title: Sample ID 1773 disseminated cell sample from patient with advanced prostate cancer

tag: Disseminated-cell sample detected by EpCaM positivity and isolated by micropipetting from the bone marrow of a patient with advanced prostate cancer. 10-20 disseminated cells from each patient were pooled and amplified by ligation mediated PCR then labeled by random priming for array CGH analysis. Patient was Gleason grade 7, TNM stage T3aN1, was treated by radical retropubic prostatectomy (RRP), and received no hormone therapy. Bone marrow was collected just prior to RRP.


title: Heart Tissue_Trex1WT/RAG2KO_A

status: Public on Aug 22 2008

type: RNA

city: New Haven

first: Daniel

middle: B

last: Stetson

state: CT

address: 300 Cedar Street

department: Immunobiology

country: USA

institute: Yale University

description: Heart ventricle tissue

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Affymetrix MAS 5.0 software analysis

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Affymetrix protocol

extract_protocol: Heart tissue was homogenized in RNABee, and total RNA was prepared using conventional techniques.

tag: Heart tissue from Trex1 WT, RAG2 KO on C57 Bl/6 background, 119 days old, male


title: Heart Tissue_Trex1WT/RAG2KO_B

description: Heart ventricle tissue

tag: Heart tissue from Trex1 WT, RAG2 KO on C57/Bl6 background, 134 days old, male


title: Sample ID 1677_replicate3 disseminated cell sample from patient with advanced prostate cancer

status: Public on Aug 17 2008

type: genomic

city: Seattle

first: Ilona

middle: N

last: Holcomb

state: WA

address: 1100 Fairview Ave N

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: On microgram each of tumor and reference DNA labeled with Cy5 and Cy3, respectively, were combined and briefly dried by Speedvac. The samples were resuspended in hybridization mix (50% formamide, 10% dextran sulfate, 3x SSC, 1.5% SDS) and heated to 70°C for 10 minutes, followed by 1-hour incubation at 37°C to allow blocking of repetitive sequences by human Cot-1 DNA. After incubation, samples were applied to the microarray under a coverslip and hybridized at 37°C for 18 hours. After hybridization, the arrays were then washed in 50% formamide and 2x SSC (pH 7.0) for 20 minutes at 45°C, followed by a 7-minute wash at room temperature in 0.1 mol/L NaPO4 (pH 8.0) and 0.1% NP40. After washing, the arrays were dried by centrifugation at 600 rpm for 5 minutes.

scan_protocol: Arrays were scanned with a GenePix 4000A scanner (Axon Instruments, Inc., Union City, CA); fluorescence data were processed with GenePix 3.0 image analysis software (Axon Instruments, Inc.). For each spot, log2 ratio = log2(Cy5/Cy3) and average log2 intensity = [log2(Cy5) + log2(Cy3)]/2 were calculated, where Cy5 and Cy3 refer to the median foreground fluorescent signals of the tumor and reference DNA, respectively. Background subtraction was not used because it conferred no benefit in tests run on cell lines with varying numbers of X chromosome copies.

data_processing: The log2 ratios on each array were normalized and corrected for intensity-based location adjustment with a block-level loess algorithm (as described in Yang YH, Dudoit S, Luu P, Speed TP Normalization for cDNA microarray Bittner ML Chen Y Dorsel AN Dougherty ER eds. . Microarrays: optical technologies and informatics 2001141-52. SPIE, Society for Optical Engineering Bellingham, WA).

molecule: genomic DNA

organism: Homo sapiens

source_name: Disseminated cell sample from patient with advanced prostate cancer.

label_protocol: Array CGH bioprime kit (Invitrogen)

extract_protocol: 10-20 cells amplified directly in collection tube by ligation mediated pcr (as per method described in Klein CA, Schmidt-Kittler O, Schardt JA, Pantel K, Speicher MR and Riethmuller G. Comparative genomic hybridization, loss of heterozygosity, and DNA sequence analysis of single cells. Proc Natl Acad Sci U S A 1999;96: 4494-4499.)

tag: Replicate 3 of three biological replicates collected from the same patient. Disseminated-cell sample detected by EpCaM positivity and isolated by micropipetting from the bone marrow of a patient with advanced prostate cancer. 10-20 disseminated cells from each patient were pooled and amplified by ligation mediated PCR then labeled by random priming for array CGH analysis. Patient was TNM stage M+ and was treated by chemical castration.

source_name: normal female reference DNA

extract_protocol: DNA was isolated using a QIAamp DNA Blood Mini Kit (Qiagen)

tag: Normal female genomic DNA isolated from peripheral blood. The DNA equivalent to 10-20 cells was then amplified by  ligation mediated PCR


title: Sample ID 1677_replicate1 disseminated cell sample from patient with advanced prostate cancer

tag: Replicate 1 of three biological replicates collected from the same patient. Disseminated-cell sample detected by EpCaM positivity and isolated by micropipetting from the bone marrow of a patient with advanced prostate cancer. 10-20 disseminated cells from each patient were pooled and amplified by ligation mediated PCR then labeled by random priming for array CGH analysis. Patient was TNM stage M+ and was treated by chemical castration.


title: Sample ID 1776 disseminated cell sample from patient with advanced prostate cancer

tag: Disseminated-cell sample detected by EpCaM positivity and isolated by micropipetting from the bone marrow of a patient with advanced prostate cancer. 10-20 disseminated cells from each patient were pooled and amplified by ligation mediated PCR then labeled by random priming for array CGH analysis. Patient was TNM stage M+, treated retropubic prostatectomy (RRP), and received chemical castration. Bone marrow was collected just prior to RRP.


title: Sample ID 1924 disseminated cell sample from patient with localized prostate cancer

extract_protocol: 10-20 cells amplified directly in collection tube by ligation mediated pcr

tag: Disseminated cell sample collected from the bone marrow of a patient with localized prostate cancer. After enrichment for epithelial cells, EpCaM (CD326; a pan-epithelial cell antigen)positive cells were identified and isolated into pools of cells by micropipetting. The pools of 10-20 disseminated cells from each patient were amplified by ligation mediated PCR then labeled by random priming for array CGH analysis. Patient's tumor

value: Gleason grade 7 and TNM stage T2aN0.


title: Sample ID 1922 disseminated cell sample from patient with localized prostate cancer

value: Gleason grade 7 and TNM stage T2cN0.


title: Sample ID 1923 disseminated cell sample from patient with localized prostate cancer

tag: Disseminated cell sample collected from the bone marrow of a patient with localized prostate cancer. After enrichment for epithelial cells, EpCaM (CD326; a pan-epithelial cell antigen)positive cells were identified and isolated into pools of cells by micropipetting. The pools of 10-20 disseminated cells from each patient were amplified by ligation mediated PCR then labeled by random priming for array CGH analysis.  Patient's tumor

value: Gleason grade 6 and TNM stage T2cN0.


title: Sample ID 1892 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1945 disseminated cell sample from patient with localized prostate cancer

value: Gleason grade 7 and TNM stage T3a.


title: Sample ID 1937 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1918 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1851 disseminated cell sample from patient with localized prostate cancer

value: Gleason grade 7 and TNM stage T2c.


title: Sample ID 1891 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1953 disseminated cell sample from patient with localized prostate cancer

value: Gleason grade 6 and TNM stage T2c.


title: Sample ID 1967 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1888 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1894 disseminated cell sample from patient with localized prostate cancer

value: Gleason grade unknown and TNM stage unkown.


title: Sample ID 1677_replicate2 disseminated cell sample from patient with advanced prostate cancer

tag: Replicate 2 of three biological replicates collected from the same patient. Disseminated-cell sample detected by EpCaM positivity and isolated by micropipetting from the bone marrow of a patient with advanced prostate cancer. 10-20 disseminated cells from each patient were pooled and amplified by ligation mediated PCR then labeled by random priming for array CGH analysis. Patient was TNM stage M+ and was treated by chemical castration.


title: Sample ID 1848 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 2120 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 2121 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1849 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1778 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1815 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1833 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1798 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1788 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1845 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1847 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1767 disseminated cell sample from patient with localized prostate cancer

value: Gleason grade 9 and TNM stage T3b.


title: Sample ID 1834 disseminated cell sample from patient with localized prostate cancer

value: Gleason grade 7 and TNM stage T2a.


title: Sample ID 1785 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1720 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1719 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1728 disseminated cell sample from patient with localized prostate cancer

value: Gleason grade 6 and TNM stage T2b.


title: Sample ID 1734 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1710 disseminated cell sample from patient with localized prostate cancer

value: Gleason grade unknown and TNM stage unknown.


title: Sample ID 1721 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1762 disseminated cell sample from patient with localized prostate cancer

tag: Disseminated cell sample collected from the bone marrow of a patient with localized prostate cancer. After enrichment for epithelial cells, EpCaM (CD326; a pan-epithelial cell antigen)positive cells were identified and isolated into pools of cells by micropipetting. The pools of 10-20 disseminated cells from each patient were amplified by ligation mediated PCR then labeled by random priming for array CGH analysis. Patient’s tumor

value: Gleason grade 6 and TNM stage T2a.


title: Sample ID 1658 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1586 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1636 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1688 disseminated cell sample from patient with localized prostate cancer


title: Pho_ctrl_disc_biorep6

status: Public on Aug 01 2008

city: Cambridge

first: Steve

last: Russell

address: Downing Street

department: Department of Genetics

country: United Kingdom

institute: University of Cambridge

description: group4: ctrl ChIP using disc chromatin, pre-immune serum in wildtype, chromatin prep 6, hybridisation 1

hyb_protocol: Amplified ChIP DNA was fragmented to 50-100bp by treatment with DNAse I for 10min at 37 ºC and 10min at 99 ºC (0.02 U/ug, Epicentre; size distribution of fragmented DNA was verified on a 2% agarose gel). The fragmented DNA was then end-labeled with 70nM of bio-ddATP (Perkin Elmer) using 6-10U of terminal transferase (TdT, Roche) per 1 ug of fragmented DNA in 1x TdT buffer (Roche) and 5mM CoCl2 (Roche) for 2 hours at 37 ºC. The labeled DNA material was subsequently hybridized to the microarrays for 18 hours at 45 ºC in a 3M TMAC/1X MES-based solution.

scan_protocol: Chips were scanned on an Affymetrix GeneChip Scanner according to the manufacturer’s recommendations.

data_processing: Sample and control were analysed together in groups (1-4) using the TiMAT package. Affymetrix CEL files were converted into chromosomal enrichment profiles using the TiMAT2 package (http://bdtnp.lbl.gov/TiMAT/TiMAT2/). Probe mapping information (“bpmap”) to D. melanogaster genome release 4 was obtained from David Nix. Each CEL file was visualised for manual inspection and artefacts were masked using CelMasker. Normalisation was subsequently performed with CelProcessor using default parameters. Enrichment profiles were generated using ScanChip, outputting windowed enrichment signals and Wilcoxon Rank Sum scores.

label: TdT labeled

organism: Drosophila melanogaster

source_name: T3 discs (haltere, 3rd leg)

label_protocol: 10-20 ng of ChIP and control DNA samples were amplified using a random-primed PCR method according to Affymetrix recommendations (Affymetrix Chromatin Immunoprecipitation Assay Protocol; http://www.affymetrix.com/support/technical/manuals.affx). Purified DNAs were then fragmented, TdT labeled, and hybridized to the Affymetrix Drosophila genome Tiling Array 1.0 (reverse part no. 520,054) as described previously (Manak et al. 2006).

growth_protocol: Embryo collections were performed at 25 ºC and L3 larvae were raised at 25 ºC.

