title: WRKY23-overexpressor_Mmt-inoculated_rep2


title: WRKY23-overexpressor_Mmt-inoculated_rep3

status: Public on Aug 01 2009

type: RNA

city: Sainte-Foy

first: Armand

last: Séguin

state: Quebec

department: Laurentian Forestry Centre

country: Canada

institute: Natural Resources Canada

description: Gene expression data from infected tissues with Melampsora medusae f. sp. tremuloidae (Mmt).

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Poplar Genome Array. GeneChips were washed and stained in the Fluidics protocol EukGE_WS2v5_450.

scan_protocol: GeneChip scanner.

data_processing: Robust Multichip Average (RMA) via FlexArray software package (http://genomequebec.mcgill.ca/FlexArray).

label: biotin

molecule: total RNA

organism: Populus tremula x Populus alba

source_name: WRKY23-overexpressor leaf discs, Mmt-inoculated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Wildtype and WRKY23-overexpressor plants of Populus tremula x P. alba clone INRA 717 1-B4 were grown in a mixture of peatmoss, vermiculite and turface (4:2:1) with a photoperiod of 16-h day/8-h night at 24°C/20°C.  Melampsora medusae f. sp. tremuloidae (Mmt) were maintained on Populus tremuloides according to Boyle et al., 2005 [Boyle B, Hamelin RC, Seguin A (2005) In vivo monitoring of obligate biotrophic pathogen growth by kinetic PCR. Applied and Environmental Microbiology 71: 1546-1552].

extract_protocol: Total RNA were extracted from frozen leaf tissues according to Chang et al., 1993 [Chang S, Puryear J, Cairney J (1993) A simple and efficient method for isolating RNA from pine trees. Plant Molecular Biology Reporter 11: 113-116] and were purified on RNeasy columns (RNeasy Plant Mini Kit, Qiagen). Following a DNase I treatment (Qiagen), 10 μg of total RNA from each biological sample were used for each microarray experiment.

treatment_protocol: Leaf discs (2-cm diameter) prepared from leaf LPI9 (leaf plastochron index) of 1-m tall plants were inoculated on the abaxial side with Melampsora medusae f. sp. tremuloidae (Mmt) urediniospores suspended in 0.01% tween at a density of 500 spores per cm2 or were mock-inoculated with 0.01% tween (control). After inoculation, discs were kept on wet paper in petri dishes and incubated in a growth chamber at 18°C with a 16-h photoperiod until sample collection at 5 dpi.

tag: tissue

value: Leaf discs from fully expanded leaf LPI9 (leaf plastochron index)

tag: genotype


title: Slide 215 Ewe 10 and 12

city: College Station

first: Thomas

last: Spencer

state: TX

address: 442 Kleberg Center

department: Animal Science

country: USA

institute: Texas A&M University

description: One array is included in one slide.

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit (Genisphere Inc., Hatfield, PA) using dual channel design with dye-swapping.  Microarray slides were prepared by placing them approximately 6-8 cm above a 50oC water bath for 10 sec followed by snap drying on a heat block at 65oC for 5 sec and then allowing them to cool at room temperature for 1 min; this process was repeated four times for each slide.  Slides were then UV crosslinked at 1800 J.  Following UV crosslinking, slides were washed in 1% SDS (Ambion, Austin, TX) for 5 min on a gently rotating platform, rinsed twice in nuclease free water (Invitrogen), and subsequently washed for 3 min in 100% ethanol with gentle agitation.  Slides were then placed in 50 ml conical tubes and dried by centrifugation at <1000 X g for 4 min.  Dried slides were stored in a light-tight slide box until hybridization.  At the time of hybridization, 130 μl of concentrated cDNA (combined samples) was mixed with 2 μl LNA dT blocker, 118 μl nuclease free water, and 250 μl 2X Enhanced Hybridization Buffer (Genisphere) and denatured at 80ºC for 10 min.  An Agilent gasket slide was utilized for the first hybridization step.  Following assembly of the hybridization chamber, slides were hybridized at 58oC for 16 h.  Slides were washed and dried according to manufacturer’s instructions, and a second hybridization reagent containing the capture reagents was made according to instructions.  All subsequent steps were performed under minimal light conditions.  Dried slides were then hybridized with 50 μl of the 3DNA hybridization mix, coverslipped, placed in a humidified 50 ml conical tube and hybridized at 58oC for 4 h in the dark.  Following removal of coverslips, slides were washed and dried according to manufacturer’s instructions.

scan_protocol: Arrays were scanned at 5 μm resolution on a GenePix Personal 4100A (Molecular Devices Corporation, Sunnyvale, CA) and images were saved in the TIFF format.  Auto photomultiplier tube (PMT) settings were selected and adjusted so that the ratio of overall intensities between two channels (Cy3 and Cy5) was 0.95 to 1.05.  The signal intensities of all spots on each image were quantified by Genepix Pro 6.0 software (Molecular Devices Corporation, Downingtown, PA), and data were saved as .txt files for further analysis.

data_processing: The signal intensity of each probe was divided by that of negative control to filter the genes which were not expressed.  Signal intensities were normalized by LOWESS within the R statistics package.  To correct for background signal, median signal intensity and median background intensity was used to normalize the data by LOWESS.  A mixed model that included the fixed effects of dye (Cy3 and Cy5) as well as random effects of slide and array was used to analyze the normalized data by SAS (SAS Institute, Cary, NC).  Comparisons were conducted as follows: day 9 CO vs day 9 P4; day 9 CO vs day 12 CO; and day 12 CO vs day 12 P4.  P-value and fold changes between each comparison for each gene were calculated.  False discovery rate (FDR) was calculated by R program according to Benjamini and Hochberg's method.  The P-value and FDR was set at 0.05 for statistical analyses to identify differentially expressed genes.

organism: Ovis aries

source_name: Ovis aries endometrium ewe 10 day 12 progesterone treated

label_protocol: Preparation of cDNA was performed according to the manufacturer’s instructions.  Briefly, endometrial total RNA (9 µg) from each ewe (n=5 per day and treatment) was reverse-transcribed with Superscript II (Invitrogen, Carlsbad, CA) with the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labeling reagents.  Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was co-hybridized with a cDNA sample from the opposite treatment for direct comparison of differences between treatments.

extract_protocol: Total cellular RNA was isolated from frozen ipsilateral endometrium using Trizol reagent (Gibco-BRL, Bethesda, MD) according to manufacturer’s instructions. The quantity and quality of total RNA was determined by spectrometry and Agilent BioAnalyzer 2100 (Agilent, Palo Alto, CA) using the RNA 6000 Nano Labchip kit (Agilent), respectively in accordance with the manufacturer’s instructions. Endometrial RNA was subsequently processed through an RNeasy Mini Kit (Qiagen, Valencia, CA) according to manufacturer’s instructions.

treatment_protocol: Ewe was bred at estrus (day 0) and received daily exogenous injections of progesterone (25 mg in corn oil vehicle) from days 1.5 to 12 post-mating.

value: endometrium

tag: developmental stage

value: day 12 of pregnanacy

tag: treatment

value: progesterone in corn oil vehicle

source_name: Ovis aries endometrium ewe 12 day 12 corn oil treated

treatment_protocol: Ewe was bred at estrus (day 0) and received daily exogenous injections of corn oil vehicle from days 1.5 to 12 post-mating.

value: corn oil vehicle


title: Slide 214 Ewe 4197 and 4172

description: One array is included in one slide.

source_name: Ovis aries endometrium ewe 4197 day 9 progesterone treated

treatment_protocol: Ewe was bred at estrus (day 0) and received daily exogenous injections of progesterone (25 mg in corn oil vehicle) from days 1.5 to 9 post-mating.

value: day 9 of pregnanacy

source_name: Ovis aries endometrium ewe 4172 day 9 corn oil treated

treatment_protocol: Ewe was bred at estrus (day 0) and received daily exogenous injections of corn oil vehicle from days 1.5 to 9 post-mating.


title: wildtype_Mmt-inoculated_rep1

description:
Gene expression data from infected tissues with Melampsora medusae f. sp. tremuloidae (Mmt).
Processed with WRKY23-overexpressor plants.

source_name: wildtype leaf discs, Mmt-inoculated

value: wildtype


title: wildtype_Mmt-inoculated_rep2


title: wildtype_Mmt-inoculated_rep3


title: Slide 211 Ewe 40094 and 4133

description: One array is included in one slide.

source_name: Ovis aries endometrium ewe 4094 day 9 corn oil treated

source_name: Ovis aries endometrium ewe 4133 day 9 progesterone treated


title: Slide 219 Ewe 3195 and 3227

description: One array is included in one slide.

source_name: Ovis aries endometrium ewe 3195 day 12 progesterone treated

source_name: Ovis aries endometrium ewe 3227 day 12 corn oil treated


title: wildtype_mock-inoculated_rep2

description: Gene expression data from non-infected tissues.

source_name: wildtype leaf discs, mock-inoculated


title: WRKY23-overexpressor_mock-inoculated_rep3

source_name: WRKY23-overexpressor leaf discs, mock-inoculated


title: wildtype_mock-inoculated_rep3


title: Slide 212 Ewe 4155 and 4099

description: One array is included in one slide.

source_name: Ovis aries endometrium ewe 4155 day 9 progesterone treated

source_name: Ovis aries endometrium ewe 4099 day 9 corn oil treated


title: WRKY23-overexpressor_mock-inoculated_rep1


title: WRKY23-overexpressor_mock-inoculated_rep2


title: H3K27me3 of CpG island in RWPE1

status: Public on Jul 31 2009

type: genomic

city: Shinagawa-ku

first: Hideyuki

last: Takeshima

state: Tokyo

department: Institute for Advanced Life Sciences

country: Japan

institute: Hoshi University

description: To recover immunocomplex, Dynabeads protein A (Dynal) was used.

hyb_protocol: Labelled DNA mixed with cot-1 DNA and Agilent blocking solution was hybridized to microarray for 40 hours at 67℃ and 10 rpm rotation.  Microarrays was washed according to Agilent protocol.

scan_protocol: The microarray was scanned with an Agilent G2565BA microarray scanner (Agilent Technologies).

data_processing: Scanned data was analyzed with Feature Extraction Ver.9.1 and normalized (Background subtraction) using Agilent G4477AA ChIP Analytics 1.3 software.

molecule: genomic DNA

organism: Homo sapiens

source_name: Sonicated RWPE1 chromatin (WCE)

label_protocol: Cross-link was reversed at 65℃, DNA was recovered with RNaseA and proteinase K treatment, followed by phenol extraction and ethanol precipitation, and dissolved in 100 μl of 1 x TE. 500 ng of DNA was labeled using Agilent Genomic DNA labeling Kit PLUS (5188-5309).

extract_protocol: About 1 x 10e7 cells were cross-linked with 1 % formaldehyde, lysed, and sonicated with a Bioruptor UCD-250 (Cosmo Bio, Tokyo, Japan).

tag: cell line

value: Normal prostatic epithelial cell line, RWPE1

tag: cell fraction

value: WCE

source_name: Sonicated RWPE1 chromatin (IP)

label_protocol: Solubilized chromatin was diluted 10-fold in dilution buffer [50 mM Tris-HCl, pH 8.0, 167 mM NaCl, 1.1 % (w/v) Triton X-100, 0.11 % (w/v) sodium deoxycholate (DOC)], and incubated with antibody against H3K27me3 (07-449, Millipore) at 4ºC overnight.  Immuno-complexes were collected with Dynabeads Protein A, washed with 1 x RIPA buffer [50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, 1 % (w/v) Triton X-100, 0.1 % (w/v) SDS, 0.1 % (w/v) DOC] containing 150 mM NaCl, 1 x RIPA buffer containing 500 mM NaCl, LiCl wash buffer [10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5 % (w/v) NP-40, 0.5 % (w/v) DOC] and 1 x TE containing 50 mM NaCl.  After cross-link reversal, DNA was recovered with RNaseA and proteinase K treatment, followed by phenol extraction and ethanol precipitation, and dissolved in 100 μl of 1 x TE.  500 ng of DNA was labeled using Agilent Genomic DNA labeling Kit PLUS (5188-5309).

