title: Lung Cancer Cell Line RVH6849

city: Toronto

first: Shirley

last: Tam

state: Ontario

address: 661 University Avenue, Suite 510, MaRS Building, West Tower

department: Genome Technologies

country: Canada

institute: Ontario Institute for Cancer Research

hyb_protocol: Microarray labeling, hybridization and scanning was performed according to the manufacturer's recommendations by the University Health Networks (UHN) Microarray Centre (Toronto, Ontario, Canada).

data_processing: Image files were quantified in BeadStudio Version 3.3.8 (Illumina) and raw data output were loaded into the R statistical environment (v2.14.0) using the lumi package (v2.6.0) implemented in the Bioconductor libraries. The probes were re-annotated against miRBase v16, log2 transformed and normalized using the Robust Spline Normalization (RSN) algorithm. No background correction was performed.

source_name: Total RNA from RVH6849 cells

growth_protocol: Cells were cultured in RPMI-1640, supplemented with 10% FBS and 1X Penicillin/Streptomycin.  Xenografts were grown by subcutaneous injection of two million trypsin-dissociated tumor cells into non-obese diabetic/severe combined immunodeficient mice.

extract_protocol: Total RNA was isolated from confluent cell lines or fresh-frozen xenograft tissues using Trizol reagent (Life Technologies, Carlsbad, CA, USA) according to the manufacturer's instructions, followed by Dnase I treatment (Life Technologies) and purification using the Qiagen RNeasey kit (Qiagen, Venlo, Netherlands).  RNA quantity and quality was assessed using the Qubit Fluorometer (Life Technologies), NanoDrop 1000 (Nanodrop Technologies, Wilmington, DE, USA), and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Not Applicable


title: Lung Xenograft RVH6849

status: Public on Oct 22 2013

type: RNA

scan_protocol: Microarray labeling, hybridization and scanning was performed according to the manufacturer's recommendations by the University Health Networks (UHN) Microarray Centre (Toronto, Ontario, Canada).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Total RNA from RVH6849 xenograft

tag: cell line


title: Lung Xenograft H520

source_name: Total RNA from H520 xenograft

label_protocol: Microarray labeling, hybridization and scanning was performed according to the manufacturer's recommendations by the University Health Networks (UHN) Microarray Centre (Toronto, Ontario, Canada).


title: PR+NR breast cancer BC_4560224043_A

city: Amsterdam

first: Jelle

middle: Johannes

last: ten Hoeve

address: Plesmanlaan 121

department: Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were between-array normalised using simple scaling (SSN) subsequently log2 transformed

label: Biotin

source_name: 14G core needle breast tumor biopsy

label_protocol: Total RNA was amplified and biotin labeled using the Illumina® TotalPrep™-96 RNA kit. All steps were performed according to standard protocol.

extract_protocol: From the frozen biopsies approximately 30 sections of 30-μm thickness were used for total RNA isolation with RNABee (Campro Scientific, Amersfoort, The Netherlands). Isolated total RNA was subsequently DNase-treated by using the Qiagen RNase-free DNase kit and RNeasy spin columns (Qiagen, West Sussex, U.K.) and dissolved in RNase-free H2O.

tag: response breast

value: PR+NR [Partial Response + No Response]

tag: response

value: NOCR [No complete response]

tag: ihc er percentage

tag: ihc pr percentage

tag: intrinsic molecular subtype

value: Normal

tag: treatment

value: PTC

tag: clinical subtype

tag: tissue

value: breast cancer tumor


title: Lung Cancer Cell Line H1264

source_name: Total RNA from H1264 cells


title: pCR+npCR mamma breast cancer BC_4560224053_D

value: pCR+npCR mamma [pathological complete response + near pathological complete response mamma]

value: CR [(pathological) complete response]


title: LNCaP_ DCC_2

city: Copenhagen

first: Charlotte

last: Svensson

state: Please select one

address: Blegdamsvej 3

department: Novo Nordisk foundation center for protein research

country: Denmark

institute: University of copenhagen

description:
androgen status, negative
LNCaP grown in DCC (steroid-depleted) medium_No2

hyb_protocol: 1.5 ug of Cy3-labelled 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 manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: LNCaP cells, DCC serum containing medium

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

growth_protocol: LNCaP cells wre grown in RPMI1648 supplemented with 10%FBS or alternatively supplemented with 5% dextran-coated charcoal stripped(DCC) FBS.

extract_protocol: Qiagen's RNAeasy RNA extraction kit

treatment_protocol: Steroid depletion was achieved by incubating with DCC containing medium for 5 days and treatment of DCC cultured cells with synthestic androgen (R1881, 10nM) was perfomed overnight (16h).

value: LNCaP

value: DCC serum containing medium


title: PR+NR breast cancer BC_4560224053_C


title: LNCaP_FBS_1

description:
androgen status, positive
LNCaP grown in normal (steroid-containing) medium_No1

source_name: LNCaP cells, FBS containing medium

value: FBS containing medium


title: Lung Cancer Cell Line H520

source_name: Total RNA from H520 cells


title: PR+NR breast cancer BC_4560224074_E

value: LumB


title: Lung Xenograft H1264

source_name: Total RNA from H1264 xenograft


title: pCR+npCR mamma breast cancer BC_4560224078_D


title: PR+NR breast cancer BC_4560224078_E

value: Basal


title: LNCaP_FBS_2

description:
androgen status, positive
LNCaP grown in normal (steroid-containing) medium_No2


title: UF 715133-1 control

city: Qingdao

first: Qing

last: Kong

state: Shandong

address: Yushan Road 5

department: Food Science and Engineering

country: China

institute: Ocean University of China

description: Gene expression profile not affected by Bacillus megaterium in Aspergillus flavus NRRL 3357 in UF 715133-1

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to microarrays (Agilent-040537) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x15k array slides ( Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software(Agilent) 10.7.1.1 using default parameters to obtain background subtracted  and spatially detrended Processed Signal intensities. Then the data were normalised using quantile normalisation with GeneSpring 12.0.

organism: Aspergillus flavus

source_name: UF 715133-1 control, 7days

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low Input Quick-Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop 2000 Spectrophotometer.