extract_protocol: Chromatin was prepared from a minimum of 100 discs or 200mg embryos. Chromatin preparation and ChIP were performed as described previously (Birch-Machin et al. 2005; Adryan et al. 2007). For Pc target analysis the specific reaction used chromatin from the Pc-GFP fly line immunopurified using anti-GFP, and the control reaction used wild type chromatin immunopurified using anti-GFP. For Pho analysis wild type chromatin was used with anti-Pho for the specific reaction and pre-immune antiserum for the control.

treatment_protocol: Chromatin from embryos aged between 0 to 16 h after egg laying was purified as described previously (Birch-Machin et al 2005; Adryan et al. 2007). For the preparation of chromatin from T3 imaginal discs (haltere and third leg) late 3rd instar larvae were dissected in ice-cold Schneider's Medium. Dissected discs were washed with PBS, fixed in PBS/1.5% formaldehyde for 20 min and washed with PBS. Batches of material were snap-frozen in liquid N2 and stored at -80 ºC.

tag: L3 larval T3 discs


title: Pho_disc_biorep4

description: group4: Pho ChIP using disc chromatin, anti-Pho in wildtype, chromatin prep 1, hybridisation 1


title: Pho_disc_biorep5


title: Sample ID 1588 disseminated cell sample from patient with localized prostate cancer

value: Gleason grade 9 and TNM stage T2cN0.


title: Pho_ctrl_disc_biorep5

description: group4: ctrl ChIP using disc chromatin, pre-immune serum in wildtype, chromatin prep 5, hybridisation 1


title: Pho_ctrl_disc_biorep4

description: group4: ctrl ChIP using disc chromatin, pre-immune serum in wildtype, chromatin prep 4, hybridisation 1


title: Pho_disc_biorep6


title: Sample ID 1617 disseminated cell sample from patient with localized prostate cancer

value: Gleason grade 7 and TNM stage T2aNo.


title: Pc_ctrl_disc_biorep6

description: group3: ctrl ChIP using disc chromatin, anti-GFP in wildtype, chromatin prep 6, hybridisation 1


title: Sample ID 1682 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1654 disseminated cell sample from patient with localized prostate cancer


title: Pc_ctrl_disc_biorep5

description: group3: ctrl ChIP using disc chromatin, anti-GFP in wildtype, chromatin prep 5, hybridisation 1


title: Sample ID 1527 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1695 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1585 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1508 disseminated cell sample from patient with localized prostate cancer

source_name: Sample ID 1508 - disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1685 disseminated cell sample from patient with localized prostate cancer


title: Sample ID 1300 disseminated cell sample from patient with localized prostate cancer


title: Pc_ctrl_disc_biorep4

description: group3: ctrl ChIP using disc chromatin, anti-GFP in wildtype, chromatin prep 4, hybridisation 1


title: Pc_disc_biorep6

description: group3: Pc ChIP using disc chromatin, anti-GFP in Pc-GFP flies, chromatin prep 3, hybridisation 1


title: Pc_disc_biorep4

description: group3: Pc ChIP using disc chromatin, anti-GFP in Pc-GFP flies, chromatin prep 1, hybridisation 1


title: Pho_ctrl_embryo_biorep3

description: group2: ctrl ChIP using whole-embryo chromatin, pre-immune serum in wildtype, chromatin prep 3, hybridisation 1

source_name: whole-embryo chromatin

tag: 0-16h AEL embryo


title: Pc_disc_biorep5

description: group3: Pc ChIP using disc chromatin, anti-GFP in Pc-GFP flies, chromatin prep 2, hybridisation 1


title: Pho_ctrl_embryo_biorep2

description: group2: ctrl ChIP using whole-embryo chromatin, pre-immune serum in wildtype, chromatin prep 2, hybridisation 1


title: Pho_embryo_biorep3

description: group2: Pho ChIP using whole-embryo chromatin, anti-Pho in wildtype, chromatin prep 3, hybridisation 1


title: Pho_embryo_biorep2

description: group2: Pho ChIP using whole-embryo chromatin, anti-Pho in wildtype, chromatin prep 2, hybridisation 1


title: Pc_ctrl_embryo_biorep3_techrep1

description: group1: ctrl ChIP using whole-embryo chromatin, anti-GFP in wildtype, chromatin prep 3, hybridisation 1


title: Pho_embryo_biorep1

description: group2: Pho ChIP using whole-embryo chromatin, anti-Pho in wildtype, chromatin prep 1, hybridisation 1


title: Pc_ctrl_embryo_biorep2_techrep3

description: group1: ctrl ChIP using whole-embryo chromatin, anti-GFP in wildtype, chromatin prep 2, hybridisation 3


title: Pc_ctrl_embryo_biorep3_techrep2

description: group1: ctrl ChIP using whole-embryo chromatin, anti-GFP in wildtype, chromatin prep 3, hybridisation 2


title: Pc_ctrl_embryo_biorep1_techrep1

description: group1: ctrl ChIP using whole-embryo chromatin, anti-GFP in wildtype, chromatin prep 1, hybridisation 1


title: Pc_embryo_biorep2_techrep1

description: group1: Pc ChIP using whole-embryo chromatin, anti-GFP in Pc-GFP flies, chromatin prep 2, hybridisation 1


title: Pc_embryo_biorep2_techrep2

description: group1: Pc ChIP using whole-embryo chromatin, anti-GFP in Pc-GFP flies, chromatin prep 2, hybridisation 2


title: Pc_embryo_biorep3_techrep1

description: group1: Pc ChIP using whole-embryo chromatin, anti-GFP in Pc-GFP flies, chromatin prep 3, hybridisation 1


title: Pc_ctrl_embryo_biorep2_techrep2

description: group1: ctrl ChIP using whole-embryo chromatin, anti-GFP in wildtype, chromatin prep 2, hybridisation 2


title: Pc_embryo_biorep1_techrep1

description: group1: Pc ChIP using whole-embryo chromatin, anti-GFP in Pc-GFP flies, chromatin prep 1, hybridisation 1


title: Pc_embryo_biorep3_techrep2

description: group1: Pc ChIP using whole-embryo chromatin, anti-GFP in Pc-GFP flies, chromatin prep 3, hybridisation 2


title: Pc_embryo_biorep1_techrep3

description: group1: Pc ChIP using whole-embryo chromatin, anti-GFP in Pc-GFP flies, chromatin prep 1, hybridisation 3


title: Pc_embryo_biorep2_techrep3

description: group1: Pc ChIP using whole-embryo chromatin, anti-GFP in Pc-GFP flies, chromatin prep 2, hybridisation 3


title: Pc_embryo_biorep1_techrep2

description: group1: Pc ChIP using whole-embryo chromatin, anti-GFP in Pc-GFP flies, chromatin prep 1, hybridisation 2


title: Pc_ctrl_embryo_biorep2_techrep1

description: group1: ctrl ChIP using whole-embryo chromatin, anti-GFP in wildtype, chromatin prep 2, hybridisation 1


title: Pc_ctrl_embryo_biorep1_techrep2

description: group1: ctrl ChIP using whole-embryo chromatin, anti-GFP in wildtype, chromatin prep 1, hybridisation 2


title: Pc_ctrl_embryo_biorep1_techrep3

description: group1: ctrl ChIP using whole-embryo chromatin, anti-GFP in wildtype, chromatin prep 1, hybridisation 3


title: Rahman H2O2 replicate 2

city: Stanford

first: Gretchen

middle: Marie

last: Ehrenkaufer

state: CA

address: Grant S-143, 300 Pasteur Dr.

department: Microbiology and Immunology

institute: Stanford Uninversity

description: Trophozoites treated  1 hr with 1mM H2O2

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: GCOS scaling only- target 500

organism: Entamoeba histolytica

source_name: Trophozoites treated  1 hr with 1mM H2O2

label_protocol: Affymetrix single amplification

tag: Strain

value: Rahman

tag: Media

value: TYI

tag: Long term axenic growth


title: Rahman H2O2 replicate 1

description: Trophozoites treated 1 hr with 1 mM H2O2


title: H2O2_replicate_3

description: Trophozoites treated for 1.5 h with 1mM H2O2

source_name: Trophozoites treated for 1.5 hr with 1mM H2O2


title: DPTA_replicate_1

description: Trophozoites treated 1 hr with 200 uM DPTA-NONOate


title: DPTA_replicate_3

source_name: Trophozoites treated 1 hr with 200 uM DPTA-NONOate


title: Rahman H2O2 replicate 3

description: Trophozoites treated 1 hr with 1mM H2O2

source_name: Trophozoites treated 1 hr with 1mM H2O2


title: H2O2_replicate_2

source_name: Trophozoites treated 1 hr with 1 mM H2O2


title: DPTA_replicate_2


title: H2O2_replicate_1


title: Control fibroblast (C4.gpr)

city: Prague

first: Viktor

last: Stranecky

address: Ke Karlovu 2

department: 1st Faculty of Medicine

country: Czech Republic

institute: Charles University

hyb_protocol: 825ng of Cy3 and Cy5 labelled aRNA were hybridized competitively for 17 hrs in a 65° C, according to the manufacturer's recommnded protocol (Two-Color Microarray-Based Gene expression Analysis, Agilent) .

scan_protocol: The hybridized slides were scanned with GenePix 4200A scanner (Axon Instrument, Union City, CA) with PMT gains adjusted to obtain highest intensity unsaturated images. Gene PixPro software (Axon Instruments) was used for image analysis the of TIFF files, as generated by the scanner.

data_processing: Data from individual arrays were background corrected (using normexp method),  log transformed and normalized using Loess and G-quantile functions. Normalization was performed in R statistic environment using Limma package

source_name: Total RNA from control fibroblast labeled with Cyanine-5 (red)

label_protocol: 500 ng of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

growth_protocol: Skin fibroblasts were cultured in the Dulbecco’s modified Eagle’s medium supplemented by 10 % fetal calf serum, 20mM HEPES pH 7.5, 0.2 % NaHCO3 and gentamycin 0.02 mg/ml at 37°C and 5 % CO2 in air

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

treatment_protocol: For experiments, confluent cell were harvested using 0.05 % trypsine and 0.02 % EDTA

tag: fibroblast

source_name: Total RNA from reference HeLa cell lines labeled with Cyanine-3 (green)

tag: HeLa


title: fib_ZT10

city: Tokushima

first: Tomoko

last: Kawai

address: 3-18-15 Kuramoto-cho

department: Institute of Health Biosciences

country: Japan

institute: The University of Tokushima Graduate School

description: Four bezafibrate-treated mice at time ZT10 are divided by the control sample for all present spots.

hyb_protocol: Hybridizations were performed using GE Hybridization Kit (P/N 5188-5242) and GE Wash Buffer 1 and 2 (P/N 5188-5325, -5326) as following Agilent's protocol.

scan_protocol: Microarrays were scanned using Agilent’s DNA Microarray Scanner BA (P/N G2565BA) and data extracted using Agilent's Feature Extraction software, version 9.5 (P/N G2567AA).

data_processing: Data were processed using Agilent’s GeneSpring® GX software, version 7.3 (P/N G1745). Data were transformed by setting all measurements less than 0.01. Data points that did not have detectable signal and those that represent microarray controls were labeled as Absent, those representing either non-uniform or saturated features were labeled as Marginal, and all remaining data points were labeled as Present. All data points were 50 percentile scaled using the 50 percentile of signal intensity value that cut off 10 for data points labeled as Present. Then the data from each "spot ID" was subdivided by that of control sample.

