title: op50 4/29 sma6 4hrs

status: Public on Nov 06 2008

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28347.gif
Measurement: time(absolute) 4 h
Infection: OP50
Strain Name: sma-6(wk7)

hyb_protocol: see Proc Natl Acad Sci U S A. 2006;103:14086-14091

scan_protocol: Scanner Make = Axon Instruments (V1.00); Scanner Model = GenePix 4000B

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

organism: Caenorhabditis elegans

source_name: sma-6 mutants exposed to E. coli OP50- 4 hours

source_name: Common reference- Mixed stage N2 worm culture


title: op50 6/29 N2 4hrs

type: RNA

country: USA

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19596.gif
Measurement: time(absolute) 4 h
Infection: OP50
Strain Name: N2

molecule: total RNA

source_name: N2 worms exposed to E. coli OP50-4 hours

label_protocol: see Proc Natl Acad Sci U S A. 2006;103:14086-14091

tag: Common reference- Mixed stage N2 worm culture


title: pa14 4/29 sma6 4hrs

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28346.gif
Measurement: time(absolute) 4 h
Infection: PA14
Strain Name: sma-6(wk7)

source_name: sma-6 mutants exposed to P. aeruginosa PA14- 4 hours

extract_protocol: see Proc Natl Acad Sci U S A. 2006;103:14086-14091


title: pa14 4/21 n2 24hrs

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28296.gif
Measurement: time(absolute) 24 h
Infection: PA14
Strain Name: N2

source_name: N2 worms exposed to P. aeruginosa PA14- 24 hours


title: pa14 4/22 n2 24hrs

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28291.gif
Measurement: time(absolute) 24 h
Infection: PA14
Strain Name: N2

tag: N2 worms exposed to P. aeruginosa PA14- 24 hours


title: hues6Neuron

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Drive, Room 3114

department: SCRM

institute: UCSD

description: NE cells were cultured (submitted)

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: Image analysis and base calling was done using Gerald (Illumina pipeline), and reads aligned to human (hg17) using Megablast.

label: not applicable

organism: Homo sapiens

source_name: NE

label_protocol: not applicable

growth_protocol: ES and NP cells were cultured as described in Yeo et al. Plos Computational Biology 2007

extract_protocol: Small RNA cloning was performed as described in White et al. Science 2008.

treatment_protocol: Ref. to manuscript

tag: small RNA cloning


title: pa14 4/23 n2 24hrs

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28290.gif
Measurement: time(absolute) 24 h
Infection: PA14
Strain Name: N2


title: hues6NP

description: NP cells were cultured as described in Yeo et al. PLoS Computational Biology, 2007

source_name: NP


title: op50 4/22 n2 24hr

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28264.gif
Measurement: time(absolute) 24 h
Infection: OP50
Strain Name: N2

source_name: N2 worms exposed to E. coli OP50- 24 hours


title: op50 5/29 new N2 4hrs

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19660.gif
Measurement: time(absolute) 4 h
Infection: OP50
Strain Name: N2

source_name: N2 worms exposed to E. coli OP50- 4 hours


title: hues6

description: ES cells were cultured as described in Yeo et al. PLoS Computational Biology, 2007

source_name: ESC


title: pa14 629new 4hr

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19659.gif
Measurement: time(absolute) 4 h
Infection: PA14
Strain Name: N2

source_name: N2 worms exposed to P. aeruginosa PA14 - 4 hours

source_name: Common reference- mixed stage N2 worms culture


title: daf-2_OP50_4

description:
Simple annotation: C. elegans, innate immunity
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64219.gif
Measurement: time(absolute) 24 h
Infection: OP50
Strain Name: daf-2(e1370)

source_name: Reference

tag: Reference


title: pa14 5/29 n2 4hr

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27967.gif
Measurement: time(absolute) 4 h
Infection: PA14
Strain Name: N2

source_name: N2 worms exposed to P. aeruginosa PA14- 4 hours


title: daf-2_OP50_2

description:
Simple annotation: C. elegans, innate immunity
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64217.gif
Measurement: time(absolute) 24 h
Infection: OP50
Strain Name: daf-2(e1370)


title: daf-2_PA14_4

description:
Simple annotation: C. elegans, innate immunity
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64222.gif
Measurement: time(absolute) 24 h
Infection: PA14
Strain Name: daf-2(e1370)


title: daf-2_OP50_3

description:
Simple annotation: C. elegans, innate immunity
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64218.gif
Measurement: time(absolute) 24 h
Infection: OP50
Strain Name: daf-2(e1370)


title: pa14 sma6 7/30 4hrs

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27364.gif
Measurement: time(absolute) 4 h
Infection: PA14
Strain Name: sma-6(wk7)

tag: sma-6 mutants exposed to P. aeruginosa PA14- 4 hours


title: op50 sma6 7/30 4hrs

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27363.gif
Measurement: time(absolute) 4 h
Infection: OP50
Strain Name: sma-6(wk7)

tag: sma-6 mutants exposed to E. coli OP50- 4 hours


title: daf-2_OP50_1

description:
Simple annotation: C. elegans, innate immunity
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64216.gif
Measurement: time(absolute) 24 h
Infection: OP50
Strain Name: daf-2(e1370)


title: daf-2_PA14_3

description:
Simple annotation: C. elegans, innate immunity
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64215.gif
Measurement: time(absolute) 24 h
Infection: PA14
Strain Name: daf-2(e1370)


title: daf-2_PA14_2

description:
Simple annotation: C. elegans, innate immunity
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64221.gif
Measurement: time(absolute) 24 h
Infection: PA14
Strain Name: daf-2(e1370)


title: op50 sma6 7/2 4hrs

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27361.gif
Measurement: time(absolute) 4 h
Infection: OP50
Strain Name: sma-6(wk7)


title: op50 5/07 N2 4hr

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19293.gif
Measurement: time(absolute) 4 h
Infection: OP50
Strain Name: N2

tag: N2 worms exposed to E. coli OP50- 4 hours


title: pa14 5/7 n2 4hr

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27966.gif
Measurement: time(absolute) 4 h
Infection: PA14
Strain Name: N2

tag: N2 worms exposed to P. aeruginosa PA14- 4 hours


title: op50 4/21 n2 24hr

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28263.gif
Measurement: time(absolute) 24 h
Infection: OP50
Strain Name: N2

tag: N2 worms exposed to E. coli OP50- 24 hours


title: daf-2_PA14_1

description:
Simple annotation: C. elegans, innate immunity
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64220.gif
Measurement: time(absolute) 24 h
Infection: PA14
Strain Name: daf-2(e1370)


title: E.ch-p200 HG18 1 of 2

status: Public on Nov 05 2008

type: genomic

city: Galveston

first: Bing

last: Zhu

state: TX

address: 301 University Boulevard

institute: utmb

description: Chip-chip p200 infected THP1 cells

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: A two-array set representing whole-genome promoter (5 kb) tiling, containing 385,000 probes (50- to 75-mer) from ~60,000 human transcripts was obtained from Nimblegen Systems.  Labeling and hybridization of E. chaffeensis ChIP samples was performed by Nimblegen Systems.  For each spot on the array, log2-ratio of Cy5 labeled p200 IP sample versus the Cy3-labeled input DNA sample (not taken through immunoprecipitation steps) was calculated.  The intensity ratio of p200 IP to input DNA was plotted versus genomic position to identify regions where increased signal (i.e. DNA fragment enrichment) was observed relative to the control sample.  Positions identified as p200 binding sites on the human 5 kb promoter array were identified by using NimbleScan, and peaks detected by searching for four or more probes above the specified cutoff values, ranging from 90% to 15% using a 500 bp sliding window.  The cutoff value is a percentage of a hypothetical maximum (mean ± standard deviation), and the ratio data was randomized 20 times to determine the probability of false positives.  Each peak was then assigned a false discovery rate (FDR) score based on the randomization.

molecule: genomic DNA

source_name: p200 ChIP DNA from highly infected (95%) THP-1cells by Ehrlichia chaffeensis

label_protocol: 1 µg ChIP DNA and input DNA were directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers and  Cy3 nonamersper based on the manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: THP-1 cells were cultured for 7 days in the presence of E. chaffeensis

extract_protocol: ChIP was performed on highly infected (95%) THP-1 cells seven days after infection using ChIP-IT Express kit (Active Motif, Carlsbad, CA) with anti-E. chaffeensis p200 antibody and normal human IgG according to the manufacturer’s instructions.  Amplicons were prepared by adapting the standard protocol for whole-genome amplification using the GenomePlex WGA kit (Sigma-Aldrich)  except the initial random fragmentation step was eliminated and DNA from entire ChIP and input was amplified.

tag: Age

value: 7 days infection in culture

tag: Tissue

tag: Antibody

source_name: Input DNA from uninfected THP-1 cells

growth_protocol: THP-1 cells were cultured for 7 days

value: no

value: 7 days in culture,


title: op50 n2 11/19 24hr

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/28186.gif
Measurement: time(absolute) 24 h
Infection: OP50
Strain Name: N2


title: UPC2M2K31A, experiment 2

city: Memphis

first: Katherine

middle: S

last: Barker

state: TN

address: 881 Madison Avenue, Room 305

department: Clinical Pharmacy

institute: University of Tennessee Health Science Center

description: The scanned images were analyzed using software resident in GeneChip Operating System v2.0 (Affymetrix).

hyb_protocol: The cRNA pellet was suspended in 10 µl of RNase-free water and 10 µg was fragmented by ion-mediated hydrolysis at 95 °C for 35 min in 200 mM Tris-acetate (pH 8.1), 500 mM potassium acetate, 150 mM magnesium acetate. The fragmented cRNA was hybridized for 16 h at 45 °C to the C. albicans NimbleExpress GeneChip arrays. Arrays were washed at 25 °C with 6 × SSPE, 0.01% Tween 20 followed by a stringent wash at 50 °C with 100 mM MES, 0.1 M NaCl, 0.01% Tween 20. Hybridizations and washes employed the Affymetrix Fluidics Station 450 using their standard EukGE-WS2v5 protocol. The arrays were then stained with phycoerythrein-conjugated streptavidin (Molecular Probes).

scan_protocol: The fluorescence intensities were determined using the GCS 3000 high-resolution confocal laser scanner (Affymetrix).

data_processing: Sample loading and variations in staining were standardized by scaling the average of the fluorescent intensities of all genes on an array to a constant target intensity (250). The signal intensity for each gene was calculated as the average intensity difference, represented by [Σ(PM − MM)/(number of probe pairs)], where PM and MM denote perfect-match and mismatch probes.  The scaled gene expression values from GeneChip Operating System v2.0 software were generated using the MAS5.0 algorithm.

label: Biotin

organism: Candida albicans

source_name: UPC2 S2 allele in UPC2 disruption strain A, experiment 2

label_protocol: cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription using the T7 promoter-coupled double-stranded cDNA as template and the Bioarray HighYield RNA Transcript Labeling Kit

growth_protocol: Cell grown for 3 hours until log phase.

extract_protocol: Total RNA was isolated using the hot SDS-phenol method (31). Frozen cells were suspended in 12 ml of 50 mM sodium acetate (pH 5.2), 10 mM EDTA at room temperature, after which 1 ml of 20% sodium dodecyl sulphate and 12 ml of acid phenol (Fisher Scientific) were added. This mixture was incubated 10 min at 65 °C with mixing each minute, cooled on ice for 5 min, and centrifuged for 15 min at 12,000g. Supernatants were transferred to new tubes containing 15 ml of chloroform, mixed, and centrifuged at 200g for 10 min. The aqueous layer was removed to new tubes, RNA was precipitated with 1 volume isopropanol and 0.1 volume 2 M sodium acetate (pH 5.0), and then collected by centrifugation at 17,000g for 35 min at 4 °C. The RNA pellet was suspended in 10 ml of 70% ethanol, collected again by centrifugation, and suspended in nuclease-free water.


title: SC5314, experiment 2

source_name: Genome strain SC5314

tag: Genome strain SC5314


title: UPC2M2K21A, experiment 2

source_name: UPC2 S1 allele in UPC2 disruption strain A, experiment 2


title: UPC2M4A, experiment 2

source_name: UPC2 disruption strain in SC5314 strain A, experiment 2


title: UPC2M2K31B, experiment 2

source_name: UPC2 S2 allele in UPC2 disruption strain B, experiment 2


title: UPC2M2K31B, experiment 1

source_name: UPC2 S2 allele in UPC2 disruption strain B, experiment 1


title: UPC2M2K31A, experiment 1

source_name: UPC2 S2 allele in UPC2 disruption strain A, experiment 1


title: UPC2M2K21B, experiment 1

source_name: UPC2 S1 allele in UPC2 disruption strain B, experiment 1


title: UPC2M2K21A, experiment 1

source_name: UPC2 S1 allele in UPC2 disruption strain A, experiment 1


title: UPC2M4A, experiment 1

source_name: UPC2 disruption strain in SC5314 strain A, experiment 1


title: SC5314, experiment 1

tag: Cells grown for 3 hours until log phase.