tag: antibody

value: IP


title: RNA polymerase II binding at CpG island in HMEC

source_name: Sonicated HMEC chromatin (WCE)

value: Normal mammary epithelial cells, HMEC

source_name: Sonicated HMEC chromatin (IP)

label_protocol: Solubilized chromatin was diluted 10-fold in dilution buffer [50 mM Tris-HCl, pH 8.0, 167 mM NaCl, 1.1 % (w/v) Triton X-100, 0.11 % (w/v) sodium deoxycholate (DOC)], and incubated with antibody against pol II (ab5095, Abcam) at 4ºC overnight.  Immuno-complexes were collected with Dynabeads Protein A, washed with 1 x RIPA buffer [50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, 1 % (w/v) Triton X-100, 0.1 % (w/v) SDS, 0.1 % (w/v) DOC] containing 150 mM NaCl, 1 x RIPA buffer containing 500 mM NaCl, LiCl wash buffer [10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5 % (w/v) NP-40, 0.5 % (w/v) DOC] and 1 x TE containing 50 mM NaCl.  After cross-link reversal, DNA was recovered with RNaseA and proteinase K treatment, followed by phenol extraction and ethanol precipitation, and dissolved in 100 μl of 1 x TE.  500 ng of DNA was labeled using Agilent Genomic DNA labeling Kit PLUS (5188-5309).

value: pol II


title: wildtype_mock-inoculated_rep1


title: T-cells_individual_UC282

city: Geneva

first: Emmanouil

middle: T

last: Dermitzakis

address: 1 Rue Michel-Servet

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva Medical School

description: One of three cell types derived from umbilical cords of 85 individuals

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Intensity values were log2 transformed and normalized independently for each cell type (quantile normalization for sample replicates, and median normalization across individuals). Each cell type was then renormalized using the mean of the medians of each cell type expression values

source_name: Primary T-cells

label_protocol: Biotinylated cRNA was prepared through two one-quarter scale Message Amp II reactions (Ambion, Foster City, CA).

growth_protocol: Cord blood was collected in 50 ml falcon tubes containing 10 ml of anti-coagulants (Sodium citrate, EDTA- Sigma, St. Louis, MO) and kept at 4oC for less than 24 hours prior to treatment. For separation, cord blood was diluted 2 fold in PBS (Invitrogen), layered on Ficoll-Paque (GE Healthcare Lifesciences, Chalfont St. Giles, United Kingdom) and centrifuged for 30 min at 800g. The mononuclear cell layer was removed, washed twice in 40 ml of PBS and re-suspended in 1 ml of RPMI 20% FCS, 1% antibiotics (Amimed, Basel, Switzerland).  For fibroblast preparation, cord tissue was finely cut under sterile conditions in 1 ml DMEM 10% FCS, 1% antibiotics (Amimed), transferred to a T25 flask and cultured upside-down for 12 hours to allow cells to attach to plastic. Flasks were then turned and left for about 1 week until fibroblast clusters appear. Fibroblasts were then expanded with standard procedures.  For preparation of EBV-immortalized lymphoblastoid cell lines (LCLs), 300 ul of re-suspended cells and 100 ul of EBV were transferred to a 24-well plate well, and cultured in an incubator at 37 oC, 5 % CO2. Fresh medium was added and replaced every 2-3 days. Cells were kept in culture for no less than 21 days prior to freezing.  For PHA stimulated T-cell preparation, re-suspended mononuclear cells were diluted to a concentration of 1 x 106 cells/ml in RPMI  (Invitrogen) with 5 ug/ml of PHA (Sigma), and cultured for 5 days with 2/3 medium replacement after 2.5 days. A subset of samples was characterized by flow cytometric analysis for expression of CD3, CD25 and CD69 (Becton Dickinson, Franklin Lakes, NJ) revealing a homogenous activated T-cell population.

extract_protocol: Total RNA was extracted from fibroblasts, LCLs, and T-cells and was prepared with RNeasy columns with on-column DNAse treatment (Qiagen,  Venlo, The Netherlands), quantified with NanoDrop (Thermo Scientific, Waltham, MA) and analyzed with a 2100 Bioanalyzer (Agilent, Santa Clara, CA). Two one-quarter scale Message Amp II reactions (Ambion, Foster City, CA) were performed for each RNA extraction with 200 ng of total RNA.

tag: cell type

value: Primary T-cells

tag: gender

value: Female


title: H3K9me3 of CpG island in RWPE1

label_protocol: Solubilized chromatin was diluted 10-fold in dilution buffer [50 mM Tris-HCl, pH 8.0, 167 mM NaCl, 1.1 % (w/v) Triton X-100, 0.11 % (w/v) sodium deoxycholate (DOC)], and incubated with antibody against H3K9me3 (07-442, Millipore) at 4ºC overnight.  Immuno-complexes were collected with Dynabeads Protein A, washed with 1 x RIPA buffer [50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, 1 % (w/v) Triton X-100, 0.1 % (w/v) SDS, 0.1 % (w/v) DOC] containing 150 mM NaCl, 1 x RIPA buffer containing 500 mM NaCl, LiCl wash buffer [10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5 % (w/v) NP-40, 0.5 % (w/v) DOC] and 1 x TE containing 50 mM NaCl.  After cross-link reversal, DNA was recovered with RNaseA and proteinase K treatment, followed by phenol extraction and ethanol precipitation, and dissolved in 100 μl of 1 x TE.  500 ng of DNA was labeled using Agilent Genomic DNA labeling Kit PLUS (5188-5309).


title: RNA polymerase II binding at CpG island in RWPE1

label_protocol: Solubilized chromatin was diluted 10-fold in dilution buffer [50 mM Tris-HCl, pH 8.0, 167 mM NaCl, 1.1 % (w/v) Triton X-100, 0.11 % (w/v) sodium deoxycholate (DOC)], and incubated with antibody against pol II (ab5095, Abcam, Cambridge, UK) at 4ºC overnight.  Immuno-complexes were collected with Dynabeads Protein A, washed with 1 x RIPA buffer [50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, 1 % (w/v) Triton X-100, 0.1 % (w/v) SDS, 0.1 % (w/v) DOC] containing 150 mM NaCl, 1 x RIPA buffer containing 500 mM NaCl, LiCl wash buffer [10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5 % (w/v) NP-40, 0.5 % (w/v) DOC] and 1 x TE containing 50 mM NaCl.  After cross-link reversal, DNA was recovered with RNaseA and proteinase K treatment, followed by phenol extraction and ethanol precipitation, and dissolved in 100 μl of 1 x TE.  500 ng of DNA was labeled using Agilent Genomic DNA labeling Kit PLUS (5188-5309).


title: H3K4me3 of CpG island in RWPE1

label_protocol: Solubilized chromatin was diluted 10-fold in dilution buffer [50 mM Tris-HCl, pH 8.0, 167 mM NaCl, 1.1 % (w/v) Triton X-100, 0.11 % (w/v) sodium deoxycholate (DOC)], and incubated with antibody against H3K4me3 (07-473, Millipore, Billerica, MA) at 4ºC overnight.  Immuno-complexes were collected with Dynabeads Protein A, washed with 1 x RIPA buffer [50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, 1 % (w/v) Triton X-100, 0.1 % (w/v) SDS, 0.1 % (w/v) DOC] containing 150 mM NaCl, 1 x RIPA buffer containing 500 mM NaCl, LiCl wash buffer [10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5 % (w/v) NP-40, 0.5 % (w/v) DOC] and 1 x TE containing 50 mM NaCl.  After cross-link reversal, DNA was recovered with RNaseA and proteinase K treatment, followed by phenol extraction and ethanol precipitation, and dissolved in 100 μl of 1 x TE. 500 ng of DNA was labeled using Agilent Genomic DNA labeling Kit PLUS (5188-5309).


title: H3Ac of CpG island in HMEC

label_protocol: Cross-link was reversed at 65℃, DNA was recovered with RNaseA and proteinase K treatment, followed by phenol extraction and ethanol precipitation, and dissolved in 100 μl of 1 x TE..  500 ng of DNA was labeled using Agilent Genomic DNA labeling Kit PLUS (5188-5309).

label_protocol: Solubilized chromatin was diluted 10-fold in dilution buffer [50 mM Tris-HCl, pH 8.0, 167 mM NaCl, 1.1 % (w/v) Triton X-100, 0.11 % (w/v) sodium deoxycholate (DOC)], and incubated with antibody against H3Ac (06-599, Millipore) at 4ºC overnight.  Immuno-complexes were collected with Dynabeads Protein A, washed with 1 x RIPA buffer [50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, 1 % (w/v) Triton X-100, 0.1 % (w/v) SDS, 0.1 % (w/v) DOC] containing 150 mM NaCl, 1 x RIPA buffer containing 500 mM NaCl, LiCl wash buffer [10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5 % (w/v) NP-40, 0.5 % (w/v) DOC] and 1 x TE containing 50 mM NaCl.  After cross-link reversal, DNA was recovered with RNaseA and proteinase K treatment, followed by phenol extraction and ethanol precipitation, and dissolved in 100 μl of 1 x TE.  500 ng of DNA was labeled using Agilent Genomic DNA labeling Kit PLUS (5188-5309).


title: T-cells_individual_UC277

treatment_protocol: Cord blood was collected in 50 ml falcon tubes containing 10 ml of anti-coagulants (Sodium citrate, EDTA- Sigma, St. Louis, MO) and kept at 4oC for less than 24 hours prior to treatment. For separation, cord blood was diluted 2 fold in PBS (Invitrogen), layered on Ficoll-Paque (GE Healthcare Lifesciences, Chalfont St. Giles, United Kingdom) and centrifuged for 30 min at 800g. The mononuclear cell layer was removed, washed twice in 40 ml of PBS and re-suspended in 1 ml of RPMI 20% FCS, 1% antibiotics (Amimed, Basel, Switzerland).  For fibroblast preparation, cord tissue was finely cut under sterile conditions in 1 ml DMEM 10% FCS, 1% antibiotics (Amimed), transferred to a T25 flask and cultured upside-down for 12 hours to allow cells to attach to plastic. Flasks were then turned and left for about 1 week until fibroblast clusters appear. Fibroblasts were then expanded with standard procedures.  For preparation of EBV-immortalized lymphoblastoid cell lines (LCLs), 300 ul of re-suspended cells and 100 ul of EBV were transferred to a 24-well plate well, and cultured in an incubator at 37 oC, 5 % CO2. Fresh medium was added and replaced every 2-3 days. Cells were kept in culture for no less than 21 days prior to freezing.  For PHA stimulated T-cell preparation, re-suspended mononuclear cells were diluted to a concentration of 1 x 106 cells/ml in RPMI  (Invitrogen) with 5 ug/ml of PHA (Sigma), and cultured for 5 days with 2/3 medium replacement after 2.5 days. A subset of samples was characterized by flow cytometric analysis for expression of CD3, CD25 and CD69 (Becton Dickinson, Franklin Lakes, NJ) revealing a homogenous activated T-cell population.

value: Male


title: H3K4me3 of CpG island in HMEC

label_protocol: Solubilized chromatin was diluted 10-fold in dilution buffer [50 mM Tris-HCl, pH 8.0, 167 mM NaCl, 1.1 % (w/v) Triton X-100, 0.11 % (w/v) sodium deoxycholate (DOC)], and incubated with antibody against H3K4me3 (07-473, Millipore, Billerica, MA) at 4ºC overnight.  Immuno-complexes were collected with Dynabeads Protein A, washed with 1 x RIPA buffer [50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, 1 % (w/v) Triton X-100, 0.1 % (w/v) SDS, 0.1 % (w/v) DOC] containing 150 mM NaCl, 1 x RIPA buffer containing 500 mM NaCl, LiCl wash buffer [10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5 % (w/v) NP-40, 0.5 % (w/v) DOC] and 1 x TE containing 50 mM NaCl.  After cross-link reversal, DNA was recovered with RNaseA and proteinase K treatment, followed by phenol extraction and ethanol precipitation, and dissolved in 100 μl of 1 x TE.  500 ng of DNA was labeled using Agilent Genomic DNA labeling Kit PLUS (5188-5309).


title: H3K9me3 of CpG island in HMEC


title: T-cells_individual_UC285


title: T-cells_individual_UC313


title: T-cells_individual_UC284


title: Slide 210 Ewe 4008 and 4028

description: One array is included in one slide.

source_name: Ovis aries endometrium ewe 4008 day 9 progesterone treated

source_name: Ovis aries endometrium ewe 4028 day 9 corn oil vehicle treated

treatment_protocol: Ewe was bred at estrus (day 0) and received daily exogenous injections of corn oil vehicle (2 ml) from days 1.5 to 9 post-mating.


title: T-cells_individual_UC295


title: T-cells_individual_UC304


title: H3K27me3 of CpG island in HMEC


title: H3Ac of CpG island in RWPE1

label_protocol: Cross-link was reversed at 65℃, DNA was recovered with RNaseA and proteinase K treatment, followed by phenol extraction and ethanol precipitation, and dissolved in 100 μl of 1 x TE.  500 ng of DNA was labeled using Agilent Genomic DNA labeling Kit PLUS (5188-5309).