growth_protocol: Wild-type A. flavus strain NRRL 3357 was used as the pathogenic fungus and maintained on potato dextrose agar (PDA) medium (containing the extract of 200 g boiled potato, 20 g glucose and 20 g agar in 1 liter of distilled water) at 4°C. Spore suspensions were prepared by washing the surface of the 7-day-old sporulating cultures of A. flavus on PDA plate with 0.1% Tween 80 solution in sterile distilled water. Spores were counted with a haemocytometer and then were diluted to desired concentrations (5 × 106 spores/ml and 1 × 106 spores/ml) with 0.1% Tween 80 solution. The marine antagonist B. megaterium used in this study was isolated from the Yellow Sea of East China, which was identified by morphological, physiological, and chemotaxonomic features of the organism and confirmed by 16S rRNA based phylogenetic analysis. Bacteria cells were prepared by growing cultures in beef extract peptone broth (BEPB: beef extract, 3 g/l; peptone, 10 g/l; sodium chloride, 5 g/l) for 24 h at 37°C with shaking at 200 rpm. The cells were harvested by centrifuging at 8000 rpm (10000 g) for 45 s and were washed twice with sterile distilled water to remove the growth medium. The cells were counted by platecount method and then were diluted with sterile distilled water to desired concentration (1 × 108 CFU/ml). Two types of peanut varieties, UF 715133-1 and Jinhua 1012, from a collection of Shandong Peanut Institute, were selected in this study. UF 715133-1 is a kind of peanut that could resist to A. flavus invasion, while Jinhua 1012 is susceptible to A. flavus. Before treatments, the peanut kernels were washed with tap water, then surfaced-disinfected with 0.1% sodium hypochlorite for 1 min, cleaned with tap water and air dried prior to wounding.Two types of peanut varieties, UF 715133-1 and Jinhua 1012, from a collection of Shandong Peanut Institute, were selected in this study. UF 715133-1 is a kind of peanut that could resist to A. flavus invasion, while Jinhua 1012 is susceptible to A. flavus. Before treatments, the peanut kernels were washed with tap water, then surfaced-disinfected with 0.1% sodium hypochlorite for 1 min, cleaned with tap water and air dried prior to wounding.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent 2100 Bioanalyser.

treatment_protocol: The effect of B. megaterium on aflatoxin biosynthesis and genes expression of pathogen was firstly tested in potato dextrose broth (PDB) and glucose minimal salts medium (MM). The cell suspension of B. megaterium (concentration in PDB and MM was finally adjusted to 108 CFU/ml) or sterile distilled water as a control was added into the 100 ml beaker flask containing 15 ml PDB or MM, respectively. Then 100 μl of spore suspension (5 × 106 spores/ml) of A. flavus were added into each beaker flask. After 48 h of incubation at 28°C at 200 rpm, mycelia were collected, fresh frozen with liquid nitrogen, ground to a fine powder in liquid nitrogen, and stored at -80°C for further analysis. The effect of B. megaterium on aflatoxin biosynthesis and genes expression in the A. flavus fungal pathogen was also tested in two types of peanut kernels, UF 715133-1 and Jinhua 1012, respectively. Peanut kernels were wounded (6 mm diameter and approximately 3 mm deep) using a sterile borer and then 20 μl of 1 × 108 CFU/ml cell suspension of B. megaterium was inoculated on wounded peanut kernels respectively. Sterile distilled water was also used for inoculation as control. Two hours after bacterial inoculation, 10 μl A. flavus spore suspension was inoculated into each wound at a concentration of 106 spores/ml. The kernels were placed in artificial weather chamber to maintain high humidity (85%) and incubated at 28°C for 7 days. Each treatment was replicated three times with 20 peanut kernels in each test. The mycelia on kernels were harvested at day 7 and fresh frozen immediately in liquid nitrogen, ground into powder, and stored at -80°C for further analysis.

value: UF 715133-1 control

tag: time

value: 7 d

value: mycelia

tag: age

value: 7 days


title: Lung Xenograft H460

source_name: Total RNA from H460 xenograft


title: Lung Cancer Cell Line H460

source_name: Total RNA from H460 cells


title: pCR+npCR mamma breast cancer BC_4560224088_C

value: LumA


title: UF 715133-1 treatment

description: Gene expression profile affected by Bacillus megaterium in Aspergillus flavus NRRL 3357 in UF 715133-1

source_name: UF 715133-1 treatment, 7days

value: UF 715133-1 treatment


title: Lung Xenograft A549

source_name: Total RNA from A549 xenograft


title: PR+NR breast cancer BC_4560224089_C

value: PR+NR [Partial Response + No Response]

value: NOCR [No complete response]


title: Jinhua 1012 treatment

description: Gene expression profile affected by Bacillus megaterium in Aspergillus flavus NRRL 3357 in Jinhua 1012

source_name: Jinhua 1012 treatment, 7days

value: Jinhua 1012 treatment


title: siSpt4; CIT(+); Replicate #3

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description:
Sample name: #3 C
Raw data file: EM03P11.gpr

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: F635 Median column as Red signal. The raw Red signal data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.The raw Red signal data　intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. Detected signals for each gene were normalized by global normalization method (the median of the detected signal intensity was adjusted to 30).

organism: Mus musculus

source_name: CH12F3-2A cell line

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Cells were maintained in RPMI 1640 supplemented with 10% FCS, 50microM 2-mercaptoethanol, 5% NCTC, 20mM HEPES, 2mM L-glutamine

extract_protocol: RNA samples were extracted from cells using RNeasy mini kit (Qiagen).

treatment_protocol: siRNA oligonucleotides were introduced to CH12F3-2A cells by AMAXA electroporation.  The cells were then cultured for 24hours, stimulated by CD40L, IL4, TGFb (CIT), and cultured for another 24 hours.

value: CH12F3-2A cell line derived from B cell lymphoma

tag: cit-induced switching

value: IgA

tag: genotype/variation

value: Spt4 knockdown


title: pCR+npCR mamma breast cancer BC_4560224088_F

value: pCR+npCR mamma [pathological complete response + near pathological complete response mamma]

value: CR [(pathological) complete response]

value: PTC

value: breast cancer tumor


title: Jinhua 1012 control

description: Gene expression profile not affected by Bacillus megaterium in Aspergillus flavus NRRL 3357 in Jinhua 1012

source_name: Jinhua 1012 control, 7days

value: Jinhua 1012 control


title: Lung Cancer Cell Line A549

source_name: Total RNA from A549 cells


title: siSpt5; CIT(+); Replicate #3

description:
Sample name: #4 C
Raw data file: EM03P12.gpr

value: Spt5 knockdown


title: siSpt5; CIT(+); Replicate #2

description:
Sample name: #4 B
Raw data file: EM03P07.gpr


title: siControl; CIT(+); Replicate #3

description:
Sample name: #2 C
Raw data file: EM03P10.gpr

value: Control


title: MM control

description: Gene expression profile not affected by Bacillus megaterium in Aspergillus flavus NRRL 3357 in MM

source_name: MM control, 48 h

value: MM control

value: mycelia


title: NA breast cancer BC_4560224089_A

value: NA [Not Available]

value: PD [progressive disease]

value: Normal


title: pCR+npCR mamma breast cancer BC_4560224089_B

value: CR+kl [(pathological) complete response breast, positive lymph nodes]

value: LumB


title: MM treatment

description: Gene expression profile affected by Bacillus megaterium in Aspergillus flavus NRRL 3357 in MM

source_name: MM treatment, 48 h

value: MM treatment


title: siSpt4; CIT(+); Replicate #2

description:
Sample name: #3 B
Raw data file: EM03P06.gpr

value: CH12F3-2A cell line derived from B cell lymphoma

value: IgA


title: pCR+npCR mamma breast cancer BC_4531933041_E

source_name: 14G core needle breast tumor biopsy

value: pCR+npCR mamma [pathological complete response + near pathological complete response mamma]


title: siControl; CIT(+); Replicate #2

description:
Sample name: #2 B
Raw data file: EM03P02.gpr


title: PDB control

description: Gene expression profile not affected by Bacillus megaterium in Aspergillus flavus NRRL 3357 in PDB

source_name: PDB control, 48 h

value: PDB control


title: Lung Xenograft RVH6849

description: color-coded tags

scan_protocol: The samples were prepared for nCounter miRNA expression profiling according to the manufacturer’s recommendations (NanoString, Seattle, WA, USA) by the University Health Networks (UHN) Microarray Centre (Toronto, Ontario, Canada).  For each sample, a scan of 600 fields-of-view (FOV) was imaged.