title: UPC2M4B, experiment 1

source_name: UPC2 disruption strain in SC5314 strain B, experiment 1


title: HES2_Mir122WT_rep2

city: Jerusalem

first: Galit

last: Tzur

address: Kiryat Hadassah

department: Gene Therapy

country: Israel

institute: Hadassah University Hospital

description: Effect of wt versus mutant hsa-miR-122 overexpression on spontaneous hESC differentiation.

hyb_protocol: According to Affymetrix protocol

scan_protocol: According to Affymetrix protocol

data_processing: normalized using RMA (R2.1.0 package)

label: biotin

source_name: hESC transduced with WT miR-122-expressing lentiviral vector

label_protocol: According to Affymetrix protocol

growth_protocol: Prior to differentiation - on foreskin-derived feeder cells with complete KO medium with bFGF

extract_protocol: Extraction with Trizol and purification with phenol / chloroform using PLG tubes

treatment_protocol: Two-week spontaneous differentiation in KO medium without feeder cells and bFGF

tag: Cell line

value: human ES cell HES2


title: Resistant clinical isolate S2, experiment 1

hyb_protocol: The cRNA pellet was suspended in 10 μl of RNase-free water and 10 μg was fragmented by ion-mediated hydrolysis at 95 °C for 35 min in 200 mM Tris-acetate (pH 8.1), 500 mM potassium acetate, 150 mM magnesium acetate. The fragmented cRNA was hybridized for 16 h at 45 °C to the C. albicans NimbleExpress GeneChip arrays. Arrays were washed at 25 °C with 6 × SSPE, 0.01% Tween 20 followed by a stringent wash at 50 °C with 100 mM MES, 0.1 M NaCl, 0.01% Tween 20. Hybridizations and washes employed the Affymetrix Fluidics Station 450 using their standard EukGE-WS2v5 protocol. The arrays were then stained with phycoerythrein-conjugated streptavidin (Molecular Probes).

source_name: Clinical resistant isolate, experiment 1

tag: Clinical resistant isolate S2.


title: HES2_Mir122Mut_rep3

source_name: hESC transduced with mutant miR-122-expressing lentiviral vector


title: Susceptible clinical isolate S1, experiment 2

source_name: Clinical susceptible isolate, experiment 2

tag: Clinical susceptible isolate S1


title: ING4 ChIP-chip + Doxorubicin treatment

first: Tiffany

last: Hung

address: 371 SERRA MALL

institute: Stanford University

description: HG18 array 1 of 2

hyb_protocol: standard manufacturer's protocol

scan_protocol: Arrays were scanned with Axon scanner at 5 um resolution according to standard Nimblegen protocols

data_processing: Arrays were processed using Nimblegens standard protocol for Nimblescan 2.4 ChIP data extraction

source_name: ChIP DNA

label_protocol: Nimblegen ChIP labeling protocol (1 ug of Amplified ChIP DNA, direct incorporation of cy labeled primers with klenow extension)

growth_protocol: DMEM + 10% FBS

extract_protocol: ChIP samples collected as in http://www.genomecenter.ucdavis.edu/farnham/pdf/FarnhamLabChIP%20Protocol.pdf

treatment_protocol: Doxorubicin 400 ng/ul, 4 hours

tag: HT1080 cell line stably expressing Flag-ING4

source_name: Input DNA


title: Resistant clinical isolate S2, experiment 2

source_name: Clinical resistant isolate, experiment 2

tag: Clinical resistant isolate S2


title: HES2_Mir122WT_rep1


title: HES2_Mir122Mut_rep2


title: HES2_Mir122Mut_rep1


title: Total RNA RBM35A+

city: Buffalo

first: Yurij

last: Ionov

state: NY

address: Elm and Carlton streets

department: Cancer Genetics

institute: Roswell Park Cancer Institute

description: The biotin-labeled target synthesis reactions, as well as the Affymetrix HG-U95Av2 GeneChip arrays hybridization, staining, and scanning, were performed using Affymetrix standard protocols (Affymetrix, Santa Clara, CA).

hyb_protocol: Samples were hybridized to the Affymetrix HG-U95Av2 GeneChips according to manufacturer's instructions in the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.

scan_protocol: HG-U95Av2 GeneChips were scanned using Affymetrix GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions.

data_processing: Affymetrix HG-U95Av2 data were imported as .CEL files into R using the Affy scripting library. Quantile normalization between the arrays and signal estimation was performed using bioconductor gcRMA.quant command

source_name: LS180 colon carcinoma cell line

label_protocol: The analysis was performed at the Gene Expression facility of Roswell Park Cancer Institute, as follows.  Ten micrograms of total RNA from RBM35+ and RBM35- cells were used to synthesize double-stranded cDNA using a SuperScript II reverse transcriptase kit (Invitrogen).  Biotinylated cRNA was synthesized from double-stranded cDNA using the Enzo Bioarray High Yield transcript labeling kit (EnzoLife Sciences), then purified using the GeneChip sample cleanup module (Affymetrix) and fragmented.  Fragmented cRNA was hybridized to Affymetrix HG-U95Av2 GeneChips.

extract_protocol: Tet-off LS180 -RBM35A cells with restored expression of RBM35A protein (incubated without Dox for at least six days) and their parental cells maintained in the presence of Dox were grown to no more than 80% confluency in 100mm-diameter plates with the indicated cells were harvested for each polysomal analysis.  The medium was removed and total RNA was extracted using TRIZOL reagent according to manufactureres instructions. The pellets were washed twice with 75% ethanol and resuspended in RNAse-free water.

tag: LS180 colon carcinoma cell line expressing RBM35A protein


title: Total RNA RBM35A-

tag: LS180 colon carcinoma cell line not expressing RBM35A protein


title: Susceptible clinical isolate S1, experiment 1

source_name: Clinical susceptible isolate, experiment 1


title: ING4 PHD mutant ChIP-chip + Doxorubicin treatment

description: HG18 array 1 of 2

tag: HT1080 cell line stably expressing Flag-ING4-D213A


title: UPC2M2K21B, experiment 2

source_name: UPC2 S1 allele in UPC2 disruption strain B, experiment 2


title: ING4 PHD mutant ChIP-chip

description: HG18 array 1 of 2

tag: HT1080 cell line stably expressing ING4-D213A


title: Breast 74 nulliparous case HuIII

status: Public on Nov 04 2008

city: Philadelphia

first: Julia

last: Santucci-Pereira

state: PA

address: 333 Cottman Ave, P2051

institute: Fox Chase Cancer Center

description: Biological replicate: 8 of 8- Nulliparous case

hyb_protocol: The Cy5-labeled probes (15 μl) were combined with its corresponding human reference Cy3-labeled probes (15 μl). The probes were denatured at 98˚C for 3 min and spun at 13,000 rpm for 3 min at room temperature. The products were pipetted onto arrays, coverslips were applied, and the slides were placed in a hybridization chamber (GeneMachines, from GeneMachines Company). Arrays were incubated in a water bath at 42˚C for 16 h, and subsequently washed with 0.5X SSC, 0.01% (wt/vol) SDS, followed by 0.06X SSC, at room temperature for 10 min each. Slides were spun for 5 min at 800 rpm (130 g) at room temperature.

scan_protocol: Arrays were read with a Affymetrix 428 fluorescent scanner (MWG Technologies) at 10 μm resolution and variable photomultiplier tube (PMT) voltage settings to obtain the maximal signal intensities with <1% (wt/vol) probe saturation. The resulting images were analyzed using ImaGene version 4.2 and GeneSight version 4.0 (Biodiscovery, Inc., San Diego, CA) software.

data_processing: For detecting the differential expression of genes background correction using the normexp method in Linear Models for Microarray Data was done for adjusting the local median background.An offset of 100 was used for both channels to further damp down the variability of log ratios for low-intensity spots. The resulting log ratios were normalized by using the print-tip group Lowess method with span 0.4.

source_name: Breast biopsy from nulliparous case

label_protocol: The total RNA was amplified using a PCR method based on dT-T7-RNA amplification. We have adopted the direct labeling of probes with using 5 μg of amplified RNA (8 μl) combined with amine-modified random primer (2 μg/μl, 1 μl) and RNase inhibitor (5 ug/μl, 1 ul). μl). The mix was incubated at 70˚C for 10 min, and then chilled on ice for 10 min. Primer-RNA solution was added to the reverse transcriptase mix (5X first-strand buffer, 6 μl; 50X aa-dUTP/dNTPs (25 mM dATP, dGTP, and dCTP, 15 mM dTTP, and 10 mM aminoallyl-dUTP), 0.6 μl; DTT, 0.1 M, 3 μl; SuperScript II reverse transcriptase (Invitrogen/Life Technologies), 2 μl) and incubated at 42˚C for 2 h. The reaction was terminated by adding EDTA (0.5 M, 10 μl), and the RNA was hydrolyzed with NaOH (1 M, 10 μl) at 65˚C for 30 min. Probes were cleaned with a QIAquick PCR purification kit (Qiagen); the Cy3- and Cy5-labeled products were combined, followed by 500 μl of Buffer PB. The samples were applied to QIA quick columns. Elutes were partially dried in a vacuum centrifuge and then resuspended in 15 μl of hybridization buffer.

extract_protocol: From laser capture microdissection samples the RNA was extracted using TRIzol according with manufacturer's protocol

tag: Age at diagnosis:55

tag: Age at first birth

tag: Parity status:Nulliparous case

tag: Breast biopsy diagnosis:Invasive ductal carcinoma

source_name: Universal human reference

extract_protocol: not applicable

tag: Stratagene Human Reference


title: Breast 72 nulliparous case HuIII

description: Biological replicate: 6 of 8- Nulliparous case

tag: Age at diagnosis:57

label_protocol: direct labeling of probes with using 5 μg of amplified RNA (8 μl) combined with amine-modified random primer (2 μg/μl, 1 μl) and RNase inhibitor (5 ug/μl, 1 ul). μl). The mix was incubated at 70˚C for 10 min, and then chilled on ice for 10 min. Primer-RNA solution was added to the reverse transcriptase mix (5X first-strand buffer, 6 μl; 50X aa-dUTP/dNTPs (25 mM dATP, dGTP, and dCTP, 15 mM dTTP, and 10 mM aminoallyl-dUTP), 0.6 μl; DTT, 0.1 M, 3 μl; SuperScript II reverse transcriptase (Invitrogen/Life Technologies), 2 μl) and incubated at 42˚C for 2 h. The reaction was terminated by adding EDTA (0.5 M, 10 μl), and the RNA was hydrolyzed with NaOH (1 M, 10 μl) at 65˚C for 30 min. Probes were cleaned with a QIAquick PCR purification kit (Qiagen); the Cy3- and Cy5-labeled products were combined, followed by 500 μl of Buffer PB. The samples were applied to QIA quick columns. Elutes were partially dried in a vacuum centrifuge and then resuspended in 15 μl of hybridization buffer.