extract_protocol: About 1 x 107 cells were cross-linked with 1 % formaldehyde, lysed, and sonicated with a Bioruptor UCD-250 (Cosmo Bio, Tokyo, Japan).


title: DNA methylation of CpG island in ZR-75-1

description: To recover methylated DNA with anti-5-methyl cytidine antibody, Dynabeads protein A (Dynal) was used.

data_processing: Scanned data was analyzed with Feature Extraction Ver.9.1 and normalized (Background subtraction) using Agilent G4477AA ChIP Analytics 1.3 software.  Our original parameter, Me value was calculated using normalized log ratio and P[Xbar]. The Me value linearly correlates with the fraction of methylated DNA molecules in CpG islands in samples with various overall DNA methylation levels.

source_name: Sonicated ZR-75-1 genomic DNA (WCE)

label_protocol: One μg of DNA was labeled using Agilent Genomic DNA labeling Kit PLUS (5188-5309)

extract_protocol: DNA lysis buffer plus proteinase K. Phenol/Chloroform extraction. Ethanol precipitation. RNase treatment.

value: Breast cancer cell line, ZR-75-1

source_name: Sonicated ZR-75-1 genomic DNA (IP)

label_protocol: Five μg of genomic DNA was sonicated by a VP-5s homogenizer (TAITEC, Saitama, Japan).  After heat denaturation, DNA was incubated with antibody against 5-methyl cytidine (Diagnode, Liége, Belgium) in 1 x IP buffer [10 mM Na-phosphate, pH 7.0, 140 mM NaCl, 0.05 % (w/v) Triton X-100] at 4ºC overnight.  Immuno-complexes were collected with Dynabeads Protein A (Invitrogen Dynal AS, Oslo, Norway), washed with 1 x IP buffer four times, treated with Proteinase K treatment, and purified by phenol extraction and ethanol precipitation.  4.33 μg of DNA was labeled using Agilent Genomic DNA labeling Kit PLUS (5188-5309).

value: 5-methyl cytidine


title: T-cells_individual_UC271


title: T-cells_individual_UC276


title: DNA methylation of CpG island in MDA-MB-468

source_name: Sonicated MDA-MB-468 genomic DNA (WCE)

value: Breast cancer cell line, MDA-MB-468

source_name: Sonicated MDA-MB-468 genomic DNA (IP)


title: DNA methylation of CpG island in HMEC

source_name: Sonicated HMEC genomic DNA (WCE)

source_name: Sonicated HMEC genomic DNA (IP)


title: DNA methylation of CpG island in RWPE1

source_name: Sonicated RWPE1 genomic DNA (WCE)

source_name: Sonicated RWPE1 genomic DNA (IP)

label_protocol: Five μg of genomic DNA was sonicated by a VP-5s homogenizer (TAITEC, Saitama, Japan).  After heat denaturation, DNA was incubated with antibody against 5-methyl cytidine (Diagnode, Liége, Belgium) in 1 x IP buffer [10 mM Na-phosphate, pH 7.0, 140 mM NaCl, 0.05 % (w/v) Triton X-100] at 4ºC overnight.  Immuno-complexes were collected with Dynabeads Protein A (Invitrogen Dynal AS, Oslo, Norway), washed with 1 x IP buffer four times, treated with Proteinase K treatment, and purified by phenol extraction and ethanol precipitation.  4.33 μg of DNA was labeled using Agilent Genomic DNA labeling Kit PLUS (5188-5309)


title: T-cells_individual_UC270


title: T-cells_individual_UC226


title: T-cells_individual_UC234


title: T-cells_individual_UC243


title: T-cells_individual_UC223


title: T-cells_individual_UC255


title: T-cells_individual_UC253


title: T-cells_individual_UC187


title: T-cells_individual_UC188


title: T-cells_individual_UC227


title: T-cells_individual_UC251


title: DNA methylation of CpG island in Du145

source_name: Sonicated Du145 genomic DNA (WCE)

value: Prostate cancer cell line, Du145

source_name: Sonicated Du145 genomic DNA (IP)


title: DNA methylation of CpG island in MCF7

source_name: Sonicated MCF7 genomic DNA (WCE)

value: Breast cancer cell line, MCF7

source_name: Sonicated MCF7 genomic DNA (IP)


title: DNA methylation of CpG island in LNCaP

source_name: Sonicated LNCaP genomic DNA (WCE)

value: Prostate cancer cell line, LNCaP

source_name: Sonicated LNCaP genomic DNA (IP)


title: T-cells_individual_UC218

source_name: Primary T-cells


title: T-cells_individual_UC217


title: DNA methylation of CpG island in 22Rv1

source_name: Sonicated 22Rv1genomic DNA (WCE)

value: Prostate cancer cell line, 22Rv1

source_name: Sonicated 22Rv1genomic DNA (IP)


title: T-cells_individual_UC181


title: DNA methylation of CpG island in PC3

source_name: Sonicated PC3 genomic DNA (WCE)

value: Prostate cancer cell line, PC3

source_name: Sonicated PC3 genomic DNA (IP)


title: T-cells_individual_UC180


title: T-cells_individual_UC183


title: T-cells_individual_UC176


title: T-cells_individual_UC228


title: T-cells_individual_UC177


title: T-cells_individual_UC164


title: T-cells_individual_UC155


title: T-cells_individual_UC167


title: T-cells_individual_UC140


title: T-cells_individual_UC172


title: T-cells_individual_UC141


title: T-cells_individual_UC130


title: T-cells_individual_UC128


title: T-cells_individual_UC169


title: T-cells_individual_UC117


title: T-cells_individual_UC139


title: T-cells_individual_UC137


title: T-cells_individual_UC119


title: T-cells_individual_UC125


title: T-cells_individual_UC144


title: T-cells_individual_UC124


title: T-cells_individual_UC121


title: T-cells_individual_UC152


title: T-cells_individual_UC116


title: T-cells_individual_UC114


title: T-cells_individual_UC122


title: T-cells_individual_UC113


title: T-cells_individual_UC115


title: T-cells_individual_UC108


title: T-cells_individual_UC112


title: T-cells_individual_UC110


title: T-cells_individual_UC103


title: T-cells_individual_UC100


title: T-cells_individual_UC88


title: T-cells_individual_UC97


title: T-cells_individual_UC94


title: T-cells_individual_UC93


title: T-cells_individual_UC87


title: T-cells_individual_UC83


title: T-cells_individual_UC78


title: T-cells_individual_UC105


title: T-cells_individual_UC81


title: T-cells_individual_UC51


title: T-cells_individual_UC55


title: T-cells_individual_UC49


title: T-cells_individual_UC86


title: T-cells_individual_UC79


title: T-cells_individual_UC62


title: T-cells_individual_UC60


title: T-cells_individual_UC48


title: T-cells_individual_UC42


title: T-cells_individual_UC70


title: T-cells_individual_UC50


title: T-cells_individual_UC225


title: T-cells_individual_UC19


title: T-cells_individual_UC45


title: T-cells_individual_UC18


title: T-cells_individual_UC34


title: LCLs_individual_UC313

source_name: EBV-transformed B-cells

value: EBV-transformed B-cells


title: T-cells_individual_UC95


title: LCLs_individual_UC304


title: T-cells_individual_UC24


title: LCLs_individual_UC285


title: T-cells_individual_UC25


title: LCLs_individual_UC284


title: LCLs_individual_UC295


title: T-cells_individual_UC41


title: LCLs_individual_UC226


title: LCLs_individual_UC271


title: LCLs_individual_UC253


title: LCLs_individual_UC243


title: LCLs_individual_UC225


title: LCLs_individual_UC218


title: LCLs_individual_UC227


title: LCLs_individual_UC223


title: LCLs_individual_UC187


title: LCLs_individual_UC277


title: LCLs_individual_UC181


title: LCLs_individual_UC255


title: LCLs_individual_UC282


title: LCLs_individual_UC251


title: LCLs_individual_UC228


title: LCLs_individual_UC270


title: LCLs_individual_UC217


title: LCLs_individual_UC276


title: LCLs_individual_UC234


title: LCLs_individual_UC188


title: LCLs_individual_UC183


title: LCLs_individual_UC176


title: LCLs_individual_UC172


title: LCLs_individual_UC180


title: LCLs_individual_UC137


title: LCLs_individual_UC169


title: LCLs_individual_UC128


title: LCLs_individual_UC167


title: LCLs_individual_UC155


title: LCLs_individual_UC144


title: LCLs_individual_UC141


title: LCLs_individual_UC164


title: LCLs_individual_UC125


title: LCLs_individual_UC116


title: LCLs_individual_UC122


title: LCLs_individual_UC110


title: LCLs_individual_UC114


title: LCLs_individual_UC130


title: LCLs_individual_UC140


title: LCLs_individual_UC115


title: LCLs_individual_UC121


title: LCLs_individual_UC139


title: LCLs_individual_UC117


title: LCLs_individual_UC124


title: LCLs_individual_UC113


title: LCLs_individual_UC112


title: LCLs_individual_UC108


title: LCLs_individual_UC119


title: LCLs_individual_UC103


title: LCLs_individual_UC105


title: LCLs_individual_UC97


title: LCLs_individual_UC100


title: LCLs_individual_UC88


title: LCLs_individual_UC87


title: LCLs_individual_UC94


title: LCLs_individual_UC81


title: LCLs_individual_UC79


title: LCLs_individual_UC86


title: LCLs_individual_UC95


title: LCLs_individual_UC78


title: LCLs_individual_UC49


title: LCLs_individual_UC62


title: LCLs_individual_UC60


title: LCLs_individual_UC48


title: LCLs_individual_UC34


title: LCLs_individual_UC45


title: LCLs_individual_UC50


title: LCLs_individual_UC70


title: LCLs_individual_UC25


title: LCLs_individual_UC24


title: LCLs_individual_UC41


title: LCLs_individual_UC42


title: LCLs_individual_UC55


title: Fibroblasts_individual_UC313

source_name: Primary fibroblasts

value: Primary fibroblasts


title: LCLs_individual_UC19


title: Fibroblasts_individual_UC304


title: LCLs_individual_UC18


title: Fibroblasts_individual_UC295


title: Fibroblasts_individual_UC285


title: Fibroblasts_individual_UC282


title: LCLs_individual_UC83


title: LCLs_individual_UC152


title: Fibroblasts_individual_UC284


title: LCLs_individual_UC177


title: Fibroblasts_individual_UC277


title: Fibroblasts_individual_UC276


title: Fibroblasts_individual_UC270


title: Fibroblasts_individual_UC255


title: Fibroblasts_individual_UC271


title: Fibroblasts_individual_UC243


title: Fibroblasts_individual_UC228


title: Fibroblasts_individual_UC253


title: Fibroblasts_individual_UC218


title: Fibroblasts_individual_UC227


title: Fibroblasts_individual_UC251


title: Fibroblasts_individual_UC234


title: Fibroblasts_individual_UC217


title: Fibroblasts_individual_UC226


title: Fibroblasts_individual_UC225


title: Fibroblasts_individual_UC223


title: Fibroblasts_individual_UC187


title: Fibroblasts_individual_UC188


title: Fibroblasts_individual_UC176


title: Fibroblasts_individual_UC181


title: Fibroblasts_individual_UC183


title: Fibroblasts_individual_UC172


title: Fibroblasts_individual_UC177


title: Fibroblasts_individual_UC155


title: Fibroblasts_individual_UC169


title: Fibroblasts_individual_UC164


title: Fibroblasts_individual_UC180


title: Fibroblasts_individual_UC152


title: Fibroblasts_individual_UC167


title: Fibroblasts_individual_UC144


title: LCLs_individual_UC93


title: Fibroblasts_individual_UC140


title: Fibroblasts_individual_UC130


title: LCLs_individual_UC51


title: Fibroblasts_individual_UC137


title: Fibroblasts_individual_UC128


title: Fibroblasts_individual_UC125


title: Fibroblasts_individual_UC121


title: Fibroblasts_individual_UC119


title: Fibroblasts_individual_UC139


title: Fibroblasts_individual_UC114


title: Fibroblasts_individual_UC112


title: Fibroblasts_individual_UC113


title: Fibroblasts_individual_UC124


title: Fibroblasts_individual_UC122


title: Fibroblasts_individual_UC105


title: Fibroblasts_individual_UC115


title: Fibroblasts_individual_UC117


title: Fibroblasts_individual_UC116


title: ILMN-4b-MCF7-4

city: Jacksonville

first: Yan

middle: W.