data_processing: Prior to data normalization, nCounter data imaging quality control (QC) metrics were assessed.  There was no significant discrepancy between the FOVs attempted and the FOVs counted.  The binding density for the samples ranged between 0.24 and 0.72 – within the typical recommended range.  The raw data was loaded into the R statistical environment (v2.14.0), and re-annotated against miRBase v16.  Prior to normalization, probes indicated to have some level of background were corrected using probe level adjustment factors.  Then, the geometric mean of the positive controls was used for code count normalization, while the background was estimated using the mean of the negative controls.  Sample input amounts were normalized to the geometric mean of five housekeeping mRNA controls (ACTB, B2M, GAPDH, RPL19 and RPL10) included in the assay, and finally, to total miRNA count.

source_name: Total RNA from RVH6849 xenograft


title: siSpt5; CIT(+); Replicate #1

description:
Sample name: #4 A
Raw data file: EM03906.gpr


title: Lung Xenograft H520

description: color-coded tags

hyb_protocol: The samples were prepared for nCounter miRNA expression profiling according to the manufacturer’s recommendations (NanoString, Seattle, WA, USA) by the University Health Networks (UHN) Microarray Centre (Toronto, Ontario, Canada).

source_name: Total RNA from H520 xenograft


title: PDB treatment

description: Gene expression profile affected by Bacillus megaterium in Aspergillus flavus NRRL 3357 in PDB

source_name: PDB treatment, 48 h

value: PDB treatment


title: NA breast cancer BC_4560224084_F

value: NOCR [No complete response]

value: LumA

value: PTC

value: breast cancer tumor


title: Lung Cancer Cell Line RVH6849

description: color-coded tags

source_name: Total RNA from RVH6849 cells

label_protocol: The samples were prepared for nCounter miRNA expression profiling according to the manufacturer’s recommendations (NanoString, Seattle, WA, USA) by the University Health Networks (UHN) Microarray Centre (Toronto, Ontario, Canada).


title: Lung Cancer Cell Line H520

description: color-coded tags

source_name: Total RNA from H520 cells


title: siControl; CIT(+); Replicate #1

description:
Sample name: #2 A
Raw data file: EM03903.gpr

value: Control


title: pCR+npCR mamma breast cancer BC_5357957054_E

value: CR [(pathological) complete response]


title: Lung Xenograft H460

description: color-coded tags

source_name: Total RNA from H460 xenograft


title: PR+NR breast cancer BC_4531933059_F

value: PR+NR [Partial Response + No Response]


title: siSpt4; CIT(+); Replicate #1

description:
Sample name: #3 A
Raw data file: EM03905.gpr

value: Spt4 knockdown


title: Lung Cancer Cell Line H460

description: color-coded tags

source_name: Total RNA from H460 cells


title: MCF10A deltaHer2 1

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

hyb_protocol: Hybridized for 16 h to GeneChip Human Gene 1.0 ST arrays (Affymetrix)

scan_protocol: GeneChip Scanner 3000 with an autoloader according to the manufacturer’s instructions

data_processing: Expression values were normalized and probeset-level values calculated with robust multi-array average (RMA) as implemented in the R/Bioconductor package affy (R version 2.14)

source_name: human epithelial  cells  MCF10A Detla-HER2

label_protocol: GeneChip WT cDNA Synthesis Kit and a GeneChip WT Terminal Labeling Kit (Affymetrix)

growth_protocol: MCF10A cells were cultured in DMEM/F12 medium (Invitrogen) supplemented with 5% horse serum (Hyclone), 20 ng/ml epidermal growth factor (EGF) (Peprotech), 0.5 µg/ml hydrocortisone (Sigma), 100 ng/ml cholera toxin (Sigma), 10 µg/ml insulin (Sigma), 100 IU/ml penicillin, and 100 µg/ml streptomycin. For 3D cultures, DMEM/F12 medium was supplemented with 2% horse serum, 5 ng/ml EGF, 0.5 µg/ml hydrocortisone, 100 ng/ml cholera toxin, 10 µg/ml insulin, 100 IU/ml penicillin, and 100 µg/ml streptomycin

extract_protocol: RNA was extracted with TRIzol reagent (Sigma)

treatment_protocol: Prior anaylysis the cells were grown for 16 hours in DMEM/F12 medium supplemented with 100 IU/ml penicillin, and 100 µg/ml streptomycin

tag: transgene


title: pCR+npCR mamma breast cancer BC_4560224084_D


title: MCF10A deltaHer2 3


title: PR+NR breast cancer BC_4531933070_D


title: pCR+npCR mamma breast cancer BC_5357957058_D


title: MCF10A deltaHer2 2


title: pCR+npCR mamma breast cancer BC_4531933070_C


title: pCR+npCR mamma breast cancer BC_4531933083_F


title: Lung Xenograft H1264

description: color-coded tags

source_name: Total RNA from H1264 xenograft


title: pCR+npCR mamma breast cancer BC_4531933059_D


title: MCF10A HER2wt 2

source_name: human epithelial  cells  MCF10A WT-HER2

value: HER2 wild type


title: Lung Cancer Cell Line H1264

description: color-coded tags

source_name: Total RNA from H1264 cells


title: MCF10A HER2wt 1


title: MCF10A HER2wt 3


title: pCR+npCR mamma breast cancer BC_4531933072_F

value: CR+kl [(pathological) complete response breast, positive lymph nodes]


title: Lung Xenograft A549

description: color-coded tags

source_name: Total RNA from A549 xenograft


title: pCR+npCR mamma breast cancer BC_4531933083_D


title: Lung Cancer Cell Line A549

description: color-coded tags

source_name: Total RNA from A549 cells


title: PR+NR breast cancer BC_4560224007_D


title: pCR+npCR mamma breast cancer BC_4560224066_B


title: MCF10A control 3

source_name: human epithelial  cells  MCF10A Parental

value: control


title: pCR+npCR mamma breast cancer BC_4560224008_E

value: Normal


title: MCF10A control 2


title: MCF10A control 1


title: 377743

city: Houston

first: Anne

middle: Chinenye

last: Katchy

state: Texas

address: 3605 Cullen Blvd, Room 3021

department: CNRCS, Biology and Biochemistry

country: USA

institute: University of Houston

hyb_protocol: Hybridization was performed at 42 °C for at least 40 hours after pooling of samples for each array. Subsequent to hybridization the slides were washed in three SDS/SSC wash buffers of stepwise lower stringency.

scan_protocol: Slides were scanned using an Axon GenePix 4400A (MDS Analytical Technologies) to obtain TIFF files.