title: Breast 71 nulliparous case HuIII

description: Biological replicate: 5 of 8- Nulliparous case

tag: Age at diagnosis:87


title: Breast 73 nulliparous case HuIII

description: Biological replicate: 7 of 8- Nulliparous case

tag: Breast biopsy diagnosis:Invasive lobular carcinoma


title: Breast 69 nulliparous case HuIII

description: Biological replicate: 3 of 8- Nulliparous case

tag: Age at diagnosis:77


title: UPC2M4B, experiment 2

source_name: UPC2 disruption strain in SC5314 strain B, experiment 2


title: Breast 65 nulliparous control HuIII

description: Biological replicate: 6 of 7- Nulliparous control

source_name: Breast biopsy from nulliparous control

tag: Age at diagnosis:50

tag: Parity status:Nulliparous control

tag: Breast biopsy diagnosis:Apocrine metaplasia, stromal fibrosis


title: Breast 63 nulliparous control HuIII

description: Biological replicate: 4 of 7- Nulliparous control

tag: Age at diagnosis:51

tag: Breast biopsy diagnosis:Fibroadenoma, papilloma


title: Breast 59 parous case HuIII

description: Biological replicate: 39 of 39- Parous case

source_name: Breast biopsy from parous case

tag: Age at diagnosis:63

tag: Parity status:Parous case

tag: Breast biopsy diagnosis:Invasive ductal carcinoma and DCIS


title: Breast 68 nulliparous case HuIII

description: Biological replicate: 2 of 8- Nulliparous case

tag: Age at diagnosis:68

tag: Breast biopsy diagnosis:Invasive ductal and lobular carcinoma


title: Breast 70 nulliparous case HuIII

description: Biological replicate: 4 of 8- Nulliparous case

tag: Age at diagnosis:74

tag: Age at first birth

tag: Parity status:Nulliparous case


title: E.ch-p200 HG18 2 of 2

description: Chip-chip p200 THP1 cells

source_name: p200 ChIP DNA from highly infected (95%) THP-1cells by Ehrlichia chaffeensis

tag: Age

tag: Tissue

tag: Antibody

source_name: Input DNA from uninfected THP-1 cells


title: Breast 64 nulliparous control HuIII

description: Biological replicate: 5 of 7- Nulliparous control

tag: Age at diagnosis:53

tag: Breast biopsy diagnosis:Stromal fibrosis

tag: Stratagene Human Reference


title: Breast 58 parous case HuIII

description: Biological replicate: 38 of 39- Parous case

tag: Age at diagnosis:66


title: Breast 66 nulliparous control HuIII

description: Biological replicate: 7 of 7- Nulliparous control

tag: Age at diagnosis:58

tag: Parity status:Nulliparous control

tag: Breast biopsy diagnosis:Adenosis


title: Breast 60 nulliparous control HuIII

description: Biological replicate: 1 of 7- Nulliparous control

tag: Age at diagnosis:65


title: Breast 67 nulliparous case HuIII

description: Biological replicate: 1 of 8- Nulliparous case

tag: Breast biopsy diagnosis:Invasive ductal carcinoma


title: Breast 61 nulliparous control HuIII

description: Biological replicate: 2 of 7- Nulliparous control

tag: Age at diagnosis:62

tag: Breast biopsy diagnosis:Fibroadenoma


title: Breast 56 parous case HuIII

description: Biological replicate: 36 of 39- Parous case

tag: Age at diagnosis:61

tag: Parity status:Parous case


title: Breast 57 parous case HuIII

description: Biological replicate: 37 of 39- Parous case

tag: Age at diagnosis:60

tag: Age at first birth


title: Breast 51 parous case HuIII

description: Biological replicate: 31 of 39- Parous case

tag: Age at diagnosis:73

tag: Breast biopsy diagnosis:Invasive lobular carcinoma and LCIS


title: Breast 52 parous case HuIII

description: Biological replicate: 32 of 39- Parous case

tag: Age at diagnosis:70

tag: Breast biopsy diagnosis:Invasive lobular carcinoma


title: Breast 53 parous case HuIII

description: Biological replicate: 33 of 39- Parous case

tag: Age at diagnosis:92

tag: Breast biopsy diagnosis:Invasive lobular Carcinoma

tag: Stratagene Human Reference


title: Breast 50 parous case HuIII

description: Biological replicate: 30 of 39- Parous case

tag: Age at diagnosis:58


title: Breast 55 parous case HuIII

description: Biological replicate: 35 of 39- Parous case

tag: Breast biopsy diagnosis:Invasive ductal carcinoma and DCIS


title: Breast 54 parous case HuIII

description: Biological replicate: 34 of 39- Parous case


title: Breast 48 parous case HuIII

description: Biological replicate: 28 of 39- Parous case

tag: Age at diagnosis:75


title: Breast 47 parous case HuIII

description: Biological replicate: 27 of 39- Parous case

tag: Age at diagnosis:79

tag: Breast biopsy diagnosis:Invasive ductal carcinoma


title: Breast 49 parous case HuIII

description: Biological replicate: 29 of 39- Parous case

tag: Age at diagnosis:82


title: Breast 46 parous case HuIII

description: Biological replicate: 26 of 39- Parous case

tag: Age at diagnosis:76


title: Breast 38 parous case HuIII

description: Biological replicate: 18 of 39- Parous case

tag: Age at diagnosis:65

tag: Parity status:Parous case


title: Breast 33 parous case HuIII

description: Biological replicate: 15 of 39- Parous case

tag: Age at diagnosis:67

tag: Age at first birth


title: Breast 39 parous case HuIII

description: Biological replicate: 19 of 39- Parous case

tag: Age at diagnosis:74


title: Breast 41 parous case HuIII

description: Biological replicate: 21 of 39- Parous case


title: Breast 34 parous case HuIII

description: Biological replicate: 16 of 39- Parous case

tag: Age at diagnosis:55


title: Breast 44 parous case HuIII

description: Biological replicate: 24 of 39- Parous case

tag: Breast biopsy diagnosis:Invasive lobular carcinoma


title: Breast 35 parous case HuIII

description: Biological replicate: 17 of 39- Parous case


title: Breast 40 parous case HuIII

description: Biological replicate: 20 of 39- Parous case

tag: Age at diagnosis:62


title: Breast 42 parous case HuIII

description: Biological replicate: 22 of 39- Parous case

tag: Age at diagnosis:81


title: Breast 45 parous case HuIII

description: Biological replicate: 25 of 39- Parous case

tag: Stratagene Human Reference


title: Breast 31 parous case HuIII

description: Biological replicate: 13 of 39- Parous case

tag: Breast biopsy diagnosis:Invasive Ductal carcinoma


title: Breast 43 parous case HuIII

description: Biological replicate: 23 of 39- Parous case

tag: Age at diagnosis:56

tag: Breast biopsy diagnosis:Invasive ductal carcinoma and DCIS


title: Breast 30 parous case HuIII

description: Biological replicate: 12 of 39- Parous case

tag: Age at diagnosis:59

tag: Breast biopsy diagnosis:Invasive Ductal carcinoma and DCIS


title: Breast 32 parous case HuIII

description: Biological replicate: 14 of 39- Parous case

tag: Age at diagnosis:84

tag: Breast biopsy diagnosis:Invasive ductal carcinoma


title: Breast 28 parous case HuIII

description: Biological replicate: 10 of 39- Parous case

tag: Age at diagnosis:76

tag: Breast biopsy diagnosis:Mucinous adenocarcinoma


title: Breast 27 parous case HuIII

description: Biological replicate: 9 of 39- Parous case

tag: Age at diagnosis:75

tag: Parity status:Parous case


title: Breast 26 parous case HuIII

description: Biological replicate: 8 of 39- Parous case

tag: Age at first birth


title: Breast 29 parous case HuIII

description: Biological replicate: 11 of 39- Parous case

tag: Age at diagnosis:78


title: Breast 24 parous case HuIII

description: Biological replicate: 6 of 39- Parous case

tag: Age at diagnosis:57


title: Breast 23 parous case HuIII

description: Biological replicate: 5 of 39- Parous case

tag: Age at diagnosis:72


title: Breast 21 parous case HuIII

description: Biological replicate: 3 of 39- Parous case

tag: Age at diagnosis:55

tag: Breast biopsy diagnosis:Invasive Ductal and lobular carcinoma


title: Breast 25 parous case HuIII

description: Biological replicate: 7 of 39- Parous case

tag: Age at diagnosis:74

tag: Breast biopsy diagnosis:Invasive ductal and lobular carcinoma

tag: Stratagene Human Reference


title: Breast 22 parous case HuIII

description: Biological replicate: 4 of 39- Parous case

tag: Age at diagnosis:60


title: Breast 18 parous control HuIII

description: Biological replicate: 17 of 17- Parous control

source_name: Breast biopsy from parous control

tag: Parity status:Parous control

tag: Breast biopsy diagnosis:Benign breast disease


title: ING4 ChIP-chip

description: HG18 array 1 of 2

tag: Ht1080 cell line stably expressing Flag-ING4


title: Breast 15 parous control HuIII

description: Biological replicate: 15 of 17- Parous control

tag: Breast biopsy diagnosis:Adenosis


title: Breast 4 parous control HuIII

description: Biological replicate: 4 of 17- Parous control

tag: Age at diagnosis:61

tag: Breast biopsy diagnosis:Fibrocystic changes


title: Breast 6 parous control HuIII

description: Biological replicate: 6 of 17- Parous control

tag: Breast biopsy diagnosis:Fibroadenoma, adenosis


title: Breast 5 parous control HuIII

description: Biological replicate: 5 of 17- Parous control

tag: Age at first birth

tag: Breast biopsy diagnosis:Ductal hyperplasia, mild


title: Breast 9 parous control HuIII

description: Biological replicate: 9 of 17- Parous control

tag: Age at diagnosis:64


title: Breast 7 parous control HuIII

description: Biological replicate: 7 of 17- Parous control

tag: Age at diagnosis:52

tag: Breast biopsy diagnosis:Adenosis, ductal ectasia


title: Breast 11 parous control HuIII

description: Biological replicate: 11 of 17- Parous control

tag: Age at diagnosis:59

tag: Breast biopsy diagnosis:Papilloma


title: Breast 20 parous case HuIII

description: Biological replicate: 2 of 39- Parous case

tag: Parity status:Parous case

tag: Breast biopsy diagnosis:Invasive Ductal Carcinoma


title: Breast 10 parous control HuIII

description: Biological replicate: 10 of 17- Parous control

tag: Age at diagnosis:71

tag: Stratagene Human Reference


title: Breast 19 parous case HuIII

description: Biological replicate: 1 of 39- Parous case

tag: Breast biopsy diagnosis:Invasive Ductal carcinoma


title: Breast 17 parous control HuIII

description: Biological replicate: 16 of 17- Parous control

tag: Age at diagnosis:72

tag: Parity status:Parous control


title: Breast 1 parous control HuIII

description: Biological replicate: 1 of 17- Parous control

tag: Age at diagnosis:50


title: Breast 12 parous control HuIII

description: Biological replicate: 12 of 17- Parous control

tag: Age at diagnosis:63


title: Breast 13 parous control HuIII

description: Biological replicate: 13 of 17- Parous control

tag: Age at diagnosis:61

tag: Breast biopsy diagnosis:Stromal fibrosis


title: Breast 14 parous control HuIII

description: Biological replicate: 14 of 17- Parous control

tag: Age at diagnosis:77

tag: Age at first birth

tag: Breast biopsy diagnosis:Adenosis


title: Breast 2 parous control HuIII

description: Biological replicate: 2 of 17- Parous control

tag: Breast biopsy diagnosis:Ductal hyperplasia


title: Breast 8 parous control HuIII

description: Biological replicate: 8 of 17- Parous control

tag: Breast biopsy diagnosis:Apocrine metaplasia


title: Breast 3 parous control HuIII

description: Biological replicate: 3 of 17- Parous control

tag: Age at diagnosis:55

tag: Breast biopsy diagnosis:Fibroadenoma


title: Breast 70 nulliparous case HuI

description: Biological replicate: 4 of 8- Nulliparous case

hyb_protocol: The Cy5-labeled probes (15 μl) were combined with its corresponding human reference Cy3-labeled probes (15 μl). The probes were denatured at 98˚C for 3 min and spun at 13,000 rpm for 3 min at room temperature. The products were pipetted onto arrays, cover

scan_protocol: Arrays were read with a Affymetrix 428 fluorescent scanner (MWG Technologies) at 10 μm resolution and variable photomultiplier tube (PMT) voltage settings to obtain the maximal signal intensities with <1% (wt/vol) probe saturation. The resulting images we

label_protocol: The total RNA was amplified using a PCR method based on dT-T7-RNA amplification. We have adopted the direct labeling of probes with using 5 μg of amplified RNA (8 μl) combined with amine-modified random primer (2 μg/μl, 1 μl) and RNase inhibitor (5 ug/μl, 1 ul).

tag: Age at diagnosis:74

tag: Parity status:Nulliparous case

tag: Breast biopsy diagnosis:Invasive ductal carcinoma


title: Breast 72 nulliparous case HuI

description: Biological replicate: 6 of 8- Nulliparous case

tag: Age at diagnosis:57

label_protocol: direct labeling of probes with using 5 μg of amplified RNA (8 μl) combined with amine-modified random primer (2 μg/μl, 1 μl) and RNase inhibitor (5 ug/μl, 1 ul).

tag: Stratagene Human Reference


title: Breast 71 nulliparous case HuI

description: Biological replicate: 5 of 8- Nulliparous case

tag: Age at diagnosis:87


title: Skeletal Muscle versus Liver Animal 4

city: East Lansing

first: Catherine

middle: W.

last: Ernst

state: MI

address: 3330 Anthony Hall

department: Animal Science

institute: Michigan State University

description: The tissue samples compared on this array are part of an experiment to validate the swine protein annotated oligonucleotide microarray.

hyb_protocol: Labeled aRNAs were purified and combined with 65 µl of Slide Hyb #1 solution (Ambion, Inc.) and denatured at 70C for 5 min. Hybridizations were performed in sealed hybridization cassettes (ArrayIt, TeleChem International, Inc., Sunnyvale, CA, USA) for 18 h at a humid 54C. Following hybridization, slides were washed in 2X SSC/0.5% SDS and 0.1X SSC/0.1% SDS solutions for 10 min each. The slides were rinsed in a 0.1X SSC solution and nuclease-free water and dried by centrifugation.