source_name: hypothalamus from 4 bezafibrate-treated mice at ZT10

label_protocol:
Sample labeling, array processing and scanning, and data extraction were performed as described in One-Color Microarray-Based Gene Expression Analysis – Protocol. These protocols are available for download at http://www.chem.agilent.com/scripts/generic.asp?lpage=11617&indcol=N&prodcol=Y.
The microarrays used were Agilent’s Whole Mouse Genome Oligo Microarrays (P/N G4122F). Probe sequence information is publicly available at http://www.chem.agilent.com/cag/bsp/bsp_register.asp.
Labeled cRNAs were generated from 400 ng of total RNA using Agilent’s Low RNA Input Linear Amplification Kit (P/N 5188-5339).

extract_protocol: The square area containing the hypothalamus was dissected from the brain immediately after decapitation at ZT10 and stored in RNAlater stabilization reagent for two hours. Total RNA was isolated following Qiagen's RNA isolation protocol (RNeasy Mini kit; Qiagen P/N 74104, Hilden, Germany). Contaminating DNA was removed using an RNase-free DNase set (Qiagen P/N 79254) during the process of RNA purification. The quality of the purified RNA applicable for microarray analysis was assessed by Agilent 2100 Bioanalyzer using an RNA 6000 Nano Labchip kit (Agilent Technologies).

treatment_protocol: Mice of 8wks age were fed with a normal diet (MF, Oriental Yeast, Tokyo, Japan) for two weeks, after which their feed was supplemented with 0.5% bezafibrate (Sigma Chemical Co., St. Louis, MO, USA) for two weeks. After that, the mice were returned to their normal diet for five weeks.

tag: The time of sacrifice; ZT10

tag: These mice were fed diet including 0.5% bezafibrate between 11 and 12 wks age.

tag: Equivalent amount of total RNA from hypothalamus of 4 bezafibrate-treated mice were mixed equally and used for microarray.

source_name: Hypothalamus from 4 control mice at ZT10

label_protocol:
Sample labeling, array processing and scanning, and data extraction were performed as described in One-Color Microarray-Based Gene Expression Analysis â?? Protocol. These protocols are available for download at http://www.chem.agilent.com/scripts/generic.asp?lpage=11617&indcol=N&prodcol=Y.
The microarrays used were Agilentâ??s Whole Mouse Genome Oligo Microarrays (P/N G4122F). Probe sequence information is publicly available at http://www.chem.agilent.com/cag/bsp/bsp_register.asp.
Labeled cRNAs were generated from 400 ng of total RNA using Agilentâ??s Low RNA Input Linear Amplification Kit (P/N 5188-5339).

tag: Strain; ICR, Gender; Male, Age; 17 wks, Tissue; Hypothalamus, The time of sacrifice; ZT10.

tag: Equivalent amount of total RNA from hypothalamus of 4 mice were mixed equally and used for microarray.


title: Control fibroblast (C9.gpr)


title: Control fibroblast (C5.gpr)


title: colon_0h_rep2

city: Adelaide

first: Joanne

last: Bowen

state: South Australia

address: North Terrace

department: Medical Oncology

country: Australia

institute: Royal Adelaide Hospital

description: Gene expression data from large intestine not treated with irinotecan

hyb_protocol: A total hybridisation volume of 300ul was prepared for each sample and 200ul loaded into a Rat 230 version 2.0 GeneChip.  The chip was hybridised at 45C for 16 hours in an oven with a rotating wheel at 60rpm.  After hybridisation the chip was washed using the appropriate fluidics script in the Affymetrix Fluidics Station 450.

scan_protocol: Chips were scanned using the Affymetrix GeneChip Scanner 3000. The scanner operating software, GCOS, converts the signal on the chip into a DAT file, which is used for generating subsequent CEL and CHP files for analysis.

data_processing: Data was normalised using robust multiarray average approach with additional background adjustment using sequence information to estimate probe affinity for nonspecific binding

organism: Rattus norvegicus

source_name: DA rat colon control

label_protocol: A total of 7ug was labelled using the Affymetrix One Cycle cDNA synthesis kit (Millenium Sciences cat no. 900431).  The subsequent cDNA was cleaned using the Affymetrix GeneChip Sample Cleanup kit (Millenium Sciences cat no. 900371). Biotin was incorporated into the resultant cRNA using the Affymetrix IVT labelling kit (Millenium Sciences cat no. 900449).  After the IVT process, the labelled cRNA was cleaned using the above GeneChip Sample Cleanup kit. A total of 20ug of labelled cRNA was then fragmented to the 50-200bp size range and quality control checked using the Bioanalyser 2100 using the NanoChip protocol.  Samples were then prepared for hybridisation to the Rat 230 version 2.0 GeneChip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes 1x Hybridisation Buffer (100mM MES, 1m NaCl, 20mM EDTA, 0.01% Tween-20), 0.1mg/ml Herring Sperm DNA, 0.5mg/ml BSA, and 7% DMSO.

growth_protocol: Rats were housed individually with free access to food and water

extract_protocol: Extraction of RNA was carried out by NucleoSpin RNA II kit (Machery Nagel, Germany) as per manufacturer's instructions. Rat total RNA was quality ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.

treatment_protocol: Rats received a single intraperitoneal injection of irinotecan while under light halothane anaesthetic (2% in 1.5 L O2). At the specified time point, rats were killed by exsanguination and cervical dislocation. The GIT was removed immediately and flushed with chilled isotonic saline.  Sections of whole stomach, jejunum and colon were snap frozen in LN2 and stored at -70C until extraction.

tag: Gender

value: female

tag: Age

value: 10 weeks


title: colon_72h_rep1

description: Gene expression data from large intestine treated with irinotecan

source_name: DA rat colon treated 72 h


title: Control fibroblast (C6.gpr)


title: colon_0h_rep1


title: colon_1h_rep1

source_name: DA rat colon treated 1 h


title: colon_24h_rep2

source_name: DA rat colon treated 24 h


title: colon_72h_rep2


title: fib_ZT22

description: Four bezafibrate-treated mice at time ZT22 are divided by the control sample for all present spots.

source_name: Hypothalamus from 4 bezafibrate-treated mice at ZT22

extract_protocol: The square area containing the hypothalamus was dissected from the brain immediately after decapitation at ZT22 and stored in RNAlater stabilization reagent for two hours. Total RNA was isolated following Qiagen's RNA isolation protocol (RNeasy Mini kit; Qiagen P/N 74104, Hilden, Germany). Contaminating DNA was removed using an RNase-free DNase set (Qiagen P/N 79254) during the process of RNA purification. The quality of the purified RNA applicable for microarray analysis was assessed by Agilent 2100 Bioanalyzer using an RNA 6000 Nano Labchip kit (Agilent Technologies).

tag: Strain; ICR, Gender; Male, Age; 17 wks, Tissue; Hypothalamus, The time of sacrifice; ZT22.

source_name: Hypothalamus from 4 control mice at ZT22


title: Control fibroblast (C8.gpr)


title: colon_6h_rep1

source_name: DA rat colon treated 6 h


title: jejunum_72h_rep2

description: Gene expression data from small intestine treated with irinotecan

source_name: DA rat jejunum treated 72 h


title: Control fibroblast (C3.gpr)


title: colon_6h_rep2


title: colon_24h_rep1


title: colon_1h_rep2


title: Control fibroblast (C7.gpr)


title: jejunum_24h_rep2

source_name: DA rat jejunum treated 24 h


title: Control fibroblast (C2.gpr)


title: Control fibroblast (C1.gpr)


title: jejunum_6h_rep2

source_name: DA rat jejunum treated 6 h


title: Patient fibroblast (P13.gpr)

source_name: Total RNA from patient fibroblast labeled with Cyanine-5 (red)


title: Patient fibroblast (P12.gpr)


title: Patient fibroblast (P11.gpr)


title: jejunum_24h_rep1


title: Patient fibroblast (P10.gpr)


title: Patient fibroblast (P7.gpr)


title: Patient fibroblast (P2.gpr)


title: Patient fibroblast (P8.gpr)


title: stomach_72h_rep2

description: Gene expression data from stomach treated with irinotecan

source_name: DA rat stomach treated 72 h


title: Patient fibroblast (P9.gpr)


title: stomach_72h_rep1


title: Patient fibroblast (P5.gpr)


title: jejunum_0h_rep2

description: Gene expression data from small intestine not treated with irinotecan

source_name: DA rat jejunum control


title: Patient fibroblast (P4.gpr)


title: Patient fibroblast (P6.gpr)


title: stomach_6h_rep2

source_name: DA rat stomach treated 6 h


title: stomach_24h_rep2

source_name: DA rat stomach treated 24 h


title: stomach_24h_rep1


title: jejunum_1h_rep1

source_name: DA rat jejunum treated 1 h


title: jejunum_6h_rep1


title: Patient fibroblast (P1.gpr)

source_name: Total RNA from reference HeLa cell lines labeled with Cyanine-3 (green)


title: jejunum_0h_rep1


title: jejunum_1h_rep2


title: stomach_0h_rep2

description: Gene expression data from stomach not treated with irinotecan

source_name: DA rat stomach control


title: mouse on chow-4a

city: Amsterdam

first: Douwe

last: Molenaar

address: De Boelelaan 1085

department: Systems Bioinformatics

country: Netherlands

institute: Vrije Universiteit Amsterdam

description: mouse on chow-4a

hyb_protocol: Two individual differentially, labeled cDNAs were, incubated at 95° C for 3', cooled down to 68° C and, mixed (final-volume 20 µl)., To these mixed cDNAs, 180 µl of pre-heated (68°, C) Slidehyb#1 hybridization, buffer (Ambion Austin USA), was added and the, resulting solution was, applied on a pre-heated, slide (68° C). Slides were, then hybridized at 44° C for, 16 hours. Subsequently, slides were washed at, 42°C once in 1 x, SSC/0.2% SDS and twice, in 1 x SSC and dried by, centrifugation (1 x SSC is, 0.15 M NaCl and 0.15 M, Sodium Citrate).