data_processing: Manual processing of data was carried out in GenePix Pro 6.1 to identify possible major issues. Subsequent analysis was carried out in the R environment using the following packages: Bioconductor bundle, Limma, Aroma, KTH. Print-tip lowess was used for normalization and empirical Bayes t-test for statistical analysis. Cut-offs set as described in article.

source_name: vehicle-treated B6

label_protocol: Labeling was carried out with aminoallyl-modified dUTP incorporated during cDNA synthesis using Superscript III (Invitrogen). Incubation with Cy3 or Cy5 monoreactive NHS-ester dured 30 min.

extract_protocol: RNA extraction was from frozen tissue using TRIzol reagent (Invitrogen Carlsbad, CA) in accordance with manufacturer’s protocol.

tag: background strain

source_name: BPA-treated B6


title: PR+NR breast cancer BC_4544460088_D

source_name: 14G core needle breast tumor biopsy

value: LumB


title: OSCC sample8

type: genomic

city: miyazaki city

first: kentarou

last: nagai

state: miyazaki

department: medical

institute: Miyazaki university

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: We analyzed copy number analysis of Affymetrix 250K SNP arrays by CNAG ver3.0. Genotyping data were genered by DynamicModel 3.0  algorithm.

molecule: genomic DNA

source_name: oral squamous cell carcinoma tissue 8

label_protocol: Standard Affymetrix procedures

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

treatment_protocol: Samples were extracted in the center of tumor, not dissected.

tag: Sex

value: male

tag: Stage

value: Ⅱ

tag: region

value: tongue

tag: clinical stage

tag: differentiation

value: moderately


title: pCR+npCR mamma breast cancer BC_4560224008_B

tag: response breast

value: pCR+npCR mamma [pathological complete response + near pathological complete response mamma]

tag: response

tag: ihc er percentage


title: F4 replicate 2

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

description: Fertile Chinese cabbage floral buds (>5.0mm); contain mature pollen grains (replicate 2).

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.probe file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Brassica rapa subsp. pekinensis

source_name: Fertile Chinese cabbage floral buds

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Fertile plants (MsfMs) and sterile plants (MsMS) were obtained by planting seeds from a cross between male fertile (MsfMs) and sterile (MsMS) plants, segregated to a 1:1 ratio. The seeds were sown and grown in a greenhouse at Chungnam National University in spring and autumn of 2009 and 2010. After flowering, MsfMs and MsMS plants were identified and floral buds were sampled from at least 10 plants with transcriptome profiles representing ' f' difference, each at different developmental stages. The bud samples were divided into three and four pools for sterile and fertile buds, respectively, and stored at -70 degree until use.

extract_protocol: Total RNA was isolated from samples using an easy-BLUE TM total RNA extraction kit (Invitrogen, NY, U.S.A.) and was then purified using an RNeasy MinElute TM Cleanup Kit (Qiagen, Germany). For biological repeats, RNAs were extracted from two samples collected in 2009 and 2010, and subjected to microarray analysis.

value: floral bud

tag: phenotype

value: fertile

tag: size

tag: developmental stage

value: mature pollen grains


title: 377741


title: F4 replicate 1

description: Fertile Chinese cabbage floral buds (>5.0mm); contain mature pollen grains (replicate 1).

tag: tissue


title: 377742


title: 377740


title: F3 replicate 2

description: Fertile Chinese cabbage floral buds (2.5mm≤ buds ≤5.0 mm); after tetrad stage, but before mature pollen (replicate 2).

value: 2.5mm≤ buds ≤5.0 mm

value: after tetrad stage, but before mature pollen grains


title: pCR+npCR mamma breast cancer BC_4531933043_A

value: CR [(pathological) complete response]

tag: ihc pr percentage

tag: intrinsic molecular subtype

tag: treatment

value: PTC

tag: clinical subtype

value: breast cancer tumor


title: PR+NR breast cancer BC_4531933043_E

value: PR+NR [Partial Response + No Response]

value: PD [progressive disease]


title: Patient 10

hyb_protocol: Hybridized for 16 h at 37 C with rotary shaking (250 rpm). Hybridization buffer and washing protocol were according to the protocol supplied by TORAY Industries, Inc.

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0 (Axon Instruments).

data_processing: F635 Median column as Red signal. The raw Red signal data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots' signal intensities of 95% confidence intervals. The raw Red signal data intensities greater than 2 standard deviations (SDs) of the background signal intensity were considered to be valid. Detected signals for each gene were normalized by the global normalization method (the median of the detected signal intensity was adjusted to 20).

source_name: Bone marrow, gastric adenocarcinoma stage IV

label_protocol: Amino Allyl aRNA was synthesized by the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion #1753). CyeDye coupling and fragmentation were performed as per the protocol supplied by TORAY Industries, Inc.

growth_protocol: Bone marrow samples were stored at -80℃ until RNA extraction.

extract_protocol: RNA samples were extracted from cells using the RNeasy mini kit (Qiagen).

value: bone marrow

tag: primary tumor

value: gastric adenocarcinoma

value: IV

tag: peritoneal dissemination

value: present


title: PR+NR breast cancer BC_4531933046_D

value: NOCR [No complete response]

value: Normal


title: F3 replicate 1

description: Fertile Chinese cabbage floral buds (2.5mm≤ buds ≤5.0 mm); after tetrad stage, but before mature pollen (replicate 1).


title: F2 replicate 2

description: Fertile Chinese cabbage floral buds (2.0mm≤ buds ≤2.5 mm); contain tetrad stage pollen grains (replicate 2).

value: 2.0mm≤ buds ≤2.5 mm

value: tetrad stage pollen grains


title: Lung Cancer Cell Line RVH6849

data_processing: CT values were determined using the SDS software (Life Technologies, Carlsbad, CA, USA) with automatic baseline and threshold settings.  The data was loaded into the R statistical environment (v2.14.0) and pre-processed.  Triplicate CT values were averaged and normalized to the geometric mean of hsa-let-7g, hsa-miR-191 and hsa-miR-335-3p, which were selected as endogenous controls.  CT values greater than 36 were considered to be below the limit of detection.  Fold changes were calculated as Xenograft-Cell Line.  Matrix non-normalized contains the mean of triplicate raw CT values.  Matrix normalized contains log2|2^-ΔCT| values; where ΔCT = CT_target - CT_endogenous_controls.  Fold Change contains CT values of xenografts compared to CT values of cell lines (ΔCT_xenograft - ΔCT_cell_line).

label: FAM

source_name: Total RNA from RVH6849 cells

label_protocol: cDNA for each miRNA of interest was synthesized from an input of five nanograms total RNA using the TaqMan® microRNA Reverse Transcription Reagents and specific reverse transcription primers (Life Technologies, Carlsbad, CA, USA).  Real-time PCR with TaqMan® probes was performed on a Life Technologies ViiA™ 7 Real-Time PCR System (Life Technologies, Carlsbad, CA, USA) using the following conditions: 10 min at 95°C, followed by 40 cycles of 95°C for 30 sec and 60°C for 1 min.  All assays were performed in triplicates.