last: Asmann

state: FL

address: 4500 San Pablo Road South

institute: Mayo Clinic

hyb_protocol: The single-stranded PCR product was hybridized to the Sentrix Array Matrix (SAM), where the labelled strand binds to the bead on the array containing the complementary address sequence

scan_protocol: Illumina BeadArray Reader

data_processing: The goals of this study were to understand variability due to SAM, extraction, dilution and technical replication.  Note that normalization by definition removes systematic variation from the data.  Thus, we present an initial set of analyses using un-normalized data in order to fully understand the systematic effects of interest in this study.  However, since most analyses will be performed only after normalization, we also present results on normalized data.  The raw miRNA expression values were exported from the BeadStudio software without background subtraction or normalization for all 735 probes.  All data are presented on the log base 2 scale. Normalizations were performed using fastlo, a model-based nonlinear normalization similar to cyclic loess

source_name: MCF7 Cell Line (breast adenocarcinoma)

label_protocol: Varying amounts of total RNA were polyadenylated and then converted to cDNA using a biotinylated oligo-dT primer with a universal PCR sequence at its 5’ end.  This was followed by annealing of a miRNA-specific oligonucleotide pool (MSO) which consists of three parts: a universal PCR priming site at the 5’ end, an address sequence complementary to a capture sequence on the BeadArray and a microRNA-specific sequence at the 3’ end.  Extension of MSO was facilitated by addition of a polymerase, but only if their 3’ bases were complementary to the cognate sequence in the cDNA template.  Common primers were used to amplify the cDNA templates; the primer complimentary to the BeadArray was fluorescently labelled.

growth_protocol: Colon cancer tissues from patients were fresh frozen. The total RNAs for the cell lines were supplied by Illumina

extract_protocol: Total RNA was extracted using Trizol® LS (Invitrogen, Corp., Carlsbad, CA).

tag: sam plate

tag: amount of rna

tag: extraction

value: b


title: Fibroblasts_individual_UC108


title: Fibroblasts_individual_UC110


title: Fibroblasts_individual_UC97


title: Fibroblasts_individual_UC95


title: Fibroblasts_individual_UC94


title: Fibroblasts_individual_UC100


title: ILMN-3b--293-4

source_name: HEK 293 Cell Line (embryonic kidney)


title: ILMN-4a-MCF7-4

value: a


title: Fibroblasts_individual_UC103


title: Fibroblasts_individual_UC93


title: Fibroblasts_individual_UC88


title: ILMN-2a-PC3-4

source_name: PC3 Cell Line (prostate adenocarcinoma)


title: ILMN-1a-Hela-4

source_name: Hela Cell Line (cervical adenocarcinoma)

value: Hela


title: ILMN-3a-293-4


title: ILMN-1b-Hela-4


title: T200-919-1a-3

source_name: Colon Cancer Tissue

value: colon cancer


title: Fibroblasts_individual_UC141


title: T200-565-2a-3


title: ILMN-2b-PC3-4


title: Fibroblasts_individual_UC86


title: Fibroblasts_individual_UC81


title: Fibroblasts_individual_UC87


title: Fibroblasts_individual_UC78


title: Fibroblasts_individual_UC83


title: T200-919-2a-3


title: Fibroblasts_individual_UC79


title: T200-45-1a-3


title: T200-565-1a-3


title: T200-45-2a-3


title: Fibroblasts_individual_UC62


title: Fibroblasts_individual_UC70


title: T200-165-2a-3


title: Fibroblasts_individual_UC60


title: Fibroblasts_individual_UC55


title: Fibroblasts_individual_UC51


title: T200-133-2a-3


title: ILMN-4b-MCF7-3


title: T200-133-1a-3


title: ILMN-3b--293-3


title: Fibroblasts_individual_UC50


title: Fibroblasts_individual_UC45


title: Fibroblasts_individual_UC42


title: T200-165-1a-3


title: Fibroblasts_individual_UC48


title: ILMN-1b-Hela-3


title: ILMN-2b-PC3-3


title: Fibroblasts_individual_UC41


title: ILMN-2a-PC3-3


title: Fibroblasts_individual_UC34


title: T800-565-1a-2


title: T800-45-2a-2


title: Fibroblasts_individual_UC19


title: Fibroblasts_individual_UC24


title: Fibroblasts_individual_UC18


title: 5nM-Testosterone-with100nM-VitD_rep2

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: LNCaP passage#16

hyb_protocol: nimblegen standard protocol for 4-plex arrays

data_processing: RMA values were derived using standard parameters in NimbleScan software

label_protocol: Nimblegen one-color cy3 labeling

growth_protocol: LNCaP cells were grown in RPMI-1640 media with 10% fetal bovine serume supplemented with 100U penicillin and 0.1 mg/mL streptomycin in 37°C with 5%CO2 and 85% humidity.

extract_protocol: Total RNA was extracted using the RNeasy Midi kit (Qiagen Inc., Valencia, CA, USA) DNA was removed by on-column DNase digestion. RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Center for Functional Genomics at State University of New York at Albany (Rensselaer, NY, USA)

treatment_protocol: LNCaP cells were plated at 1x10^6 cells per 150 x 25mm dish with 25mL of growth media, and allowed to adhere for 48h prior to treatment. Each treatment was prepared at 6x concentration, so that 5mL of treatment soultion was added to the 25mL growth media.

value: LNCaP


title: ILMN-3a-293-3


title: 5nM-Testosterone-with100nM-VitD_rep1

description: LNCaP passage#15

scan_protocol: nimblegen standard protocol for 4-plex arrays


title: T800-45-1a-2


title: T50-565-a-2

value: 50 ng


title: ILMN-1a-Hela-3


title: T50-45-a-2


title: T800-565-2a-2


title: 5nM-Testosterone-with100nM-VitD_rep3

description: LNCaP passage#17


title: No-Testosterone-withVitD_rep3

description: LNCaP passage#17

source_name: No-Testosterone-withVitD


title: No-Testosterone-withVitD_rep2

description: LNCaP passage#16


title: Fibroblasts_individual_UC25

value: Female


title: 5nM-Testosterone_rep3

description: LNCaP passage#17


title: T400-565-1a-2


title: T400-565-2a-2


title: T400-45-2a-2


title: T400-45-1a-2


title: 5nM-Testosterone_rep2

description: LNCaP passage#16


title: 5nM-Testosterone_rep1

description: LNCaP passage#15


title: T25-565-a-2

value: 25 ng


title: T25-45-a-2


title: No-Testosterone_rep1

description: LNCaP passage#15

source_name: No-Testosterone


title: No-Testosterone_rep3

description: LNCaP passage#17


title: T200-919-2a-2


title: No-Testosterone_rep2

description: LNCaP passage#16


title: T200-919-1a-2


title: T200-565-1a-2


title: T200-565-2a-2


title: Tumor sample of the patient 19

city: Brest

first: Sylvia

last: Quéméner

address: 49 rue Felix le Dantec

country: France

description:
Tumor sample of the patient 19
We made 2 RNA extractions for each sample when it was possible from the same biopsie. The first one is called F for forward and R, reverse for the second extremity of the biopsie. So we have two gpr files. The .txt recapitulates the results for the 2 .gpr for each sample.

hyb_protocol: Cy3 and Cy5 samples were mixed and hybridized for 16h at 42°C. Slides were sequentially washed.

scan_protocol: Scanned on a Scanexpress- Perkin Elmer

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal. Home made (MADSCAN) software was used for the normalization. This soft use 3 types of methods : Rank Invariant method, Spatial approach definition and scaled Lowess fitness.

label_protocol: 0.5µg total RNA was amplified and labelled using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion) and CyDye Post Labelling Reactive Dyes (Amersham). After reverse transcription, second strand cDNA was subsequently synthesized following the manufacturer's protocol. In vitro transcription was then achieved concomitantly with aminoallyl-dUTP incorporation to perform labelling with cyanins (Cy5 for the reference sample and Cy3 for individual samples)

extract_protocol: Total RNA extracted from Macherey-Nagel total RNA and protein isolation kit

tag: patient

value: Ethmoïd sinus

tag: tumor

value: ITAC adenocarcinomas (Intestine Type)

tag: wood dust exposure

value: no

source_name: total RNA from pooled normal samples

value: controlateral sinus (control)


title: Tumor sample of the patient 14

description:
Tumor sample of the patient 14
We made 2 RNA extractions for each sample when it was possible from the same biopsie. The first one is called F for forward and R, reverse for the second extremity of the biopsie. So we have two gpr files. The .txt recapitulates the results for the 2 .gpr for each sample.

value: yes


title: ILMN-4a-MCF7-3


title: Tumor sample of the patient 16

description:
Tumor sample of the patient 16
We made 2 RNA extractions for each sample when it was possible from the same biopsie. The first one is called F for forward and R, reverse for the second extremity of the biopsie. So we have two gpr files. The .txt recapitulates the results for the 2 .gpr for each sample.


title: Tumor sample of the patient 12

description:
Tumor sample of the patient 12
We made 2 RNA extractions for each sample when it was possible from the same biopsie. The first one is called F for forward and R, reverse for the second extremity of the biopsie. So we have two gpr files. The .txt recapitulates the results for the 2 .gpr for each sample.


title: T200-165-2a-2


title: T200-165-1a-2


title: T200-45-2a-2


title: Tumor sample of the patient 9

description:
Tumor sample of the patient 9
We made 2 RNA extractions for each sample when it was possible from the same biopsie. The first one is called F for forward and R, reverse for the second extremity of the biopsie. So we have two gpr files. The .txt recapitulates the results for the 2 .gpr for each sample.


title: T200-133-2a-2


title: T200-45-1a-2


title: Tumor sample of the patient 10

description:
Tumor sample of the patient 10
We made 2 RNA extractions for each sample when it was possible from the same biopsie. The first one is called F for forward and R, reverse for the second extremity of the biopsie. So we have two gpr files. The .txt recapitulates the results for the 2 .gpr for each sample.


title: T200-133-1a-2


title: Fibroblasts_individual_UC49

value: Male


title: T100-45-a-2


title: T100-565-a-2


title: ILMN-4b-MCF7-2


title: No-Testosterone-withVitD_rep1

description: LNCaP passage#15


title: Tumor sample of the patient 6

description:
Tumor sample of the patient 6
We made 2 RNA extractions for each sample when it was possible from the same biopsie. The first one is called F for forward and R, reverse for the second extremity of the biopsie. So we have two gpr files. The .txt recapitulates the results for the 2 .gpr for each sample.

value: colloïd adenocarcinoma


title: Tumor sample of the patient 5

description:
Tumor sample of the patient 5
We made 2 RNA extractions for each sample when it was possible from the same biopsie. The first one is called F for forward and R, reverse for the second extremity of the biopsie. So we have two gpr files. The .txt recapitulates the results for the 2 .gpr for each sample.


title: Tumor sample of the patient 8

description:
Tumor sample of the patient 8
We made 2 RNA extractions for each sample when it was possible from the same biopsie. The first one is called F for forward and R, reverse for the second extremity of the biopsie. So we have two gpr files. The .txt recapitulates the results for the 2 .gpr for each sample.


title: ILMN-4a-MCF7-2


title: ILMN-3b--293-2


title: ILMN-3a-293-2


title: ILMN-2a-PC3-2


title: ILMN-2b-PC3-2


title: Normal sample of the patient 16

description:
Normal sample of the patient 16
We made 2 RNA extractions for each sample when it was possible from the same biopsie. The first one is called F for forward and R, reverse for the second extremity of the biopsie. So we have two gpr files. The .txt recapitulates the results for the 2 .gpr for each sample.

value: Controlateral sinus


title: Normal sample of the patient 14

description:
Normal sample of the patient 14
We made 2 RNA extractions for each sample when it was possible from the same biopsie. The first one is called F for forward and R, reverse for the second extremity of the biopsie. So we have two gpr files. The .txt recapitulates the results for the 2 .gpr for each sample.


title: ILMN-1b-Hela-2


title: T200-565-2b-1


title: Normal sample of the patient 19

description:
Normal sample of the patient 19
We made 2 RNA extractions for each sample when it was possible from the same biopsie. The first one is called F for forward and R, reverse for the second extremity of the biopsie. So we have two gpr files. The .txt recapitulates the results for the 2 .gpr for each sample.


title: Normal sample of the patient 12

description:
Normal sample of the patient 12
We made 2 RNA extractions for each sample when it was possible from the same biopsie. The first one is called F for forward and R, reverse for the second extremity of the biopsie. So we have two gpr files. The .txt recapitulates the results for the 2 .gpr for each sample.