scan_protocol: Fluorescent images were detected by a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA) and fluorescence intensity data were collected using GenePix software (Molecular Devices) after spot alignment. Median intensity values for each dye channel were stored as comma-separated values data files.

data_processing: Loess normalized log-ratio of Cy5 versus Cy3 intensities. No background correction.

organism: Sus scrofa

source_name: Skeletal Muscle Animal 4

label_protocol: Five µg of total RNA were reverse transcribed with a T7 oligo(dT) primer using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion Inc., Austin, TX, USA) according to the manufacturer’s instructions. Following first-strand and second-strand synthesis and purification, the cDNAs were in vitro transcribed to synthesize multiple copies of amino allyl-modified aRNAs. After purification, aRNAs were labeled with N-hydroxysuccinate (NHS) ester Cy3  (GE Healthcare, UK).

extract_protocol: Total RNA from 1.0 g of tissue was extracted using TRIzol reagent (Invitrogen Corp., Carlsbad, CA, USA) according to the manufacturer’s instructions. RNA concentration and quality were determined with an RNA 6000 Pico LabChip® kit using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Palo Alto, CA, USA).

tag: Tissue

value: Skeletal Muscle;

tag: Gender

value: Female;

tag: Age

value: 165 days.

source_name: Liver Animal 4

label_protocol: Five µg of total RNA were reverse transcribed with a T7 oligo(dT) primer using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion Inc., Austin, TX, USA) according to the manufacturer’s instructions. Following first-strand and second-strand synthesis and purification, the cDNAs were in vitro transcribed to synthesize multiple copies of amino allyl-modified aRNAs. After purification, aRNAs were labeled with N-hydroxysuccinate (NHS) ester Cy5  (GE Healthcare, UK).

value: Liver;


title: Breast 73 nulliparous case HuI

description: Biological replicate: 7 of 8- Nulliparous case

tag: Breast biopsy diagnosis:Invasive lobular carcinoma


title: Uterine Endothelium versus Skeletal Muscle Animal 4

source_name: Uterine Endothelium Animal 4

value: Uterine Endothelium;


title: Breast 65 nulliparous control HuI

description: Biological replicate: 6 of 7- Nulliparous control

tag: Age at diagnosis:50

tag: Parity status:Nulliparous control

tag: Breast biopsy diagnosis:Apocrine metaplasia, stromal fibrosis


title: Breast 67 nulliparous case HuI

description: Biological replicate: 1 of 8- Nulliparous case

tag: Age at diagnosis:53

tag: Age at first birth


title: Breast 68 nulliparous case HuI

description: Biological replicate: 2 of 8- Nulliparous case

tag: Age at diagnosis:68

tag: Breast biopsy diagnosis:Invasive ductal and lobular carcinoma


title: Breast 66 nulliparous control HuI

description: Biological replicate: 7 of 7- Nulliparous control

tag: Age at diagnosis:58

tag: Breast biopsy diagnosis:Adenosis


title: Brain versus Uterine Endothelium Animal 4

source_name: Brain Animal 4

value: Brain;


title: Liver versus Brain Animal 4


title: Breast 64 nulliparous control HuI

description: Biological replicate: 5 of 7- Nulliparous control

tag: Breast biopsy diagnosis:Stromal fibrosis


title: Skeletal Muscle versus Uterine Endothelium Animal 3

source_name: Skeletal Muscle Animal 3

source_name: Uterine Endothelium Animal 3


title: Breast 56 parous case HuI

description: Biological replicate: 36 of 39- Parous case

tag: Age at diagnosis:61

tag: Parity status:Parous case

tag: Breast biopsy diagnosis:Invasive ductal carcinoma


title: Uterine Endothelium versus Brain Animal 2

source_name: Uterine Endothelium Animal 2

tag: Tissue

source_name: Brain Animal 2


title: Breast 74 nulliparous case HuII

description: Biological replicate: 8 of 8- Nulliparous case

data_processing: For detecting the differential expression of genes background correction using the normexp method in Linear Models for Microarray Data was done for adjusting the local median background.An offset of 100 was used for both channels to further damp down the variability of log ratios for low-intensity spots. The resulting log ratios were normalized by using the print-tip group Lowess method with span 0.4

tag: Age at diagnosis:55

tag: Parity status:Nulliparous case

tag: Stratagene Human Reference


title: Brain versus Skeletal Muscle Animal 3

source_name: Brain Animal 3

tag: Gender

tag: Age


title: Breast 59 parous case HuI

description: Biological replicate: 39 of 39- Parous case

tag: Age at diagnosis:63

tag: Breast biopsy diagnosis:Invasive ductal carcinoma and DCIS


title: Breast 69 nulliparous case HuI

description: Biological replicate: 3 of 8- Nulliparous case

source_name: Breast biopsy from nulliparous case

tag: Age at diagnosis:77

tag: Age at first birth


title: Breast 61 nulliparous control HuI

description: Biological replicate: 2 of 7- Nulliparous control

tag: Age at diagnosis:62

tag: Parity status:Nulliparous control

tag: Breast biopsy diagnosis:Fibroadenoma

source_name: Universal human reference


title: Breast 74 nulliparous case HuI


title: Breast 53 parous case HuI

description: Biological replicate: 33 of 39- Parous case

tag: Age at diagnosis:92

tag: Breast biopsy diagnosis:Invasive lobular Carcinoma


title: Brain Versus Skeletal Muscle Animal 2

source_name: Skeletal Muscle Animal 2


title: Uterine Endothelium versus Liver Animal 3

source_name: Liver Animal 3


title: Breast 73 nulliparous case HuII

tag: Age at diagnosis:57

tag: Breast biopsy diagnosis:Invasive lobular carcinoma


title: Breast 55 parous case HuI

description: Biological replicate: 35 of 39- Parous case

source_name: Breast biopsy from parous case

tag: Age at diagnosis:60

tag: Parity status:Parous case


title: Breast 57 parous case HuI

description: Biological replicate: 37 of 39- Parous case

tag: Breast biopsy diagnosis:Invasive ductal carcinoma


title: Breast 63 nulliparous control HuI

description: Biological replicate: 4 of 7- Nulliparous control

source_name: Breast biopsy from nulliparous control

tag: Age at diagnosis:51

tag: Breast biopsy diagnosis:Fibroadenoma, papilloma

tag: Stratagene Human Reference


title: Breast 72 nulliparous case HuII

description: Biological replicate: 6 of 8- Nulliparous case

tag: Parity status:Nulliparous case


title: Breast 71 nulliparous case HuII

description: Biological replicate: 5 of 8- Nulliparous case

tag: Age at diagnosis:87


title: Breast 54 parous case HuI

description: Biological replicate: 34 of 39- Parous case

tag: Age at diagnosis:70


title: Breast 58 parous case HuI

description: Biological replicate: 38 of 39- Parous case

tag: Age at diagnosis:66

tag: Age at first birth

tag: Breast biopsy diagnosis:Invasive ductal carcinoma and DCIS


title: Breast 69 nulliparous case HuII

tag: Age at diagnosis:77


title: Liver versus Brain Animal 3

description: The tissue samples compared on this array are part of an experiment to validate the swine protein annotated oligonucleotide microarray.

tag: Tissue

tag: Gender

tag: Age


title: Breast 51 parous case HuI

description: Biological replicate: 31 of 39- Parous case

tag: Age at diagnosis:73

tag: Breast biopsy diagnosis:Invasive lobular carcinoma and LCIS


title: Breast 62 nulliparous control HuI

description: Biological replicate: 3 of 7- Nulliparous control

tag: Age at diagnosis:58

tag: Parity status:Nulliparous control

tag: Breast biopsy diagnosis:Papilloma


title: Skeletal Muscle versus Liver Animal 2

source_name: Liver Animal 2


title: Breast 50 parous case HuI

description: Biological replicate: 30 of 39- Parous case

tag: Parity status:Parous case

tag: Breast biopsy diagnosis:Invasive ductal carcinoma


title: Breast 52 parous case HuI

description: Biological replicate: 32 of 39- Parous case

tag: Breast biopsy diagnosis:Invasive lobular carcinoma

tag: Stratagene Human Reference


title: Breast 49 parous case HuI

description: Biological replicate: 29 of 39- Parous case

tag: Age at diagnosis:82


title: Liver versus Uterine Endothelium Animal 2


title: Breast 70 nulliparous case HuII

description: Biological replicate: 4 of 8- Nulliparous case

tag: Age at diagnosis:74

tag: Parity status:Nulliparous case


title: Breast 68 nulliparous case HuII

description: Biological replicate: 2 of 8- Nulliparous case

tag: Age at diagnosis:68

tag: Age at first birth

tag: Breast biopsy diagnosis:Invasive ductal and lobular carcinoma


title: Skeletal Muscle versus Uterine Endothelium Animal 1

source_name: Skeletal Muscle Animal 1

tag: Tissue

tag: Gender

source_name: Uterine Endothelium Animal 1


title: MLL-germline_ALL_H3K79 (7 samples)

city: Plantagenet

first: Madeleine

middle: E.

last: Lemieux

state: ON

address: 275 Main St., Suite 252

country: Canada

institute: Bioinfo

description: MLL-germline ALL H3K79 ChIP: ALL05008.CEL, ALL05016.CEL, ALL05031.CEL, ALL05048.CEL, ALL05157.CEL, ALL05165.CEL, ALL05004.CEL

hyb_protocol: 3 micrograms of labelled material was hybridized according to the standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol

data_processing: Regions of above-background signal were identified by Model-based Analysis of Tiling array (MAT) software (http://chip.dfci.harvard.edu/~wli/MAT/) run with bandwidth = 300, max gap = 300, minimum probes = 10 and p-value cutoff = 1x10e-5 and using a bpmap for human NCBI genome build 36 (Hg18) downloaded from the MAT website.

source_name: H3K79me2 ChIP of MLL-germline ALL bone marrow

label_protocol: Each ChIP was amplified using ligation-mediated PCR (LM-PCR). Labeling was according to standard Affymetrix protocols.

extract_protocol: 3-10×10e5 cells were used. Briefly, cells were cross-linked by addition of 1% formaldehyde for 10 min at room temp. Cross-linking was terminated by adding final 125 mM glycine and cells were washed with cold PBS containing PMSF, collected by centrifugation and washed in PBS twice. The pellet was resuspended in SDS buffer (50 mM Tris-Cl pH 8.1; 100 mM NaCl; 0.5% SDS; 5 mM EDTA; 0.2% NaN3 and protease inhibitors) and snap frozen.  After thawing the nuclear pellets were collected by centrifugation and resuspended in ChIP buffer (50mM Tris 8.1; 100mM NaCl; 0.3% SDS; 1.5% Triton X-100; 5 mM EDTA; 0.2% NaN3; and protease inhibitors). Cells were sonicated to fragment DNA to an average size of 0.5-1 kb. The sample was centrifuged at 10000g at 4° C for 10 min, the supernatant collected and pre-cleared with protein-A beads at 4°C for 2 hrs. The sample was then incubated with anti-dimethyl H3K79 antibody (ab# ab3594) and protein-A beads at 4°C overnight. Immunoprecipitated protein-DNA complexes were sequentially washed with Mixed Micelle buffer (20 mM Tris pH 8.1; 150mM NaCl; 5mM EDTA; 0.5% SDS; 1% Triton X-100; 6% Sucrose), buffer 500 (0.1% Deoxycholate, 1% Triton X-100, 1 mM EDTA, 50 mM HEPES pH 7.5, 500 mM NaCl), LiCl buffer (250 mM LiCl, 0.5% NP-40, 0.5% Deoxycholate, 1 mM EDTA, 10 mM Tris-Cl pH 8.1) and TE buffer (10 mM Tris-Cl pH 7.5, 1 mM EDTA). All washes were for 5 min at 4C. Protein-DNA complexes were eluted in TE with 1%SDS buffer supplemented with proteinase K (500u) for 3 hrs at 55oC. The sample was treated with RNase A and DNA fragments were purified using Qiagen's PCR purification kit, and eluted in 100 ul of TE buffer.

