneChip Scanner 3000.

data_processing: The probe level measurements (PM and MM) were generated using Affymetrix Gtype software. Microarray data were normalized using a modified RMA method.

label: Biotin

source_name: micro-dissected tumor tissue

label_protocol: As per manufacturer (Affymetrix).

extract_protocol: Germline DNA was extracted and purified using standard methods and microdisected DNA was followed the ptotocol from Puregene DNA purification Tissue Kit (Gentra System Inc).

value: esophageal squamous cell carcinoma

tag: digestion enzyme

value: Hpa II


title: Biofilm_Wascana_Creek_Sulfamethazine_rep1


title: Biofilm_Wascana_Creek_Sulfamethoxazole_rep2


title: tumor T28_Hpa2_Sty

description: Hybridized to 250K_Sty


title: tumor T26_Hpa2_Sty

description: Hybridized to 250K_Sty


title: Biofilm_Wascana_Creek_Gemfibrozil_rep3


title: tumor T24_Hpa2_Sty

description: Hybridized to 250K_Sty


title: Biofilm_Wascana_Creek_Sulfamethoxazole_rep3


title: Sarcoma tumor PT10DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT1DD

description: Hybridized to 250K_Sty


title: tumor T27_Hpa2_Sty

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT5DD

description: Hybridized to 250K_Sty


title: tumor T23_Hpa2_Sty

description: Hybridized to 250K_Sty


title: Biofilm_Wascana_Creek_Gemfibrozil_rep2


title: tumor T29_Hpa2_Sty

description: Hybridized to 250K_Sty


title: Biofilm_Wascana_Creek_Sulfamethoxazole_rep1


title: tumor T25_Hpa2_Sty

description: Hybridized to 250K_Sty


title: tumor T22_Hpa2_Sty

description: Hybridized to 250K_Sty


title: tumor T20_Hpa2_Sty

description: Hybridized to 250K_Sty


title: tumor T21_Hpa2_Sty

description: Hybridized to 250K_Sty


title: Biofilm_Wascana_Creek_Erythromycin_rep3


title: Biofilm_Wascana_Creek_Gemfibrozil_rep1


title: tumor T17_Hpa2_Sty

description: Hybridized to 250K_Sty


title: Biofilm_Wascana_Creek_Erythromycin_rep1


title: tumor T15_Hpa2_Sty

description: Hybridized to 250K_Sty


title: tumor T16_Hpa2_Sty

description: Hybridized to 250K_Sty


title: Biofilm_Wascana_Creek_Control_rep3


title: Biofilm_Wascana_Creek_Erythromycin_rep2


title: tumor T14_Hpa2_Sty

description: Hybridized to 250K_Sty


title: Biofilm_Wascana_Creek_Control_rep2


title: tumor T11_Hpa2_Sty

description: Hybridized to 250K_Sty


title: tumor T10_Hpa2_Sty

description: Hybridized to 250K_Sty


title: tumor T6_Hpa2_Sty

description: Hybridized to 250K_Sty


title: Biofilm_Wascana_Creek_Control_rep1


title: tumor T7_Hpa2_Sty

description: Hybridized to 250K_Sty


title: tumor T3_Hpa2_Sty

description: Hybridized to 250K_Sty


title: tumor T5_Hpa2_Sty

description: Hybridized to 250K_Sty


title: tumor T9_Hpa2_Sty

description: Hybridized to 250K_Sty


title: tumor T2_Hpa2_Sty

description: Hybridized to 250K_Sty


title: normal N28_Hpa2_Sty

description: Hybridized to 250K_Sty

source_name: micro-dissected adjacent normal tissue

value: epithelium


title: Sarcoma tumor PT14DD

description: Hybridized to 250K_Sty


title: tumor T1_Hpa2_Sty

description: Hybridized to 250K_Sty


title: normal N25_Hpa2_Sty

description: Hybridized to 250K_Sty


title: normal N26_Hpa2_Sty

description: Hybridized to 250K_Sty


title: normal N19_Hpa2_Sty

description: Hybridized to 250K_Sty


title: normal N22_Hpa2_Sty

description: Hybridized to 250K_Sty


title: normal N21_Hpa2_Sty

description: Hybridized to 250K_Sty


title: normal N27_Hpa2_Sty

description: Hybridized to 250K_Sty


title: Stau2 replicate 5

type: other

city: Montréal

first: Luc

last: DesGroseillers

state: Québec

address: 2900 Edouard Montpetit

department: Biochimie

institute: Université de Montréal

description: Brains were homogenized and cell extracts were immunoprecipitated using anti-Stau2 antibody and co-IPed mRNAs were purified.

hyb_protocol: Standard Illumina procedure

scan_protocol: Hybridized chips were scanned using an Illumina iScan System. Results were recorded using the BeadStudio software platform.

data_processing: Data were processed with the FlexArray 1.2 software. RMA background adjustment was performed but no normalization was done. Variance stabilization: log base2. Data were analyzed by t-test (equal-variance t-statistic). To identify mRNAs that specifically copurify with Staufen2, signal intensities obtained for specific IPs were compared with the baseline signal intensities of control IPs using the FlexArray 1.2 software. Each probe set presenting a fold enrichment over control of more than 8 (p value < 0.002) was scored as a potential Staufen2-associated mRNA.

molecule: other

organism: Rattus norvegicus

source_name: P18 embryonic brain from Sprague-Dawley rats.

label_protocol: Illumina® TotalPrep™ RNA Amplification Kit from Ambion

extract_protocol: TriZol reagent

treatment_protocol: Immunoprecipitation was performed on cell extracts prepared from whole brains of E17-E18 Sprague Dawley rat embryos. Cells were dissociated with a manual putter and lysed in 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 0.5% Triton X-100, 15 mM EGTA, 1 mM DTT and complete EDTA-free protease inhibitor cocktail (Roche). Cell lysates were centrifuged at 10 000 rpm for 10 min. After centrifugation, the supernatants were incubated with a rabbit anti-Stau2 antibody for 2 hours at 4°C, then with a 50% protein A-sepharose slurry for 2 hours at 4°C. Immune complexes were washed five times with the lysis buffer and eluted from the resin by heating at 95°C for 5 minutes in elution buffer (100 mM Tris-HCl pH 7.4, 200 mM DTT and 4% SDS). RNAs were isolated by Trizol (Invitrogen) extraction.

value: P18 embryonic brain

tag: strain

value: Sprague-Dawley rats.


title: normal N17_Hpa2_Sty

description: Hybridized to 250K_Sty


title: normal N18_Hpa2_Sty

description: Hybridized to 250K_Sty


title: normal N23_Hpa2_Sty

description: Hybridized to 250K_Sty


title: normal N16_Hpa2_Sty

description: Hybridized to 250K_Sty


title: normal N20_Hpa2_Sty

description: Hybridized to 250K_Sty


title: tumor T12_Hpa2_Sty

description: Hybridized to 250K_Sty


title: Ctrl 5

description: Brains were homogenized and cell extracts were immunoprecipitated using preimmune antibody and co-IPed mRNAs were purified.

treatment_protocol: Control immunoprecipitation was performed on cell extracts prepared from whole brains of E17-E18 Sprague Dawley rat embryos. Cells were dissociated with a manual putter and lysed in 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 0.5% Triton X-100, 15 mM EGTA, 1 mM DTT and complete EDTA-free protease inhibitor cocktail (Roche). Cell lysates were centrifuged at 10 000 rpm for 10 min. After centrifugation, the supernatants were incubated with a rabbit preimmune antibody for 2 hours at 4°C, then with a 50% protein A-sepharose slurry for 2 hours at 4°C. Immune complexes were washed five times with the lysis buffer and eluted from the resin by heating at 95°C for 5 minutes in elution buffer (100 mM Tris-HCl pH 7.4, 200 mM DTT and 4% SDS). RNAs were isolated by Trizol (Invitrogen) extraction.


title: tumor T19_Hpa2_Sty

description: Hybridized to 250K_Sty


title: tumor T18_Hpa2_Sty

description: Hybridized to 250K_Sty


title: tumor T13_Hpa2_Sty

description: Hybridized to 250K_Sty


title: normal N14_Hpa2_Sty

description: Hybridized to 250K_Sty


title: Ctrl 4


title: Stau2 replicate 4


title: normal N13_Hpa2_Sty

description: Hybridized to 250K_Sty


title: Stau2 replicate 3

description: Brains were homogenized and cell extracts were immunoprecipitated using anti-Staufen2 antibody and co-IPed mRNAs were purified.


title: Ctrl 3


title: normal N24_Hpa2_Sty

description: Hybridized to 250K_Sty


title: normal N12_Hpa2_Sty

description: Hybridized to 250K_Sty


title: tumor T8_Hpa2_Sty

description: Hybridized to 250K_Sty


title: normal N11_Hpa2_Sty

description: Hybridized to 250K_Sty


title: tumor T4_Hpa2_Sty

description: Hybridized to 250K_Sty


title: 3h-MAA 5mM/3h-Control mouse TM3 cells/Replicate #2

type: RNA

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: The RNA expression profile for TM3 cell culture pool (n=3)) treated with 5mM MAA for 3hr  and untreated TM3 cells in duplicate wells (n=3) is given as a normalized ratio.

hyb_protocol: Hybridization was performed using 0.825 µg of Alexa 555-labeled aRNA and 0.825 µg of Alexa 647-labeled aRNA. Agilent’s SureHyb hybridization chambers were used in a hybridization oven and rotation rack for 17 hr at 65° C at 10 rpm. After hybridization, the slides were washed per Agilent’s SSPE wash protocol.

scan_protocol: Slides were scanned using an Agilent dual laser scanner using the extended dynamic range option, which utilizes two 5 um scans of each slide at settings of PMT 100% and PMT 10% to increase signal dynamic range and avoid feature saturation. TIFF images were analyzed using Agilent’s feature extraction software (version 9.5.3, protocol GE2-v5_91_0806).