growth_protocol: Cells were cultured in RPMI-1640, supplemented with 10% FBS and 1X Penicillin/Streptomycin.  Xenografts were grown by subcutaneous injection of two million trypsin-dissociated tumor cells into non-obese diabetic/severe combinted immunodeficient mice.

extract_protocol: Total RNA was isolated from confluent cell lines or fresh-frozen xenograft tissues using Trizol reagent (Life Technologies, Carlsbad, CA, USA) according to the manufacturer's instructions, followed by DNase I treatment (Life Technologies) and purification using the Qiagen RNeasy kit (Qiagen, Venlo, Netherlands).  RNA quantity and quality was assessed using the Qubit Fluorometer (Life Technologies), NanoDrop 1000 (Nanodrop Technologies, Wilmington, DE, USA), and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

tag: cell line


title: Patient 9

tag: Stage


title: OSCC sample7

source_name: oral squamous cell carcinoma tissue 7

tag: age

tag: Sex

value: male

value: Ⅱ

tag: region

value: tongue

tag: clinical stage

value: well differentiated


title: PR+NR breast cancer BC_4531933046_A

tag: response breast

tag: response

tag: ihc er percentage


title: OSCC sample3

source_name: oral squamous cell carcinoma tissue 3

value: Ⅲ

tag: differentiation


title: OSCC sample5

source_name: oral squamous cell carcinoma tissue 5

value: female

value: gingiva

value: moderately


title: OSCC sample4

source_name: oral squamous cell carcinoma tissue 4


title: Lung Xenograft H460

source_name: Total RNA from H460 xenograft


title: Lung Xenograft H520

source_name: Total RNA from H520 xenograft


title: Lung Cancer Cell Line H460

source_name: Total RNA from H460 cells


title: OSCC sample2

source_name: oral squamous cell carcinoma tissue 2


title: Lung Xenograft RVH6849

source_name: Total RNA from RVH6849 xenograft


title: Patient 4

source_name: Bone marrow, gastric adenocarcinoma stage III

tag: tissue

value: III

value: absent


title: F2 replicate 1

description: Fertile Chinese cabbage floral buds (2.0mm≤ buds ≤2.5 mm); contain tetrad stage pollen grains (replicate 1).

value: floral bud

tag: phenotype

value: fertile

tag: size

tag: developmental stage


title: Patient 7

value: bone marrow

value: gastric adenocarcinoma

value: IV

value: present


title: Patient 8


title: S3 replicate 2

description: Sterile Chinese cabbage floral buds (>2.5 mm); contain aberrant pollen grains (replicate 2).

source_name: Sterile Chinese cabbage floral buds

value: sterile

value: aberrant pollen grains


title: Oral dysplasia sample8

source_name: oral dysplasia 8

value: male

value: Ⅱ


title: Patient 5


title: F1 replicate 1

description: Fertile Chinese cabbage floral buds (<2.0 mm); contain before tetrad stage pollen grains (replicate 1).

value: before tetrad stage pollen grains


title: pCR+npCR mamma breast cancer BC_4531933092_F

source_name: 14G core needle breast tumor biopsy

value: pCR+npCR mamma [pathological complete response + near pathological complete response mamma]

value: CR [(pathological) complete response]

tag: ihc pr percentage

tag: intrinsic molecular subtype

tag: treatment

value: PTC

tag: clinical subtype

value: breast cancer tumor


title: Patient 6

tag: primary tumor

tag: Stage

tag: peritoneal dissemination


title: F1 replicate 2

description: Fertile Chinese cabbage floral buds (<2.0 mm); contain before tetrad stage pollen grains (replicate 2).


title: pCR+npCR mamma breast cancer BC_4531933069_B

value: CR+kl [(pathological) complete response breast, positive lymph nodes]

value: LumA


title: Oral dysplasia sample4

source_name: oral dysplasia 4

tag: age

tag: Sex

value: female

tag: region

value: buccal

value: Tis

value: verrucos


title: Lung Cancer Cell Line H1264

source_name: Total RNA from H1264 cells

tag: cell line


title: Lung Xenograft H1264

source_name: Total RNA from H1264 xenograft


title: S3 replicate 1

description: Sterile Chinese cabbage floral buds (>2.5 mm); contain aberrant pollen grains (replicate 1).

value: floral bud


title: pCR+npCR mamma breast cancer BC_4531933069_F

tag: response breast

tag: response

tag: ihc er percentage


title: OSCC sample1

source_name: oral squamous cell carcinoma tissue 1

value: Ⅳ

value: palate

tag: clinical stage

tag: differentiation

value: well differentiated


title: Oral dysplasia sample7

source_name: oral dysplasia 7

value: male

value: Ⅰ

value: tongue


title: Patient 3

tag: tissue

value: bone marrow

value: gastric adenocarcinoma

value: III

value: absent


title: Lung Xenograft A549

source_name: Total RNA from A549 xenograft


title: Lung Cancer Cell Line A549

source_name: Total RNA from A549 cells


title: OSCC sample6

source_name: oral squamous cell carcinoma tissue 6

value: floor of mouth


title: Lung Cancer Cell Line H520

source_name: Total RNA from H520 cells


title: S2 replicate 1

description: Sterile Chinese cabbage floral buds (1.5 mm≤ buds ≤2.5 mm); contain tetrad stage pollen grains (replicate 1).

tag: phenotype

value: sterile

tag: size

value: 1.5 mm≤ buds ≤2.5 mm

tag: developmental stage

value: tetrad stage pollen grains


title: Oral dysplasia sample6

source_name: oral dysplasia 6

value: female

value: Ⅱ


title: S2 replicate 2

description: Sterile Chinese cabbage floral buds (1.5 mm≤ buds ≤2.5 mm); contain tetrad stage pollen grains (replicate 2).

value: floral bud


title: Patient 2


title: Patient 1


title: Oral dysplasia sample5

source_name: oral dysplasia 5


title: Oral dysplasia sample1

source_name: oral dysplasia 1


title: Oral dysplasia sample2

source_name: oral dysplasia 2

value: moderately


title: Articular cartilage tissue from the condylus medialis femoris GeneFL22

status: Public on Oct 21 2013

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz Institute for Farm Animal Biology (FBN)

description: Gene expression data from articular cartilage tissues of a Duroc x Pietrain crossbreed population

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42°C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

organism: Sus scrofa

source_name: Articular cartilage surface

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: status of osteochondrosis disoder

value: non-affected


title: Articular cartilage tissue from the medial part of condylus humeri GeneFL21

value: affected


title: Articular cartilage tissue from the medial part of condylus humeri GeneFL20


title: S1 replicate 2

description: Sterile Chinese cabbage floral buds (<1.5 mm); contain before tetrad stage pollen grains (replicate 2).

source_name: Sterile Chinese cabbage floral buds

value: before tetrad stage pollen grains


title: Articular cartilage tissue from the medial part of condylus humeri GeneFL17


title: Oral dysplasia sample3

source_name: oral dysplasia 3

value: gingiva

value: well differentiated


title: Articular cartilage tissue from the medial part of condylus humeri GeneFL18


title: S1 replicate 1

description: Sterile Chinese cabbage floral buds (<1.5 mm); contain before tetrad stage pollen grains (replicate 1).