tag: MLL-germline ALL bone marrow


title: Breast 67 nulliparous case HuII

description: Biological replicate: 1 of 8- Nulliparous case

tag: Age at diagnosis:53


title: Breast 66 nulliparous control HuII

description: Biological replicate: 7 of 7- Nulliparous control

tag: Age at diagnosis:58

tag: Breast biopsy diagnosis:Adenosis


title: Breast 65 nulliparous control HuII

description: Biological replicate: 6 of 7- Nulliparous control

tag: Age at diagnosis:50

tag: Parity status:Nulliparous control

tag: Breast biopsy diagnosis:Apocrine metaplasia, stromal fibrosis


title: CD34_CD19_H3K79 (5 samples)

description: normal CD34+CD19+ H3K79 CHIP:  CD34_CD19_1.CEL, CD34_CD19_2.CEL, CD34_CD19_3.CEL, CD34_CD19_4.CEL, CD34_CD19_5.CEL

source_name: H3K79me2 ChIP of normal CD34+ CD19+ cells

tag: Purified normal bone marrow CD34+ CD19+ lympoid progenitors


title: Breast 47 parous case HuI

description: Biological replicate: 27 of 39- Parous case

tag: Age at diagnosis:79

tag: Parity status:Parous case

tag: Breast biopsy diagnosis:Invasive ductal carcinoma

tag: Stratagene Human Reference


title: MLL-rearranged_ALL_H3K79 (5 samples)

description: MLL-rearranged ALL H3K79 CHIP: MLL-AF4_061505_HsProm.CEL, MLL-AF4_A37_HsProm.CEL, MLL-AF4_06078_HsProm.CEL, MLL-ENL_06078_HsProm.CEL, MLL-AF4_05015_HsProm.CEL

source_name: H3K79me2 ChIP of MLL-rearranged ALL bone marrow

tag: MLL-rearranged ALL bone marrow


title: Liver vs Skeletal Muscle sample 1

source_name: Liver animal 1

tag: Age

source_name: Skeletal Muscle animal 1


title: Uterine Endothelium versus Brain Animal 1

source_name: Brain Animal 1


title: Breast 48 parous case HuI

description: Biological replicate: 28 of 39- Parous case

tag: Age at diagnosis:75

tag: Age at first birth


title: Breast 60 nulliparous control HuI

description: Biological replicate: 1 of 7- Nulliparous control

tag: Age at diagnosis:65


title: Breast 64 nulliparous control HuII

description: Biological replicate: 5 of 7- Nulliparous control

tag: Breast biopsy diagnosis:Stromal fibrosis


title: Breast 45 parous case HuI

description: Biological replicate: 25 of 39- Parous case


title: VUB26passage10

city: Brussels

first: Claudia

last: Spits

address: Laarbeeklaan 101

department: Embryology and Genetics

country: Belgium

institute: Vrije Universiteit Brussel

hyb_protocol: Array-CGH was performed as described by Vermeesch, J.R. et al. J. Histochem. Cytochem. 53, 413–422 (2005). 1500 ng of each labelled DNA were cohybridized. Hybridization time was between 24 and 72 hours

scan_protocol: Slides were scanned either using an Axon GenePix 4000B scanner (raw data files in gpr format) or a Agilent dual laser DNA microarray scanner G2566AA (Raw data files in txt format).

data_processing: All data is lowess normalized. The scan images were processed and data was normalized with using GenePix Pro software or the Agilent Feature Extraction Software v9.5.The final steps of data analysis were performed using Excel (Microsoft). The data obtained from the Agilent software was converted from log10 to log2.

source_name: Female reference DNA

label_protocol: Samples were labelled using the BioPrime Array CGH Genomic Labelling System; (Invitrogen, Carlsbad, CA) and Cy5- and Cy3-labelled dCTPs (GE Healthcare, Buckinghamshire, UK ), following the protocol as described by the manufacturer

growth_protocol: Human embryonic stem cells derived and cultured as described by Mateizel, I. et al. Hum. Reprod. 21, 503-511 (2006).

extract_protocol: Standard phenol-clorophorm DNA extraction followed by an ethanol precipitation and resuspended in distilled water

tag: 46, XX reference DNA

source_name: VUB26 passage 10

tag: Human embryonic stem cells


title: Breast 58 parous case HuII

description: Biological replicate: 38 of 39- Parous case

tag: Age at diagnosis:66

tag: Breast biopsy diagnosis:Invasive ductal carcinoma and DCIS


title: Breast 61 nulliparous control HuII

description: Biological replicate: 2 of 7- Nulliparous control

tag: Age at diagnosis:62

tag: Parity status:Nulliparous control

tag: Breast biopsy diagnosis:Fibroadenoma


title: Breast 44 parous case HuI

description: Biological replicate: 24 of 39- Parous case

tag: Age at diagnosis:82

tag: Breast biopsy diagnosis:Invasive lobular carcinoma


title: Breast 59 parous case HuII

description: Biological replicate: 39 of 39- Parous case

tag: Age at diagnosis:63

tag: Parity status:Parous case


title: Breast 57 parous case HuII

description: Biological replicate: 37 of 39- Parous case

tag: Age at diagnosis:60

tag: Breast biopsy diagnosis:Invasive ductal carcinoma

tag: Stratagene Human Reference


title: VUB24passage31

source_name: VUB24 passage 31

source_name: Male reference DNA

tag: 46, XY reference DNA


title: Breast 62 nulliparous control HuII

description: Biological replicate: 3 of 7- Nulliparous control

tag: Age at diagnosis:58

tag: Age at first birth

tag: Breast biopsy diagnosis:Papilloma

source_name: Universal human reference


title: Breast 60 nulliparous control HuII

tag: Age at diagnosis:65

tag: Breast biopsy diagnosis:Adenosis


title: VUB24passage10

source_name: VUB24 passage 10

tag: Human embryonic stem cells

tag: 46, XX reference DNA


title: Brain versus Liver Animal 1

description: The tissue samples compared on this array are part of an experiment to validate the swine protein annotated oligonucleotide microarray.