data_processing: Linear and LOWESS normalization as determined using Agilent's Feature Extraction software

label: Alexa 647

organism: Mus musculus

source_name: TM3 Leydig cells, MAA-treated

label_protocol: RNA samples were amplified as antisense-RNA (aRNA) while incorporating aminoallyl modified bases using the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 per the vendor’s protocol (Epicentre, Madison, WI).  Five µg of each aminoallyl-aRNA sample was fluorescent labeled using Alexa 555 or Alexa 647 by incubating with an amine-reactive dye conjugate for 1 hr at room temperature.  Unincorporated dye was removed using an RNeasy column (Qiagen, Valencia, CA).  Dye incorporation efficiency was determined using a Nanodrop spectrophotometer.

extract_protocol: Trizol extraction of RNA

tag: cell line

value: TM3 Leydig cell

value: Testis

tag: agent

value: MAA

tag: dose

tag: time

label: Alexa 555

source_name: TM3 Leydig cells, control

value: Control


title: 24h-MAA 5mM/24h-Control mouse TM3 cells/Replicate #2

description: The RNA expression profile for TM3 cell culture pool (n=3)) treated with 5mM MAA for 24hr  and untreated TM3 cells in duplicate wells (n=3) is given as a normalized ratio.


title: normal N4_Hpa2_Sty

description: Hybridized to 250K_Sty


title: Ctrl 6


title: 8h-MAA 1mM/8h-Control mouse TM3 cells/Replicate #2

description: The RNA expression profile for TM3 cell culture pool (n=3)) treated with 1mM MAA for 8hr  and untreated TM3 cells in duplicate wells (n=3) is given as a normalized ratio.


title: normal N5_Hpa2_Sty

description: Hybridized to 250K_Sty


title: Stau2 replicate 1

treatment_protocol: Immunoprecipitation was performed on cell extracts prepared from whole brains of E17-E18 Sprague Dawley rat embryos. Cells were dissociated with a manual putter and lysed in 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 0.5% Triton X-100, 15 mM EGTA, 1 mM DTT and complete EDTA-free protease inhibitor cocktail (Roche). Cell lysates were centrifuged at 10 000 rpm for 10 min. After centrifugation, the supernatants were incubated with a rabbit anti-Staufen2 antibody for 2 hours at 4°C, then with a 50% protein A-sepharose slurry for 2 hours at 4°C. Immune complexes were washed five times with the lysis buffer and eluted from the resin by heating at 95°C for 5 minutes in elution buffer (100 mM Tris-HCl pH 7.4, 200 mM DTT and 4% SDS). RNAs were isolated by Trizol (Invitrogen) extraction.


title: normal N30_Hpa2_Sty

description: Hybridized to 250K_Sty


title: normal N8_Hpa2_Sty

description: Hybridized to 250K_Sty


title: normal N6_Hpa2_Sty

description: Hybridized to 250K_Sty


title: Ctrl1

description: Brains were homogenized and cell extracts were immunoprecipitated using pre-immune antibody and co-IPed mRNAs were purified.


title: blood B30_Hpa2_Sty

description: Hybridized to 250K_Sty

source_name: venous blood

value: blood


title: normal N15_Hpa2_Sty

description: Hybridized to 250K_Sty


title: normal N2_Hpa2_Sty

description: Hybridized to 250K_Sty


title: normal N1_Hpa2_Sty

description: Hybridized to 250K_Sty


title: blood B28_Hpa2_Sty

description: Hybridized to 250K_Sty


title: normal N10_Hpa2_Sty

description: Hybridized to 250K_Sty


title: Stau2

source_name: Embryonic brain

treatment_protocol: Immunoprecipitation of Staufen2-containing mRNPs was performed on cell extracts prepared from whole brains of E17-E18 Sprague Dawley rat embryos. Cells were dissociated with a manual putter and lysed in 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 0.5% Triton X-100, 15 mM EGTA, 1 mM DTT and complete EDTA-free protease inhibitor cocktail (Roche). Cell lysates were centrifuged at 10 000 rpm for 10 min. After centrifugation, the supernatants were incubated with a rabbit polyclonal anti-Staufen2 antibodies for 2 hours at 4°C, then with a 50% protein A-sepharose slurry for 2 hours at 4°C. Immune complexes were washed five times with the lysis buffer and eluted from the resin by heating at 95°C for 5 minutes in elution buffer (100 mM Tris-HCl pH 7.4, 200 mM DTT and 4% SDS). RNAs were isolated by Trizol (Invitrogen) extraction.


title: 8h-MAA 5mM/8h-Control mouse TM3 cells/Replicate #1

description: The RNA expression profile for TM3 cell culture pool (n=3)) treated with 5mM MAA for 8hr  and untreated TM3 cells in duplicate wells (n=3) is given as a normalized ratio.


title: blood B29_Hpa2_Sty

description: Hybridized to 250K_Sty


title: Ctrl 2


title: normal N3_Hpa2_Sty

description: Hybridized to 250K_Sty


title: blood B27_Hpa2_Sty

description: Hybridized to 250K_Sty


title: 8h-MAA 1mM/8h-Control mouse TM3 cells/Replicate #1


title: blood B26_Hpa2_Sty

description: Hybridized to 250K_Sty


title: blood B25_Hpa2_Sty

description: Hybridized to 250K_Sty


title: 24h-MAA 1mM/24h-Control mouse TM3 cells/Replicate #2

description: The RNA expression profile for TM3 cell culture pool (n=3)) treated with 1mM MAA for 24hr  and untreated TM3 cells in duplicate wells (n=3) is given as a normalized ratio.


title: 3h-MAA 1mM/3h-Control mouse TM3 cells/Replicate #2

description: The RNA expression profile for TM3 cell culture pool (n=3)) treated with 1mM MAA for 3hr  and untreated TM3 cells in duplicate wells (n=3) is given as a normalized ratio.


title: blood B22_Hpa2_Sty

description: Hybridized to 250K_Sty


title: normal N29_Hpa2_Sty

description: Hybridized to 250K_Sty


title: 3h-MAA 5mM/3h-Control mouse TM3 cells/Replicate #1


title: 24h-MAA 1mM/24h-Control mouse TM3 cells/Replicate #1


title: blood B23_Hpa2_Sty

description: Hybridized to 250K_Sty


title: normal N9_Hpa2_Sty

description: Hybridized to 250K_Sty


title: 24h-MAA 5mM/24h-Control mouse TM3 cells/Replicate #1


title: normal N7_Hpa2_Sty

description: Hybridized to 250K_Sty


title: blood B18_Hpa2_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample327

city: Oslo

first: Hans Kristian

middle: Moen

last: Vollan

address: Ullernschausseen 100

department: Dept of genetics

country: Norway

institute: The norwegian Radium Hospital

hyb_protocol: Cot-1 DNA, Agilent blocking agent and Hybridization buffer were added to the Cy3 and Cy5 labeled gDNA mix. Hybridization to microarray rotating in a hybridization oven at 65ºC for 40 hrs.

scan_protocol: Washing of microarrays with Agilent wash buffer 1 and 2, followed by acetonitrile and Agilent Stabilization and Drying Solution. Images scanned with Agilent Microarray Scanner, G2565CA.

data_processing: Data processed with Agilent Feature Extraction v10.1.1 with default settings using protocols CGH-v4_95_Feb07 and CGH-v4_91_2

source_name: Tumor (primary breast cancer)

label_protocol: 1ug of genomic DNA from tumor and reference was digested using AluI and RsaI for 2 hrs on 37ºC and 20 min on 65ºC for inactivation of enzymes. The samples were labeled using Agilent DNA Lebeling Kit PLUS (containing random primers, 10X dNTPs, exo-Klenow-polymerase, buffer and Cy3- and Cy5-dUTPs). Samples labeled with Cy5 and reference with Cy3. Standard protocol was followed.

extract_protocol: DNA was isolated from snap frozen tumor tissue using chloroform/phenol extraction followed by ethanol precipitation (Nucler Acid Extractor 340A; Applied Biosystems, Foster City, CA, USA).

treatment_protocol: No preoperative treatment. Samples collected at time of primary surgery.

tag: gender

value: Female

tag: disease state

value: breast cancer

tag: age at onset (years)

tag: histology

value: Ductal

tag: histologic grade

tag: m-status (0=mx and m0, 1=m1)

tag: pgr-status

source_name: Genomic DNA, Promega

tag: reference

value: Promega pooled female genomic DNA


title: blood B20_Hpa2_Sty

description: Hybridized to 250K_Sty

tag: tissue


title: BreastCancer_Ull-sample328

tag: er-status


title: blood B19_Hpa2_Sty

description: Hybridized to 250K_Sty


title: blood B17_Hpa2_Sty

description: Hybridized to 250K_Sty


title: blood B21_Hpa2_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample329


title: blood B13_Hpa2_Sty

description: Hybridized to 250K_Sty


title: blood B24_Hpa2_Sty

description: Hybridized to 250K_Sty


title: blood B16_Hpa2_Sty

description: Hybridized to 250K_Sty


title: blood B14_Hpa2_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample326


title: 8h-MAA 5mM/8h-Control mouse TM3 cells/Replicate #2


title: BreastCancer_Ull-sample325


title: 3h-MAA 1mM/3h-Control mouse TM3 cells/Replicate #1

description: The RNA expression profile for TM3 cell culture pool (n=3) treated with 1mM MAA for 3hr  and untreated TM3 cells in duplicate wells (n=3) is given as a normalized ratio.