title: Articular cartilage tissue from the medial part of condylus humeri GeneFL16


title: Articular cartilage tissue from the condylus medialis femoris GeneFL14


title: Articular cartilage tissue from the condylus medialis femoris GeneFL23


title: Articular cartilage tissue from the medial part of condylus humeri GeneFL19


title: Articular cartilage tissue from the condylus medialis femoris GeneFL13


title: Articular cartilage tissue from the medial part of condylus humeri GeneFL15


title: Articular cartilage tissue from the condylus medialis femoris GeneFL10


title: Articular cartilage tissue from the medial part of condylus humeri GeneFL12


title: Articular cartilage tissue from the condylus medialis femoris GeneFL4


title: Articular cartilage tissue from the medial part of condylus humeri GeneFL11


title: Articular cartilage tissue from the medial part of condylus humeri GeneFL6


title: Articular cartilage tissue from the medial part of condylus humeri GeneFL8


title: Articular cartilage tissue from the medial part of condylus humeri GeneFL2


title: Articular cartilage tissue from the condylus medialis femoris GeneFL9


title: Articular cartilage tissue from the medial part of condylus humeri GeneFL7


title: Articular cartilage tissue from the condylus medialis femoris GeneFL5


title: Articular cartilage tissue from the condylus medialis femoris GeneFL3


title: NCI10314

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Drive, CB 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-213

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were analyzed with Agilent software.

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken

source_name: Human Reference B

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-208

extract_protocol: Qiagen Rneasy Mini

tag: reference

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

source_name: Normal Tissue Adjacent to Breast Tumor

tag: mammographic density

tag: mammographic dense area

tag: microenvironment subtype

value: Active;Stromal proportion_tertile1;Epithelial proportion_tertile2;Adipose proportion_tertile3


title: NCI10240

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-195

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-190

value: Inactive;Stromal proportion_tertile3;Epithelial proportion_tertile1;Adipose proportion_tertile1


title: Articular cartilage tissue from the medial part of condylus humeri GeneFL1


title: NCI10242

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-196

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-191

value: Active;Stromal proportion_tertile1;Epithelial proportion_tertile1;Adipose proportion_tertile3


title: NCI10233

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-192

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-187

value: Inactive;Stromal proportion_tertile2;Epithelial proportion_tertile3;Adipose proportion_tertile2


title: NCI10246

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-199

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-194

value: Inactive;Stromal proportion_tertile2;Epithelial proportion_tertile2;Adipose proportion_tertile2


title: NCI10235

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-193

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-188

value: Active


title: NCI10247

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-200

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-195

value: Inactive;Stromal proportion_tertile3;Epithelial proportion_tertile2;Adipose proportion_tertile1


title: NCI10254

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-202

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-197

value: Inactive;Stromal proportion_tertile2;Epithelial proportion_tertile1;Adipose proportion_tertile2


title: NCI10259

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-203

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-198

value: Active;Stromal proportion_tertile2;Epithelial proportion_tertile3;Adipose proportion_tertile2


title: NCI10308

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-210

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-205

value: Active;Stromal proportion_tertile1;Epithelial proportion_tertile3;Adipose proportion_tertile2


title: NCI10286

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-207

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-202


title: NCI10230

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-190

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-185


title: NCI10304

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-209

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-204

value: Inactive


title: NCI10309

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-211

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-206


title: NCI10206

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-186

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-181


title: NCI10276

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-205

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-200


title: NCI10243

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-197

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-192


title: NCI10310

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-212

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-207

value: Active;Stromal proportion_tertile1;Epithelial proportion_tertile3;Adipose proportion_tertile3


title: NCI10284

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-206

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-201


title: NCI10194

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-181

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-176


title: NCI10196

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-182

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-177


title: NCI10188

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-179

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-174


title: NCI10231

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-191

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-186

value: Active;Stromal proportion_tertile2;Epithelial proportion_tertile1;Adipose proportion_tertile3


title: NCI10269

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-204

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-199


title: NCI10198

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-184

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-179


title: NCI10225

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-189

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-184

value: Inactive;Stromal proportion_tertile3;Epithelial proportion_tertile3;Adipose proportion_tertile1


title: NCI10244

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-198

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-193


title: NCI10189

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-180

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-175


title: NCI10175

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-178

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-173


title: NCI10171

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-176

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-171


title: NCI10174

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-177

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-172


title: NCI10169

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-175

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-170


title: NCI10161

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-172

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-167


title: NCI10317

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-214

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-209


title: NCI10122

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-159

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-154


title: NCI10163

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-173

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-168


title: NCI10156

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-171

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-166


title: NCI10130

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-160

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-155


title: NCI10115

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-156

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-151


title: NCI10131

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-161

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-156


title: NCI10119

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-157

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-152


title: NCI10149

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-169

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-164


title: NCI10108

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-154

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-149


title: NCI10066

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-142

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-137


title: NCI10070

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-143

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-138

value: Inactive;Stromal proportion_tertile3;Epithelial proportion_tertile2;Adipose proportion_tertile2


title: NCI10138

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-165

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-160


title: NCI10077

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-148

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-143


title: NCI10145

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-167

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-162


title: NCI10097

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-152

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-147


title: NCI10091

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-150

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-145


title: NCI10044

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-136

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-131


title: NCI10083

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-149

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-144


title: NCI10060

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-139

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-134

value: Active;Stromal proportion_tertile2;Epithelial proportion_tertile1;Adipose proportion_tertile2


title: NCI10104

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-153

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-148

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: NCI10168

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-174

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-169


title: NCI10691

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-273

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-268


title: NCI10062

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-140

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-135


title: NCI10701

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-275

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-270

value: Active;Stromal proportion_tertile2;Epithelial proportion_tertile3;Adipose proportion_tertile1


title: NCI10075

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-146

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-141

value: Active;Stromal proportion_tertile1;Epithelial proportion_tertile2;Adipose proportion_tertile3


title: NCI10150

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-170

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-165

value: Active;Stromal proportion_tertile1;Epithelial proportion_tertile1;Adipose proportion_tertile3


title: NCI10547

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-266

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-261


title: ECSC_VPA and 5aza-treated_rep4

city: Yufu city

first: Yukie

last: Kawano

state: Oita

address: idaigaoka 1-1

department: Obstetrics and Gynecology

institute: Oita University

description: cells were incubated for 72 h with VPA and 5aza

hyb_protocol: Gene Expression Hybridization kit was used for hybridization in accordance with the manufacture's instructions (Agilent Technologies).

scan_protocol: Microarray images were obtained by using a laser confocal scanner G2565BA (Agilent Technologies).