scan_protocol: Using the Scan Array, Express microarray, scanner. 1.Turn on the, scanner and the computer, (in this order) 2.Login:, scanner 3.Double click the, 'ScanArray Express' icon, 4.Switch on lasers 1 and 3, at least 15 minutes prior to, scanning arrays 5.Click the, 'File' button This is to, prevent you from, accidentally turning off the, laser after the 15 minutes, warming-up phase 6.Insert, the slide with the array-side, up and the label towards, the outside. On Agilent, slides the array side is the, side with the label that has, the word Agilent"""" on it, 7.Press 'Scan | Prescan', 8.Put resolution at 50 m, select both labels used, and set PMT values for, both channels 9.Press, 'Start' 10.Press 'Palette ', 'Green' as soon as, projection of the image has, started (first dye) select the, red colour as soon as, scanning of the second, layer (second dye) has, started 11.Adjust PMT, values to balance signals, obtained for both, channels. If necessary do, a few low-resolution scans, to obtain a optimal balance, 12.Click the 'Scan' button, again 13.Select frame for, high resolution scan adjust, resolution (to 10 m) and, scan the array for both, dyes 14.Press 'File | Save', to save the files 'Save all', saves both dye layers, Create a new folder for, each array 'Save all' saves, the signals from both layers, in individual files 15.Switch, off the lasers

data_processing: Only data from channel 2 , were used. After blank probe spots  were removed, array  measurements were first  normalized using quantile  normalization in R  (http://www.r-project.org).  Pearsons correlation on  the quantile-normalized  data was used to  determine overall similarity  between the culture  medium and  mouse-derived L.  plantarum transcriptome  data. The statistical  significance of the  differences was calculated  from the variation in the  biological replicates using  Student's t-test on log(ratio)  values. A FDR (false  discovery rate) adjustment  of the p-values was  performed (Smyth, 2004).  The list of differentially  expressed genes were  projected onto the  metabolic pathways known  for L. plantarum (Teusink  et al., 2006) using the  Simpheny software  (Genomatica, Inc., San  Diego, USA) and Cluster  (Eisen et al, 1998) to  display the gene  expression patterns. Only  genes with FDR adjusted  p-values less than 0.05,  corresponding to at most  5% false positives were  displayed. Analysis was  also assisted by  LacPlantCyc (Teusink et  al., 2005)

organism: Lactiplantibacillus plantarum WCFS1

source_name: mouse 30

label_protocol: This protocol describes direct Cy3 labelling of sheared DNA (as prepared by Total DNA isolation and shearing). This labelled DNA can be used as a normalizer in comparative expression experiments (hybridisations to cDNAs) or for strain diversity comparisons (DNA-DNA hybridisations). The protocol describes a modified application of the BioPrime array CGH labelling kit (Invitrogen 18095-012). For more detailed information concerning the kit check the manufacturer’s manual (Invitrogen 18095-013 and 18095-014; pdf document available in BASE). Ordering chemicals Cy3-dUTP solutions can be ordered at Amersham at 25 nmol scale (PA53022) or 250 nmol scale (PA53032). The concentration of the labelled nucleotide in both cases is 1 mM. For labelling DNA with Cy5 Cy5-dUTP is also available (PA55022) or 250 nmol scale (PA55032) NOTE: do not order labelled UTP’s (lacking the d), since they will not work, obviously!! Low-dTTP nucleotide mix Low-dTTp nucleotide mix (10x) 5 µl 	100 mM dCTP 5 µl

extract_protocol: THMS buffer" THMS 25 g	1 M Tris.HCl  pH = 8 300 ul

tag: mouse#

value: 30; diet:Chow;


title: MRS-2

data_processing: After blank probe spots  were removed, array  measurements were first  normalized using quantile  normalization in R  (http://www.r-project.org).  Pearsons correlation on  the quantile-normalized  data was used to  determine overall similarity  between the culture  medium and  mouse-derived L.  plantarum transcriptome  data. The statistical  significance of the  differences was calculated  from the variation in the  biological replicates using  Student's t-test on log(ratio)  values. A FDR (false  discovery rate) adjustment  of the p-values was  performed (Smyth, 2004).  The list of differentially  expressed genes were  projected onto the  metabolic pathways known  for L. plantarum (Teusink  et al., 2006) using the  Simpheny software  (Genomatica, Inc., San  Diego, USA) and Cluster  (Eisen et al, 1998) to  display the gene  expression patterns. Only  genes with FDR adjusted  p-values less than 0.05,  corresponding to at most  5% false positives were  displayed. Analysis was  also assisted by  LacPlantCyc (Teusink et  al., 2005)

source_name: Lplantarum MRS#2

tag: Medium

value: MRS; Growth phase:exponential


title: mouse on chow-1a

description: mouse on chow-1a

source_name: mouse 26

value: 26; diet:Chow;


title: stomach_1h_rep2

source_name: DA rat stomach treated 1 h


title: stomach_1h_rep1


title: Chow-3

source_name: Lplantarum Chow#3

value: Chow; Growth phase:exponential;


title: stomach_0h_rep1


title: stomach_6h_rep1


title: CDM-2

source_name: Lplantarum CDM#2

value: CDM; Growth phase:exponential; C-source:glucose


title: MRS-3

source_name: Lplantarum MRS#3


title: MRS-1

source_name: Lplantarum MRS#1


title: Chow-1

source_name: Lplantarum Chow#1


title: Chow-2

source_name: Lplantarum Chow#2


title: mouse on western-1

description: mouse on western-1

source_name: mouse 65

value: 65; diet:Western;


title: CDM-1

source_name: Lplantarum CDM#1


title: Patient fibroblast (P3.gpr)

source_name: Total RNA from patient fibroblast labeled with Cyanine-5 (red)


title: mouse on chow-3a

description: mouse on chow-3a

source_name: mouse 29

value: 29; diet:Chow;


title: jejunum_72h_rep1

source_name: DA rat jejunum treated 72 h


title: mouse on chow-4b

description: mouse on chow-4b


title: RA-treated 48hr rep4

status: Public on Jul 31 2008

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

description: Biological replicate 4 of 6; flip labeling.

hyb_protocol: Genomic Solutions hybridization station and hybridization buffer

scan_protocol: Scanned and quantified using a Perkin Elmer ScanArray Express scanner and software

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal using Perkin Elmer software

source_name: B16 melanoma cells

label_protocol: Invitrogen Superscript cDNA direct labeling system

extract_protocol: Total RNA extracted using Tri reagent following manufacturer's instructions

treatment_protocol: Treated with DMSO only

tag: B16 cell line

tag: DMSO treated (mock transfected)

tag: Treatment

value: 48 hr

tag: Treated with 10 uMol all-trans Retinoic Acid in DMSO


title: RA-treated 48hr rep5

description: Biological replicate 5 of 6; standard labeling.

treatment_protocol: Treated with 10 uMol all-trans Retinoic Acid in DMSO

tag: all-trans retinoic acid treated

tag: Treated with DMSO only


title: mouse on western-3

description: mouse on western-3

source_name: mouse 61

value: 61; diet:Western;


title: RA-treated 48hr rep3

description: Biological replicate3 of 6; standard labeling.


title: RA-treated 48hr rep2

description: Biological replicate 2 of 6; flip labeling.


title: mouse on chow-2a

description: mouse on chow-2a

source_name: mouse 27

value: 27; diet:Chow;


title: RA-treated 24hr rep2

value: 24 hr


title: RA-treated 24hr rep4


title: mouse on chow-1b

description: mouse on chow-1b


title: RA-treated 24hr rep3


title: RA-treated 24hr rep6

description: Biological replicate 6 of 6; flip labeling.


title: RA-treated 24hr rep5


title: RA-treated 48hr rep6


title: RA-treated 10hr rep6

value: 10 hr


title: RA-treated 48hr rep1

description: Biological replicate 1 of 6; standard labeling.


title: RA-treated 24hr rep1


title: RA-treated 10hr rep4


title: RA-treated 10hr rep5


title: RA-treated 10hr rep3


title: RA-treated 4hr rep4

value: 4 hr


title: RA-treated 4hr rep6


title: RA-treated 10hr rep2


title: RA-treated 10hr rep1


title: RA-treated 4hr rep5


title: RA-treated 4hr rep3


title: RA-treated 4hr rep2


title: RA-treated 4hr rep1


title: B16 vs melan-a, rep 6

description: B16 vs melan-a, replicate 6 of 6; flip labeling

hyb_protocol: Used Agilent hybridization solution and Biomicrosystem MAUI hybridization station, both according to manufacturers' instructions. Hybridization was for 16hr at 60C.

scan_protocol: Scanned on an Perkin Elmer ScanArray Express scanner.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Imagene software (Biodiscovery)  was used.

source_name: melan-a cells

extract_protocol: Total RNA extracted using tri-reagent following manufacturer's instructions

tag: Growth medium

value: RPMI 1640

tag: Strain

source_name: B16 cells

value: DMEM


title: B16 vs melan-a, rep 4

description: B16 vs melan-a, replicate 4 of 6; flip labeling


title: B16 vs melan-a, rep 1

description: B16 vs melan-a, replicate 1 of 6; standard labeling


title: B16 vs melan-a, rep 3

description: B16 vs melan-a, replicate 3 of 6; standard labeling


title: B16 vs melan-a, rep 5

description: B16 vs melan-a, replicate 5 of 6; standard labeling


title: mouse on western-2

description: mouse on western-2


title: mouse on chow-3b

description: mouse on chow-3b


title: Imaginal disc from Df(2R)ED50000 3rd instar larvae  (dye swap 1)

status: Public on Jul 15 2008

first: Edwige

last: Hiriart

address: Hills Road

department: Laboratory of Molecular Biology

institute: MRC

description: Analysis of the effect of hmgd deletion on gene expression in Drosophila embryos.

hyb_protocol: Genomics Solution GeneTAC hybridisation station with Ocimum hybridisation buffer. Hybridisation and washing described in detail at http://www.flychip.org.uk/protocols/hybridisation/hyb_oligoMWG.php

scan_protocol: Axon 4000B scanner using standard protocols (http://www.flychip.org.uk/protocols/imaging/scanning2.php)

data_processing: Spot finding and quantitation via the Dapple package. Normalisation accross the XX biological replicates for all YY

source_name: wild type DrosDel w118iso, 2iso, 3iso

label_protocol: Standard Klenow labelling of double stranded DNA (http://www.flychip.org.uk/protocols/gene_expression/klenow.php) using 3 to 5 microgrammes of total RNA.

extract_protocol: Approximately 50 imaginal discs from 3rd instar larvae were dissected and transferred into an eppendorf tube containing 100microlitres of TRIzol.  Tissues were stored at -80 C until homogenization and RNA extraction. 8 independent samples were taken.

tag: RNA from imaginal disc from wild type DrosDel w118iso, 2iso, 3iso 3rd instar larvae

extract_protocol: Approximately 50 imaginal discs from 3rd instar larvae were dissected and transferred into an eppendorf tube containing 100microlitres of TRIzol.  Tissues were stored at -80 C until homogenization and RNA extraction. 4 independent samples were taken.

tag: RNA from imaginal disc from Df(2R)ED50000 3rd instar larvae


title: B16 vs melan-a, rep 2

description: B16 vs melan-a, replicate 2 of 6; flip labeling


title: Imaginal disc from Df(2R)ED50000 3rd instar larvae  (1)

extract_protocol: Approximately 50 imaginal discs from 3rd instar larvae were dissected and transferred into an eppendorf tube containing 100ml of TRIzol.  Tissues were stored at -80 C until homogenization and RNA extraction. 4 independent samples were taken.

extract_protocol: Approximately 50 imaginal discs from 3rd instar larvae were dissected and transferred into an eppendorf tube containing 100ml of TRIzol.  Tissues were stored at -80 C until homogenization and RNA extraction. 8 independent samples were taken.


title: Brain from Df(2R)ED50000 3rd instar larvae  (dye swap 2)

extract_protocol: Approximately 25 brains from 3rd instar larvae were dissected and transferred into an eppendorf tube containing 100microlitres of TRIzol.  Tissues were stored at -80 C until homogenization and RNA extraction. 8 independent samples were taken.

tag: RNA from brain from wild type DrosDel w118iso, 2iso, 3iso 3rd instar larvae

extract_protocol: Approximately 25 brains from 3rd instar larvae were dissected and transferred into an eppendorf tube containing 100microlitres of TRIzol.  Tissues were stored at -80 C until homogenization and RNA extraction. 4 independent samples were taken.

tag: RNA from brain from Df(2R)ED50000 3rd instar larvae


title: Imaginal disc from Df(2R)ED50000 3rd instar larvae  (2)


title: Embryos (stage 0-11) from Df(2R)ED50000 strain (2)

label_protocol: Standard direct incorporation of Cy dyes during 1st strand cDNA synthesis (http://www.flychip.org.uk/protocols/gene_expression/direct_labelling.php) using 50 microgrammes of total RNA

extract_protocol: 0-11 stage embryos were collected from agar plates with a brush, transferred in a mesh, washed in water and dechoroniated for 2 minutes in 50% (v/v) solution of sodium hypochlorite. After extensive washing, the embryos were transferred into an eppendorf tube containing 500 ml of TRIzol. Embryos were stored at -80 C until homogenization and RNA extraction. 4 independent samples were taken.