title: Stau2 replicate 2


title: blood B12_Hpa2_Sty

description: Hybridized to 250K_Sty


title: blood B15_Hpa2_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample324


title: blood B11_Hpa2_Sty

description: Hybridized to 250K_Sty


title: tumor T30_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: blood B8_Hpa2_Sty

description: Hybridized to 250K_Sty


title: tumor T26_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample320


title: blood B7_Hpa2_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample321

value: Lobular


title: BreastCancer_Ull-sample319


title: tumor T29_gDNA_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample322


title: blood B5_Hpa2_Sty

description: Hybridized to 250K_Sty


title: blood B6_Hpa2_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample323


title: tumor T29_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: tumor T30_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T28_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: blood B9_Hpa2_Sty

description: Hybridized to 250K_Sty


title: blood B1_Hpa2_Sty

description: Hybridized to 250K_Sty


title: tumor T27_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: blood B4_Hpa2_Sty

description: Hybridized to 250K_Sty


title: tumor T28_gDNA_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample318


title: BreastCancer_Ull-sample317


title: blood B3_Hpa2_Sty

description: Hybridized to 250K_Sty


title: blood B10_Hpa2_Sty

description: Hybridized to 250K_Sty


title: tumor T25_gDNA_Sty

description: Hybridized to 250K_Sty


title: blood B2_Hpa2_Sty

description: Hybridized to 250K_Sty


title: tumor T26_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T27_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T24_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample316


title: tumor T25_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: tumor T23_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T19_gDNA_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample315


title: tumor T22_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T21_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T23_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample312


title: tumor T18_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T17_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T22_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: tumor T21_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: tumor T24_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T15_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T16_gDNA_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample313


title: tumor T11_gDNA_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample310


title: tumor T18_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: tumor T14_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T13_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T20_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample308


title: BreastCancer_Ull-sample309


title: tumor T9_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T8_gDNA_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample314


title: tumor T16_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: tumor T19_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: tumor T4_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T12_gDNA_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample307


title: tumor T10_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T5_gDNA_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample306


title: tumor T20_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T6_gDNA_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample305

tag: tumor cell prct


title: tumor T3_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T14_Hpa2_Nsp

description: Hybridized to 250K_Nsp

tag: digestion enzyme


title: normal N30_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T1_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T2_gDNA_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample304


title: BreastCancer_Ull-sample303


title: tumor T12_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: tumor T11_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: tumor T13_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: normal N26_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T15_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: tumor T17_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: normal N28_gDNA_Sty

description: Hybridized to 250K_Sty


title: normal N27_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T10_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: tumor T7_gDNA_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample300

value: Mixed duct-lob


title: tumor T9_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: normal N29_gDNA_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample299


title: normal N22_gDNA_Sty

description: Hybridized to 250K_Sty


title: normal N24_gDNA_Sty

description: Hybridized to 250K_Sty


title: normal N25_gDNA_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample301


title: BreastCancer_Ull-sample311


title: normal N23_gDNA_Sty

description: Hybridized to 250K_Sty


title: normal N17_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T8_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: normal N20_gDNA_Sty

description: Hybridized to 250K_Sty


title: normal N15_gDNA_Sty

description: Hybridized to 250K_Sty


title: normal N16_gDNA_Sty

description: Hybridized to 250K_Sty


title: normal N21_gDNA_Sty

description: Hybridized to 250K_Sty


title: normal N19_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T5_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: tumor T7_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample297

value: Medullary


title: tumor T4_Hpa2_Nsp

description: Hybridized to 250K_Nsp

value: esophageal squamous cell carcinoma


title: BreastCancer_Ull-sample295


title: BreastCancer_Ull-sample296


title: tumor T3_Hpa2_Nsp

description: Hybridized to 250K_Nsp

value: Hpa II


title: BreastCancer_Ull-sample293


title: normal N14_gDNA_Sty

description: Hybridized to 250K_Sty

value: epithelium


title: BreastCancer_Ull-sample294


title: normal N12_gDNA_Sty

description: Hybridized to 250K_Sty


title: normal N10_gDNA_Sty

description: Hybridized to 250K_Sty


title: normal N18_gDNA_Sty

description: Hybridized to 250K_Sty


title: normal N4_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T2_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: tumor T1_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample292


title: normal N9_gDNA_Sty

description: Hybridized to 250K_Sty


title: normal N13_gDNA_Sty

description: Hybridized to 250K_Sty


title: normal N7_gDNA_Sty

description: Hybridized to 250K_Sty


title: normal N6_gDNA_Sty

description: Hybridized to 250K_Sty


title: normal N3_gDNA_Sty

description: Hybridized to 250K_Sty


title: normal N29_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: normal N30_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: normal N8_gDNA_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample291


title: normal N2_gDNA_Sty

description: Hybridized to 250K_Sty


title: normal N5_gDNA_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample290


title: BreastCancer_Ull-sample288


title: blood B28_gDNA_Sty

description: Hybridized to 250K_Sty


title: blood B29_gDNA_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample289


title: normal N26_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: normal N25_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: normal N28_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: normal N1_gDNA_Sty

description: Hybridized to 250K_Sty


title: blood B30_gDNA_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample287


title: BreastCancer_Ull-sample286


title: normal N24_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: normal N27_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: blood B27_gDNA_Sty

description: Hybridized to 250K_Sty


title: normal N23_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: blood B25_gDNA_Sty

description: Hybridized to 250K_Sty


title: blood B22_gDNA_Sty

description: Hybridized to 250K_Sty


title: blood B21_gDNA_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample284


title: BreastCancer_Ull-sample302


title: normal N21_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: blood B24_gDNA_Sty

description: Hybridized to 250K_Sty


title: blood B20_gDNA_Sty

description: Hybridized to 250K_Sty


title: blood B23_gDNA_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample283

value: Mucinous


title: normal N20_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: normal N22_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: normal N19_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample298


title: BreastCancer_Ull-sample285

value: DCIS


title: BreastCancer_Ull-sample282


title: blood B17_gDNA_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample281


title: normal N18_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: blood B18_gDNA_Sty

description: Hybridized to 250K_Sty


title: blood B14_gDNA_Sty

description: Hybridized to 250K_Sty


title: blood B12_gDNA_Sty

description: Hybridized to 250K_Sty


title: blood B13_gDNA_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample279


title: BreastCancer_Ull-sample280


title: normal N11_gDNA_Sty

description: Hybridized to 250K_Sty


title: tumor T6_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: blood B26_gDNA_Sty

description: Hybridized to 250K_Sty


title: blood B19_gDNA_Sty

description: Hybridized to 250K_Sty


title: normal N16_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: blood B15_gDNA_Sty

description: Hybridized to 250K_Sty


title: blood B16_gDNA_Sty

description: Hybridized to 250K_Sty


title: normal N17_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: blood B11_gDNA_Sty

description: Hybridized to 250K_Sty


title: blood B10_gDNA_Sty

description: Hybridized to 250K_Sty


title: blood B6_gDNA_Sty

description: Hybridized to 250K_Sty


title: leukocytes_day3_rep1

first: Bjørg

last: Mikalsen

address: Sognsveien 20

department: Division of Pathology

institute: Oslo University Hospital

hyb_protocol: Hybridization was performed as described in the protocol from Affymetrix.

scan_protocol: Arrays were scanned in a GeneChip Scanner 3000 (Affymetrix).

data_processing: The data was normalized using robust multi-chip averaging (RMA) with default settings in the Bioconductor affy package (endothelial cell and leukocyte samples separately). Detection p-values were calculated with the 'mas5calls' function using default parameters.

label: biotin

source_name: leukocytes, allograft day 3

label_protocol: Biotinylated cRNA was prepared according to the one-cycle Affymetrix protocol.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit and QIAshredders (Qiagen, UK) as described in the spin protocol.

treatment_protocol: Heart grafts were transplanted into the neck of the recipient using a cuff-based technique. After harvesting, the heart was minced and endothelial cells (EC) enriched using a CD31 antibody (clon 3A12) and MACS beads (Miltenyi). Leukocytes were depleted from the cell suspension before EC enrichment by a CD45 antibody (Ox1 clone) and Dynabeads (Dynal/Invitrogen).

tag: strain

value: Lewis

value: transplanted heart

tag: cell type

value: leukocyte

value: male


title: leukocytes_day4

source_name: leukocytes, allograft day 4


title: blood B7_gDNA_Sty

description: Hybridized to 250K_Sty

value: blood


title: leukocytes_day2

source_name: leukocytes, allograft day 2


title: leukocytes_day3_rep2


title: BreastCancer_Ull-sample277

value: Female


title: blood B4_gDNA_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample274

value: breast cancer


title: blood B8_gDNA_Sty

description: Hybridized to 250K_Sty


title: normal N13_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: isograft_day4_rep2

source_name: endothelial cells, isograft day 4

value: endothelium


title: isograft_day4_rep3


title: blood B5_gDNA_Sty

description: Hybridized to 250K_Sty


title: blood B3_gDNA_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample271

value: Ductal

value: Promega pooled female genomic DNA


title: isograft_day3_rep3

source_name: endothelial cells, isograft day 3


title: blood B1_gDNA_Sty

description: Hybridized to 250K_Sty


title: BreastCancer_Ull-sample278


title: BreastCancer_Ull-sample276


title: normal N11_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: normal N15_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample275


title: normal N14_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: blood B2_gDNA_Sty

description: Hybridized to 250K_Sty


title: isograft_day4_rep1


title: BreastCancer_Ull-sample273


title: BreastCancer_Ull-sample272


title: normal N9_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: normal N12_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: isograft_day3_rep2


title: isograft_control_rep2

source_name: endothelial cells, normal heart

value: normal heart


title: isograft_day2_rep3

source_name: endothelial cells, isograft day 2


title: isograft_control_rep1


title: isograft_day2_rep2


title: normal N7_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: isograft_day2_rep1