tag: Tissue

tag: Gender

tag: Age

source_name: Liver Animal 1


title: Breast 63 nulliparous control HuII

description: Biological replicate: 4 of 7- Nulliparous control

source_name: Breast biopsy from nulliparous control

tag: Age at diagnosis:51

tag: Parity status:Nulliparous control

tag: Breast biopsy diagnosis:Fibroadenoma, papilloma


title: Breast 55 parous case HuII

description: Biological replicate: 35 of 39- Parous case

source_name: Breast biopsy from parous case

tag: Age at diagnosis:60

tag: Parity status:Parous case

tag: Breast biopsy diagnosis:Invasive ductal carcinoma and DCIS


title: Breast 46 parous case HuI

description: Biological replicate: 26 of 39- Parous case

tag: Age at diagnosis:76

tag: Stratagene Human Reference


title: Breast 56 parous case HuII

description: Biological replicate: 36 of 39- Parous case

tag: Age at diagnosis:61

tag: Age at first birth

tag: Breast biopsy diagnosis:Invasive ductal carcinoma


title: VUB20_CMT1Apassage18

source_name: VUB20_CMT1A passage 18


title: Breast 42 parous case HuI

description: Biological replicate: 22 of 39- Parous case

tag: Age at diagnosis:81


title: Breast 43 parous case HuI

description: Biological replicate: 23 of 39- Parous case

tag: Age at diagnosis:56


title: Breast 41 parous case HuI

description: Biological replicate: 21 of 39- Parous case

tag: Age at diagnosis:65


title: Breast 52 parous case HuII

description: Biological replicate: 32 of 39- Parous case

tag: Age at diagnosis:70

tag: Breast biopsy diagnosis:Invasive lobular carcinoma


title: Breast 51 parous case HuII

description: Biological replicate: 31 of 39- Parous case

tag: Age at diagnosis:73

tag: Breast biopsy diagnosis:Invasive lobular carcinoma and LCIS


title: VUB19_DM1passage32

source_name: VUB19_DM1 passage 32

tag: Human embryonic stem cells

tag: 46, XY reference DNA


title: Breast 53 parous case HuII

description: Biological replicate: 33 of 39- Parous case

tag: Age at diagnosis:92

tag: Breast biopsy diagnosis:Invasive lobular Carcinoma


title: Breast 40 parous case HuI

description: Biological replicate: 20 of 39- Parous case

tag: Age at diagnosis:62

tag: Parity status:Parous case

tag: Breast biopsy diagnosis:Invasive ductal carcinoma and DCIS


title: Breast 49 parous case HuII

description: Biological replicate: 29 of 39- Parous case

tag: Age at diagnosis:82

tag: Stratagene Human Reference


title: Breast 50 parous case HuII

description: Biological replicate: 30 of 39- Parous case

tag: Age at diagnosis:58

tag: Age at first birth

tag: Breast biopsy diagnosis:Invasive ductal carcinoma


title: Breast 54 parous case HuII

description: Biological replicate: 34 of 39- Parous case


title: VUB20_CMT1Apassage7

source_name: VUB20_CMT1A passage 7


title: Breast 39 parous case HuI

description: Biological replicate: 19 of 39- Parous case

tag: Age at diagnosis:74


title: Breast 38 parous case HuI

description: Biological replicate: 18 of 39- Parous case

tag: Age at diagnosis:65


title: Breast 47 parous case HuII

description: Biological replicate: 27 of 39- Parous case

tag: Age at diagnosis:79


title: Breast 48 parous case HuII

description: Biological replicate: 28 of 39- Parous case

tag: Age at diagnosis:75


title: Breast 32 parous case HuI

description: Biological replicate: 14 of 39- Parous case

tag: Age at diagnosis:84


title: VUB13_FXSpassage43

source_name: VUB13_FXS passage 43

tag: Human embryonic stem cells

tag: 46, XX reference DNA


title: Breast 42 parous case HuII

tag: Age at diagnosis:81


title: Breast 33 parous case HuI

description: Biological replicate: 15 of 39- Parous case

tag: Age at diagnosis:67


title: Breast 30 parous case HuI

description: Biological replicate: 12 of 39- Parous case

tag: Age at diagnosis:59

tag: Breast biopsy diagnosis:Invasive Ductal carcinoma and DCIS


title: Breast 41 parous case HuII

tag: Parity status:Parous case


title: Breast 31 parous case HuI

description: Biological replicate: 13 of 39- Parous case

tag: Age at diagnosis:76

tag: Breast biopsy diagnosis:Invasive Ductal carcinoma


title: Breast 34 parous case HuI

description: Biological replicate: 16 of 39- Parous case

tag: Age at diagnosis:55

tag: Breast biopsy diagnosis:Invasive ductal carcinoma and DCIS

tag: Stratagene Human Reference


title: Breast 34 parous case HuII

tag: Age at first birth


title: Breast 39 parous case HuII

tag: Age at diagnosis:74

tag: Breast biopsy diagnosis:Invasive ductal carcinoma


title: Breast 35 parous case HuII

description: Biological replicate: 17 of 39- Parous case

tag: Age at diagnosis:75


title: Breast 38 parous case HuII

tag: Age at diagnosis:65


title: VUB13_FXSpassage45

source_name: VUB13_FXS passage 45

tag: Human embryonic stem cells


title: Breast 40 parous case HuII

tag: Age at diagnosis:62


title: VUB13_FXSpassage30

source_name: VUB13_FXS passage 30

tag: 46, XX reference DNA


title: Breast 33 parous case HuII

tag: Age at diagnosis:67


title: Breast 43 parous case HuII

description: Biological replicate: 23 of 39- Parous case

tag: Age at diagnosis:56


title: Breast 44 parous case HuII

description: Biological replicate: 24 of 39- Parous case

tag: Age at diagnosis:82

tag: Breast biopsy diagnosis:Invasive lobular carcinoma


title: VUB15passage18

tag: 46, XY reference DNA

source_name: VUB15 passage 18


title: Breast 46 parous case HuII

description: Biological replicate: 26 of 39- Parous case

tag: Age at diagnosis:76

tag: Parity status:Parous case


title: VUB17passage7

source_name: VUB17 passage 7


title: VUB19_DM1passage5

source_name: Human embryonic stem cells

source_name: VUB19_DM1 passage 5


title: Breast 45 parous case HuII

description: Biological replicate: 25 of 39- Parous case


title: Breast 29 parous case HuI

description: Biological replicate: 11 of 39- Parous case

tag: Age at diagnosis:78

tag: Breast biopsy diagnosis:Mucinous adenocarcinoma


title: VUB13_FXSpassage28

source_name: VUB13_FXS passage 28

source_name: Female reference DNA


title: Breast 35 parous case HuI

tag: Age at first birth

tag: Breast biopsy diagnosis:Invasive ductal carcinoma and DCIS

source_name: Universal human reference

tag: Stratagene Human Reference


title: Breast 32 parous case HuII

tag: Age at diagnosis:84

tag: Breast biopsy diagnosis:Invasive ductal carcinoma


title: VUB09_FSHD.2passage88

source_name: VUB09_FSHD.2 passage 88

tag: Human embryonic stem cells


title: Breast 31 parous case HuII

tag: Breast biopsy diagnosis:Invasive Ductal carcinoma


title: VUB11_FXSpassage45

tag: 46, XX reference DNA

source_name: VUB11_FXS passage 45


title: VUB09_FSHD.2passage100

source_name: VUB09_FSHD.2 passage 100


title: Breast 30 parous case HuII

source_name: Breast biopsy from parous case

tag: Age at diagnosis:59

tag: Breast biopsy diagnosis:Invasive Ductal carcinoma and DCIS


title: Breast 28 parous case HuI

description: Biological replicate: 10 of 39- Parous case


title: VUB09_FSHD.2passage40

source_name: VUB09_FSHD.2 passage 40


title: Breast 26 parous case HuII

description: Biological replicate: 8 of 39- Parous case

tag: Age at diagnosis:75


title: Breast 29 parous case HuII


title: Breast 27 parous case HuII

description: Biological replicate: 9 of 39- Parous case


title: Breast 24 parous case HuII

description: Biological replicate: 6 of 39- Parous case

tag: Age at diagnosis:57


title: Breast 25 parous case HuII

description: Biological replicate: 7 of 39- Parous case

tag: Age at diagnosis:74

tag: Breast biopsy diagnosis:Invasive ductal and lobular carcinoma


title: Breast 27 parous case HuI

tag: Parity status:Parous case


title: Breast 26 parous case HuI


title: Breast 25 parous case HuI


title: Breast 19 parous case HuII

description: Biological replicate: 1 of 39- Parous case

tag: Age at diagnosis:71


title: Breast 24 parous case HuI


title: VUB09_FSHD.1passage28

source_name: Male reference DNA

tag: 46, XY reference DNA

source_name: VUB09_FSHD.1 passage 28


title: VUB07.2passage131

source_name: VUB07.2 passage 131


title: Breast 23 parous case HuII

description: Biological replicate: 5 of 39- Parous case

tag: Age at diagnosis:72

tag: Age at first birth


title: Breast 18 parous control HuII

description: Biological replicate: 17 of 17- Parous control

source_name: Breast biopsy from parous control

tag: Age at diagnosis:60

tag: Parity status:Parous control

tag: Breast biopsy diagnosis:Benign breast disease

tag: Stratagene Human Reference


title: VUB08_MFSpassage49

source_name: VUB08_MFS passage 49

tag: Human embryonic stem cells


title: Breast 23 parous case HuI

tag: Breast biopsy diagnosis:Invasive ductal carcinoma


title: Breast 17 parous control HuII

description: Biological replicate: 16 of 17- Parous control

tag: Breast biopsy diagnosis:Adenosis


title: Breast 22 parous case HuI

description: Biological replicate: 4 of 39- Parous case


title: Breast 20 parous case HuII

description: Biological replicate: 2 of 39- Parous case

tag: Age at diagnosis:61

tag: Breast biopsy diagnosis:Invasive Ductal Carcinoma


title: VUB07.2passage122

source_name: VUB07.2 passage 122

tag: 46, XX reference DNA


title: Breast 14 parous control HuII

description: Biological replicate: 14 of 17- Parous control

tag: Age at diagnosis:77


title: Breast 22 parous case HuII


title: Breast 21 parous case HuII

description: Biological replicate: 3 of 39- Parous case

tag: Age at diagnosis:55

tag: Breast biopsy diagnosis:Invasive Ductal and lobular carcinoma


title: Breast 13 parous control HuII

description: Biological replicate: 13 of 17- Parous control

tag: Breast biopsy diagnosis:Stromal fibrosis


title: Breast 21 parous case HuI

tag: Parity status:Parous case


title: Breast 12 parous control HuII

description: Biological replicate: 12 of 17- Parous control

tag: Age at diagnosis:63

tag: Breast biopsy diagnosis:Ductal hyperplasia, mild


title: Breast 15 parous control HuII

description: Biological replicate: 15 of 17- Parous control

tag: Age at diagnosis:78

tag: Age at first birth


title: VUB07.2passage77

source_name: VUB07.2 passage 77


title: Breast 19 parous case HuI

tag: Age at diagnosis:71

tag: Breast biopsy diagnosis:Invasive Ductal carcinoma


title: Breast 18 parous control HuI

tag: Age at diagnosis:60

tag: Parity status:Parous control

tag: Breast biopsy diagnosis:Benign breast disease

tag: Stratagene Human Reference


title: Breast 20 parous case HuI

tag: Age at diagnosis:61

tag: Breast biopsy diagnosis:Invasive Ductal Carcinoma


title: VUB06.2passage21

source_name: VUB06.2 passage 21

tag: Human embryonic stem cells

tag: 46, XX reference DNA


title: Breast 7 parous control HuII

description: Biological replicate: 7 of 17- Parous control

tag: Age at diagnosis:52

tag: Breast biopsy diagnosis:Adenosis, ductal ectasia


title: Breast 8 parous control HuII

description: Biological replicate: 8 of 17- Parous control

tag: Age at diagnosis:77

tag: Breast biopsy diagnosis:Apocrine metaplasia


title: VUB06.1passage64

source_name: VUB06.1 passage 64


title: Breast 17 parous control HuI

tag: Age at diagnosis:72

tag: Breast biopsy diagnosis:Adenosis


title: Breast 6 parous control HuII

description: Biological replicate: 6 of 17- Parous control

tag: Age at first birth

tag: Breast biopsy diagnosis:Fibroadenoma, adenosis


title: Breast 9 parous control HuII

description: Biological replicate: 9 of 17- Parous control

tag: Age at diagnosis:64


title: Breast 10 parous control HuII

description: Biological replicate: 10 of 17- Parous control

tag: Age at diagnosis:71


title: Breast 15 parous control HuI

tag: Age at diagnosis:78

tag: Parity status:Parous control


title: VUB05_HD.2passage106

source_name: VUB05_HD.2 passage 106

tag: 46, XY reference DNA


title: VUB07.1passage32

source_name: VUB07.1 passage 32

source_name: Female reference DNA


title: Breast 13 parous control HuI

tag: Age at diagnosis:61

tag: Breast biopsy diagnosis:Stromal fibrosis

source_name: Universal human reference

tag: Stratagene Human Reference


title: Breast 2 parous control HuII

description: Biological replicate: 2 of 17- Parous control

tag: Age at diagnosis:59

tag: Breast biopsy diagnosis:Ductal hyperplasia


title: Breast 1 parous control HuII

description: Biological replicate: 1 of 17- Parous control

tag: Age at diagnosis:50

tag: Breast biopsy diagnosis:Fibrocystic changes


title: Breast 3 parous control HuII

description: Biological replicate: 3 of 17- Parous control

tag: Age at diagnosis:55

tag: Breast biopsy diagnosis:Fibroadenoma


title: VUB05_HD.2passage103

source_name: VUB05_HD.2 passage 103

tag: Human embryonic stem cells


title: Breast 14 parous control HuI

tag: Age at diagnosis:77

tag: Age at first birth

tag: Breast biopsy diagnosis:Adenosis


title: Breast 5 parous control HuII

description: Biological replicate: 5 of 17- Parous control

tag: Breast biopsy diagnosis:Ductal hyperplasia, mild


title: VUB05_HD.2passage97

source_name: VUB05_HD.2 passage 97


title: Breast 4 parous control HuII

description: Biological replicate: 4 of 17- Parous control


title: Arabidopsis leaves-mock infection with buffer-17 dpi; used as control rep 3

city: London

first: Mohan

last: babu

state: Ontario

address: 1391 Sandford

department: Virology

institute: AAFC

description: Labelling, hybridization, and detection of hybridization signals were performed as per Affymetrix standard protocol

hyb_protocol: As per Affymetrix protocol

scan_protocol: As per Affymetrix protocol

data_processing: Hybridization signals obtained from the scanned array images were quantified using MAS5.0 expression analysis algorithm, implemented in the Affymetrix GCOS (Gene Chip Operating) software version 1.2. Raw MAS5.0 data files obtained from scanned array images were imported into GeneSpring microarray analysis software version 7.3.1 (Silicon Genetics, Redwood City, CA, USA).

label: Single color

organism: Arabidopsis thaliana

label_protocol: As per Affymetrix protocol

growth_protocol: Arabidopsis grown at standard green house conditions

extract_protocol: Trizol reagent to extract total RNA

treatment_protocol: Protoplasts transfected with PPV infection

tag: Arabidopsis leaves mock infected with buffer at 17 dpi were used as control.


title: Breast 11 parous control HuI

description: Biological replicate: 11 of 17- Parous control

tag: Parity status:Parous control

tag: Breast biopsy diagnosis:Papilloma


title: VUB05_HD.1passage86

source_name: VUB05_HD.1 passage 86

tag: 46, XY reference DNA


title: VUB05_HD.2passage75

source_name: VUB05_HD.2 passage 75


title: Breast 9 parous control HuI

tag: Age at diagnosis:64


title: Arabidopsis leaves-mock infection with buffer-17 dpi; used as control rep 2


title: VUB06.1passage36

tag: 46, XX reference DNA

source_name: VUB06.1 passage 36


title: small RNAs from zili mutant zebrafish gonads

city: Groningen

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

description: The isolated small RNAs were separated on a denaturing 15% polyacrylamide (PAA) gel and stained with SYBRgreenII.  The population of small RNAs with a length of 19-40 bases was obtained by passive elution of the RNAs from the gel.  The RNAs were precipitated with ethanol and dissolved in water. The gel purified RNAs were first poly(A)-tailed using poly(A) polymerase followed by ligation of a RNA adapter to the 5'-phosphate of the RNAs.  First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and M-MLV-RNase H- reverse transcriptase.  Incubation temperatures were 42ºC for 15 min, ramp to 55ºC followed by 55ºC for 5 min. The resulting cDNAs were then PCR-amplified to about 40 ng/ul using a high fidelity DNA polymerase.  The cDNAs were purified using the Macherey & Nagel NucleoSpin Exctract II kit and subsequently sequenced using the 454 platform (Roche).

data_processing: adapter sequences (ctATCGgaccttggctgtcactca and polyA) were trimmed and inserts mapped to the zebrafish genome

organism: Danio rerio

extract_protocol: Gonads from 5 weeks old fish were flash frozen and small RNA species were isolated using the mirVana miRNA isolation kit.

tag: 5 week old hu3173 animals (TL background)


title: Breast 12 parous control HuI

tag: Age at diagnosis:63

tag: Stratagene Human Reference


title: Ziwi-IP small RNAs from zebrafish testes

type: other

description: The RNAs were poly(A)-tailed using poly(A) polymerase followed by ligation of a RNA adapter to the 5'-phosphate of the small RNAs.  First-strand cDNA synthesis was performed using an oligo(dT)-linker primer and M-MLV-RNase H- reverse transcriptase.  The cDNA was PCR amplificated for 16 cycles according to the instructions of 454 Live Sciences. Equal amounts of bar coded cDNA were mixed.  The 125 - 140 bp fraction of the cDNA pool was obtained by fractionation of the cDNA on a preparative 6% polyacrylamide (PAA) gel.  The eluted cDNA was purified using the Macherey & Nagel NucleoSpin Extract II kit and was seqeunced on 454 GS FLX system.

data_processing: adapter sequences (ctCCGAgaccttggctgtcactca and polyA) were trimmed and inserts mapped to the zebrafish genome.

molecule: other

extract_protocol: Assay: immunoprecipotation Antibody: Ziwi affinity purified antibody.  Procedure: tissues were sonicated for 1 minute at 4ºC and centrifuged for 10 minutes at 12.000 rpm at 4ºC.  Supernatant was used for IP. One IP generally contains 30ul Dynabeads (Invitrogen), 3 testes, and Ziwi antibody 1:200 in a total volume of 500ul.  IP lysis buffer contains 25mM TrisHCl pH7.5, 150mM NaCl, 1.5mM MgCl2, 1% TritonX100, 1mM DTT, protease inhibitors.  Beads, antibodies and lysate were incubated for 2 h at 4ºC while rotating. Beads were washed three times with wash buffer (25mM TrisHCl pH7.5, 300mM NaCl, 1.5mM MgCl2, 1mM DTT).  Beads were used for Trizol (Invitrogen) RNA isolation.

tag: testes from adult TL


title: Breast 10 parous control HuI

tag: Age at diagnosis:71


title: Breast 8 parous control HuI

tag: Breast biopsy diagnosis:Apocrine metaplasia


title: Arabidopsis leaves-mock infection with buffer-17 dpi; used as control rep 1


title: small RNAs from wild-type zebrafish gonads

data_processing: adapter sequences (ctAGGTgaccttggctgtcactca and polyA) were trimmed and inserts mapped to the zebrafish genome

tag: 5 week old TL animals


title: PPV infection in Arabidopsis leaves-17 days post inoculation rep 3

source_name: Arabidopsis leaves infected with PPV at 17 days post inoculation


title: Breast 7 parous control HuI

tag: Age at diagnosis:52

tag: Breast biopsy diagnosis:Adenosis, ductal ectasia


title: Zili-IP small RNAs from zebrafish testes

data_processing: adapter sequences (ctGCTCgaccttggctgtcactca and polyA) were trimmed and inserts mapped to the zebrafish genome

extract_protocol: Assay: immunoprecipotation Antibody: Zili affinity purified antibody.  Procedure: tissues were sonicated for 1 minute at 4ºC and centrifuged for 10 minutes at 12.000 rpm at 4ºC.  Supernatant was used for IP. One IP generally contains 30ul Dynabeads (Invitrogen), 3 testes, and Zili antibody 1:250 in a total volume of 500ul.  IP lysis buffer contains 25mM TrisHCl pH7.5, 150mM NaCl, 1.5mM MgCl2, 1% TritonX100, 1mM DTT, protease inhibitors.  Beads, antibodies and lysate were incubated for 2 h at 4ºC while rotating. Beads were washed three times with wash buffer (25mM TrisHCl pH7.5, 300mM NaCl, 1.5mM MgCl2, 1mM DTT).  Beads were used for Trizol (Invitrogen) RNA isolation.