data_processing:
Feature Extraction software (Version 9.5.3.1, Agilent Technologies) with the manufacturer’s recommended settings was applied for the microarray image analysis.
The resulting data were subsequently imported into GeneSpring GX software version 11.5 (Agilent Technologies) to yield gene expression profiles. To eliminate the mRNAs which are not expressed in either untreated ECSCs or VPA-treated ECSCs, mRNAs were filtered based on raw signal intensity (100<, at least 50% of each group has values within range) and flag (at least 50% cases have good flags), and then 18,621 were left. The data for a given mRNA were then normalized  to the median of that mRNA in the four untreated ECSCs. Among the 18,621 mRNAs, differentially expressed mRNAs were identified statistically by using a filter based on a fold change of >5.0 combined with the Student t-test (p< 0.05) (Volcano plot), with the Benjamini-Hochberg adjustment for false discovery rate (FDR).

source_name: ECSC, VPA and 5aza-treated, replicate 4

label_protocol: Total RNA was labeled with Cy3 and amplified with the Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) and subjected to a microarray analysis.

growth_protocol: Endometriotic tissues were obtained from premenopausal patients who had undergone a salpingo-oophorectomy or evisceration for the treatment of ovarian endometriotic cysts (n=25, aged 30-39 years). Normal endometrial tissues were obtained from premenopausal patients who had undergone hysterectomies for subserosal leiomyoma and had no evidence of endometriosis (n=22, aged 37-41 years). Endometriotic tissues (n=5) and normal endometrial tissues (n=5) were fixed in 7% neutral buffered formaldehyde solution, embedded in paraffin, and processed for immunohistochemical staining. Isolated ECSCs and NESCs were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 100 IU/ml of penicillin, 50 mg/ml of streptomycin, and 10% 21 heat-inactivated fetal bovine serum (FBS) (all obtained from Gibco-BRL, Gaithersburg, MD, USA) at 37°C in 5% CO2 in air.

extract_protocol: Total RNA from untreated ECSCs (n=4), VPA-treated ECSCs (n=4), 5aza-treated ECSCs (n=4) and VPA and 5aza-treated ECSCs (n=4) was extracted with the RNeasy Mini kit (Qiagen, Valencia, CA, USA) and subjected to a gene expression microarray analysis.

treatment_protocol: Subconfluent ECSCs cultured in 10-cm dishes (Corning, New York, NY, USA) were further incubated for 72 h with or without VPA (8 mM).

tag: cell type

value: primary cell type of endometriotic cyst stromal cells (ESCS)


title: NCI10555

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-268

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-263

value: Inactive;Stromal proportion_tertile2;Epithelial proportion_tertile2;Adipose proportion_tertile2


title: NCI10550

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-267

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-262

value: Active


title: NCI10522

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-265

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-260

value: Inactive;Stromal proportion_tertile1;Epithelial proportion_tertile2;Adipose proportion_tertile3


title: NCI10689

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-272

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-267


title: ECSC_VPA and 5aza-treated_rep3

source_name: ECSC, VPA and 5aza-treated, replicate 3


title: ECSC_5aza-treated_rep4

description: cells were incubated for 72 h with 5-aza-2'-deoxycytidine (5aza)

source_name: ECSC, 5aza-treated, replicate 4


title: NCI10148

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-168

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-163

value: Inactive;Stromal proportion_tertile3;Epithelial proportion_tertile1;Adipose proportion_tertile1


title: ECSC_VPA and 5aza-treated_rep2

source_name: ECSC, VPA and 5aza-treated, replicate 2


title: NCI10683

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-269

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-264


title: NCI10518

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-263

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-258


title: ECSC_5aza-treated_rep3

source_name: ECSC, 5aza-treated, replicate 3


title: ECSC_5aza-treated_rep2

source_name: ECSC, 5aza-treated, replicate 2


title: NCI10692

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-274

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-269


title: NCI10511

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-261

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-256

value: Active;Stromal proportion_tertile3;Epithelial proportion_tertile2;Adipose proportion_tertile1


title: ECSC_VPA-treated_rep4

description: cells were incubated for 72 h with 11mM VPA

data_processing:
Feature Extraction software (Version 9.5.3.1, Agilent Technologies) with the manufacturer’s recommended settings was applied for the microarray image analysis.
The resulting data were subsequently imported into GeneSpring GX software version 11.5 (Agilent Technologies) to yield gene expression profiles. To eliminate the mRNAs which are not expressed in either untreated ECSCs or VPA-treated ECSCs, mRNAs were filtered based on raw signal intensity (100<, at least 50% of each group has values within range) and flag (at least 50% cases have good flags), and then 18,621 were left. The data for a given mRNA were then normalized to the median of that mRNA in the four untreated ECSCs. Among the 18,621 mRNAs, differentially expressed mRNAs were identified statistically by using a filter based on a fold change of >5.0 combined with the Student t-test (p< 0.05) (Volcano plot), with the Benjamini-Hochberg adjustment for false discovery rate (FDR).

source_name: ECSC, VPA-treated, replicate 4

extract_protocol: Total RNA from untreated ECSCs (n=4) and VPA-treated ECSCs (n=4) was extracted with the RNeasy Mini kit (Qiagen, Valencia, CA, USA) and subjected to a gene expression microarray analysis.


title: ECSC_VPA-treated_rep3

description: cells were incubated for 72 h with 10mM VPA

source_name: ECSC, VPA-treated, replicate 3


title: ECSC_5aza-treated_rep1

source_name: ECSC, 5aza-treated, replicate 1


title: ECSC_VPA and 5aza-treated_rep1

source_name: ECSC, VPA and 5aza-treated, replicate 1


title: NCI10513

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-262

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-257


title: ECSC_VPA-treated_rep2

description: cells were incubated for 72 h with 9mM VPA

source_name: ECSC, VPA-treated, replicate 2


title: NCI10520

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-264

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-259

value: Inactive;Stromal proportion_tertile2;Epithelial proportion_tertile3;Adipose proportion_tertile1


title: NCI10505

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-258

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-253

value: Active;Stromal proportion_tertile2;Epithelial proportion_tertile3;Adipose proportion_tertile2


title: NCI10486

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-255

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-250


title: NCI10506

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-259

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-254

value: Inactive;Stromal proportion_tertile3;Epithelial proportion_tertile2;Adipose proportion_tertile1


title: NCI10482

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-253

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-248


title: NCI10498

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-257

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-252


title: NCI10685

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-270

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-265


title: ECSC_untreated_rep3

description: untreated

hyb_protocol: Gene Expression Hybridization kit was used for hybridization in accordance with the manufacture's instructions (Agilent Technologies).

source_name: ECSC, untreated, replicate 3

label_protocol: Total RNA was labeled with Cy3 and amplified with the Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) and subjected to a microarray analysis.


title: ECSC_VPA-treated_rep1

description: cells were incubated for 72 h with 8mM VPA

source_name: ECSC, VPA-treated, replicate 1


title: ECSC_untreated_rep4

description: untreated

source_name: ECSC, untreated, replicate 4


title: ECSC_untreated_rep2

description: untreated

source_name: ECSC, untreated, replicate 2


title: ECSC_untreated_rep1

description: untreated

source_name: ECSC, untreated, replicate 1


title: NCI10465

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-251

source_name: Human Reference B

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-246

source_name: Normal Tissue Adjacent to Breast Tumor


title: NCI10455

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-250

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-245

value: Inactive;Stromal proportion_tertile2;Epithelial proportion_tertile3;Adipose proportion_tertile2


title: NCI10469

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-252

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-247


title: Hmeso MM line transfected with shCon, biological rep 2

city: Burlington

first: Arti

last: Shukla

state: VT

address: 89 Beaumont Avenue

department: Pathology

institute: University of Vermont

description:
Gene expression data in epithelioid mesothelioma cell line transfected with shCon plasmid
Transfected MM lineERK1>70% inhibited

hyb_protocol: Biotin-labeled cDNA fragments that were hybridized to the probe array at 45 oC for 16 h.