title: BreastCancer_Ull-sample270


title: allograft_day4_rep2

source_name: endothelial cells, allograft day 4

value: DA (Dark Agouti)


title: allograft_day4_rep3


title: allograft_day3_rep2

source_name: endothelial cells, allograft day 3


title: normal N10_Hpa2_Nsp

description: Hybridized to 250K_Nsp

source_name: micro-dissected adjacent normal tissue


title: isograft_control_rep3


title: allograft_day4_rep1


title: normal N8_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample269


title: allograft_day3_rep1


title: blood B9_gDNA_Sty

description: Hybridized to 250K_Sty


title: normal N5_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample267


title: allograft_day2_rep2

source_name: endothelial cells, allograft day 2


title: normal N6_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: allograft_day2_rep3


title: normal N1_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample266


title: normal N3_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: normal N2_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: allograft_control_rep3


title: BreastCancer_Ull-sample265


title: allograft_control_rep2


title: isograft_day3_rep1


title: normal N4_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: allograft_day2_rep1


title: BreastCancer_Ull-sample264

value: Lobular


title: BreastCancer_Ull-sample263


title: blood B30_Hpa2_Nsp

description: Hybridized to 250K_Nsp

value: Hpa II


title: Control normal fat NF117

description: Gene expression data from control normal fat

scan_protocol: Flourescence was measured by confocal scanner (Agilent, Palo Alto, CA)

data_processing: Signal intensity data was generated with Affymetrix Microarray Suite version 5.0 software with default parameters. Expression values were estimated with robust multi-array average (RMA) using standard background correction. RMA-normalized expression data is provided in log base 2 scale.

source_name: Human control normal fat

label_protocol: Per manufacturer's instructions

extract_protocol: Total RNA was extracted from macro-dissected cryomolds and homogenized in QIAzol lysis reagent

value: Human fat

tag: disease status

value: Normal control

tag: sample id


title: BreastCancer_Ull-sample262


title: Control normal fat NF119


title: BreastCancer_Ull-sample261


title: allograft_control_rep1


title: BreastCancer_Ull-sample268


title: Sarcoma tumor PT182PL

description: Gene expression data from soft-tissue sarcoma tumor

source_name: Soft-tissue sarcoma

value: Soft-tissue sarcoma


title: blood B27_Hpa2_Nsp

description: Hybridized to 250K_Nsp

source_name: venous blood


title: BreastCancer_Ull-sample258


title: BreastCancer_Ull-sample257


title: blood B29_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT180PL


title: allograft_day3_rep3


title: BreastCancer_Ull-sample260


title: Sarcoma tumor PT178PL


title: blood B28_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT179PL


title: Control normal fat NF84


title: BreastCancer_Ull-sample256


title: Sarcoma tumor PT176PL


title: blood B23_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: blood B25_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample259


title: Sarcoma tumor PT174PL


title: Sarcoma tumor PT172PL


title: Sarcoma tumor PT169PL


title: BreastCancer_Ull-sample253


title: Sarcoma tumor PT171PL


title: Sarcoma tumor PT170PL


title: blood B24_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample255


title: blood B21_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: blood B26_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: blood B19_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT166PL


title: Sarcoma tumor PT165PL


title: Sarcoma tumor PT167PL


title: Sarcoma tumor PT164PL


title: blood B18_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: blood B20_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT163PL


title: Sarcoma tumor PT161PL


title: BreastCancer_Ull-sample249


title: Sarcoma tumor PT162PL


title: BreastCancer_Ull-sample251


title: BreastCancer_Ull-sample250


title: blood B22_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: blood B16_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT157MRC


title: blood B17_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT158MRC


title: BreastCancer_Ull-sample247

value: Other


title: Sarcoma tumor PT168PL


title: Sarcoma tumor PT154MRC


title: blood B14_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample254


title: blood B13_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT156MRC


title: Sarcoma tumor PT153MRC


title: Sarcoma tumor PT152MRC


title: BreastCancer_Ull-sample244


title: BreastCancer_Ull-sample246


title: BreastCancer_Ull-sample245


title: blood B15_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample243


title: Sarcoma tumor PT149MRC


title: Sarcoma tumor PT159PL


title: Sarcoma tumor PT160PL


title: Sarcoma tumor PT150MRC


title: blood B10_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample241


title: blood B11_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT143MRC


title: Sarcoma tumor PT147MRC


title: Sarcoma tumor PT145MRC


title: Sarcoma tumor PT144MRC


title: Sarcoma tumor PT146MRC


title: Sarcoma tumor PT148MRC


title: BreastCancer_Ull-sample252


title: blood B12_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT142MRC


title: BreastCancer_Ull-sample240

value: Medullary


title: Sarcoma tumor PT140MRC


title: Sarcoma tumor PT137MF


title: blood B5_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: blood B3_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT133MF


title: BreastCancer_Ull-sample239

value: Tubulolobular


title: Sarcoma tumor PT134MF


title: BreastCancer_Ull-sample238


title: blood B2_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: blood B6_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample236


title: Sarcoma tumor PT135MF


title: Sarcoma tumor PT131MF


title: Sarcoma tumor PT151MRC


title: BreastCancer_Ull-sample237


title: BreastCancer_Ull-sample234


title: BreastCancer_Ull-sample235


title: blood B4_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: blood B1_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample233


title: Sarcoma tumor PT130MF


title: blood B7_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample232


title: Sarcoma tumor PT128MF


title: Sarcoma tumor PT129MF


title: tumor T29_gDNA_Nsp

description: Hybridized to 250K_Nsp

source_name: micro-dissected tumor tissue

value: esophageal squamous cell carcinoma


title: tumor T30_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT124MF


title: Sarcoma tumor PT139MRC


title: Sarcoma tumor PT122MF


title: Sarcoma tumor PT125MF


title: Sarcoma tumor PT123MF


title: Sarcoma tumor PT141MRC


title: BreastCancer_Ull-sample248

source_name: Tumor (primary breast cancer)


title: BreastCancer_Ull-sample242

source_name: Genomic DNA, Promega


title: Sarcoma tumor PT126MF


title: BreastCancer_Ull-sample229


title: Sarcoma tumor PT121MF


title: Sarcoma tumor PT120MF


title: blood B9_Hpa2_Nsp

description: Hybridized to 250K_Nsp

value: blood


title: tumor T27_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT138MRC


title: Sarcoma tumor PT115MF


title: Sarcoma tumor PT119MF


title: tumor T28_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample231

value: Female


title: Sarcoma tumor PT113MF


title: tumor T26_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: blood B8_Hpa2_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT116MF


title: BreastCancer_Ull-sample227

value: breast cancer

value: Male

value: Promega reference genomic DNA


title: tumor T25_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample225


title: BreastCancer_Ull-sample226

value: Ductal


title: BreastCancer_Ull-sample228

value: Promega pooled female genomic DNA


title: tumor T23_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample230


title: tumor T24_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT108MF


title: BreastCancer_Ull-sample224


title: tumor T21_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: tumor T22_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT110MF


title: Sarcoma tumor PT109MF


title: Sarcoma tumor PT111MF


title: Sarcoma tumor PT114MF


title: Sarcoma tumor PT105MF


title: Sarcoma tumor PT107MF


title: Sarcoma tumor PT104MF


title: Sarcoma tumor PT112MF


title: Sarcoma tumor PT106MF


title: Sarcoma tumor PT118MF


title: Sarcoma tumor PT100MF


title: Sarcoma tumor PT103MF


title: BreastCancer_Ull-sample222


title: BreastCancer_Ull-sample221


title: BreastCancer_Ull-sample220


title: tumor T17_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: tumor T20_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT99LMS


title: Sarcoma tumor PT101MF


title: Sarcoma tumor PT102MF


title: BreastCancer_Ull-sample223


title: Sarcoma tumor PT95LMS


title: BreastCancer_Ull-sample219


title: tumor T15_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT97LMS


title: tumor T16_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: tumor T18_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT94LMS


title: Sarcoma tumor PT92LMS


title: BreastCancer_Ull-sample218

value: Mucinous


title: Sarcoma tumor PT96LMS


title: Sarcoma tumor PT91LMS


title: BreastCancer_Ull-sample217


title: tumor T14_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT98LMS


title: Sarcoma tumor PT88LMS


title: Sarcoma tumor PT93LMS


title: BreastCancer_Ull-sample216


title: Sarcoma tumor PT90LMS


title: BreastCancer_Ull-sample214


title: tumor T12_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT85LMS


title: Sarcoma tumor PT84LMS


title: Sarcoma tumor PT86LMS


title: tumor T11_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT82LMS


title: Sarcoma tumor PT81LMS


title: Sarcoma tumor PT80LMS


title: tumor T13_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: tumor T8_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT79LMS


title: BreastCancer_Ull-sample209


title: BreastCancer_Ull-sample210


title: BreastCancer_Ull-sample211


title: tumor T10_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: tumor T19_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample215

value: Lobular


title: BreastCancer_Ull-sample212


title: BreastCancer_Ull-sample208


title: tumor T6_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT76LMS


title: Sarcoma tumor PT73LMS


title: Sarcoma tumor PT87LMS


title: tumor T9_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: tumor T4_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT49DD


title: tumor T5_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT50DD


title: Sarcoma tumor PT44DD


title: Sarcoma tumor PT89LMS


title: BreastCancer_Ull-sample205


title: tumor T3_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT83LMS


title: Sarcoma tumor PT78LMS


title: BreastCancer_Ull-sample204


title: BreastCancer_Ull-sample213


title: Sarcoma tumor PT40DD


title: Sarcoma tumor PT42DD


title: tumor T2_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT38DD


title: Sarcoma tumor PT37DD


title: BreastCancer_Ull-sample206


title: BreastCancer_Ull-sample202


title: BreastCancer_Ull-sample203


title: Sarcoma tumor PT39DD


title: BreastCancer_Ull-sample200


title: BreastCancer_Ull-sample201


title: normal N30_gDNA_Nsp

description: Hybridized to 250K_Nsp

value: epithelium


title: Sarcoma tumor PT36DD


title: normal N29_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: normal N27_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: normal N28_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample199


title: BreastCancer_Ull-sample207


title: Sarcoma tumor PT35DD


title: tumor T1_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: normal N26_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample198


title: normal N24_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: tumor T7_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: U266 cell line RNA polymerase II

city: Omaha

first: Himabindu

last: Ramachandrareddy

state: NE

address: 600 South 42nd st

department: Pathology and microbiology

institute: University of Nebraska Medical Center

description: ChIP-chip U266 RNA PolII

hyb_protocol: The labeled ChIP DNA was precipitated and hybridized to the custom arrays by Roche-Nimblegen according to the manufacturers instructions (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: The arrays were scanned using a MS200 Microarray Scanner by Roche-Nimblegen as per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Data processing from the scanned images was performed by Roche-Nimblegen using NimbleScan software (http://www.nimblegen.com/products/lit/lit.html).