title: VUB05_HD.1passage58

source_name: VUB05_HD.1 passage 58

tag: Human embryonic stem cells


title: PPV infection in Arabidopsis leaves-17 days post inoculation rep 2

tag: Arabidopsis leaves infected with PPV at 17 days post inoculation


title: VUB04_CFpassage66

source_name: VUB04_CF passage 66

source_name: Male reference DNA


title: PPV infection in Arabidopsis leaves-17 days post inoculation rep 1


title: Zili-IP small RNAs from zebrafish ovaries

data_processing: adapter sequences (ctCGCAgaccttggctgtcactca and polyA) were trimmed and inserts mapped to the zebrafish genome

extract_protocol: Assay: immunoprecipotation Antibody: Zili affinity purified antibody.  Procedure: tissues were sonicated for 1 minute at 4ºC and centrifuged for 10 minutes at 12.000 rpm at 4ºC.  Supernatant was used for IP. One IP generally contains 30ul Dynabeads (Invitrogen), 1/2 ovary, and Zili antibody 1:250 in a total volume of 500ul.   IP lysis buffer contains 25mM TrisHCl pH7.5, 150mM NaCl, 1.5mM MgCl2, 1% TritonX100, 1mM DTT, protease inhibitors.  Beads, antibodies and lysate were incubated for 2 h at 4ºC while rotating. Beads were washed three times with wash buffer (25mM TrisHCl pH7.5, 300mM NaCl, 1.5mM MgCl2, 1mM DTT).  Beads were used for Trizol (Invitrogen) RNA isolation.

tag: ovary from adult TL


title: VUB04_CFpassage117

source_name: VUB04_CF passage 117


title: VUB05_HD.1passage51

source_name: VUB05_HD.1 passage 51


title: VUB04_CFpassage23

source_name: VUB04_CF passage 23


title: PPV deletion mutant-Arabidopsis protoplasts-12hpt-used as control rep 2

tag: Arabidopsis protoplasts transfected with PPV deletion mutant at 12 hpt; used as control.


title: Dendritic cell DNA-allergy susceptible d14 mice-rep9

city: Boston

first: Alexey

last: Fedulov

state: MA

address: 75 Francis St.

department: Brigham and Women's Hospital

institute: Harvard Medical School

description: Cy3 labels portion of DNA sample treated with methylation-sensitive nucleases, Cy5 is untreated portion

hyb_protocol: Competitive hybridization to probes, each of which cover 50 bp, results in changes in the ratio of fluorescence depending on methylation-driven nuclease sensitivity: in an unmethylated sample nuclease destroys the DNA in the green-labeled portion, so only red-labeled fragments hybridize; in a methylated sample nuclease does not perform so both portions hybridize returning mixed fluorescence. Therefore demethylation leads to increased binding of the red-labeled fragments. The ratio of untreated (red) versus treated (green) will now be proportionate to hybridization at each probe. Respectively, higher ratios are obtained if hybridization is lower (unmethylated).

scan_protocol: commercial service provided by Switchgear Genomics

data_processing: These ratios are normalized with background adjustment to obtain ‘z-scores’. A z-score is a dimensionless value which represents the number of standard deviations from the background control (which behaves as fully methylated DNA). Z-scores are quantitative log2-transformed data proportionate to the methylation of the interrogated target, which allow comparison of samples from different chips and batches. They are calculated as: [(exp log2 ratio)-(mean log2 ratio of negs)] / (stdev log2 ratio of negs). A typical threshold value of 1.6 or more indicates that the site has a >95% chance of being demethylated. Of notice is the fact that each z-score is a summary of fluorescence ratio for 3 adjacent probes, this ‘frame’ shifts one probe at a time, so each probe is also included into 3 of the z-scores; this should be taken into consideration during validation. For this reason there is also less z-score data raws than fluorescence data raws. Fluorescence reading, normalization, background adjustment and the resulting z-scores are provided by the company’s bioinformatics facility along with the annotation file. Raw values are also provided

organism: Mus musculus

source_name: Splenic CD11c+ dendritic cell - allergy susceptible (methylase treated)

label_protocol: The assay relies on sensitivity to restriction endonucleases conferred by the absence of methylation on cytosine residues. A cocktail of methylation-sensitive nucleases (with 99.9% efficiency and specificity for unmethylated DNA) is used to digest half of each genomic DNA sample, prior to differential fluorescent labeling (Cy 5 red for the nuclease-untreated sample; Cy3 green for the treated).

growth_protocol: Maternal sensitization is achieved by initial i.p. injections of 5 μg OVA with 1 mg alum in 0.1 ml PBS into mice at 3 and 7 days of age. After weaning, female mice are exposed to aerosols of allergen (3% (w/v) OVA (grade V, Sigma-Aldrich) in PBS, pH 7.4) for 10 min on 3 consecutive days at 4, 8, and 12 wk of age, and then mated with normal male mice. The aerosol exposure is performed within individual compartments of a mouse pie chamber (Braintree Scientific, Braintree, MA) using a Pari IS2 nebulizer (Sun Medical Supply, Kansas City, KS) connected to air compressor (PulmoAID; DeVilbiss, Somerset, PA). These female mice were shown to consistently have strong allergic airway inflammation and evidence of Th2 polarization.

extract_protocol: Dendritic cells were isolated from splenocyte suspension using magnetic cell separation (Miltenyi). Genomic DNA was isolated using Qiagen procedure.

treatment_protocol: All neonate mice are untreated, genetically and environmentally identical.

tag: Strain

value: BALB/c

tag: Age

value: 14 day old

tag: Mothers

value: allergic asthma

tag: Organ

value: spleen

tag: Cell type

value: dendritic cells

source_name: Splenic CD11c+ dendritic cell - allergy susceptible (untreated)


title: Breast 5 parous control HuI

source_name: Breast biopsy from parous control

tag: Age at diagnosis:55

tag: Age at first birth

tag: Parity status:Parous control

tag: Breast biopsy diagnosis:Ductal hyperplasia, mild


title: Breast 6 parous control HuI

tag: Age at diagnosis:61

tag: Breast biopsy diagnosis:Fibroadenoma, adenosis

tag: Stratagene Human Reference


title: Breast 4 parous control HuI

tag: Breast biopsy diagnosis:Fibrocystic changes


title: Breast 3 parous control HuI

tag: Breast biopsy diagnosis:Fibroadenoma


title: VUB05_HD.1passage65

tag: 46, XY reference DNA

source_name: VUB05_HD.1 passage 65

tag: Human embryonic stem cells


title: PPV deletion mutant-Arabidopsis protoplasts-12hpt-used as control rep 1

tag: Arabidopsis protoplasts transfected with PPV deletion mutant at 12 hpt; used as control.


title: PPV deletion mutant-Arabidopsis protoplasts-12hpt-used as control rep 3

source_name: Arabidopsis protoplasts transfected with PPV deletion mutant at 12 hpt; used as control


title: PPV infection_Arabidopsis protoplast cells_12 hpt rep 2

source_name: Arabidopsis protoplasts transfected with PPV infection at 12hpt


title: Dendritic cell DNA-allergy susceptible d14 mice-rep7

tag: Strain


title: VUB03_DM1.2passage98

source_name: VUB03_DM1.2 passage 98

source_name: Female reference DNA

tag: 46, XX reference DNA


title: PPV infection_Arabidopsis protoplast cells_12 hpt rep 1

tag: Arabidopsis protoplasts transfected with PPV infection at 12hpt


title: Dendritic cell DNA-allergy susceptible d14 mice-rep6

tag: Age

tag: Mothers

tag: Organ


title: Dendritic cell DNA-allergy susceptible d14 mice-rep5

tag: Cell type


title: Dendritic cell DNA-allergy susceptible d14 mice-rep8


title: PPV infection_Arabidopsis protoplast cells_12 hpt rep 3


title: VUB03_DM1.1passage30

source_name: VUB03_DM1.1 passage 30


title: Ziwi-IP small RNAs from zebrafish ovaries

data_processing: adapter sequences (ctCAGCgaccttggctgtcactca and polyA) were trimmed and inserts mapped to the zebrafish genome

extract_protocol: Assay: immunoprecipotation Antibody: Ziwi affinity purified antibody.  Procedure: tissues were sonicated for 1 minute at 4ºC and centrifuged for 10 minutes at 12.000 rpm at 4ºC.  Supernatant was used for IP. One IP generally contains 30ul Dynabeads (Invitrogen), 1/2 ovary, and Ziwi antibody 1:200 in a total volume of 500ul.  IP lysis buffer contains 25mM TrisHCl pH7.5, 150mM NaCl, 1.5mM MgCl2, 1% TritonX100, 1mM DTT, protease inhibitors.  Beads, antibodies and lysate were incubated for 2 h at 4ºC while rotating. Beads were washed three times with wash buffer (25mM TrisHCl pH7.5, 300mM NaCl, 1.5mM MgCl2, 1mM DTT).  Beads were used for Trizol (Invitrogen) RNA isolation.

tag: ovary from adult TL


title: Dendritic cell DNA-allergy susceptible d14 mice-rep4


title: VUB02.2passage109

source_name: VUB02.2 passage 109


title: PPV deletion mutant_Arabidopsis protoplasts_6hpt_Control rep 3

source_name: PPV deletion mutant transfected with Arabidopsis protoplasts at 6hpt; used as control


title: Breast 1 parous control HuI

tag: Age at diagnosis:50

tag: Age at first birth

tag: Parity status:Parous control

source_name: Universal human reference


title: VUB02.2passage219

source_name: VUB02.2 passage 219


title: VUB02.1passage21

source_name: Male reference DNA

source_name: VUB02.1 passage 21


title: Breast 2 parous control HuI

tag: Age at diagnosis:59

tag: Breast biopsy diagnosis:Ductal hyperplasia

tag: Stratagene Human Reference


title: PPV infection-Arabidopsis protoplasts-6h post transfection rep 3

source_name: PPV infection in Arabidopsis protoplasts at 6hpt


title: PPV infection-Arabidopsis protoplasts-6h post transfection rep 2

tag: PPV infection in Arabidopsis protoplasts at 6hpt


title: Dendritic cell DNA-allergy susceptible d14 mice-rep2


title: Dendritic cell DNA-allergy susceptible d14 mice-rep1


title: PPV deletion mutant_Arabidopsis protoplasts_6hpt_Control rep 1

tag: PPV deletion mutant transfected with Arabidopsis protoplasts at 6hpt; used as control


title: VUB01.2passage55

tag: 46, XY reference DNA

source_name: VUB01.2 passage 55

tag: Human embryonic stem cells


title: PPV infection-Arabidopsis protoplasts-6h post transfection rep 1


title: PPV deletion mutant-Arabidopsis protoplasts-3h control rep 3

source_name: protoplast transfected with PPV deletion mutant at 3hpt


title: VUB01.1passage31

source_name: VUB01.1 passage 31


title: Dendritic cell DNA-normal control d14 mice-rep9

source_name: Splenic CD11c+ dendritic cell - normal control (methylase treated)

tag: Strain

value: normal controls

source_name: Splenic CD11c+ dendritic cell - normal control (untreated)

value: spleen,


title: Dendritic cell DNA-normal control d14 mice-rep8


title: Dendritic cell DNA-normal control d14 mice-rep6


title: Dendritic cell DNA-normal control d14 mice-rep7


title: MLLAF4_BM_H3K79 (6 samples)

description: MLLAF4 BM H3K79 CHIP: MLLAF4-224_MmProm.CEL (hit & run Cre), MLLAF4-226_MmProm.CEL (hit & run Cre), MLLAF4-227_MmProm.CEL (hit & run Cre), MLLAF4-228_MmProm.CEL (hit & run Cre), MLLAF4-654_MmProm.CEL (Mx1Cre), MLLAF4-992_MmProm.CEL (Mx1Cre)

data_processing: Regions of above-background signal were identified by Model-based Analysis of Tiling array (MAT) software (http://chip.dfci.harvard.edu/~wli/MAT/) run with bandwidth = 300, max gap = 300, minimum probes = 10 and p-value cutoff = 1x10e-5 and using a bpmap for mouse NCBI genome build 36 (Mm8) downloaded from the MAT website.