title: T200-919-1b-1


title: T200-919-2a-1


title: T200-919-2b-1


title: ILMN-1a-Hela-2


title: T200-919-1a-1


title: Normal sample of the patient 10

description:
Normal sample of the patient 10
We made 2 RNA extractions for each sample when it was possible from the same biopsie. The first one is called F for forward and R, reverse for the second extremity of the biopsie. So we have two gpr files. The .txt recapitulates the results for the 2 .gpr for each sample.


title: T200-565-1a-1


title: Normal sample of the patient 9

description:
Normal sample of the patient 9
We made 2 RNA extractions for each sample when it was possible from the same biopsie. The first one is called F for forward and R, reverse for the second extremity of the biopsie. So we have two gpr files. The .txt recapitulates the results for the 2 .gpr for each sample.


title: T200-45-2b-1


title: Normal sample of the patient 8

description:
Normal sample of the patient 8
We made 2 RNA extractions for each sample when it was possible from the same biopsie. The first one is called F for forward and R, reverse for the second extremity of the biopsie. So we have two gpr files. The .txt recapitulates the results for the 2 .gpr for each sample.


title: T200-565-1b-1


title: T200-45-1a-1


title: T200-45-2a-1


title: Normal sample of the patient 5

description:
Normal sample of the patient 5
We made 2 RNA extractions for each sample when it was possible from the same biopsie. The first one is called F for forward and R, reverse for the second extremity of the biopsie. So we have two gpr files. The .txt recapitulates the results for the 2 .gpr for each sample.


title: Normal sample of the patient 6

description:
Normal sample of the patient 6
We made 2 RNA extractions for each sample when it was possible from the same biopsie. The first one is called F for forward and R, reverse for the second extremity of the biopsie. So we have two gpr files. The .txt recapitulates the results for the 2 .gpr for each sample.


title: T200-165-2b-1


title: T200-45-1b-1


title: T200-565-2a-1


title: T200-165-2a-1


title: T200-133-1b-1


title: T200-165-1b-1


title: T200-133-2b-1


title: T200-133-2a-1


title: T200-165-1a-1


title: T200-133-1a-1


title: T100-919-2b-1


title: T100-565-2b-1


title: T100-919-1a-1


title: T100-919-2a-1


title: T100-919-1b-1


title: T100-45-2b-1


title: T100-565-1a-1


title: T100-45-2a-1


title: T100-45-1b-1


title: T100-165-2b-1


title: T100-165-1a-1


title: T100-165-1b-1


title: T100-133-2b-1


title: T100-565-1b-1


title: T100-133-1a-1


title: T100-133-1b-1


title: T100-133-2a-1


title: ILMN-4b-MCF7-1


title: T100-565-2a-1


title: ILMN-4a-MCF7-1


title: ILMN-3b--293-1


title: ILMN-2a-PC3-1


title: T100-45-1a-1


title: ILMN-1b-Hela-1


title: ILMN-2b-PC3-1


title: T100-165-2a-1


title: ILMN-1a-Hela-1


title: ILMN-3a-293-1


title: anr mutant early stationary #2

city: Bunkyo-ku

first: Hiroyuki

last: Arai

address: Yayoi 1-1-1

department: Department of Biotechnology

institute: The University of Tokyo

description: GeneChip Hybridization Oven 640 and Fluidics Station 450 were used for target hybridization and staining under the control of the Affymetrix GeneChip Operating Software.

hyb_protocol: Target hybridization, staining, and scanning were performed according to the instructions designed for the Pseudomonas aeruginosa genome array by Affymetrix.

scan_protocol: Affymetrix GeneChip Scanner 3000 was used.

data_processing: The Affymetrix GeneChip Operating Software was used for data acquisition and processing.

organism: Pseudomonas aeruginosa

source_name: strain PAO6261 (anr), early stationary phase #2

label_protocol: Enzo BioArray terminal labeling kit

growth_protocol: P. aeruginosa strains were cultivated aerobically in LB medium in Erlenmeyer flasks. Total RNA was extracted when optical density at 600 nm was 1.4.

extract_protocol: Total RNA was extracted by a hot-phenol method. After contaminated DNA was eliminated by RQ1 DNase (Promega) treatment, RNA was purified by RNeasy mini columns (Qiagen).

treatment_protocol: The culture was mixed with 2 volumes of RNAprotect Bacterial Reagent (Qiagen) before RNA purification.

tag: growth phase

value: early stationary phase #2

value: anr mutant


title: roxSR mutant exponential #2

source_name: strain ROX1 (roxSR), exponential phase #2

growth_protocol: P. aeruginosa strains were cultivated aerobically in LB medium in Erlenmeyer flasks. Total RNA was extracted when optical density at 600 nm was 0.3.

value: exponential phase #2

value: roxSR mutant


title: anr mutant exponential #1

source_name: strain PAO6261 (anr), exponential phase #1

value: exponential phase #1


title: roxSR mutant early stationary #1

source_name: strain ROX1 (roxSR), early stationary phase #1

value: early stationary phase #1


title: roxSR mutant exponential #1

source_name: strain ROX1 (roxSR), exponential phase #1


title: roxSR mutant early stationary #2

source_name: strain ROX1 (roxSR), early stationary phase #2


title: anr mutant exponential #2

source_name: strain PAO6261 (anr), exponential phase #2


title: PAO1ut early stationary #2

source_name: strain PAO1ut, early stationary phase #2

value: wild type


title: PAO1ut early stationary #1

source_name: strain PAO1ut, early stationary phase #1


title: PAO1ut exponential #2

source_name: strain PAO1ut, exponential phase #2


title: Stmn1-WT v Stmn1-null Array 3

city: Bethlehem

first: Danielle

middle: N.

last: Ringhoff

state: PA

address: 111 Research Drive

department: Biological Sciences

institute: Lehigh University

hyb_protocol: default Agilent protocol

scan_protocol: default Agilent protocol

data_processing: default Agilent protocol

organism: Mus musculus

source_name: Total RNA extraction from tissue culture of stmn1 +/+ embryonic fibroblasts

label_protocol: Followed Agilent protocol for linear amplification of cDNA sample labeling.

extract_protocol: Used Trizol Extration from cultured cells followed by BioChip quality check, DNase treatment, quantification of RNA.

tag: strain

value: embryonic fibroblasts

source_name: Total RNA extraction from tissue culture of stmn1 -/- embryonic fibroblasts

value: stmn1 -/-


title: vector control, biological rep1

city: Boston

first: Shingo

last: Kajimura

state: MA

address: 44 Binney Street

department: Department of Cell Biology

institute: Harvard Medical School

description: PRDM16 regulated genes

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The array data were analyzed using the DNA-Chip Analyzer (dChip) software.

source_name: C2C12 mouse myoblasts expressing vector

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

growth_protocol: DMEM containing 10% FBS suppliment with penicillin and streptomycin

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

treatment_protocol: retroviruses expressing mouse PRDM16 or empty vector were transduced in myoblasts supplemented with 8 μg/ml polybrene.  48 hours after the infection, cells were selected with puromycin.

value: C2C12 myoblast


title: PAO1ut exponential #1

source_name: strain PAO1ut, exponential phase #1


title: Stmn1-WT v Stmn1-null Array 4


title: vector control, biological rep2

description: PRDM16 regulated genes


title: vector control, biological rep3

description: PRDM16 regulated genes


title: Stmn1-WT v Stmn1-null Array 2


title: PRDM16, biological rep3

description: PRDM16 regulated genes

source_name: C2C12 mouse myoblasts expressing PRDM16


title: MM.1S cells cultured alone

first: Manoj

last: Bhasin

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

description: Affymetrix HG-U133A plus 2.0 gene expression data from multiple myeloma MM.1S cells cultured alone

hyb_protocol: Following fragmentation, ~2 microg of cRNA were hybridized for 16 hr at 45C on Human Genome 133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: Data was MAS5 algorithm from affymetrix

label: Biotin

source_name: Human

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from ~2 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).


title: anr mutant early stationary #1

source_name: strain PAO6261 (anr), early stationary phase #1


title: Transcription profiles of NTG-treated E. coli imp fabI(G93V) and its control strain in the presence of triclosan

city: Daejeon

first: BJ

last: Yu

address: 52 Eoeun-dong Yuseong-gu

department: Systems Microbiology Research Center

country: South Korea

institute: KRIBB

description: no additional information

hyb_protocol: The dried labeled probes were resuspended in 30 mL hybridization buffer (25% formamide, 5xSSC, 0.1% SDS, 10% dextran sulfate) and incubated at 95 °C for 5 min to denature the labeled probes. Each labeled probe was mixed and applied to the microarray slide and covered with a cover-slip. Hybridization was carried out in a humidified slide chamber (Corning) submerged in a 42 °C water bath for over 16 h. The cover-slips were removed by incubation for 1 min in wash buffer I (2xSSC and 0.1% SDS) prewarmed to 42 °C, and the slides were washed sequentially in washing buffer I at 42 °C for 10 min in the dark, washing buffer II (0.1xSSC and 0.1% SDS) at room temperature for 10 min in the dark, and twice in washing buffer III (0.1xSSC) at room temperature for 1 min. Finally, the slides were dried by centrifugation at 700 rpm for 5 min.

scan_protocol: Scanned on a GenePix 4000B scanner (Axon Instruments). The resulting images were analyzed using GenePix Pro 6.0 software (Axon Instruments), and the data were imported into Genespring software for further analysis.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software GX 7.3 was used.

organism: Escherichia coli

source_name: NTG-treated E. coli imp fabI(G93V) [E. coli IFN5]

label_protocol: The purified RNA (40 mg) was mixed with 2 mL of bacterial random primer (3 mg/mL), 10mL 5xFirst strand buffer (Invitrogen) 5 mL 0.1M DTT, 1 mL 50xaminoallyl-dNTP mixture (0.5 mM each of dATP, dGTP, dCTP and dTTP), 1mL RNasin (40 U/mL) (Promega) and 2 mL reverse transcriptase (200 U/mL) (Invitrogen), and was incubated at 42°C for 1 h. After a further incubation with 1 mL reverse transcriptase (200 U/mL) at 42 °C for 1 h, 16.5 mL 1M NaOH and 16.5 mL 0.5 M EDTA were added to the mixture and incubated at 65 °C for 15 min to degrade the RNA. HCl (16.5 mL, 1M) was added to neutralize the mixture. The synthesized cDNA mixtures were purified using Microcon YM-30 (Millipore) and eluted. The purified cDNA was mixed with 1 m L 1M Na2CO3 (pH 9.0) and 2 mL Cy3-OSu or Cy5-OSu (Amersham Pharmacia Biotech) and incubated at room temperature for 1 h in the dark. The two labeled cDNA samples to be compared were purified using a QIAquick PCR purification kit (Qiagen), and the eluted cDNA was dried by SpeedVac.

growth_protocol: The cells were cultivated in 100 ml LB broth containing 2 mg/L Cm with  50 mg/L triclosan and harvested in mid-logarithmic growth phase (OD600=1.1).

extract_protocol: Total RNA extracted using RNAprotect Bacterial Reagent (Qiagen) and an RNeasy Mini kit (Qiagen).

treatment_protocol: Treatment of sub-lethal triclosan; 50 mg/L triclosan

value: E. coli imp 4231(G93V)

tag: passage

tag: imp mutation

value: contains a 23 codon deletion allele in imp (increased membrane permeability),substitution of the 94th codon of fabI, NTG treatment; fabI(G93V), substitution of Gly(the 94th codon) of fabI with Val, NTG treatment to be high resistance to triclosan

tag: ntg treatment

tag: agent

value: triclosan

source_name: E. coli imp fabI(G94V) [control]

treatment_protocol: No triclosan treatment

value: E. coli imp 4231(G93V), substitution of the 94th codon of fabI

value: contains a 23 codon detion allele in imp (increased membrane permeability),substitution of the 94th codon of fabI; fabI(G93V), substitution of Gly(the 94th codon) of fabI with Val


title: Transcription profiles of NTG-treated E. coli imp fabI(G93V) and its control strain in the absence of triclosan

description: no additional information

source_name: NTG-treated E. coli imp fabI(G93V) [E. coli IFN4]

growth_protocol: The cells were cultivated in 100 ml LB broth containing 2 mg/L Cm without triclosan and harvested in mid-logarithmic growth phase (OD600=1.0).

value: contains a 23 codon deletion allele in imp (increased membrane permeability),substitution of the 93th codon of fabI, NTG treatment; fabI(G93V), substitution of Gly(the 93th codon) of fabI with Val, NTG treatment to be high resistance to triclosan

value: yes

value: no triclosan

source_name: E. coli imp fabI(G93V) [control]

value: E. coli imp 4231(G93V), substitution of the 93th codon of fabI

value: contains a 23 codon detion allele in imp (increased membrane permeability),substitution of the 93th codon of fabI; fabI(G93V), substitution of Gly(the 93th codon) of fabI with Val


title: MM.1S cells cultured with pDCs

description: Affymetrix HG-U133A plus 2.0 gene expression data from multiple myeloma MM.1S cells cultured with pDCs

tag: cell line


title: PRDM16, biological rep2

description: PRDM16 regulated genes


title: mRNA expression in RWPE1

description: The signal intensities were normalized so that the average of all of the genes on a GeneChip would be 500.

hyb_protocol: Labeled cRNA was hybridized to microarray for 16 hours at 45℃.

scan_protocol: The microarray was stained and scanned according to the protocol from Affymetrix.

data_processing: Scanned data was analyzed with GeneChip Operating Software (ver1.4).

molecule: polyA RNA

source_name: Total RNA from RWPE1

label_protocol: From 8 μg of total RNA, the first-strand cDNA was synthesized with SuperScript III reverse transcriptase (Invitrogen, Groningen, the Netherlands) and a T7-(dT)24 primer, and the double-stranded cDNA was then synthesized. From the double-stranded cDNA, biotin-labeled cRNA was prepared using a BioArray HighYield RNA transcript labeling kit (Enzo, Farmingdale). Labeled cRNA (20 μg) was fragmented.