source_name: RNA polymerase II ChIP DNA from U266 cell line

label_protocol: 1µg each of control Input and experimental ChIP DNA were labelled by Roche-Nimblegen using Cy3-random heptamer and Cy5-random heptamer, respectively, according to manufacturer's protocols. (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: cells were grown in RPMI1640 medium with 10%FBS, 1mM L-Glutamine and Penicillin and Streptomycin

extract_protocol: For analysis of Histone modifications, native ChIP without formaldehyde crosslinking was performed followed by micrococcal nuclease digestion of the chromatin to obtain mononucleosomes. Briefly, 20x106 cells were lysed with the buffer (Tris-HCl pH7.6-50mM, CaCl2-1mM, TritonX-100-0.2%, Sodium Butyrate-5mM, PMSF-0.5mM, Protease Inhibitor cocktail (Sigma-Aldrich, St. Louis, MO, USA)-20ul) on ice and digested with micrococcal nuclease 1Unit (Sigma-Aldrich, St. Louis, MO, USA) in the same buffer at 37°C for 6min. The reaction was stopped by addition of Tris-HCl pH7.6 and EDTA to a final concentration of 10mM and 5mM respectively. The cell lysate was then sonicated (Intensity -3, Pulse on-20”, Pulse off- 2’, Number of pulses-6) using Fisher F550 Sonic dismembrator. The chromatin was then dialyzed into RIPA buffer (10mM Tris pH7.6, 1mMEDTA, 0.1%SDS, 0.1% Sodium deoxycholate, 1% TritonX-100) for 2hours at 4°C and proceeded to the immuno precipitation after saving 10% of the dialysate as input. For analysis of PolII binding, 100x106 cells were cross-linked with formaldehyde (1% final concentration) for 10min and then quenched with Glycine (0.125M final concentration).  The cells were washed with ice cold PBS and lysed using 5ml of the lysate buffer (1%SDS, EDTA-10mM, Tris HCl pH8.1-50mM, PMSF-1mM) on ice for 10 min. Chromatin was solubilized by performing sonication (Intensity-5, Pulse on-30”, Pulse off-1’, Number of pulses- 15) to break down the DNA to a size ranging from 200-400bp. The chromatin was then dialyzed overnight into RIPA buffer at 4°C. Chromatin equivalent to 20x106 cells was used for one ChIP experiment and 10% of it was saved as input. Chromatin immunoprecipitation was performed overnight at 4°C using specific antibody (4ug) bound protein A Dynabeads (Dynal Biotech, Oslo, Norway). The antibody- chromatin complexes were washed with RIPA buffer, High salt RIPA buffer (10mM Tris pH7.6, 1mMEDTA, 0.1%SDS, 0.1% Sodium deoxycholate, 1% TritonX-100, 300mM NaCl), Lithium chloride buffer (0.25M LiCl, 0.5% NP40, 0.5% Sodium Deoxycholate), TE+0.2% TritonX-100 and TE buffer. The DNA was eluted by incubation of the beads at 65°C in the presence of SDS and simultaneous proteinase K (Roche diagnostics) digestion. The ChIP DNA was validated for enrichment by real time quantitative-PCR amplification (primer sequences shown in the supplementary data) and the enriched input and ChIP DNA samples were later amplified.The ChIP DNA was amplified by using the LMPCR technique as described previously (Oberley et al., Methods Enzymol 376:316, 2004) with a few modifications. The ChIP DNA obtained was repaired using the DNA End Repair Kit (Epicentre Biotechnologies). dATP was added to the 3’ ends of ChIP DNA by incubating with dATP and Taq DNA polymerase (New England Biolabs) at 70°C for 30 min. The ChIP DNA was then ligated to unidirectional adaptors. The sequences of the oligonucleotides used as adaptors are as follows: Adaptor 3a-forward 5’- TCGGTAACGACTCACTTGGGTTCCT-3’ and Reverse 5’- GGAACCCAAGTG-3’, Adaptor 3b-forward 5’-TGGCAATTCCCTCACTAAAGGGCT-3’ and Reverse-5’-GCCCTTTAGTGA. The adaptors were annealed and ligated to the ChIP DNA by incubating ChIP DNA with the adaptors in excess at 16°C overnight using T4 DNA ligase (New England Biolabs). The ChIP DNA was then amplified by PCR using the following protocol: 1 cycle of 55°C 2 min, 72°C 5 min, 95°C 2 min; 30-35 rounds of amplification at 95°C 0.5 min, 55°C 0.5 min and 72°C 1 min; and final extension at 72°C for 4 min. The resulting LMPCR-amplified ChIP DNA was then purified using PCR purification kit (Qiagen) and validated for enrichment by real-time PCR to verify that the enrichment ratios are retained. The ChIP DNA was then hybridized to a custom oligonucleotide chip (NimbleGen Systems, Madison, WI).

value: Myeloma cell line

tag: chip antibody

value: RNA PolII

tag: cell line

source_name: Input DNA from U266 cell line

value: None, Input DNA


title: Sarcoma tumor PT32DD

value: Soft-tissue sarcoma


title: normal N22_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT30DD


title: Sarcoma tumor PT31DD


title: BreastCancer_Ull-sample195

tag: gender

tag: disease state


title: normal N21_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT29DD


title: BreastCancer_Ull-sample194

tag: age at onset (years)

tag: histology


title: Sarcoma tumor PT74LMS


title: SUDHL16 cell line H3K27me3

description: ChIP-chip DHL16 H3K27me3

source_name: H3K27me3 ChIP DNA from DHL16 cell line

value: Diffuse large B cell lymphoma cell line

source_name: Input DNA from DHL16 cell line


title: BreastCancer_Ull-sample192

tag: histologic grade

tag: m-status (0=mx and m0, 1=m1)


title: Naïve B cells H3K27me3

description: ChIP-chip Naïve B cells H3K27me3

source_name: H3K27me3 ChIP DNA from human primary tonsilar Naïve B cells

growth_protocol: None, ChIP was performed immediately after isolation of naïve B cells

treatment_protocol: Cells were isolated from human tonsil using miltenyi midi MACS columns

value: Naïve B cell

source_name: Input DNA from human primary tonsilar naïve B cells


title: BreastCancer_Ull-sample191

tag: pgr-status

tag: reference


title: BreastCancer_Ull-sample196

tag: er-status


title: normal N19_gDNA_Nsp

description: Hybridized to 250K_Nsp

tag: tissue


title: BreastCancer_Ull-sample197

tag: tumor cell prct


title: BreastCancer_Ull-sample190


title: U266 cell line H3K27me3

description: ChIP-chip U266 H3K27me3

source_name: H3K27me3 ChIP DNA from U266 cell line


title: BreastCancer_Ull-sample189


title: CL01 cell line H3K27me3

description: ChIP-chip CL01 H3K27me3

source_name: H3K27me3 ChIP DNA from CL01 cell line

value: Burkitt lymphoma cell line which reverted back to a phenotype similar to naïve B cells

source_name: Input DNA from CL01 cell line

value: Burkitts lymphoma cell line reverted back to naïve B cell type


title: normal N18_gDNA_Nsp

description: Hybridized to 250K_Nsp

source_name: micro-dissected adjacent normal tissue


title: normal N25_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: normal N17_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: normal N20_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample193

value: Female


title: normal N23_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: U266 cell line H3K4me1

description: ChIP-chip U266 H3K4me1

source_name: H3K4me1 ChIP DNA from U266 cell line


title: normal N15_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: normal N16_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Sarcoma tumor PT25DD


title: SUDHL16 cell line H3K4me1

description: ChIP-chip DHL16 H3K4me1

source_name: H3K4me1 ChIP DNA from DHL16 cell line


title: BreastCancer_Ull-sample188

value: breast cancer


title: Centroblasts H3K27me3

description: ChIP-chip Centroblasts H3K27me3

source_name: H3K27me3 ChIP DNA from human primary tonsilar centroblasts

growth_protocol: None, ChIP was performed immediately after isolation of centroblasts

value: Germinal center B cells

source_name: Input DNA from human primary tonsilar centroblasts


title: BreastCancer_Ull-sample187

value: Male

value: Promega reference genomic DNA


title: Naïve B cells H3K4me1

description: ChIP-chip Naïve B cells H3K4me1

source_name: H3K4me1 ChIPDNA  from human primary tonsilar Naïve B cells


title: Sarcoma tumor PT22DD

source_name: Soft-tissue sarcoma


title: CL01 cell line H3K4me1

description: ChIP-chip CL01 H3K4me1

source_name: H3K4me1 ChIP DNA from CL01 cell line


title: BreastCancer_Ull-sample184

source_name: Tumor (primary breast cancer)