source_name: H3K79me2 ChIP of MLLAF4 leukemic bone marrow

label_protocol: Each ChIP was amplified using the Sigma WGA1 kit. Labeling was according to standard Affymetrix protocols.

tag: Whole bone marrow from MLLAF4 leukemic animals


title: MLLAF4_preB_H3K79 (3 samples)

description: MLLAF4 preB H3K79 CHIP: MLLAF4_1_MmProm.CEL (Mx1Cre), MLLAF4_2_MmProm.CEL (hit-and-run Cre), MLLAF4_3_MmProm.CEL (secondary)

source_name: H3K79me2 ChIP of MLLAF4 leukemic preB cells

tag: Purified bone marrow B220+ CD43- IgM- IgD- cells from MLLAF4 leukemic animals


title: PPV deletion mutant-Arabidopsis protoplasts-3h control rep 2

tag: protoplast transfected with PPV deletion mutant at 3hpt


title: Normal_preB_H3K79 (3 samples)

description: normal preB H3K79 CHIP:  preB_1_MmProm.CEL, preB_3_MmProm.CEL, preB_3_MmProm.CEL

source_name: H3K79me2 ChIP of normal preB cells

tag: Purified normal bone marrow B220+ CD43- IgM- IgD- cells


title: PPV deletion mutant_Arabidopsis protoplasts_6hpt_Control rep 2


title: VUB01passage135

source_name: VUB01 passage 135


title: PPV deletion mutant-Arabidopsis protoplasts-3h control rep 1


title: PPV infection-Aabdiopsis protoplasts-3hpt rep 2

source_name: Arabidopsis protoplasts transfected with PPV infectious clone at 3hpt.

tag: Protoplasts transfected with PPV infection. Samples collected after 3hpt.


title: VUB01passage276


title: PPV infection-Aabdiopsis protoplasts-3hpt rep 1


title: PPV infection-Aabdiopsis protoplasts-3hpt rep 3


title: [Aiolos OBF-1]-1

status: Public on Nov 03 2008

city: Basel

first: Edward

middle: James

last: Oakeley

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: Bone marrow from an Aiolos/OBF-1 double deletion mouse

hyb_protocol: RNA was hybridised using the standard Affymetrix hybridisation protocol as per manufacturer's instructions (45°C over night)

scan_protocol: The chips were scanned using an Affymetrix genechip scanner as per manufacturer's instructions

data_processing: Expression values were estimated using the RMA algorithm implemented in Bioconductor. Further data anaylsis was performed using GeneSpring 4

source_name: Bone marrow

label_protocol: RNA was amplified and labelled using the Affymetrix 1-cycle 3'IVT protocol

growth_protocol: Mice were grown for seven weeks in our mouse facility

extract_protocol: RNA was purified using the Qiagen RNA easy protocol according to the manufacturer's insructions

treatment_protocol: Bone marrow was extracted from the mice

value: Bl6, Tissue:Bone marrow, Age:7 weeks


title: [Aiolos OBF-1]-2


title: [OBF-1]-2

description: Bone marrow from an OBF-1 deletion mouse


title: [Aiolos]-1

description: Bone marrow from an Aiolos deletion mouse


title: Dendritic cell DNA-normal control d14 mice-rep5

tag: Age

tag: Mothers

tag: Organ

tag: Cell type


title: [Aiolos]-2


title: Dendritic cell DNA-normal control d14 mice-rep4


title: [OBF-1]-1


title: Dendritic cell DNA-normal control d14 mice-rep3


title: Dendritic cell DNA-normal control d14 mice-rep2


title: Dendritic cell DNA-normal control d14 mice-rep1


title: Hippocampus veh 2

status: Public on Nov 01 2008

city: Bethesda

first: Robert

middle: H

last: Bonow

state: MD

address: 9 Memorial Drive, Building 9

department: Brain Physiology and Metabolism Section

institute: National Institute on Aging / NIH

hyb_protocol: A total of 0.75 ug of biotin-labeled cRNA was hybridized for 16 hours to Illumina's Sentrix MouseRef-8 Expression BeadChips (Illumina, San Diego, CA, USA).

scan_protocol: The arrays were washed and blocked. Biotinylated cRNA was detected with streptavidin-Cy3 and quantitated using Illumina's BeadStation 500X Genetic Analysis Systems scanner. The image data was extracted using BeadStudio software (Illumina).

data_processing: The expression data were filtered to include only probes with a consistent signal on each chip; the cutoff value was established at P < 0.02.  The resulting dataset was next analyzed with DIANE 6.0, a spreadsheet based microarray analysis program.  Using DIANE, the background was subtracted from the raw signal intensity of each gene, and the results were normalized with a Z-Score transformation.  Only 16 of the 64 total arrays are included in this GEO Archive file.

source_name: hippocampus 24h after PBS injection

label_protocol: A 0.5 ug aliquot of total RNA from each sample was labeled using the Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, USA).  RNA was first converted into single-stranded cDNA using reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter, and then the single-stranded cDNA was copied to produce double-stranded cDNA molecules.  The double-stranded cDNA was used in an overnight in vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporating biotin-16-UTP.

extract_protocol: Total RNA was extracted from hippocampus and cerebral cortex samples using Qiagen RNeasy Lipid Tissue Mini and Midi kits, respectively (Qiagen, Valencia, CA, USA).

treatment_protocol: At sacrifice, hippocampus and cerebral cortex were rapidly dissected, flash frozen at -60°C, and stored at -80°C until RNA extraction.

value: C57BL/6 and SV129/Ola cross, Age:12-15 weeks of age


title: WT-2

description: Control bone marrow


title: Hippocampus veh 3


title: Cortex lps 4

source_name: cerebral cortex 24 h after LPS injection


title: Hippocampus veh 1


title: Hippocampus lps 4

source_name: hippocampus 24h after LPS injection


title: Hippocampus veh 4


title: Hippocampus lps 1


title: Hippocampus lps 2


title: Cortex lps 2


title: Cortex veh 1

source_name: cerebral cortex 24 h after PBS injection


title: Hippocampus lps 3


title: WT-1

description: Control bone marrow


title: Cortex lps 1


title: Cortex veh 2


title: Cortex lps 3


title: Cortex veh 3


title: Cortex veh 4


title: bone_marrow_hematopoietic_stem_cells

status: Public on Oct 18 2008

type: SAGE

anchor: NlaIII

city: Vancouver

first: BCGSC

last: BC Cancer Agency

state: BC

address: 675 West 10th Avenue

department: Gene Expression

institute: Canada's Michael Smith Genome Sciences Centre

description: Murine adult bone marrow was harvested and stained as described in Dykstra et al. Cell Stem Cell 2007 and the CD45+/SP/Rho-/Lin- cells were sorted on a FACSVantage.  Individual single cell transplantation experiments into sublethally irradiated recipients confirm that the HSC purity is at ~1 in 3.

molecule: polyA RNA

source_name: Bone marrow, FACS sorted Lin-/CD45+/SP/Rho-

extract_protocol:
Starting RNA amount: ~3ng (27 cycles of PCR used)
Isolation method: Arcturus PicoPure [total RNA was extracted using the PicoPure kit (Arcturus), a column based method that isolates polyA RNA (http://www.moleculardevices.com/pages/reagents/picopure.html)]
Storage Medium: H2O
DNaseI treatment: Yes
Method of RNA (cDNA) quant: Agilent
SAGE type PCR-LongSAGE

tag: Tissue

value: Bone marrow

value: Adult

tag: FACS sorted

value: Yes, Lin-/CD45+/SP/Rho-

tag: Purity

tag: Number of cells


title: Polysomal RNA RBM35A+

status: Public on Oct 16 2008

description: The biotin-labeled target synthesis reactions, as well as the Affymetrix HG-U95Av2 GeneChip arrays hybridization, staining, and scanning, were performed using Affymetrix standard protocols (Affymetrix, Santa Clara, CA).

data_processing: Affymetrix HG-U95Av2 data were imported as .CEL files into R using the Affy scripting library. Quantile normalization between the arrays and signal estimation was performed using bioconductor gcRMA.quant command

source_name: LS180 colon carcinoma cell line

label_protocol: The analysis was performed at the Gene Expression facility of Roswell Park Cancer Institute, as follows.  Ten micrograms of total or polysomal RNA from RBM35+ and RBM35- cells were used to synthesize double-stranded cDNA using a SuperScript II reverse transcriptase kit (Invitrogen).  Biotinylated cRNA was synthesized from double-stranded cDNA using the Enzo Bioarray High Yield transcript labeling kit (EnzoLife Sciences), then purified using the GeneChip sample cleanup module (Affymetrix) and fragmented.  Fragmented cRNA was hybridized to Affymetrix HG-U95Av2 GeneChips.

extract_protocol: Tet-off LS180 -RBM35A cells with restored expression of RBM35A protein (incubated without Dox for at least six days) and their parental cells maintained in the presence of Dox were grown to no more than 80% confluency to ensure good loading of polysomes.  Two 100mm-diameter plates with the indicated cells were harvested for each polysomal analysis.  Cells were washed twice with ice-cold PBS containing 100 mkg/ml cycloheximide (Sigma), scraped, pelleted and resuspended in 5 times the size of the cell pellet volume of polysomal buffer [50 mM Tris-HCl, pH 7.5, 10 mM KCl, 1.5 mM MgCl2, 1% Triton X-100, 1% sodium deoxycholate, freshly added 5 mM DTT and 40 u/ul RNAse inhibitor(Sigma)].  Lysates were incubated on ice for 10 min with occasional mixing.  Nuclei and debris were removed by centrifugation at 13,000 rpm for 10 min at 4 degrees C.  Supernatants were recovered and 600 ul aliquots were sedimented in 10-40% continuous sucrose gradient prepared in a polysomal buffer lacking detergents by centrifugation for 90 min at 38,000 rpm, at 4 degrees C in Sorvall Ultraspeed TH-641 rotor.  Each gradient was collected in 15 fractions of ~660 ul volume.  An absorbance profile at 254 nm was used to identify polysome-associated fractions.  One volume of 8M guanidine HCl (UltraPure, Invitrogen) was added to the pooled polysomal fractions and vortexed for 3 min.  Next, 2.5 volumes of 100% ethanol was added, samples were vortexed for 1 min and stored at -20 degrees C overnight.  Samples were centrifuged for 1 h at maximum speed in the bench-top centrifuge at 4 degrees C to collect the polysomal RNA.  The pellets were air-dried for 20 min and subjected to an RNA clean-up procedure using an RNAeasy kit (Qiagen), according to the manufacturer’s instructions.  Eluted RNA was precipitated again in 1/10 volume of 3 M sodium acetate, pH 5.2 and 2.5 volumes of 100% ethanol at -20 degrees C overnight.  The pellets were washed twice with 75% ethanol and resuspended in RNAse-free water.

tag: LS180 colon carcinoma cell line expressing RBM35A protein


title: Polysomal RNA RBM35A-

tag: LS180 colon carcinoma cell line


title: Danio rerio_AB_mind bomb_24hpf_wild

status: Public on Oct 08 2008

city: Daegu

first: Sanggyu

last: Lee

address: 1370 Sankyuk-dong, Bukgu

country: South Korea

institute: Kyungpook National University

description: SAGE analysis was carried out as described (Velculescu et al., 1995) but was modified slightly according to Lee et al (Lee et al., 2007).  We performed a low-cycle PCR (14 cycles) using the GeneAmp PCR System 2400 (Applied Biosystem, Foster City, CA) to amplify 3’cDNA in order to generate a sufficient amount of templates for SAGE analysis. The sense primer used was a SAGE primer 1 (5’-GGA TTT GCT GGT GCA GTA CA-3’) or SAGE primer 2 (5’-CTG CTC GAA TTC AAG CTT CT-3’); the antisense primer used was 5’-biotin- ACT ATC TAG AGC GGC CGC TT-3’, which was located in the 3’ end of all cDNAs generated from the anchored oligo(dT) primers.

source_name: Danio rerio, AB line, 24hpf, wild-type

extract_protocol:
Total RNA was isolated from the whole embryos (24 hpf stage) using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instruction.
Poly A RNA was isolated using oligo(dT)25 beads (Dynal Biotech ASA, Oslo, Norway) according to the manufacturer’s instruction.

tag: AB line, 24hpf, wild-type, whole embryo


title: Danio rerio_AB_mind bomb_24hpf_mutant(ta52b)

source_name: Danio rerio, AB line, 24hpf, mutant(ta52b)

extract_protocol: Total RNA was isolated from the whole embryos (24 hpf stage) using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instruction. Poly A RNA was isolated using oligo(dT)25 beads (Dynal Biotech ASA, Oslo, Norway) according to the manufacturer’s instruction.

tag: AB line, 24hpf, mutant(ta52b), whole embryo