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

tag: Normal prostatic epithelial cell line, RWPE1


title: PRDM16, biological rep1

description: PRDM16 regulated genes


title: PAM765-transgenic Arabidopsis

status: Public on Jul 30 2009

city: Bunkyo

first: Kenro

last: Oshima

description: PAM765 encodes the secretory protein of Candidatus Phytoplasma asteris. Total RNA was isolated from PAM765-transgenic plant with ISOGEN (Nippon Gene), and used for the preparation of Cy3-labeled cRNA probes. Samples were subjected to microarray experiments using an Agilent Arabidopsis 3 (4 × 44K) Oligo Microarray (Agilent Technologies). All microarray experiments were performed according to the supplier’s manual. The slides were scanned with a Microarray Scanner (Agilent Technologies) at a 5-μm resolution.

hyb_protocol: The microarrays were hybridized according to the Agilent manufacture's protocol.

scan_protocol: The slides were scanned by an Agilent scanner.

data_processing: Extraction and image analysis software (Feature Extraction version 9.5.3.1; Agilent Technologies) was used to integrate each spot’s intensity.

organism: Arabidopsis thaliana

source_name: PAM765-transgenic Arabidopsis

label_protocol: RNA extracts from Arabidopsis were fluorescence labeled according to the Agilent manufacture's protocol.

extract_protocol: Total RNA was isolated with ISOGEN (Nippon Gene).

tag: 2-weeks old PAM765-transgenic Arabidopsis thaliana


title: PAM765-transgenic Arabidopsis (sample No3)


title: GUS-transgenic Arabidopsis (sample No3)

description: Total RNA was isolated from PAM765-transgenic plant with ISOGEN (Nippon Gene), and used for the preparation of Cy3-labeled cRNA probes. Samples were subjected to microarray experiments using an Agilent Arabidopsis 3 (4 × 44K) Oligo Microarray (Agilent Technologies). All microarray experiments were performed according to the supplier’s manual. The slides were scanned with a Microarray Scanner (Agilent Technologies) at a 5-μm resolution.

source_name: GUS-transgenic Arabidopsis

tag: 2-weeks old GUS-transgenic Arabidopsis thaliana


title: mRNA expression in HMEC

source_name: Total RNA from HMEC

tag: Normal mammary epithelial cells, HMEC


title: PAM765-transgenic Arabidopsis (sample No2)


title: CVID CD21low B cell, biological rep3

city: Freiburg i. Breisgau

first: Mirzokhid

last: Rakhmanov

state: BW

address: Breisacher Str. 66

department: Centre of Chronic Immunodeficiency

country: Germany

institute: University Medical Center Freiburg

description:
Gene expression data from ex vivo CD21low B cells of CVID
Ficoll gradient separated periphreal blood mononuclear cells were stained for the expression of CD19, CD21, CD27 and CD38 cell surface markers. The cells were sorted into CD19+CD27-CD38+CD21+ naive B cells and CD19hiCD27-CD38lowCD21low B cells.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Microarray Suite version 5.0 (MAS 5.0) software was used to generate CEL files using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. The CEL files were uploaded and analyzed using the dCHIP software. The signal intensities were logged, normalized using invariant set normalization method and model-based expression values were calculated.

source_name: Peripheral blood ex vivo CD21low B cells of CVID patient

label_protocol: Biotinylated cRNA were prepared using GeneChip® Two-Cycle Target Labeling kit according to the Affymetrix protocol from 100 ng total RNA (GeneChip® Expression Analysis Technical Manual, 2005-2006, Affymetrix).

treatment_protocol: No treatment, ex vivo cells

tag: protocol

value: sorted ex vivo cells

tag: phenotype

tag: diagnosis

value: CVID

tag: cell type

value: CD21low B cell


title: CVID CD21low B cell, biological rep1


title: GUS-transgenic Arabidopsis

description: Total RNA was isolated from GUS-transgenic plant with ISOGEN (Nippon Gene), and used for the preparation of Cy3-labeled cRNA probes. Samples were subjected to microarray experiments using an Agilent Arabidopsis 3 (4 × 44K) Oligo Microarray (Agilent Technologies). All microarray experiments were performed according to the supplier’s manual. The slides were scanned with a Microarray Scanner (Agilent Technologies) at a 5-μm resolution.


title: GUS-transgenic Arabidopsis (sample No2)


title: CVID CD21low B cell, biological rep2


title: CVID naive B cell, biological rep3

description:
Gene expression data from ex vivo naive B cells of CVID
Ficoll gradient separated periphreal blood mononuclear cells were stained for the expression of CD19, CD21, CD27 and CD38 cell surface markers. The cells were sorted into CD19+CD27-CD38+CD21+ naive B cells and CD19hiCD27-CD38lowCD21low B cells.

source_name: Peripheral blood ex vivo naive B cells of CVID patient

value: naive B cell


title: CVID naive B cell, biological rep2


title: CVID CD21low B cell, biological rep4


title: CVID naive B cell, biological rep1


title: HaCaT_siP63_rep3_ds2_cy5

city: Grenoble

first: Ning

last: WU

address: 17 rue des Martyrs

institute: CEA

description: this is p63 siRNA transfection. rep: biological replicate; ds: dye swap

hyb_protocol: Direct hybridization sample (Cy5 vs Cy3)

scan_protocol: Arrays were scanned with Agilent G2505B Scanner . Feature extraction was performed with Genepix Pro 6.0 software(Axon Instruments).

data_processing: The raw data from GenePix were analyzed by GeneSpring (Agilent). The data in the VALUE column correspond to lowess normalized log ratio of F635_MEDIAN vs F532_MEDIAN.

source_name: HaCaT cells transfected with p63 siRNA

label_protocol: Labeling were performed using 2.5 ug of aRNA per reaction and were carried out according to the manufacturer's rpotocol (Ambion) using the MessageAmp kit with 1/2 quantity.

growth_protocol: HaCaT cells were grown at 37°C in a humidified incubator with 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum, 105 units/liter penicillin, 50 mg/liter streptomycin, and 2 mM GlutaMax (Invitrogen).

extract_protocol: Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer's protocol and the integrity of the RNAs was verified using the Agilent Bioanalyzer.  Message RNA amplification with T7 RNA Polymerase was carried out according to the manufacturer's protocol (Ambion) using the MessageAmp kit with 1/2 quantity. aRNA integrity and yield were assessed by electrophoretic fractionation on a Bioanalyzer 2100 and a RNA6000 Nano chip (Agilent Technologies) .

treatment_protocol: Transient gene knockdown was performed by siRNA transfection. Transfection of siRNA was carried out by INTERFERin (PolyPlus transfection). 10000/cm2 cells were seeded in 6-well plate 24 hours before transfection. The mixture of siRNA and INTERFERin was prepared as described by the manufacture’s instruction. All transfections were performed at the concentration of 10 nM of siRNA.

value: HaCaT

source_name: Wild type HaCaT cells


title: HD naive B cell, biological rep1

description:
Gene expression data from ex vivo naive B cells of HD
Ficoll gradient separated periphreal blood mononuclear cells were stained for the expression of CD19, CD21, CD27 and CD38 cell surface markers. The cells were sorted into CD19+CD27-CD38+CD21+ naive B cells and CD19hiCD27-CD38lowCD21low B cells.

source_name: Peripheral blood ex vivo naive B cells of HD

value: healthy donor


title: HD naive B cell, biological rep2


title: Global gene expression profiling of human pleural mesotheliomas; meso 7

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description: 9 mesothelioma mixed type tumors were compared to the normal pleura of 4 donors.

hyb_protocol: All the hybridization, washing, staining procedures were done using a Genechip Affymetrix station (Fluidics station 450), GeneChip Scanner 3000) as raccomended by manufacturer.

scan_protocol: Scanning was done using a Genechip Affymetrix station (GeneChip Scanner 3000) as raccomended by manufacturer.

data_processing: Microarray quality control and statistical validation were performed using Bioconductor The presence of hybridization/construction artifacts was evaluated with the fitPLM function. The probe (PM) intensity distribution was evaluated using hist function (Bioconductor package affy). Probe set intensities were obtained by means of GCRMA and normalization was done according to quantiles method.Bioconductor OneChannelGUI, a graphical interface to Bioconductor packages, was used to run any of the described analyses.

source_name: mesothelioma tissue

label_protocol: Biotinylated cRNA target was produced starting from 3 µg of total RNA in according to Affymetrix (Santa Clara, CA) instructions and for each sample 15 µg were fragmented to a length of 20-200 bp

extract_protocol: Total RNA was extracted from each of the tumor and control samples using the RNeasy Mini kit (Qiagen, Valencia, CA).

tag: Mesothelioma tissue was obtained from those patients with a confirmed pathological diagnosis and who had not received prior therapy. Intraoperative malignant mesothelial samples and nodules were dissected from associated fat and connective tissue, but no microdissection was performed. H&E staining was performed to verify the presence of neoplastic cells and to determine the histological subtype. Samples were stored in RNAlater (Ambion) following the manufacturer’s protocol until RNA extraction.


title: Global gene expression profiling of human pleural mesotheliomas; meso 10


title: HD naive B cell, biological rep4


title: Global gene expression profiling of human pleural mesotheliomas; meso 6.2


title: Global gene expression profiling of human pleural mesotheliomas; meso 4


title: Global gene expression profiling of human pleural mesotheliomas; meso 38

tag: Mesothelioma tissue was obtained from those patients with a confirmed pathological diagnosis and who had not received prior therapy. Intraoperative malignant mesothelial samples and nodules were dissected from associated fat and connective tissue, but no microdissection was performed. H&E staining was performed to verify the presence of neoplastic cells and to determine the histological subtype. Samples were stored in RNAlater (Ambion) following the manufacturer’s protocol until RNA extraction. mm


title: HaCaT_siP63_rep3_ds2_cy3


title: Global gene expression profiling of human pleural mesotheliomas; meso 23


title: HD naive B cell, biological rep3


title: Global gene expression profiling of human pleural mesotheliomas; meso 21


title: HaCaT_siP63_rep2_ds2_cy5


title: Global gene expression profiling of human pleural mesotheliomas; meso 36


title: HaCaT_siP63_rep3_ds1_cy3


title: Global gene expression profiling of human pleural mesotheliomas; meso 35


title: HaCaT_siP63_rep3_ds1_cy5


title: Stmn1-WT v Stmn1-null Array 1

source_name: Total RNA extraction from tissue culture of stmn1 +/+ embryonic fibroblasts

tag: genotype

value: wild type

value: embryonic fibroblasts

source_name: Total RNA extraction from tissue culture of stmn1 -/- embryonic fibroblasts

value: stmn1 -/-


title: HaCaT_siP63_rep2_ds1_cy5


title: HaCaT_siP63_rep2_ds1_cy3


title: HaCaT_siP63_rep1_ds2_cy5


title: HaCaT_siP63_rep2_ds2_cy3


title: HaCaT_siP63_rep1_ds1_cy5


title: HaCaT_siP63_rep1_ds2_cy3


title: HaCaT_siP63_rep1_ds1_cy3


title: HaCaT_siCT_for siP63_rep3_ds1_cy3

description: this control siRNA transfection was used as an experimental control for siP63 transfection, rep: biological replicate; ds: dye swap

source_name: HaCaT cells transfected with control siRNA


title: HaCaT_siCT_for siP63_rep3_ds2_cy5


title: HaCaT_siCT_for siP63_rep3_ds2_cy3


title: H1299_WT Iressa 01h00m

city: Yokohama

first: Mariko

last: Okada

address: W518, 1-7-22, Suehiro-cho, Tsurumi-ku

institute: RIKEN RCAI

description: Gene expression induced by Iressa stimulation

hyb_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) (section2, 2.2.p3-8 & 2.3.p3-14)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with default parameter.