value: Ductal

source_name: Genomic DNA, Promega


title: normal N14_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample185


title: Sarcoma tumor PT19DD


title: Sarcoma tumor PT18DD


title: normal N11_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Naïve B cells H3K4me3

description: ChIP-chip Naïve B cells H3K4me3

source_name: H3K4me3 ChIP DNA from human  primary tonsilar Naïve B cells


title: BreastCancer_Ull-sample182


title: normal N13_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: normal N10_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample183


title: SUDHL16 cell line H3K4me3

description: ChIP-chip DHL16 H3K4me3

source_name: H3K4me3 ChIP DNA from DHL16 cell line

source_name: Input DNA from DHL16 cell line


title: normal N12_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Centroblasts H3K4me1

description: ChIP-chip centroblasts H3K4me1

source_name: H3K4me1 ChIP DNA from human primary tonsilar centroblasts


title: U266 cell line H3K4me3

description: ChIP-chip U266 H3K4me3

source_name: H3K4me3 ChIP DNA from U266 cell line

source_name: Input DNA from U266 cell line


title: Sarcoma tumor PT16DD


title: Centroblasts H3K4me3

description: ChIP-chip Centroblasts H3K4me3

source_name: H3K4me3 ChIP DNA from human  primary tonsilar centroblasts


title: normal N8_gDNA_Nsp

description: Hybridized to 250K_Nsp

source_name: micro-dissected adjacent normal tissue


title: U266 cell line H3K9,K14-diacetylated

description: ChIP-chip U266 H3-acetyl

source_name: H3-K9,K14-diacetyl ChIP DNA from U266 cell line

value: H3-K9, K14-diacetyl


title: BreastCancer_Ull-sample178

value: Lobular


title: normal N9_gDNA_Nsp

description: Hybridized to 250K_Nsp

value: epithelium


title: CL01 cell line H3K4me3

description: ChIP-chip CL01 H3K4me3

source_name: H3K4me3 ChIP DNA from CL01 cell line

source_name: Input DNA from CL01 cell line


title: BreastCancer_Ull-sample179


title: normal N6_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Naïve B cells H3K9,K14-diacetylated

description: ChIP-chip Naïve B cells H3-acetyl

source_name: H3-K9,K14-diacetyl ChIP DNA from human primary tonsilar Naïve B cells

source_name: Input DNA from human primary tonsilar naïve B cells


title: Sarcoma tumor PT17DD

source_name: Soft-tissue sarcoma


title: Sarcoma tumor PT14DD


title: Sarcoma tumor PT12DD


title: Sarcoma tumor PT10DD


title: BreastCancer_Ull-sample176


title: BreastCancer_Ull-sample180


title: BreastCancer_Ull-sample186


title: Sarcoma tumor PT6DD


title: Sarcoma tumor PT7DD


title: normal N5_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: normal N3_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: CL01 cell line H3K9,K14-diacetylated

description: ChIP-chip CL01 H3-acetyl

source_name: H3-K9,K14-diacetyl ChIP DNA from CL01 cell line


title: BreastCancer_Ull-sample174

source_name: Tumor (primary breast cancer)


title: SUDHL16 cell line H3K9,K14-diacetylated

description: ChIP-chip DHL16 H3-acetyl

source_name: H3-K9,K14-diacetyl ChIP DNA from DHL16 cell line


title: BreastCancer_Ull-sample173

source_name: Genomic DNA, Promega


title: Sarcoma tumor PT23DD


title: blood B30_gDNA_Nsp

description: Hybridized to 250K_Nsp

source_name: venous blood

value: blood


title: normal N4_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: normal N1_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample177


title: BreastCancer_Ull-sample172


title: Centroblasts H3K9,K14-diacetylated

description: ChIP-chip Centroblasts H3-acetyl

source_name: H3-K9,K14-diacetyl ChIP DNA from human primary tonsilar centroblasts

source_name: Input DNA from human primary tonsilar centroblasts


title: normal N2_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample175


title: blood B27_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample170


title: BreastCancer_Ull-sample169


title: normal N7_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: BreastCancer_Ull-sample168


title: BreastCancer_Ull-sample181


title: Lmx1b loss-of-function mutant limb at E13.5, biological rep10

first: Xiao Wei Wendy

last: Gu

state: Quebec

address: 110, avenue des Pins Ouest

department: Neural Circuit Development Laboratory

institute: IRCM

description: Lmx1b -/-  E13.5 left hindlimb_2

hyb_protocol: Labelled and fragmented cDNAs were hybridized to Affymetrix Mouse GeneChip 1.0 ST chips overnight. The chips were washed and stained by the Affymetrix Fluidics Station.

scan_protocol: Genechips were scanned according to Affymetrix protocols.

data_processing: Robust Multipchip Average (RMA) normalization was performed using the open-source R framework for microarray analysis, Aroma.affymetrix (www.aroma-project.org). Normalization parameters: (1) Background Adjust - Yes; (2) Summarization Method - PLM; (3) Quantile Normalization. Fold change values were processed using FlexArray software provided by the McGill University and Génome Québec Innovation Centre (http://genomequebec.mcgill.ca/FlexArray/).

label_protocol: Per RNA labeling, 300 nanograms of total RNA was used in conjunction with the Affymetrix recommended protocol for the GeneChip 1.0 ST chip

growth_protocol: Mouse limbs dissected from E13.5 mouse embryos

extract_protocol: Tissue was stored in RNAlater (Ambion) at -20oC prior to RNA extraction. Wild-types and Lmx1b -/- were genotyped according to Chen et al., 1998. Tissue was homogenized, total RNA extracted and purified according to manufacturer's protocol (Qiagen RNeasy Mini Kit). Purity and quantity of RNA samples were assessed using Agilent RNA 6000 Nano Kit on an Agilent Bioanalyser 2100.

tag: age

value: left hindlimb

tag: genotype

value: Lmx1b -/-


title: Sarcoma tumor PT4DD

value: Soft-tissue sarcoma

tag: disease status


title: blood B28_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Liver376T (mRNA expression)

city: Meguro-ku

first: Atsushi

last: Kaneda

state: Tokyo

address: 4-6-1 Komaba

department: RCAST

country: Japan

institute: The University of Tokyo

description: liver cancer HBV+

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45degree Celsius, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Affymetrix GCOS was used with target intensity=100.

source_name: liver cancer tissue

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

extract_protocol: Total RNAs were extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).

tag: case number

value: liver cancer tissue

value: cancer

tag: pathology

value: moderately-poorly differentiated

value: M

tag: virus

value: HBV


title: Lmx1b loss-of-function mutant limb at E13.5, biological rep8

description: Lmx1b -/-  E13.5 right hindlimb_3

value: right hindlimb


title: Liver376N (mRNA expression)

description: surrounding noncancerous liver tissue, HBV+

source_name: surrounding noncancerous liver tissue

value: surrounding noncancerous liver tissue

value: control

value: Chronic hepatitis

tag: gender


title: blood B26_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Liver375T (mRNA expression)

description: liver cancer HBV+

tag: disease state

value: moderately differentiated


title: blood B23_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Lmx1b loss-of-function mutant limb at E13.5, biological rep9

description: Lmx1b -/-  E13.5 left hindlimb_1


title: blood B25_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Lmx1b loss-of-function mutant limb at E13.5, biological rep7

description: Lmx1b -/-  E13.5 right hindlimb_2


title: BreastCancer_Ull-sample171

value: Female

value: breast cancer

tag: age at onset (years)

value: Ductal

value: Promega reference genomic DNA


title: Lmx1b loss-of-function mutant limb at E13.5, biological rep6

description: Lmx1b -/-  E13.5 right hindlimb_1


title: Liver367T (mRNA expression)

description: liver cancer HCV+

value: HCV


title: BreastCancer_Ull-sample165

tag: histology


title: BreastCancer_Ull-sample166

value: Mucinous

tag: histologic grade


title: BreastCancer_Ull-sample167

tag: m-status (0=mx and m0, 1=m1)


title: Liver375N (mRNA expression)

value: LC


title: blood B22_gDNA_Nsp

description: Hybridized to 250K_Nsp

value: blood


title: BreastCancer_Ull-sample163

tag: pgr-status


title: BreastCancer_Ull-sample164

value: Lobular

tag: reference


title: blood B21_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Lmx1b loss-of-function mutant limb at E13.5, biological rep5

description: Lmx1b -/-  E13.5 left forelimb_2

value: left forelimb

value: Lmx1b -/-


title: Liver367N (mRNA expression)

description: surrounding noncancerous liver tissue, HCV+

value: M


title: Liver365T (mRNA expression)

description: liver cancer HCV+

value: liver cancer tissue

value: cancer

value: F


title: blood B19_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: blood B20_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Lmx1b loss-of-function mutant limb at E13.5, biological rep3

description: Lmx1b -/-  E13.5 right forelimb_3

value: right forelimb


title: Lmx1b loss-of-function mutant limb at E13.5, biological rep4

description: Lmx1b -/-  E13.5 left forelimb_1


title: blood B18_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: blood B29_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Liver365N (mRNA expression)

value: surrounding noncancerous liver tissue

value: control


title: blood B17_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Lmx1b loss-of-function mutant limb at E13.5, biological rep2

description: Lmx1b -/-  E13.5 right forelimb_2


title: Liver364T (mRNA expression)

description: liver cancer HCV+

value: moderately differentiated


title: Wild-type limb at E13.5, biological rep10

description: Wild-type E13.5 left hindlimb_2

source_name: Wild-type E13.5 129Sv

value: left hindlimb

value: Wild-type


title: Liver364N (mRNA expression)

value: HCV


title: blood B14_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: blood B12_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: blood B16_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Liver363N (mRNA expression)