tag: RNA from 0-11 stage embryos from hmgd deletion strain Df(2R)ED50000

extract_protocol: 0-11 stage embryos were collected from agar plates with a brush, transferred in a mesh, washed in water and dechoroniated for 2 minutes in 50% (v/v) solution of sodium hypochlorite. After extensive washing, the embryos were transferred into an eppendorf tube containing 500 ml of TRIzol. Embryos were stored at -80 C until homogenization and RNA extraction. 8 independent samples were taken.

tag: RNA from 0-11 stage embryos from wild type DrosDel w118iso, 2iso, 3iso


title: Brain from Df(2R)ED3921 3rd instar larvae  (1)

tag: RNA from brain from Df(2R)ED3921 3rd instar larvae


title: Brain from Df(2R)ED3921 3rd instar larvae  (dye swap 1)


title: Imaginal disc from Df(2R)ED3921 3rd instar larvae  (dye swap 2)

tag: RNA from imaginal disc from Df(2R)ED3921 3rd instar larvae


title: Embryos (stage 0-11) from Df(2R)ED50000 strain (dye swap)

tag: RNA from 0-11 stage embryos from wild-type DrosDel w118iso, 2iso, 3iso


title: Brain from Df(2R)ED3921 3rd instar larvae  (dye swap 2)


title: Imaginal disc from Df(2R)ED3921 3rd instar larvae  (2)


title: Imaginal disc from Df(2R)ED3921 3rd instar larvae  (1)


title: Brain from Df(2R)ED50000 3rd instar larvae  (dye swap 1)


title: Imaginal disc from Df(2R)ED3921 3rd instar larvae  (dye swap 1)


title: Embryos (stage 0-11) from Df(2R)ED3921 strain (2)

tag: RNA from stage 0-11 embryos from hmgd/z deletion strain Df(2R)ED3921

tag: RNA from 0-11 stage embryos from wild-type Drosdel w118iso, 2iso, 3iso


title: Embryos (stage 0-11) from Df(2R)ED3921 strain (dye swap 2)

tag: RNA from 0-11 stage embryos from hmgd/z deletion strain Df(2R)ED3921


title: Imaginal disc from Df(2R)ED50000 3rd instar larvae  (dye swap 2)


title: Brain from Df(2R)ED50000 3rd instar larvae  (1)


title: Embryos (stage 0-11) from Df(2R)ED3921 strain

description: Analysis of the effect of hmgd/z deletion on gene expression in Drosophila embryos.

extract_protocol: 0-11 stage embryos were collected from agar plates with a brush, transferred in a mesh, washed in water and dechoroniated for 2 minutes in 50% (v/v) solution of sodium hypochlorite. After extensive washing, the embryos were transferred into an eppendorf tube containing 500 ml of TRIzol. Embryos were stored at -80C until homogenization and RNA extraction. 4 independent samples were taken.

tag: RNA from stage 0-11 embryos from the hmgd/z deletion strain Df(2R)ED3921

extract_protocol: 0-11 stage embryos were collected from agar plates with a brush, transferred in a mesh, washed in water and dechoroniated for 2 minutes in 50% (v/v) solution of sodium hypochlorite. After extensive washing, the embryos were transferred into an eppendorf tube containing 500 ml of TRIzol. Embryos were stored at -80C until homogenization and RNA extraction. 8 independent samples were taken.

tag: RNA from stage 0-11 embryos from  wild-type Drosdel w118iso, 2iso, 3iso


title: Embryos (stage 0-11) from Df(2R)ED50000 strain (1)


title: Embryos (stage 0-11) from Df(2R)ED3921 strain (dye swap 1)

tag: RNA from stage 0-11 embryos from wild-type DrosDel w118iso, 2iso, 3iso


title: mESCs_Tip60KD_rep2

status: Public on Jul 11 2008

city: Berkeley

first: Jason

middle: T

last: Huff

address: 211 Koshland Hall

department: Plant & Microbial Biology

institute: University of California, Berkeley

description: Sample preparation, labeling, and array hybridizations were performed according to standard protocols from the UCSF Shared Microarray Core Facilities and Agilent Technologies (http://www.arrays.ucsf.edu and http://www.agilent.com).

hyb_protocol: Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays (Agilent). Hybridizations were performed for 14 hrs, according to the manufacturers protocol (Agilent).

scan_protocol: Arrays were scanned using the Agilent microarray scanner (Agilent) and raw signal intensities were extracted with Feature Extraction v8.9 software (Agilent).

data_processing: Raw log-intensities are normalized using quantile normalization method that is proposed by Bolstad et al (2003). No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization.

source_name: Tip60 KD mouse embryonic stem cells

label_protocol: Total RNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent).

extract_protocol: RNA was isolated using Trizol reagent combined with PureLink Micro-to-Midi columns (Invitrogen).

treatment_protocol: One well of a 6-well dish of E14 cells was treated with purified esiRNA (0.33 ng/ul) and Lipofectamine 2000 (Invitrogen) for 72 hr to knockdown expression of Tip60 (Htatip).

tag: Mouse embryonic stem cell line E14


title: mESCs_Tip60KD_rep3


title: A172 glioma cells, mock, 6 hr vs. A172 glioma cells, anti-mismatch, 6 hr

status: Public on Jul 12 2008

city: boston

first: Galina

last: Gabriely

state: MA

address: 4 blackfan circle

institute: HMS

description: MiR-21 promotes glioma invasion by targeting MMP regulators.  Galina Gabriely, Tom Wurdinger, Santosh Kesari, Christine C. Esau, Julja Burchard, Peter S. Linsley and Anna M. Krichevsky.  Molecular and Cellular Biology (2008).

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

source_name: A172 glioma cells

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: A172 glioma cells, mock, 6 hr

tag: A172 glioma cells, anti-mismatch, 6 hr


title: mESCs_EGFPcontrol_rep2

source_name: EGFP control KD mouse embryonic stem cells

treatment_protocol: One well of a 6-well dish of E14 cells was treated with purified, control (EGFP) esiRNA (0.33 ng/ul) and Lipofectamine 2000 (Invitrogen) for 72 hr.


title: mESCs_Tip60KD_rep4


title: A172 glioma cells, mock, 6 hr vs. A172 glioma cells, anti-miR-21, 6 hr

tag: A172 glioma cells, anti-miR-21, 6 hr


title: A172 glioma cells, mock, 24 hr vs. A172 glioma cells, miR-21, 24 hr

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45°C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver® system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).  Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.  The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

label: Biotin is incorporated during the amplification.  This binds a streptavidin-conjugated phycoerythrin during the post-hybridization staining process that provides the measurable signal.

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

tag: A172 glioma cells, mock, 24 hr

tag: A172 glioma cells, miR-21, 24 hr


title: mESCs_Tip60KD_rep1


title: A172 glioma cells, mock, 24 hr vs. A172 glioma cells, anti-miR-21, 24 hr

tag: A172 glioma cells, anti-miR-21, 24 hr


title: Gene expression profile of MEF cells transformed by H-RasV12 and Twist2

city: Lyon

first: stéphane

last: ansieau

address: 28 rue laennec

country: France

institute: Inserm U590

description: control group

hyb_protocol: Codelink Expression Assay protocol

scan_protocol: Codelink Expression Assay protocol

data_processing: Codelink Expression analysis v4.2 software

label: Biotin

source_name: MEF cells transformed by H-RasV12 and MEF cells

label_protocol: Amplification and biotin-labeling were performed according to	the Message Amp kit II (Ambion).

extract_protocol: RNA form primary or Ras + Twist-transformed MEF cells were prepared in duplicates using an RNeasy Mini kit (Quiagen).

tag: C57/B16 x DBA2 F1 mice


title: A172 glioma cells, mock, 24 hr vs. A172 glioma cells, anti-mismatch, 24 hr

tag: A172 glioma cells, anti-mismatch, 24 hr


title: Gene expression profile of MEF transformed by the two H-RasV12 and Twist1 oncogenes

description: control group

source_name: primary MEF cells transformed by H-RasV12 and Twist1

tag: MEF from C57/B16 x DBA2 F1 mice


title: Gene expression profile of MEF cells transformed by the two H-RasV12 and Twist2 oncogenes

description: control group

source_name: Primary MEF cells transformed by H-RasV12 and Twist2

tag: MEF cells from C57/B16 x DBA2 F1 mice


title: Gene expression profile of MEF cells transformed by Ras + Twist1

description: control group

source_name: Primary MEF cells transformed by the two H-RasV12 + Twist1 oncogènes

tag: Primary fibroblasts from C57/B16 x DBA2 F1 mice


title: mESCs_EGFPcontrol_rep3


title: Complemented espR mutant (R+) rep2

status: Public on Jul 04 2008

city: San Francisco

first: Paolo

last: Manzanillo

institute: University of California at San Francisco

description:
Biological replicate 2
Complemented espR mutant (R+) rep2

hyb_protocol: Cy5 and Cy3 labelled probes were mixed and hybridized to oligonucleotide MTB arrays (Operon Biosystems) at 63 C for 18h.After hybridization, slides were washed in batch.

scan_protocol: Slides were scanned using an Axon 4000B scanner and GenePix software. Data was acquired using Spotreader 1.3.1.0 and Acuity 4.0 software

data_processing: Ratio-based normalization using Acuity 4.0

organism: Mycobacterium tuberculosis

source_name: Complemented espR mutant M.tb

label_protocol: 5 ug total RNA was reverse transcribed into cDNA using random hexamer primers in the presence of aa-dUTP. cDNA was labelled with Cy dyes (Amersham) and purified over Zymo DNA binding columns.

growth_protocol: M. tuberculosis growing in 7H9 with 0.05% Tween 80 in early log phase

extract_protocol: RNA was extracted from 50 ml of culture by beadbeating in Trizol and RNA purified with Qiagen Rneasy columns per manufacturers instructions.

tag: M. tuberculosis Erdman strain

source_name: Reference Pool

tag: Pooled from all samples used


title: ESPR- mutant (R-) rep2

description:
Biological replicate 2
ESPR- mutant (R-) rep2

source_name: espR mutant M.tb


title: A172 glioma cells, mock, 6 hr vs. A172 glioma cells, miR-21, 6 hr

tag: A172 glioma cells, miR-21, 6 hr


title: mESCs_p400KD_rep3

hyb_protocol: Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 and Cy5 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays (Agilent). Hybridization samples were paired according to group designation and dye swaps were incorporated to correct for any dye bias. Hybridizations were performed for 14 hrs, according to the manufacturers protocol (Agilent).

data_processing: This dataset was normalized using robust locally weighted regression (loess) to correct for intensity, spatial and other dye biases (Cleveland 1979, JASA 74(36): 829; Yang et al 2002, NAR 30(4)). This procedure was performed and carried out using the Bioconductor package “marray” (http://www.bioconductor.org). In the context of microarray experiments, loess normalization captures the non-linear dependence of the intensity log-ratio M = log2R-log2G = log2(R/G) on the overall intensity A= (log2R+log2G)/2.

source_name: p400 KD mouse embryonic stem cells

label_protocol: Total RNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). RNA was amplified and labeled with Cy3-CTP and Cy5-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent).

treatment_protocol: One well of a 6-well dish of E14 cells was treated with purified esiRNA (0.33 ng/ul) and Lipofectamine 2000 (Invitrogen) for 72 hr to knockdown expression of p400.