data_processing: Image files were analyzed with GeneChip Operating System (GCOS) (ver.1.2) and CEL files were processed by RMA to obtain expression level of genes. were processed by RMA to obtain expression level of genes.

source_name: lung, epithelial, Iressa, 1h

label_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) (section2, chapter1-p13-18, & 2.1.p32-33,p36-40)

growth_protocol: Prior to the growth factor (GF) treatment, cells were serum starved for 16-18 hours with serum-free RPMI medium and incubated at 37C/5% CO2. The medium was again changed 2 hr prior to the GF treatment.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) and then purified using QIAGEN Rneasy kit.

treatment_protocol: Before treatments, medium were changed with serum-free medium again and incubated at 37C for 2 hours. Followed by incubation, added inhibitor (Iressa) for 20minutes.

tag: Cell line

value: H1299 (Obtained from ATCC (American Type Culture Collection)), Organ:lung, Cell type:epithelial, Disease:carcinoma; non-small cell lung cancer, Derived from metastatic site:lymph node, Age:43 years adult, Gender:male, Ethnicity:Caucasian


title: HaCaT_siCT_for siP63_rep2_ds2_cy5


title: H1299_WT Iressa 02h00m

source_name: lung, epithelial, Iressa, 2h


title: HaCaT_siCT_for siP63_rep1_ds1_cy3


title: HaCaT_siCT_for siP63_rep2_ds2_cy3


title: H1299_WT Iressa 04h00m

source_name: lung, epithelial, Iressa, 4h


title: H1299_WT EGF_Iressa 10h00m

description: Gene expression induced by EGF and Iressa stimulation

source_name: lung, epithelial, EGF+Iressa, 10h

treatment_protocol: Before treatments, medium were changed with serum-free medium again and incubated at 37C for 2 hours. Followed by incubation, firstly added inhibitor (Iressa) for 20minutes, after that added each ligand and incubated for each time.


title: HaCaT_siCT_for siP63_rep1_ds2_cy3


title: HaCaT_siCT_for siP63_rep2_ds1_cy3


title: H1299_WT EGF_Iressa 06h00m

source_name: lung, epithelial, EGF+Iressa, 6h


title: HaCaT_siCT_for siP63_rep2_ds1_cy5


title: H1299_WT EGF_Iressa 02h00m

source_name: lung, epithelial, EGF+Iressa, 2h


title: H1299_WT Iressa 00h30m

source_name: lung, epithelial, Iressa, 30min


title: HaCaT_siCT_for siP63_rep1_ds2_cy5


title: H1299_WT EGF_Iressa 00h30m

source_name: lung, epithelial, EGF+Iressa, 30min


title: HaCaT_siMYC_rep3_ds2_cy5

description: this is MYC siRNA transfection. rep: biological replicate; ds: dye swap

source_name: HaCaT cells transfected with MYC siRNA


title: H1299_WT Iressa 10h00m

data_processing: Image files were analyzed with GeneChip Operating System (GCOS) (ver.1.2) and CEL files were processed by RMA to obtain expression level of genes.

source_name: lung, epithelial, Iressa, 10h


title: HaCaT_siCT_for siP63_rep3_ds1_cy5


title: HaCaT_siMYC_rep3_ds1_cy5


title: H1299_WT EGF_Iressa 01h00m

source_name: lung, epithelial, EGF+Iressa, 1h


title: H1299_WT Iressa 00h00m

source_name: lung, epithelial, Iressa, 0min


title: H1299_WT Iressa 06h00m

source_name: lung, epithelial, Iressa, 6h


title: H1299_WT EGF_Iressa 04h00m

source_name: lung, epithelial, EGF+Iressa, 4h


title: HaCaT_siCT_for siP63_rep1_ds1_cy5

source_name: Wild type HaCaT cells


title: HaCaT_siMYC_rep3_ds2_cy3


title: H1299_WT EGF 00h30m

description: Gene expression induced by EGF stimulation

source_name: lung, epithelial, EGF, 30min

treatment_protocol: Before treatments, medium were changed with serum-free medium again and incubated at 37C for 2 hours. Followed by incubation, added each ligand and incubated for each time.


title: H1299_WT EGF 02h00m

source_name: lung, epithelial, EGF, 2h


title: HaCaT_siMYC_rep2_ds2_cy5


title: H1299_WT EGF 04h00m

source_name: lung, epithelial, EGF, 4h


title: HaCaT_siMYC_rep2_ds1_cy3


title: HaCaT_siMYC_rep3_ds1_cy3


title: HaCaT_siMYC_rep2_ds2_cy3


title: H1299_L858R Iressa 10h00m

value: H1299 (Obtained from ATCC (American Type Culture Collection) with overexpressed EGFR having L858R point mutation, Organ:lung, Cell type:epithelial, Disease:carcinoma; non-small cell lung cancer, Derived from metastatic site:lymph node, Age:43 years adult, Gender:male, Ethnicity:Caucasian


title: H1299_WT EGF 01h00m

source_name: lung, epithelial, EGF, 1h


title: HaCaT_siMYC_rep2_ds1_cy5


title: H1299_WT EGF 10h00m

source_name: lung, epithelial, EGF, 10h


title: H1299_WT Control

description: Gene expression without stimulation

source_name: lung, epithelial, Control


title: Tumor liver at 67 week_3

city: Kashiwa

first: Akihito

last: Tsubota

state: Chiba

address: 163-1 Kashiwa-shita

department: Institute of Clinical Medicine and Research

institute: Jikei University School of Medicine

description: Gene expression data from 67 week old LEC rat tumor liver tissue

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed with GeneChip Operating Software version 1.4 (Affymetrix) using Affymetrix default analysis settings, and were normalized by robust multi-array analysis (RMA) using the R 2.6.1 statistical software together and a Bioconductor package.

organism: Rattus norvegicus

source_name: LEC rat tumor liver tissue at 67 weeks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA.

growth_protocol: Specific pathogen-free (SPF) and viral antibody-free (VAF) male LEC and LEA rats were maintained in a controlled environment.

extract_protocol: Total RNA was extracted from tissue samples using RNeasy kit (Qiagen) and digested with DNase I (Qiagen) according to the manufacturer's instructions.

tag: gender

value: male

tag: animal handling

value: specific pathogen-free (SPF), viral antibody-free (VAF)

tag: strain

value: Long Evans Cinnamon (LEC/Crj)

tag: age

value: 67 weeks old

tag: tissue

value: liver

tag: disease status

value: tumor


title: H1299_WT EGF 06h00m

source_name: lung, epithelial, EGF, 6h


title: HaCaT_siMYC_rep1_ds2_cy5

tag: cell line


title: H1299_L858R Iressa 04h00m

source_name: lung, epithelial, Iressa, 4h


title: HaCaT_siMYC_rep1_ds1_cy5


title: HaCaT_siMYC_rep1_ds2_cy3


title: Tumor liver at 67 week_1


title: H1299_L858R Iressa 06h00m


title: Liver at 26 weeks

description: Gene expression data from 26 week old LEC rat noutumor liver tissue

source_name: LEC rat liver tissue at 26 weeks

value: 26 weeks old

value: normal


title: HaCaT_siMYC_rep1_ds1_cy3

source_name: HaCaT cells transfected with MYC siRNA


title: Liver at 39 weeks

description: Gene expression data from 39 week old LEC rat noutumor liver tissue

source_name: LEC rat liver tissue at 39 weeks

value: 39 weeks old


title: Tumor liver at 67 week_2


title: Liver at 4 weeks

description: Gene expression data from 4 week old LEC rat noutumor liver tissue

source_name: LEC rat liver tissue at 4 weeks

value: 4 weeks old


title: HaCaT_siCT_for siMYC_rep3_ds1_cy3

description: this control siRNA transfection was used as an experimental control for siMYC transfection, rep: biological replicate; ds: dye swap

source_name: HaCaT cells transfected with control siRNA

value: HaCaT


title: H1299_L858R Iressa 01h00m

source_name: lung, epithelial, Iressa, 1h


title: HaCaT_siCT_for siMYC_rep3_ds2_cy3


title: H1299_L858R Iressa 02h00m

source_name: lung, epithelial, Iressa, 2h


title: HaCaT_siCT_for siMYC_rep3_ds1_cy5

source_name: Wild type HaCaT cells


title: HaCaT_siCT_for siMYC_rep2_ds2_cy3


title: Tumor liver at 67 week_4


title: HaCaT_siCT_for siMYC_rep2_ds1_cy3


title: H1299_L858R EGF_Iressa 10h00m

source_name: lung, epithelial, EGF+Iressa, 10h


title: Nontumor liver at 67 weeks_3

description: Gene expression data from 67 week old LEC rat noutumor liver tissue

source_name: LEC rat nontumor liver tissue at 67 weeks


title: H1299_L858R Iressa 00h00m

source_name: lung, epithelial, Iressa, 0min


title: HaCaT_siCT_for siMYC_rep2_ds2_cy5


title: H1299_L858R EGF_Iressa 06h00m

source_name: lung, epithelial, EGF+Iressa, 6h


title: H1299_L858R Iressa 00h30m

source_name: lung, epithelial, Iressa, 30min


title: H1299_L858R EGF_Iressa 02h00m

source_name: lung, epithelial, EGF+Iressa, 2h


title: Nontumor liver at 67 weeks_4


title: H1299_L858R EGF_Iressa 04h00m

source_name: lung, epithelial, EGF+Iressa, 4h


title: HaCaT_siCT_for siMYC_rep2_ds1_cy5


title: H1299_L858R EGF_Iressa 01h00m

source_name: lung, epithelial, EGF+Iressa, 1h


title: Control liver at 67 weeks

description: Gene expression data from 67 week old LEA rat noutumor liver tissue

source_name: LEA rat liver tissue at 67 weeks

value: Long Evans Agouti (LEA)


title: Nontumor liver at 67 weeks_2


title: H1299_L858R EGF_Iressa 00h30m

source_name: lung, epithelial, EGF+Iressa, 30min


title: HaCaT_siCT_for siMYC_rep3_ds2_cy5


title: Nontumor liver at 67 weeks_1


title: HaCaT_siCT_for siMYC_rep1_ds2_cy3


title: H1299_L858R EGF 10h00m

source_name: lung, epithelial, EGF, 10h


title: HaCaT_siCT_for siMYC_rep1_ds1_cy3


title: H1299_EGFR-WT Iressa 04h00m

source_name: lung, epithelial, Iressa, 4h

value: H1299 (Obtained from ATCC (American Type Culture Collection) with overexpressed wild type EGFR, Organ:lung, Cell type:epithelial, Disease:carcinoma; non-small cell lung cancer, Derived from metastatic site:lymph node, Age:43 years adult, Gender:male, Ethnicity:Caucasian


title: H1299_EGFR-WT EGF_Iressa 10h00m


title: H1299_EGFR-WT EGF_Iressa 06h00m


title: H1299_EGFR-WT Iressa 02h00m


title: H1299_L858R EGF 01h00m

source_name: lung, epithelial, EGF, 1h


title: HaCaT_siCT_for siMYC_rep1_ds1_cy5

source_name: HaCaT cells transfected with control siRNA


title: H1299_EGFR-WT Iressa 06h00m

source_name: lung, epithelial, Iressa, 6h


title: H1299_EGFR-WT EGF_Iressa 00h30m


title: H1299_EGFR-WT Iressa 10h00m

source_name: lung, epithelial, Iressa, 10h


title: H1299_EGFR-WT Iressa 00h00m


title: HaCaT_siCT_for siMYC_rep1_ds2_cy5

source_name: Wild type HaCaT cells


title: H1299_EGFR-WT EGF_Iressa 01h00m


title: H1299_L858R EGF 04h00m

source_name: lung, epithelial, EGF, 4h


title: H1299_L858R EGF 02h00m

source_name: lung, epithelial, EGF, 2h


title: H1299_L858R EGF 06h00m

source_name: lung, epithelial, EGF, 6h


title: H1299_EGFR-WT EGF 10h00m


title: H1299_L858R EGF 00h30m

source_name: lung, epithelial, EGF, 30min


title: H1299_EGFR-WT EGF_Iressa 02h00m


title: H1299_EGFR-WT Iressa 00h30m

source_name: lung, epithelial, Iressa, 30min


title: H1299_EGFR-WT EGF 04h00m


title: kc_mcm_1 extraction1_array2

status: Public on Jul 29 2009

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: Pan MCM2-7 Antibody;target name: MCM2-7 complex;host: Mouse;antigen: MCM2-7 complex Walker B motif;clonal: Monoclonal;purified: Crude;company: Lab;catalog: Anthony Schwacha;reference: PMID: 12403810;short description: Monoclonal antibody against purified yeast MCM complex. Works cross species.;
channel ch2 is input DNA;