value: Chronic hepatitis

value: HBV


title: blood B13_gDNA_Nsp

description: Hybridized to 250K_Nsp

value: blood


title: Wild-type limb at E13.5, biological rep8

description: Wild-type E13.5 right hindlimb_3

value: right hindlimb


title: Wild-type limb at E13.5, biological rep7

description: Wild-type E13.5 right hindlimb_2


title: Liver359N (mRNA expression)

value: LC


title: Wild-type limb at E13.5, biological rep6

description: Wild-type E13.5 right hindlimb_1


title: Liver360T (mRNA expression)

description: liver cancer HCV+


title: blood B9_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Wild-type limb at E13.5, biological rep9

description: Wild-type E13.5 left hindlimb_1


title: Liver360N (mRNA expression)


title: Wild-type limb at E13.5, biological rep5

description: Wild-type E13.5 left forelimb_2

value: left forelimb


title: blood B10_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Wild-type limb at E13.5, biological rep3

description: Wild-type E13.5 right forelimb_3


title: Liver358N (mRNA expression)

value: M


title: Lmx1b loss-of-function mutant limb at E13.5, biological rep1

description: Lmx1b -/-  E13.5 right forelimb_1

value: Lmx1b -/-


title: Wild-type limb at E13.5, biological rep4

description: Wild-type E13.5 left forelimb_1


title: blood B11_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Liver358T (mRNA expression)

description: liver cancer HBV+

value: liver cancer tissue

value: cancer


title: blood B24_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Liver363T (mRNA expression)

description: liver cancer HBV+

value: poorly differentiated


title: Liver359T (mRNA expression)

description: liver cancer HCV+

value: moderately-poorly differentiated


title: blood B7_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Liver189T (mRNA expression)

description: liver cancer HBV+


title: blood B5_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: Wild-type limb at E13.5, biological rep1

description: Wild-type E13.5 right forelimb_1

value: right forelimb


title: PFT7127

status: Public on Jul 05 2010

city: Hamburg

first: Simon

middle: A

last: Joosse

address: Martinistrasse 52

department: Institute of Tumor Biology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: As described in: Joosse SA, van Beers EH, Nederlof PM. Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. BMC Cancer. 2007 Mar 7;7:43.

label_protocol: According to the manufacturer's instructions (Kreatech Biotechnology, Amsterdam).

extract_protocol:
As decribed in:
Joosse SA, et al. Prediction of BRCA1-association in hereditary non-BRCA1/2 breast carcinomas with array-CGH. Breast Cancer Res Treat. 2008 Aug 14

tag: organ

value: mammary gland

value: invasive ductal carcinoma

source_name: Women reference pool

tag: sample

value: A pool of DNA from peripheral blood lymphocytes, from 6 apparently healthy women

value: healthy

value: female


title: Wild-type limb at E13.5, biological rep2

description: Wild-type E13.5 right forelimb_2

tag: tissue

value: Wild-type


title: Liver189N (mRNA expression)

value: surrounding noncancerous liver tissue

value: control

value: Chronic hepatitis

tag: age

value: HBV


title: PFT7048

scan_protocol: As described in: Joosse SA, van Beers EH, Nederlof PM. Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. BMC Cancer. 2007 Mar 7;7:43.


title: PFT7114

data_processing:
As described in:
Joosse SA, van Beers EH, Nederlof PM. Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. BMC Cancer. 2007 Mar 7;7:43.


title: PFT7047


title: blood B3_gDNA_Nsp

description: Hybridized to 250K_Nsp

value: blood


title: PFT7020


title: PFT6918


title: blood B6_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: blood B4_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: PFT6905


title: PFT6948


title: PFT6852


title: PFT6794


title: PFT6896


title: PFT6725


title: PFT6687


title: PFT6737


title: PFT6724


title: PFT6698


title: PFT6726


title: PFT6594


title: PFT6648


title: PFT6674


title: PFT6580


title: PFT6539


title: PFT6455


title: PFT6504


title: PFT6363


title: PFT6445


title: PFT6438


title: PFT6528


title: PFT6337


title: PFT6386


title: PFT6299


title: PFT6270


title: PFT6540


title: blood B1_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: blood B15_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: PFT6234


title: PFT6181


title: PFT6351


title: PFT6231


title: blood B8_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: PFT6208


title: PFT6075


title: PFT6143


title: PFT6074


title: PFT6077


title: PFT5891


title: PFT6060


title: PFT6061


title: PFT6078


title: PFT5826


title: PFT5836


title: PFT5864


title: PFT5737


title: PFT4882


title: PFT6047


title: PFT5824


title: PFT4883


title: PFT4880


title: PFT4592


title: PFT4589


title: PFT4588


title: blood B2_gDNA_Nsp

description: Hybridized to 250K_Nsp


title: PFT4506


title: PFT4048


title: PFT4498


title: PFT4585


title: PFT3618b2


title: PFT3066


title: PFT3529


title: PFT4497


title: PFT3031


title: PFT4182


title: PFT2946-2


title: PFT3045


title: PFT2946-1


title: PFT2545


title: PFT2967


title: PFT2227


title: PFT2572


title: PFT2193


title: PFT0928


title: HR029


title: PFT1233


title: PFT0428


title: PFT1859


title: PFT1891


title: PFT0044


title: PFT0506


title: PFT3618b1


title: PFT1936


title: Sporadic - C133

hyb_protocol: As described in: Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. Joosse SA, et al. BMC Cancer. 2007 Mar 7;7:43.

extract_protocol:
As decribed in:
Prediction of BRCA1-association in hereditary non-BRCA1/2 breast carcinomas with array-CGH.
Joosse SA, et al.
Breast Cancer Res Treat. 2008 Aug 14

tag: disease

value: infiltrating ductal carcinoma

tag: type

value: sporadic breast tumor

value: A pool of DNA from peripheral blood lymphocytes, from 7 apparently healthy women.

tag: cell type

value: peripheral blood lymphocytes

value: healthy appearing


title: Sporadic - C135

scan_protocol: As described in: Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. Joosse SA, et al. BMC Cancer. 2007 Mar 7;7:43.

extract_protocol:
Prediction of BRCA1-association in hereditary non-BRCA1/2 breast carcinomas with array-CGH.
Joosse SA, et al.
Breast Cancer Res Treat. 2008 Aug 14


title: Sporadic - C134

data_processing:
As described in:
Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material.
Joosse SA, et al.
BMC Cancer. 2007 Mar 7;7:43.


title: Sporadic - C129

label_protocol:
As described in:
Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material.
Joosse SA, et al.
BMC Cancer. 2007 Mar 7;7:43.


title: PFT3524


title: Sporadic - C131


title: Sporadic - C130


title: Sporadic - C121


title: Sporadic - C127


title: Sporadic - C120


title: Sporadic - C122


title: Sporadic - C117


title: Sporadic - C115


title: Sporadic - C118


title: Sporadic - C119


title: Sporadic - C062


title: Sporadic - C040


title: BRCA2 - B2108

tag: genotype

value: mutation in the BRCA2 gene

value: A pool of DNA from peripheral blood lymphocytes, from 7 apparently healty women.


title: BRCA2 - B2109

value: mammary gland


title: BRCA2 - B2107


title: BRCA2 - B2106


title: BRCA2 - B2100


title: BRCA2 - B2101


title: BRCA2 - B2104


title: BRCA2 - B2103


title: Sporadic - C128


title: BRCA2 - B2105


title: BRCA2 - B2098


title: BRCA2 - B2095


title: BRCA2 - B2097


title: BRCA2 - B2091


title: BRCA2 - B2093


title: BRCA2 - B2090


title: BRCA2 - B2087


title: PFT4886

value: invasive ductal carcinoma

value: A pool of DNA from peripheral blood lymphocytes, from 6 apparently healthy women


title: BRCA2 - B2084


title: BRCA2 - B2085


title: BRCA2 - B2083


title: BRCA2 - B2080


title: BRCA2 - B2079


title: BRCA2 - B2096


title: PFT4499

value: healthy

value: female


title: Sporadic - C021


title: BRCA2 - B2078


title: BRCA2 - B2060


title: BRCA2 - B2052


title: BRCA2 - B2062


title: BRCA2 - B2067


title: BRCA2 - B2058


title: BRCA2 - B2055


title: BRCA2 - B2057


title: BRCA2 - B2035

hyb_protocol: As described in: Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. Joosse SA, van Beers EH, Nederlof PM. BMC Cancer. 2007 Mar 7;7:43.

extract_protocol:
As decribed in:
Prediction of BRCA1-association in hereditary non-BRCA1/2 breast carcinomas with array-CGH.
Joosse SA, van Beers EH, Tielen IH, Horlings H, Peterse JL, Hoogerbrugge N, Ligtenberg MJ, Wessels LF, Axwijk P, Verhoef S, Hogervorst FB, Nederlof PM.
Breast Cancer Res Treat. 2008 Aug 14


title: BRCA2 - B2028

scan_protocol: As described in: Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. Joosse SA, van Beers EH, Nederlof PM. BMC Cancer. 2007 Mar 7;7:43.


title: BRCA2 - B2045


title: BRCA2 - B2040


title: BRCA2 - B2030

data_processing:
As described in:
Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material.
Joosse SA, van Beers EH, Nederlof PM.
BMC Cancer. 2007 Mar 7;7:43.

extract_protocol:
Prediction of BRCA1-association in hereditary non-BRCA1/2 breast carcinomas with array-CGH.
Joosse SA, van Beers EH, Tielen IH, Horlings H, Peterse JL, Hoogerbrugge N, Ligtenberg MJ, Wessels LF, Axwijk P, Verhoef S, Hogervorst FB, Nederlof PM.
Breast Cancer Res Treat. 2008 Aug 14


title: BRCA2 - B2025

label_protocol:
As described in:
Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material.
Joosse SA, van Beers EH, Nederlof PM.
BMC Cancer. 2007 Mar 7;7:43.