title: mESCs_EGFPcontrol_rep1


title: mESCs_EGFPcontrol_rep4


title: Gene expression profile of MEF cells

description: control group

source_name: MEF primary fibroblasts

tag: Mouse primary fibroblasts from C57/B16 x DBA2 F1 mice


title: mESCs_p400KD_rep1


title: Gene expression profile of primary MEF cells

description: control group

source_name: MEF cells


title: mESCs_p400KD_rep4


title: mESCs_p400KD_rep2


title: ESPR- mutant (R-) rep1

description:
Biological replicate 1
ESPR- mutant (R-) rep1


title: WT TB rep2

description:
Biological replicate 2
WT TB rep2

source_name: Wt M.tb


title: Complemented espR mutant (R+) rep1

description:
Biological replicate 1
Complemented espR mutant (R+) rep1


title: WT TB rep1

description:
Biological replicate 1
WT TB rep1


title: S62T5

status: Public on Jul 02 2008

city: Ciudad Real

first: Ruth

middle: Cecilia

last: Galindo

state: Ciudad Real

address: Ronda de Toledo s/n

department: Animal Health

country: Spain

institute: Instituto de Investigacion en Recursos Cinegéticos

description: Normalized (global median) ratio values obtained for each probe were averaged across replicates. Significant differences were defined as those displaying an average expression fold change greater than 2-fold (log (base 2) ratio ≥ 1.0).

hyb_protocol: Labeled total RNA (1 µg) was hybridized to the microarrays using the supplied formamide-based hybridization buffer and 24x60 mm LifterSlips slides (Erie Scientific, Portmouth, NH, USA) according to the manufacturer’s (Genisphere) instructions. Post-hybridization washes were done according to the manufacturer’s (Genisphere) instructions.

scan_protocol: Hybridization signals were measured using a ScanArray Express (PerkinElmer, Boston, MA, USA) and the images where processed using GenePix Pro version 4.0 (Axon, Union City, CA, USA).

data_processing: Normalization of log2 ratios using global median normalization

label: Cy5 Fluor

organism: Ovis aries

source_name: Infected animal 62, 15 days post infection

label_protocol: One µg total RNA was labeled using the 3DNA Array900MPX kit with Cy5 and Cy3 fluor dyes (Genisphere, Hatfield, PA, USA), the supplied random and oligo-dT primes, Superscript II (Invitrogen, Carlsbad, CA, USA), the supplied formamide-based hybridization buffer and 24x60 mm LifterSlips slides (Erie Scientific, Portmouth, NH, USA) according to the manufacturer’s (Genisphere) instructions.

growth_protocol: The rams were challenged with a total dose of 1.7 x 109 B. ovis CFU, as shown by viable cell counts made on the day of inoculation, in 60 l doses (30 l administered conjunctivally and 30 l intrapreputially).

extract_protocol: Total RNA was isolated from Buffy coat samples of experimentally infected and control sheep using TriReagent (Sigma, St. Louis, MO, USA) according to manufacturer’s instructions. The RNA was checked using the Experion™ Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA) to evaluate the quality and integrity of RNA preparations.

treatment_protocol: Each necropsy specimen was macerated in a laboratory blender  and 0.5 - 0.8 ml of tissue suspension was seeded onto each of two culture plates of the modified Thayer-Martin's medium. The plates were read after 4 and 7 days of incubation at 37 ºC in 10% CO2. The Brucella colonies were identified by colonial morphology, Gram staining, oxidase and urease tests, CO2 requirement and phage typing.

tag: Infected animal 62

label: Cy3 Fluor

source_name: Uninfected animal 62, 15 days pre infection

label_protocol: One µg total RNA was labeled using the 3DNA Array900MPX kit with Alexa Fluor dyes (Genisphere, Hatfield, PA, USA), the supplied random and oligo-dT primes, Superscript II (Invitrogen, Carlsbad, CA, USA), the supplied formamide-based hybridization buffer and 24x60 mm LifterSlips slides (Erie Scientific, Portmouth, NH, USA) according to the manufacturer’s (Genisphere) instructions.

treatment_protocol: Lack of B. ovis infection was assessed by culture.

tag: Uninfected animal 62


title: S118T7

source_name: Infected animal 118, 60 days post infection

tag: Infected animal 118

source_name: Uninfected animal 118, 15 days pre infection

tag: Uninfected animal 118


title: S118T5

source_name: Infected animal 118, 15 days post infection


title: S60T7

source_name: Infected animal 60, 60 days post infection

tag: Infected animal 60

source_name: Uninfected animal 60, 15 days pre infection

tag: Uninfected animal 60


title: subtilis_ccpN-yqfLexp_wt1

status: Public on Jul 01 2008

city: Thiverval-Grignon

first: Thierry

last: Doan

address: INRA

department: Microbiologie

institute: INRA

description: Global transcriptional profiling of Bacillus subtilis cells comparing wild-type to a ccpN-yqfL double mutant. Two-condition experiment, wt vs. ccpN0yqfL mutant. 2 totally independent experiments were performed.

hyb_protocol: Panorama B. subtilis gene macroarrays (Sigma-Genosys) containing full-length PCR products of all 4107 B. subtilis protein-coding genes in duplicate were prehybridized for 2h at 65C with 100 µg/mL herring sperm DNA, and then hybridized for 20h at 65C with the denatured radiolabelled cDNA

scan_protocol: The arrays were then exposed for 24 hours to an Imaging Plate and scanned with a STORM phosphoimager (GE Lifesciences), images of the hybridized arrays were processed and signal intensities quantified using the Array Vision software (Imaging Research, Canada)

data_processing: Data analysis was performed using Array Vision software (Imaging Research, Canada) for signals and background quantitations. The raw data were re-scaled to account for the differences in individual hybridization intensities.

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: Bacillus subtilis cells, wild-type, glucose medium

label_protocol: cDNA labelling kit were provided by Sigma-Genosys and used as recommended. 2µg total RNA was used for labeled cDNA preparation in the presence of 2,5 µL [a-33P]-dCTP (10 µCi/µL).

growth_protocol: Cells pellet for RNA extraction were obtained from cultures grown up to exponential growth phase (OD600=0.5) in TSS miminal medium (Fouet and Sonenshein, 1990) supplemented with 10g/L glucose.

extract_protocol: High-quality RNA preparation, radiolabelled cDNA synthesis and hybridization were performed as previously described (Hauser et al., 1998; Eymann et al., 2002). Cells pellet for RNA extraction were obtained from cultures grown up to exponential growth phase (OD600=0.5).

treatment_protocol: no particular treatment was performed on cells prior to extract preparation.

tag: wild-type strain 168 CA, whole cells grown in glucose medium, exponential phase (OD600 0.5)


title: S62T7

source_name: Infected animal 62, 60 days post infection


title: subtilis_ccpN-yqfLexp_mutant2

source_name: Bacillus subtilis cells, ccpN-yqfL double mutant, glucose medium

tag: ccpN-yqfL double mutant strain GM1599, whole cells grown in glucose medium, exponential phase (OD600 0.5)


title: subtilis_ccpN-yqfLexp_mutant1


title: subtilis_ccpN-yqfLexp_wt2


title: S60T5

scan_protocol: Labeled total RNA (1 µg) was hybridized to the microarrays using the supplied formamide-based hybridization buffer and 24x60 mm LifterSlips slides (Erie Scientific, Portmouth, NH, USA) according to the manufacturer’s (Genisphere) instructions. Post-hybridization washes were done according to the manufacturer’s (Genisphere) instructions.

source_name: Infected animal 60, 15 days post infection

treatment_protocol: Each necropsy specimen was macerated in a laboratory blender  and 0.5 - 0.8 ml of tissue suspension was seeded onto each of two culture plates of the modified Thayer-Martin's medium. The plates were read after 4 and 7 days of incubation at 37 ºC in 10% CO2. The Brucella colonies were identified by colonial morphology, Gram staining, oxidase and urease tests, CO2 requirement and phage typing


title: PPB3

city: Vancouver

first: Kevin

last: McElwee

state: BC

department: Dermatology and Skin Science

country: Canada

institute: University of British Columbia

description: All treated biologicaly replicated samples were hybridized with the same universal human reference RNA (reference).

scan_protocol: The two fluorescent images (Cy3 and Cy5) were scanned separately using a Perkin Elmer ScanArray Express Scanner (PerkinElmer Life And Analytical Sciences, Inc., Wellesley, MA).

data_processing: Arrays were scanned at excitation wave lengths of 532 and 635 nm to detect the Cy3 and Cy5 dyes, respectively. Image analysis and quantification were conducted with commercial software, (ImaGene 7.0 software: BioDiscovery Inc., El Segundo, CA, USA). After grid assignment, the adjusted intensity for each gene was calculated by subtracting the background. This value was used as the input for the Genespring 7.2 program (Silicon Genetics, Redwood City, CA, USA).

source_name: PPB

label_protocol: 1 ug RNA were amplified using the SenseAmp plus kit (Genisphere Inc, Hatfield, PA). The calculated A 260/280 ratio was used to determine the appropriate amount of sense RNA for labeling. sense RNA from amplification was labeled with Cy5, with the 3DNA array detection 350 kit (Genisphere) and hybridized to cDNA microarrays

growth_protocol: sample was stored in an RNA stabilization reagent

extract_protocol: Total RNA was isolated with an RNeasy Fibrous Tissue Midi Kit (Qiagen) according to the manufacturer's protocols.The quantity and quality of the RNAs was measured by electrophoresis using the Agilent 2100 bioanalyzer and RNA 6000 nano kit (Agilent Technologies, Palo Alto, CA)

treatment_protocol: sample was collected in the operating theater

tag: PPB

label_protocol: Total 10ug RNA universal human reference RNA (Stratagene, Cedar Creek, TX) was labeled with Cy3 , with the 3DNA array detection 350 kit (Genisphere) and hybridized to cDNA microarrays.

extract_protocol: The Universal Human Reference RNA is composed of total RNA isolated from cell lines representing different human tissues for optimal broad gene coverage.


title: LPP4

hyb_protocol: 3DNA array detection 350 kit (Genisphere)

source_name: LPP

tag: LPP

source_name: universal human reference RNA (Stratagene, Cedar Creek, TX)

tag: The Universal Human Reference RNA is composed of total RNA isolated from cell lines representing different human tissues for optimal broad gene coverage.


title: PPB_intra-control_4

treatment_protocol: universal human reference RNA (Stratagene, Cedar Creek, TX)


title: PPB2


title: PPB_intra-control_3


title: LPP1


title: PPB4


title: LPP_intra-control_2


title: PPB_intra-control_2


title: LPP_intra-control_4


title: HRG Untreated

city: Bangalore

first: Dipshikha

last: Chakravortty

state: Karnataka

address: C.V.Raman AVENUE

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

description: Slides were scanned at 5 micron resolution using Agilent scanner.Automated feature extraction was done using Agilent’s Feature Extraction Software.

hyb_protocol: 1650ng of labeled Sample, mixed with appropriate amount of blocking buffer and hybridization buffer (Agilent Technologies) (Web link). The hybridization mix was applied on to the backings and hybridized to custom designed 60mer s.TYPHIMURIUM microarray using sure hyb chambers at 65degC for 16 hours. Slides were washed with gene expression wash buffer 1 and 2 (Agilent Technologies) followed by Acetonitrile.

scan_protocol: Laser detection of Cyanine 3 fluorescence is performed using a confocal scanning instrument containing tuned lasers, which excite Cyanine dyes at the appropriate wavelengths.