hyb_protocol: Agilent hybridization protocol;  Setting up hybridization 1.Thaw samples on ice, in the dark 2.Set up hyb reaction: (Oligo aCGH/ChOP-on-Chip Hyb kit; Agilent) sample 25ul Ambion dH2O 175ul 10X Blocking Solution 50ul 2X Hybridization buffer 250ul 3.Inc 95C, 5 minutes 4.Spin down briefly and keep at 37C while getting slide ready 5.Place gasket with agilent side facing up on metal chamber 6.Pipet 490ul of hyb reaction on gasket 7.Lay down microarray on hyb reaction with Agilent side down. 8.Assemble metal chamber 9.inc. 16-20 hours in rotating hyb oven at 65C Washing microarrays 10.Dissamble arrays in tip box lid containing Buffer 1 (Agilent) 11.Wash slide in buffer 1 with stirring, 5 minutes 12.Wash slide in buffer 2 with stirring, 5 minutes 13.Wash slide in acetonitrile, 30 seconds 14.Wash slide in buffer 3, 30 seconds 15.Store in light proof holder and scan [edit]

scan_protocol: Array scanning protocol;  Scanning per Agilent recommendations.

data_processing: Normalization and peak calling protocol;  Agilent data files are converted to a nimblegen like format for processing by MA2C. pMA2C -- pyhton MA2C (http://liulab.dfci.harvard.edu/MA2C/MA2C.htm) Parameters are passed as a tag file which we generate in Array Scanning protocol.  Processed data are obtained using following parameters: tag file is preRC/MCM_cycE/Kc/mcm_meta.tag   genome version is r5

organism: Drosophila melanogaster

source_name: ChIP: kc_mcm_1 extraction1_array2 channel_1

label_protocol: Sequenase labeling protocol;  1.Thaw DNA samples on ice 2.Transfer to 0.2ml pcr tubes. Open tubes and place inside a 1.5ml tube 3.Speed vac samples on medium heat for approx. 15-18 minutes 4.Resusp DNA in sequenase primer mix: 5X sequenase buffer 2ul (US Biochemicals) random nonamer 5ul (NNNNNNNNN; hand mixed 25,25,25,25) Ambion dH2O 1ul 5.Thaw Cy dyes (Cy 3 dUTP and Cy 5 dUTP; Perkin Elmer) on ice and in the dark 6.Add 2ul of cy dye to DNA sample 7.Start pcr program: 95C 3' 4C 2' 37C 30' ramp 95C 2' 4C 2' 37C 30' ramp 4C hold 8.At the first 4C step in program, add the following: 5X sequenase buffer 1ul Low T 1.5ul (5ul dATP, 5ul dCTP, 5ul dGTP, 2ul dTTP, 83ul ambion dH2O) 100 mM BSA 1ul 100mM DTT 0.75ul sequenase 1ul 9.At the second 4C step, add additional sequenase and finish program sequenase buffer DLT 0.7ul sequenase 0.3ul 10.Clean samples on YM-30 microcon column (Millipore) according to directions 11.Spec samples [edit]

growth_protocol:
Cell Growth ChIP Small Scale protocol;  1. Kc cells were cultured in 150mm plates at a density of 1 x 10^6 cells/ml in Schneider's Insect Cell Medium (Invitrogen 11720-067) supplemented with 10% FBS and 1% penicillin/streptomycin/glutamine (Invitrogen 10378-016). 2. For each experiment, ~1.2 x 10^8 Kc cells were collected.
RNAi protocol;  1. Generate an ~700bp pcr product to the gene of interest 2. See technical details for making dsRNA in the T7 large scale RNA production kit (Promega #P1320) 3. Count tissue culture cells. Centrifuge 1.0 x106 cells/ml. 4. Wash cells in serum free medium (SFM) 5. Resuspend the cells in SFM. You need to resuspend them in half the volume of the plate. This makes the final volume of cells in the dish at this point 2.0 x 106. 6. Aliquot into tissue culture dish 7. Add dsRNA: 15ug per 1.0 x106 cells/ml. 8. Incubate 1h 9. Add half the volume of the dish worth of 2X medium (10% serum, 2% PSG) 10. Incubate 48h. 11. Harvest cells and continue with ChIP preparation. [edit]

extract_protocol:
ChIP crosslinking and isolation protocol;  1. Cross-link cells at room temperature with 1% formaldehyde (Ted Pella #18505) for 10 min. 2. Quench reaction with 125mM glycine for 5 min. at room temp. 3. Centrifuge cross-linked cells, 1,000 rpm, 10 min. 4. Wash cells with 2X cold 1X PBS. 5. Freeze pellet with liquid nitrogen and store at -80C for at least two hours 6. Thaw pellet on ice and prepare lysis buffers: Lysis Buffer 1: 50mM Hepes-KOH, pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1/2 mini protease tablet (Roche) per 5ml of buffer Lysis Buffer 2: 10mM Tris-HCl, pH 8.0, 200mM NaCl, 1mM EDTA, 0.5 EGTA, 1/2  protease tablet per 5ml of buffer Lysis Buffer 3: 10mM Tris-HCl, pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate,  0.5% N-lauroylsarcosine, 1/2 mini protease tablet per 5ml buffer 7. Keep lysis buffers on ice 8. Resuspend pellet in 5ml lysis buffer 1 and incubate with rotation at 4C for 10min. 9. Centrifuge, 4C, 1350xg, 5 min 10.Resuspend pellet in 5ml lysis buffer 2 and incubate with rotation at room temperature for 10 min. 11. Follow step 9 12. Resuspend in 3ml lysis buffer 3 13. sonicate extract to an average size of 1Kb. 14. Add Triton X-100 to 1%. vortex gently 15. Centrifuge at 4C, 20,000xg, 10min. 16. Aliquot extracts into ~500ul samples.
ChIP protocol;  The chromatin was immunoprecipitated with a specified antibody as described in Austin et al. (1999)

value: embryo-derived cell-line

value: se/e

tag: sex

value: Female

source_name: Input: kc_mcm_1 extraction1_array2 channel_2


title: H1299_EGFR-WT EGF 06h00m


title: kc_orc_2 extraction2_array4

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: dORC2;target name: Drosophila ORC2p;host: Rabbit;antigen: purified full length protein;clonal: Polyclonal;purified: Crude;company: Lab;catalog: Stephen P. Bell MIT;reference: Austin et al 1999;
channel ch2 is input DNA;

data_processing: Normalization and peak calling protocol;  Agilent data files are converted to a nimblegen like format for processing by MA2C. pMA2C -- pyhton MA2C (http://liulab.dfci.harvard.edu/MA2C/MA2C.htm) Parameters are passed as a tag file which we generate in Array Scanning protocol.  Processed data are obtained using following parameters: tag file is preRC/ORC/Kc/orc_meta.tag   genome version is r5

source_name: ChIP: kc_orc_2 extraction2_array4 channel_1

growth_protocol: Cell Growth ChIP Large Scale protocol;  1. Kc cells were cultured in 150mm plates at a density of 1 x 10^6 cells/ml in Schneider's Insect Cell Medium (Invitrogen 11720-067) supplemented with 10% FBS and 1% penicillin/streptomycin/glutamine (Invitrogen 10378-016). 2. For each experiment, ~3 x 108 Kc cells were collected from asynchronous cultures.

source_name: Input: kc_orc_2 extraction2_array4 channel_2


title: kc_mcm_2 extraction2_array2

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: Pan MCM2-7 Antibody;target name: MCM2-7 complex;host: Mouse;antigen: MCM2-7 complex Walker B motif;clonal: Monoclonal;purified: Crude;company: Lab;catalog: Anthony Schwacha;reference: PMID: 12403810;short description: Monoclonal antibody against purified yeast MCM complex. Works cross species.;

source_name: Input: kc_mcm_2 extraction2_array2 channel_1

source_name: ChIP: kc_mcm_2 extraction2_array2 channel_2


title: SGC7901-IRX1

city: Shanghai

first: Yingyan

address: Shanghai Ruijin 2nd Road No.197

department: Department of Surgery

country: China

institute: Shanghai Ruijin Hospital

description: Gene expression of SGC7901 transfected with pEGFP-IRX1

hyb_protocol: 1.5 ug of Cy3-labeled cRNA (specific activity>10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. Following fragmentation, 250 ml of 2x Agilent hybridization buffer was added and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarray was washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute at 37°C with GE Wash buffer 2 (Agilent), and dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing with the Agilent DNA Microarray Scanner (G2505B) using the one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel set to Green and Green PMT set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters to obtain background subtracted and spatially normalized Processed Signal intensities. Features were flagged in Feature Extraction as Feature Non-uniform  and outliers were excluded.

source_name: Gastric cancer cell line SGC7901 transfected with pEGFP-IRX1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug total RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked using a NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using Trizol solution (Invitrogen, USA) following the manufacturer's recommendations.

value: gastric cancer

tag: genome/variation

value: IRX1 overexpression


title: H1299_EGFR-WT Iressa 01h00m

source_name: lung, epithelial, Iressa, 1h


title: H1299_L858R Control

description: Gene expression without stimulation

source_name: lung, epithelial, Control

value: H1299 (Obtained from ATCC (American Type Culture Collection) with overexpressed EGFR having L858R point mutation, Organ:lung, Cell type:epithelial, Disease:carcinoma; non-small cell lung cancer, Derived from metastatic site:lymph node, Age:43 years adult, Gender:male, Ethnicity:Caucasian


title: H1299_EGFR-WT EGF 02h00m


title: kc_orc_1 extraction1_array4

source_name: ChIP: kc_orc_1 extraction1_array4 channel_1

source_name: Input: kc_orc_1 extraction1_array4 channel_2


title: PATIENT 50

city: Bethesda

first: Tetsuya

last: Okano

state: MD

address: 37 Convent Drive, Bldg 37

department: NCI

institute: NIH

description: no additional information

hyb_protocol: See associated publication (PMID: 19597153)

scan_protocol: Slides were scanned with the Axon 4000B Scanner (Molecular Device, Inc) and spot intensities were quantified with Genepix (version Pro 6.0.1.00).

data_processing: Mean intensity spot values for each sample were extracted for spots that were not flagged by the image quantification software GenePix (version Pro 6.0.1.00).  In addition, spots were removed if their background intensities were higher than their respective foreground intensities, and if quadruplicate intensity spot values differed by more than 1 (on a log2 scale).  The remaining spots were then normalized using a loess normalization modified for single channel array data, where the true spot intensity is estimated by the average of that spot across all arrays.

source_name: Japanese Cohort_H20t

label_protocol: Five μg of total RNA were converted to biotin-labeled first strand cDNA, hybridized onto the chips, and processed by direct detection of the biotin-containing transcripts by streptavidin-Alexa 647 conjugate.

extract_protocol: Total RNA used for quantification of miRNA levels was extracted from lung tissue in our laboratory using TRIZOL (Invitrogen, cat. no. 15596-026), according to the manufacturer’s procedures.

tag: hybridization date

tag: tissue type

value: Cancerous

tag: histology

value: adenocarcinoma

tag: race

value: Asian (Japanese)

tag: smoking

value: No

tag: ptnm stage

value: I

tag: egfr status


title: H1299_EGFR-WT Control

description: Gene expression without stimulation

tag: Cell line


title: PATIENT 53

description: no additional information

source_name: Japanese Cohort_H36n

tag: gender

value: wild-type


title: H1299_EGFR-WT EGF_Iressa 04h00m

source_name: lung, epithelial, EGF+Iressa, 4h


title: H1299_EGFR-WT EGF 00h30m


title: SGC7901

description: Gene expression of gastric cancer cell line SGC7901

source_name: Gastric cancer cell line SGC7901


title: PATIENT 49

description: no additional information

source_name: Japanese Cohort_H20n


title: PATIENT 51

description: no additional information

source_name: Japanese Cohort_H30n