title: BRCA2 - B2011


title: BRCA2 - B2014


title: BRCA2 - B2026


title: BRCA2 - B2010


title: BRCA2 - B2004


title: BRCA2 - B2007


title: BRCA2 - B2023


title: BRCA2 - B2015


title: BRCA2 - B2017


title: M_1

city: Irvine

first: Osvaldo

last: Marinotti

state: CA

address: University of California, Irvine

department: Molecular Biology & Biochemistry

institute: University of California, Irvine

description: Biological replicate 1 of 3.  Whole mosquitoes male non-bloodfed.

hyb_protocol: Hybridization and washing were processed as per the Agilent OneColor Microarray-Based Gene Expression Analysis Protocol (Cat# G4140-90040, Agilent technologies, Santa Clare, CA).

scan_protocol: Scanning was done according to Agilents standard protocol

data_processing: Expression signals were normalized for background within chips with the Agilent spacial correction algorithm (gprocessed signals)

organism: Aedes aegypti

source_name: whole body

label_protocol: Fifty nanograms of total RNA was amplified to cDNA using WT Ovation Pico (Cat#  3300-60, NuGen, San Carlos, CA) and 2 μg of this cDNA was labeled with Cy3 (Cat# 5190-1305, Agilent technologies, Santa Clare, CA) according to the Agilent Oligonucleotide Array-Based CGH For Genomic DNA Analysis Protocol (Cat# G4410-90010, Agilent technologies, Santa Clare, CA).

growth_protocol: Aedes aegypti mosquitoes, Liverpool strain, were maintained at 25°C, 78% relative humidity and a 18/6 h light/dark cycle.

extract_protocol: Total RNA was extracted with TRIZOL (Invitrogen) and further purified with Qiagen RNAeasy columns (Cat# 74106, Qiagen,Valencia, CA) with DNase treatment according to the manufacturer’s recommendations.  The RNA was eluted in 30ul DNase/RNase-free water. RNA quality was assessed by capillary electrophoresis using the Agilent Bioanalyzer 2100 and spectrophotometric analysis.

treatment_protocol: Larvae were fed on finely powdered fish food (Tetramind, Tetra Werke, Germany). Adults (males and females) were kept in cages with access ad libitum to raisins and water. For blood feeding, four days old adult female mosquitoes were fed on mice anaesthetized with a mixture of ketamine and xylazine. Males and females were kept together in the cage until the blood meal. Blood-fed females were transferred to a separate cage and kept without males for the remaining duration of the experiment. The transferred females were kept with access to raisins and water at all times. Egg laying was observed between 72 and 96 h PBM. Three samples composed of 20 mosquitoes each were collected for each experimental time point and stored at -80°C.

tag: strain

value: Liverpool

tag: time point

value: non-bloodfed

value: male


title: M_3

description: Biological replicate 3 of 3.  Whole mosquitoes male non-bloodfed.

tag: gender


title: M_2

description: Biological replicate 2 of 3.  Whole mosquitoes male non-bloodfed.


title: 72H_1

description: Biological replicate 1 of 3.  Whole mosquitoes 72 hours post-bloodmeal.

value: 72 hours post-bloodmeal


title: 48H_1

description: Biological replicate 1 of 3.  Whole mosquitoes 48 hours post-bloodmeal.

value: 48 hours post-bloodmeal


title: BRCA2 - B2082

value: infiltrating ductal carcinoma


title: 96H_1

description: Biological replicate 1 of 3.  Whole mosquitoes 96 hours post-bloodmeal.

value: 96 hours post-bloodmeal


title: BRCA2 - B2034


title: 96H_2

description: Biological replicate 2 of 3.  Whole mosquitoes 96 hours post-bloodmeal.


title: 96H_3

description: Biological replicate 3 of 3.  Whole mosquitoes 96 hours post-bloodmeal.


title: NBF_2

description: Biological replicate 2 of 3.  Whole mosquitoes female non-bloodfed.


title: NBF_1

description: Biological replicate 1 of 3.  Whole mosquitoes female non-bloodfed.


title: 48H_3

description: Biological replicate 3 of 3.  Whole mosquitoes 48 hours post-bloodmeal.


title: 72H_2

description: Biological replicate 2 of 3.  Whole mosquitoes 72 hours post-bloodmeal.


title: 48H_2

description: Biological replicate 2 of 3.  Whole mosquitoes 48 hours post-bloodmeal.


title: NBF_3

description: Biological replicate 3 of 3.  Whole mosquitoes female non-bloodfed.


title: 72H_3

description: Biological replicate 3 of 3.  Whole mosquitoes 72 hours post-bloodmeal.


title: 24H_3

description: Biological replicate 3 of 3.  Whole mosquitoes 24 hours post-bloodmeal.

value: 24 hours post-bloodmeal


title: 24H_1

description: Biological replicate 1 of 3.  Whole mosquitoes 24 hours post-bloodmeal.


title: 24H_2

description: Biological replicate 2 of 3.  Whole mosquitoes 24 hours post-bloodmeal.


title: 12H_1

description: Biological replicate 1 of 3.  Whole mosquitoes 12 hours post-bloodmeal.

value: 12 hours post-bloodmeal


title: pLN FDC cultured stimulated with RA+Pam2CSK4+Pam3CSK4

city: Yokohama

first: Keiichiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

institute: RIKEN

description:
from Balb/cAnNCrlCrlj wild type mice
in vitro pLN FDC RA+Pam2CSK4+Pam3CSK4

hyb_protocol: The labeled cRNA was hybridized with Mouse Genome 430 2.0 Arrays (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The image was quantified by using GCOS software.

source_name: mouse in vitro cultured FDC, stimulated 96h with RA+Pam2CSK4+Pam3CSK4

label_protocol: RNA was subjected to biotinilated cRNA synthesis by using Target Labeling kit (Affymetrix).

growth_protocol: Balb/cAnNCrlCrlj wild type mice were maintained in specific pathogen-free conditions (SPF) at the animal facility of the Research Center for Allergy and Immunology. To culture FDCs, purified FDCs were cultured in D-MEM with 10% fetal calf serum (FCS), 0.02M HEPES, 0.2mM non-essential amino acids (NEAA), TNFα (5ng/ml) and anti-LTβR (1μg/ml).

extract_protocol: Total RNA was isolated using TRIzol Reagent (Invitrogen).

treatment_protocol: To stimulate FDCs in vitro, the cells were were cultured without of with the following stimuli: Pam2CSK4 (100ng/ml), LPS (20µg/ml), all-trans-retinoic acid (RA, 40nM).

value: Balb/cAnNCrlCrlj

tag: developmental stage

value: adult

value: lymph nodes

value: follicular dendritic cells (FDCs)

tag: fdcs purified from

value: peripheral lymph nodes (pLNs)

tag: fdc type

value: in vitro pLN FDC

tag: protocol

value: FDC stimulated with RA+Pam2CSK4+Pam3CSK4


title: 3H_3

description: Biological replicate 3 of 3.  Whole mosquitoes 3 hours post-bloodmeal.

value: 3 hours post-bloodmeal

value: female


title: 3H_2

description: Biological replicate 2 of 3.  Whole mosquitoes 3 hours post-bloodmeal.

value: Liverpool


title: pLN FDC cultured stimulated with RA+Pam2CSK4+LPS

department: Research Center for Allergy and Immunology

description:
from Balb/cAnNCrlCrlj wild type mice
in vitro pLN FDC RA+Pam2CSK4+LPS

source_name: mouse in vitro cultured FDC, stimulated 96h with RA+Pam2CSK4+LPS

value: FDC stimulated with RA+Pam2CSK4+LPS


title: 12H_2

description: Biological replicate 2 of 3.  Whole mosquitoes 12 hours post-bloodmeal.


title: pLN FDC cultured stimulated with Pam3CSK4

description:
from Balb/cAnNCrlCrlj wild type mice
in vitro pLN FDC Pam3CSK4

source_name: mouse in vitro cultured FDC, stimulated 96h with Pam3CSK4

value: FDC stimulated with Pam3CSK4


title: 3H_1

description: Biological replicate 1 of 3.  Whole mosquitoes 3 hours post-bloodmeal.


title: 12H_3

description: Biological replicate 3 of 3.  Whole mosquitoes 12 hours post-bloodmeal.


title: pLN FDC cultured without stimulation

description:
from Balb/cAnNCrlCrlj wild type mice
in vitro pLN FDC NS

source_name: mouse in vitro cultured FDC, without stimulation

value: FDC without stimulation


title: pLN FDC cultured stimulated with RA+LPS

description:
from Balb/cAnNCrlCrlj wild type mice
in vitro pLN FDC RA+LPS

source_name: mouse in vitro cultured FDC, stimulated 96h with RA+LPS

value: FDC stimulated with RA+LPS


title: freshly prepared FDCs from CFA immunized pLN

description:
from Balb/cAnNCrlCrlj wild type mice
WT CFA immunized pLN FDC

source_name: mouse FDC from immunized pLNs

value: ex vivo pLN FDC

value: FDC purified from CFA immunized pLNs


title: freshly prepared FDCs from naïve pLN

description:
from Balb/cAnNCrlCrlj wild type mice
WT naïve pLN FDC

source_name: mouse FDC from naïve pLNs

value: FDC purified from naïve pLNs


title: pLN FDC cultured stimulated with RA+Pam3CSK4

description:
from Balb/cAnNCrlCrlj wild type mice
in vitro pLN FDC RA+Pam3CSK4

source_name: mouse in vitro cultured FDC, stimulated 96h with RA+Pam3CSK4

value: Balb/cAnNCrlCrlj

value: FDC stimulated with RA+Pam3CSK4