data_processing:
Analysis of feature extracted data was done using Agilent’s GeneSpring GX V 7.3.1 software. Pre-processing of the replicate experiment data was done to flag the outliers. The normalization was done using GeneSpring GX using the recommended Per Chip and Per Gene Data Transformation: Set measurements less than 0.01 to 0.01, Per Chip: Normalize to 50th percentile, Per Gene: Normalize to Specific Samples (Treated Vs Control).
 Genes with log2 ratio of 1.8 and above in replicate experiments were considered as up regulated and 0.55 and below was considered down regulated. p-value was calculated by GeneSpring GX for each gene on the basis of replicate probes to indicate statistical significance

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Salmonella typhimurium HRG Mutant Untreated

label_protocol: 1 microgram of RNA is polyadenylated  using poly-A polymerase (pAp) enzyme and labeled using Agilents Lirak kit as per manufacturer recommended protocol (www.agilent.com).

extract_protocol: Trizol bacterial RNA kit


title: HRG H2O2 Treated

source_name: Salmonella typhimurium HRG Treated

tag: Salmonella typhimurium HRG Treated


title: WT H2O2 Treated

source_name: Salmonella typhimurium Wild Type Treated


title: PPB_intra-control_1


title: LPP2


title: WT Untreated

source_name: Salmonella typhimurium Wild Type Untreated


title: LPP_intra-control_3


title: LPP_intra-control_1


title: Murine lung, wild-type, Diesel Particulate Instillation vs. Control Instillation, replicate #2 dye-reversal

status: Public on Jun 30 2008

city: Honolulu

first: John

last: Maresh

state: HI

address: 651 Ilalo

department: Medicine

institute: University of Hawaii

description: This is a standard 2 color hybridization to determine transcript-level dysregulation in the lung in response to instillation of diesel engine particulate in wild-type mice.

hyb_protocol: The microarrays were hybridized with the ASAP Micromax hybridization buffer system 16 hours at 50 degrees C. Washing was at room temp: 5 minutes in 2X SSC, 0.1% SDS, then 5 minutes in .1 X SSC, 0.1% SDS, then 5 minutes in .1 X SSC.

scan_protocol: The standard scan settings using Molecular Devices 4000B.

data_processing:
The GPR data was uploaded to Acuity software from Molecular Devices, normalized by ratio of medians. Filtered to mark Genepix flags.
Log2 fold change of median value of experimental/control.

source_name: Lungs from mice exposed to diesel particulate intratracheal instillation.

label_protocol: RNA was extracted, amplified with the oligodT-T7 method, Cy-dye labeled with Perkin Elmer Micromax ASAP system.

growth_protocol: In vivo exposure of animals.

treatment_protocol: Lungs were rapidly frozen after collection. RNA was extracted from homogenized frozen hearts in Trizol pooled from 4 animals. Purification by Qiagen RNeasy columns.

tag: RNA from lungs of mice exposed to 100 ug diesel particulate (NIST) suspension by intratracheal instillation under anesthesia, 24 h after exposure. Males. Age 8-20 weeks.

source_name: Lungs from control mice exposed to saline intratracheal instillation

extract_protocol: Trizol and Qiagen columns were used according to each manufacturer's protocols.

tag: RNA from lungs of control mice exposed to saline, 24 after exposure by intratracheal instillation under anesthesia. Males. Age 8-20 weeks.


title: LPP3


title: Murine lung, wild-type, 5 day post Diesel Particulate Instillation vs. Control Instillation

extract_protocol: Trizol and Qiagen columns were used according to each manufacturer's protocols

tag: RNA from lungs of mice exposed to 100 ug diesel particulate (NIST) suspension by intratracheal instillation under anesthesia, 24 h after exposure.


title: PPB1


title: Murine lung, Apo E (-/-), Diesel Particulate Instillation vs. Control Instillation

data_processing:
The GPR data was uploaded to Acuity software from Molecular Devices, normalized by ratio of medians.  Filtered to mark Genepix flags.
Log2 fold change of medians value of experimental/control.


title: Murine lung, wild-type, Diesel Particulate Instillation vs. Control Instillation


title: Murine heart, wild type, Diesel Particulate Instillation vs Control Instillation, replicate #2, dye reversal

description: This is a standard 2 color hybridization to determine transcript-level dysregulation in the heart in response to instillation of diesel engine particulate in wild-type mice.

hyb_protocol: Labeled probe plus Cot1, polyA, tRNA combined with 3X SSC plus 25% formamide. 16 hour hybridization with glass coverslips at 42 degrees C. Stringency washing according to manufacturer's protocol.

scan_protocol: Standard scan methodology with Genepix 4000B device(Molecular Devices)

data_processing: Results were normalized using the ratio of medians method and filtered to indicate a Genepix flag.

source_name: Heart from mice exposed to diesel particulate instillation

growth_protocol: In vivo exposure of whole animals.

tag: RNA from hearts of mice exposed to 100 ug diesel particulate (NIST) suspension, 24 after exposure by intratracheal instillation under anesthesia.

source_name: Heart from control mice exposed to saline instillation

label_protocol: GE Amersham MicroMAX direct labeling kit with incorporation of dUTP-Cy dye into cDNA. Stringency washing according to manufacturer's protocol.

extract_protocol: Trizol and Qiagen columns were used according to each manufacturer's protocol

treatment_protocol: Hearts were rapidly frozen after collection. RNA was extracted from homogenized frozen hearts in Trizol pooled from 4 animals. Purification by Qiagen RNeasy columns.

tag: RNA from hearts of control mice exposed to saline, 24 after exposure by intratracheal instillation under anesthesia.


title: Murine lung, wild-type, 5 day post-Diesel Particulate Instillation vs. Control Instillation, replicate #2 dye-reversal

tag: RNA from lungs of mice exposed to 100 ug diesel particulate (NIST) suspension by intratracheal instillation under anesthesia, 5 day after exposure.

tag: RNA from lungs of control mice exposed to saline, 5 day after exposure by intratracheal instillation under anesthesia. Males. Age 8-20 weeks.


title: Murine heart, wild type, Diesel Particulate Instillation vs Control Instillation

label_protocol: GE Amersham MicroMAX direct labeling kit with incorporation of UTP-Cy dye into cDNA.

treatment_protocol: Hearts were rapidly frozen after collection. RNA was extracted from homogenized frozen hearts in Trizol pooled from 4 animals. Purification by Qiagen RNeasy column


title: Murine lung, Apo E (-/-), Diesel Particulate Instillation vs. Control Instillation, replicate #2 dye-reversal


title: Murine heart, Apo E (-/-), Diesel Particulate Instillation vs Control Instillation

description: This is a standard 2 color hybridization to determine transcript-level dysregulation in the heart in response to instillation of diesel engine particulate.

treatment_protocol: Hearts were rapidly frozen after collection. RNA was extracted from homogenized frozen hearts in Trizol pooled from 4 animals.  Purification by Qiagen RNeasy columns.

tag: RNA from hearts of mice exposed to 100 ug diesel particulate (NIST) suspension by intratracheal instillation under anesthesia, 24 after exposure.

label_protocol: GE Amersham MicroMAX direct labeling kit with incorporation of dUTP-Cy dye into cDNA.  Stringency washing according to manufacturer's protocol.


title: S_pombe_H3K36me3ChIP_rep1&2

city: Salt Lake City

first: Timothy

middle: J

last: Parnell

state: UT

address: 2000 Circle of Hope

institute: Huntsman Cancer Institute

description: Genomic DNA associated with histone that is methylated on Histone H3 residue K36

hyb_protocol: Hybridizations and washes were performed according to manufacturer's recommended procedures (Agilent Technologies).

scan_protocol: Arrays were scanned in an Agilent G2505B Microarray Scanner using extended dynamic range software. Feature extraction of the scanned images was performed using Agilent Feature Extraction Software Version 9.5.1.

data_processing: All of the software used in this analysis is open source and available from the TiMAT2 project site, http://sourceforge.net/projects/timat2. To identify genomic regions enriched in chromatin immunoprecipitation experiments, a similar approach as that used in generating the dynamic transcriptome analysis was employed with the following exceptions. Array data was acquired from the H3K36 ChIP experiment described in this manuscript as well as from two previously published ChIP experiments: H3 and H3K9me2 (Gordon et al, 2007, MCB 27:4058-69). Both the treatment (ChIP) and control (input) biological replicas were grouped together, quantile normalized, and individual replicas median scaled to 100. A sliding window of 600bp was advanced across each chromosome. Windows containing 2 or more oligos were scored by first calculating all the relative difference pairs between the treatment and control replicas and second, taking a pseudo median of these scores. To estimate confidence in the window scores, Richard Bourgon s symmetric null R application was used to assign a p-value to each window score6. John Storey s q-value R application7 was then applied to correct for multiple testing and assign FDRs to each p-value.  Overlapping high scoring windows were merged into enriched regions and then ranked by their best window score.

organism: Schizosaccharomyces pombe

source_name: H3K36me3 ChIP elutant

label_protocol:
Round A Amplification: The DNA sample was diluted in 10 ul reaction containing 1X of Sequenase Buffer and 40 pM ChIP-A primer (5'-GTTTCCCAGTCACGATCNNNNNNNNN-3'), denatured at 94 C for 2 min, and rapid cooled to 8 C. To the reaction 5 nM dNTP, 75 nM DTT, 0.5 ug BSA, and 4 units of Sequenase enzyme (USB) was added for a final volume of 15 ul. The temperature of the reaction was slowly raised to 37 C and incubated for 8 minutes. The DNA products were denatured again by incubating at 94 C for 2 minutes, followed by rapid cooling to 8 C. An additional 4 units of Sequenase enzyme was added, the temperature slowly raised to 37C and incubated for 8 minutes. The Round A products were diluted with water to 25 ul final volume.
Round B Amplification: A 7.5 ul aliquot of round A products was used as template in a PCR reaction using 2.5 units of Platinum Taq (Invitrogen), 2 mM MgCl2, and 5 uM ChIP-B primer (5'-GTTTCCCAGTCACGATC-3'). The amplification consisted of 27 rounds of 30 seconds at 94 C, 30 seconds at 40 C, 30 seconds at 50 C, and 60 seconds at 72 C. The Round B DNA products were purified using a Qiagen PCR cleanup column and eluted in 50 ul Elution Buffer. An aliquot was checked by agarose electrophoresis and the concentration determined by OD260.
Round C labeling: An aliquot of Round B product containing 2 ug of DNA was used as template in the labeling reaction. The template DNA was diluted in 25 ul volume containing 1.2X New England Biolab Buffer 2 and 10 pM of ChIP-B primer. The DNA was denatured by incubating at 94 C for 2 minutes and rapid cooled to 8 C. To the reaction 1 nM dATP, 1 nM dTTP, 1 nM dGTP, 0.5 nM dCTP, 1 nM labeled-dCTP, and 5 units of Exo-Klenow (New England Biolabs) was added for a final volume of 30 ul. The reaction was incubated at 37 C for 3 hours. The labeled products were purified using Qiagen PCR cleanup columns (not recommended) with an additional 35% guanidine HCl wash. DNA was eluted in 30 ul Elution Buffer. Incorporation and yield was checked using a Nano-Drop spectrophotometer.

growth_protocol: Yeast growth, manipulations, and molecular biology were performed according to standard protocols. The strain was grown on yeast extract with glucose (2%) supplemented with histidine, uracil, leucine, and adenine at 32C to an optical density at 600 nm of 1.0.

extract_protocol:
Chromatin preparation: Cells were cross linked with formaldehyde (1% final concentration) for 30 minutes, quenched with 0.1 M glycine, and washed with Tris buffered saline (TBS) three times. The washed cell pellets were resuspended in 500 ul of lysis buffer (50 mM Tris-HCl pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.4 mM DTT, 1X protease inhibitors) and mechanically lysed using 0.7 mm zirconia beads in a mechanical bead beater with four 2 minute rounds. The samples were centrifuged at 20K x g for 5 minutes and the supernatant discarded. The chromatin containing pellet was resuspended in 500 ul of fresh lysis buffer and sonicated five times for 25 seconds each at 90% duty cycle at power setting 4.5. The solubilized chromatin was separated from insoluble material by centrifugation at 20K x g for 10 minutes. The protein concentration was determined by Bradford assay.
Immunoprecipitation: Antibody (4 uL) against H3K36me3 (Abcam ab9050) was coupled to 100 uL of Dynabeads (Invitrogen). The beads were then incubated with an aliquot of 1 mg of prepared chromatin in 500 ul of lysis buffer supplemented with 250 ug BSA Input chromatin overnight.  Beads with captured immunocomplexes were washed sequentially with 1 ml of lysis buffer twice, lysis buffer adjusted to 500 mM NaCl once, LiCl wash buffer (10 mM Tris-HCl pH 8, 250 mM LiCl, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1 mM EDTA) once, and TE (10 mM Tris-HCl pH 8, 1 mM EDTA) once. Immunocomplexes were released and cross links reversed by incubating the beads with 200 ul ChIP Elution Buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 1% SDS) at 65 C overnight. The DNA was purified using Qiagen PCR cleanup columns and eluted in 50 ul Elution Buffer. An aliquot of 7 ul was used in subsequent amplification and labeling procedures.

tag: Strain

tag: Genotype

value: ade6-m210, leu1-32, ura4-DS/E, mat3-M::ura4

tag: Mating type

source_name: H3K36me3 ChIP input

label_protocol: refer to Sample_label_protocol_ch1

extract_protocol:
Chromatin preparation: refer to Sample_extract_protocol_ch1
Input: An aliquot of 1 mg was reserved for input material. Input chromatin was incubated at 65 C overnight to reverse cross links. The DNA was purified using Qiagen PCR cleanup columns and eluted in 50 ul Elution Buffer. An aliquot of 2 ul was used in subsequent amplification and labeling procedures.


title: Murine heart, Apo E (-/-), Diesel Particulate Instillation vs Control Instillation, replicate #2, dye reversal

description: This is a standard 2 color hybridization to determine transcript-level dysregulation in the heart in response to instillation of diesel engine particulate. This is replicate #2, the dye reversal.

data_processing: Results were normalized using the ratio of medians method and filtered to indicate a Genepix flag.  Log2 ratio of medians fold change = ratio of experimental/control i.e. channel1/channel 2.


title: subject 29

city: Farmington

first: Winfried

last: Krueger

address: 263 Farmington Aveneu

department: Genetics & Developmental Biology

institute: University of Connecticut Health Center

description: Gene Expression Data from Umbilical Cord

hyb_protocol: the arrays were hybridized for 16 hours at 42 0C and stained in an Affymetrix Fluidics Station using a two-stage signal amplification protocol based on detection of the biotinylated targets by streptavidin-phycoeritherin (SAPE) according to Affymetrix instructions.

scan_protocol: The signal was quantified by detection of bound phycoerythericin using an Affymetrix GeneChip Scanner 3000.

data_processing: scaled data  were RMA normalized using the MAANOVA inherent algorithm.  Genes demonstrating significant regulation were determined by trivariate ANOVA analysis with the variables Smoker status, gender and blood contamination (Erythro ContaminationGroup:  grouping according to their absorbtion at 418 nm into Erythrocyte group 1 (OD418 <1.5, Erythrocyte group 2 (OD418 <2.5 and Erythrocyte group 3 (OD418 >2.5,

source_name: Umbiilical Cord from_smk

label_protocol: The RNA was further amplified as recommended by the manufacturer (Affymetrix, Santa Clara, CA). For each sample, 1.5 ug of RNA was converted into biotinylated targets. Briefly, the RNA was used for first and second strand cDNA synthesis, and the double-stranded cDNA was amplified in the presence of biotinylated ribonucleotides to generate biotinylated cRNA, which was then purified by ion exchange column chromatography.

growth_protocol: Biopsy

extract_protocol: Umbilical cord (UC) tissue midway between infant and placenta was collected within 10 minutes postpartum, cut into 1.5-cm pieces, flash frozen by immersion in liquid nitrogen and stored at -80oC. A random sample of UC tissue (~300 mg) was selected and RNA was isolated using a modified guanidinium isothiocyanate/CsCl procedure (6). Briefly, tissue was cooled with liquid nitrogen, ground to a fine powder, and transferred into a tube containing 1 ml of GTC lysis buffer (4M guanidinium isothiocyanate in 50 mM sodium citrate, TrisHCl or HEPES, 0.1 % sodium sarcosyl). Extracellular matrix was dissociated from the cells, the cells were lysed, and the genomic DNA was sheared using a Polytron mixer. For estimation of blood contamination, an aliquot was analyzed spectrophotometrically at a wavelength of 418 nm. The homogenate was then layered on top of a 1.5 ml cushion of CsCl buffer (5.7 M CsCl/10 mM sodium citrate pH7.0 and 1 mM EDTA), and centrifuged at 45,000 rpm, at 22oC, in a SW50 rotor for 23 hours. RNA sediment was dissolved in 100 ul H2O (RNAsefree), concentrated by overnight precipitation at -20oC in the presence of 0.3M NaOAc and 75% ethanol (final concentration) and sedimented for 10 min at 15,000 rpm, at 4oC,

treatment_protocol: exposure to cigarette smoke

tag: ErythroCountgroup 2, gender = f


title: subject 30

tag: ErythroCountgroup 3, gender = m


title: subject 19

source_name: Umbiilical Cord from_nonsm


title: subject 26


title: S_pombe_MMSCondition_rep1&2_slide2

description: This sample is total RNA extracted from wildtype S.pombe grown under MMS conditions and treatment

hyb_protocol: RNA samples (15 ug total RNA) were fragmented and combined with Agilent Hi-RPM GE Hybridization kit (cat#5190-0403) reagents.  These samples were hybridized to the array slides at 65C for 17 hr.  The slides were washed in 6x SSPE, 0.005% N-lauroylsarcosine for one min at room temperature and in 0.06x SSPE, 0.005% N-lauroylsarcosine for 1 min at 31C.  The slides were then incubated with 0.025mg/mL primary monoclonal mouse anti-RNA DNA hybrid antibody available in a hybridoma cell line from ATCC (HB-8730).  This was diluted in 500uL of SB+BSA (100mM MES, pH 6.6, 1M NaCl, 0.05% Tween 20, and 1 mg/mL BSA).  The 60 min incubation was at 25C.  After this incubation the slides were washed four times for three min in NSWB (6xSSPE, 0.01% Tween 20).  The secondary Cy3-labeled goat anti-mouse antibody (KPL, cat#078-18-061) was used at a concentration of 3ug/mL in 500uL of SB+BSA.  The slides were incubated with the secondary antibody for 60 min at 25C.  Finally the slides are washed four times for three min in NSWB at room temperature.

data_processing: All of the software used in this analysis is open source and available from the TiMAT2 project site, http://sourceforge.net/projects/timat2. Processing of the Agilent microarray transcriptome data was performed in three basic steps:  data normalization, sliding window summaries, and enriched region identification.  For each condition (growth and or RNA fraction) and strand, the median unadjusted signal intensities from the cy3 channel were extracted. Probes were then mapped to the April 2007 build and those with < 100 exact matches were retained. The two biological replicas for each condition were quantile normalized and scaled in two different ways.  The first was to scale the data such that the median of the zebrafish control probes was one. The second was to scale the data such that the median of the trimmed intergenic region probes was one. Trimmed intergenic probes were defined as those  > 240 bp (4 probes) from any known annotation.  Probe level oligo summaries were calculated by taking the log2 of the mean of the two biological replica probes for each condition.

source_name: S.pombe grown under MMS conditions  hybridized to slide 2

label_protocol: See Sample_hyb_protocol

growth_protocol: Yeast growth, manipulations, and molecular biology were performed according to standard protocols. Cells were cultured to an optical density at 600 nm of 0.6 and then treated as described.

extract_protocol: Yeast cells were harvested and after mechanical pulverization, the cell material was stored at -80C. Total RNA was extracted using the Ambion mirVanaTM kit.

treatment_protocol: For the methyl methane-sulfonate transcriptome, cells were treated with MMS (0.02%) for 1hr.

value: wildtype


title: subject 28

tag: ErythroCountgroup 2, gender = m


title: subject 22

tag: ErythroCountgroup 1, gender = m


title: subject 24

tag: ErythroCountgroup 3, gender = f


title: S_pombe_MinimalMediaCondition_rep1&2_slide1

description: This sample is total RNA extracted from wildtype S.pombe grown under minimal media conditions and treatment

source_name: S.pombe grown under minimal media conditions hybridized to slide 1

growth_protocol: Yeast growth, manipulations, and molecular biology were performed according to standard protocols. For the minimal medium transcriptome, cells were cultured as described in media lacking amino acids and containing 2% glucose at 32C to an optical density at 600 nm of 1.0


title: subject 18


title: subject 27


title: S_pombe_StandardCondition_rep1&2_slide1

description: This sample is total RNA extracted from wildtype S.pombe grown under standard conditions

source_name: S.pombe grown under standard conditions hybridized to slide 1

growth_protocol: Yeast growth, manipulations, and molecular biology were performed according to standard protocols. For rich medium, the strain was grown on yeast extract with glucose (2%) supplemented with histidine, uracil, leucine, and adenine at 32C to an optical density at 600 nm of 1.0.


title: subject 25


title: subject 20


title: subject 21


title: S_pombe_HeatShockCondition_rep1&2_slide1

description: This sample is total RNA extracted from wildtype S.pombe grown under heat shock conditions and treatment

data_processing: All of the software used in this analysis is open source and available from the TiMAT2 project site, http://sourceforge.net/projects/timat2. Processing of the Agilent microarray transcriptome data was performed in three basic steps:  data normalization, sliding window summaries, and enriched region identification.  For each condition (growth and or RNA fraction) and strand, the median unadjusted signal intensities from the cy3 channel were extracted. Probes were then mapped to the April 2007 build and those with < 100 exact matches were retained. The two biological replicas for each condition were quantile normalized and scaled in two different ways.  The first was to scale the data such that the median of the zebrafish control probes was one. The second was to scale the data such that the median of the trimmed intergenic region probes was one. Trimmed intergenic probes were defined as those  > 240 bp (4 probes) from any known annotation.  Probe level  Oligo  summaries were calculated by taking the log2 of the mean of the two biological replica probes for each condition.

source_name: S.pombe grown under heat shock conditions hybridized to slide 1

growth_protocol: Yeast growth, manipulations, and molecular biology were performed according to standard protocols. Cells were cultured to an optical density at 600 nm of 1.0 and then treated as described.

treatment_protocol: For the heat shock transcriptome, cells were transferred to flasks which were preheated in a 40C water bath. Cells were incubated, with shaking, for 15 min and harvested.


title: subject 16


title: subject 15

tag: ErythroCountgroup 1, gender = f


title: S_pombe_HeatShockCondition_rep1&2_slide2

source_name: S.pombe grown under heat shock conditions hybridized to slide 2