scan_protocol: The probe array were scanned (Affymetrix GeneArray Scanner, GS3000) to quantify the fluorescence intensity associated with each oligonucleotide probe

data_processing: A human U133A 2.0 array was scanned twice, the images overlaid, and the average intensities of each probe cell compiled. Microarray data were analyzed using GeneSifter software (VizX Labs, Seattle, WA) by RMA method. Data were log transformed.

source_name: Stable transfection with shCon SureSilencing plasmid

label_protocol: RNA was synthesized to ds cDNA which was then converted to amplified ss cDNA using a Nugen Ovation V2 system. ss cDNA was Biotinylated using TdT end label.

growth_protocol: All cells were incubated at 37oC and 5% CO2 and grown to approximately 80-90% confluency in DMEM/F12 medium at a 1:1 ratio containing 10% fetal bovine serum (FBS), 0.1 ug/ml hydrocortisone, 2.5 ug/ml insulin, 2.5 ug/ml transferrin and 2.5 ng/ml sodium selenite and penicillin-streptomycin (50 U/ml penicillin G, 50 ug/ml streptomycin sulfate)

extract_protocol: Total RNA was extracted from cells using an RNeasy Plus Mini kit according to the manufacturer's protocol (Qiagen, Valencia, CA). RNA was dissolved in RNAs free water and quantified using the NanoDrop spectrophotometer.

treatment_protocol: In order to obtain CREB inhibition human malignant mesothelioma cells were transfected with SureSilencing CREB1 plasmid (SuperArray Biosciences) using Lipofectamine 2000. After selecting for 15 days in G418 (400ug/ml) containing medium, limited dilution was performed to obtain clones showing ≥70% inhibition.

value: epithelioid mesothelioma cell line HMESO

tag: genotype/variation

value: control


title: 59A - rep 1

city: Montpellier

first: Bruno

last: Blondin

address: 2 place Pierre Viala

country: France

institute: INRA

description: Gene expression in sample 59A, biological rep 1

hyb_protocol: Agilent gene expression microarrays 8x15k was used for the micro array hybridization, with one-color method. Array design is based on ID 016322 completed with the 39 genes from the new region of EC1118 (Agilent Technologies, Santa Clara, CA, USA). A quantity of 600ng of labeled cRNA were hybridized for 17h in 65°C in a rotative hybridization oven (Corning) using the Expression Hybridization kit (Agilent Technologies, 5188-5242). Plate were washed with expression wash buffer kit (Agilent Technologies, 5188-5325 5188-5326).

scan_protocol: The array pictures were analyzed on a GenePix 4000B laser Scanner (Axon Instruments) and with the GenePix software PRO7

data_processing: Data normalization and statistical analysis were performed using R 2.13.1 software and the limma package. Normalization was done by the quantile method considering all arrays

organism: Saccharomyces cerevisiae

label_protocol: Cy3-labeled cRNA was synthesized with the One color RNA Spike-In kit (Agilent Technologies) and purified with RNeasy kit (Qiagen). Quality and quantity of RNA were controlled at each step by spectrometry (NanoDrop 1000, Thermo Scientific)

growth_protocol: Fermentations were performed in a synthetic SM425 medium (with 425mg/L of assimilate nitrogen pH3.3 and previously described as SM300, Bely et al, 1990) which mimics natural grape must. This medium was supplemented by 1mg/L of p-aminobenzoic acid and 14.5mg/L of iron(III) chloride. Cells sampling for RNA extraction was performed at 66gCO2/L release (70% of fermentation advancement) in stationary phase.

extract_protocol: Total RNA extraction were perform with Trizol reagent (Gibco BRL, Life Technologies), purified by isopropanol precipitation then with RNeasy kit (Qiagen).

treatment_protocol: For each condition, 10E9 cells were sampled, pelleted, washed with DEPC-treated water and freeze in methanol at -80°C.

tag: strain

tag: genotype

value: wildtype

tag: array

tag: block


title: Mill MM line transfected with shCon, biological rep 2

description:
Gene expression data in fibrosarcomatoid mesothelioma cell line transfected with shCon plasmid
Transfected MM line

tag: cell line

value: fibrosarcomatoid mesothelioma cell line H2373/PPMMill


title: Hmeso MM line transfected with shCREB1, biological rep 1

description:
Gene expression data in CREB1 inhibited epithelioid mesothelioma cell line
CREB1>70% inhibited

source_name: Stable transfection with shCREB1 SureSilencing plasmid

value: CREB inhibition


title: Hmeso MM line transfected with shCREB1, biological rep 2


title: Mill MM line transfected with shCREB1, biological rep 1

description:
Gene expression data in CREB1 inhibited fibrosarcomatoid mesothelioma cell line
CREB1>70% inhibited


title: NCI10440

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-248

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-243

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

value: Inactive


title: Mill MM line transfected with shCon, biological rep 1


title: NCI10437

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-246

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-241

value: Active;Stromal proportion_tertile1;Epithelial proportion_tertile1;Adipose proportion_tertile3


title: NCI10441

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-249

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-244


title: NCI10422

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-242

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-237


title: NCI10432

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-245

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-240

value: Active;Stromal proportion_tertile2;Epithelial proportion_tertile1;Adipose proportion_tertile2


title: Yap_knockout_replicate_2

city: Philadelphia

first: Louise

middle: C

last: Showe

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

description: Yap knockout replicate 2

hyb_protocol: Standard Illumina hybridization protocol

data_processing: Gene expression levels and detection p-values were exported using Illumina's GenomeStudioV2010.1.  Raw data were quantile normalized and then filtered to remove non-informative probes either expressed at background level or showing little variation among samples (maximum fold change < 1.2).

source_name: HEK293 cells + Yap shRNA

label_protocol: Biotinylated cRNA were prepared using the Epicentre TargetAmp Nano-g Biotin-aRNA Labeling Kit for Illumina arrays

extract_protocol: Total RNA was isolated using the modified protocol of Sigma Aldrich Tri-reagent.

value: Yap knockout


title: Yap_knockout_replicate_1

description: Yap knockout replicate 1


title: 59A - rep 3

description: Gene expression in sample 59A, biological rep 3


title: NCI10438

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-247

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-242

value: Inactive;Stromal proportion_tertile2;Epithelial proportion_tertile1;Adipose proportion_tertile2


title: 59A - rep 2

description: Gene expression in sample 59A, biological rep 2


title: Mill MM line transfected with shCREB1, biological rep 2


title: Angiomotin_knockout_replicate_3

description: Angiomotin knockout replicate 3

source_name: HEK293 cells + Amot shRNA

value: Angiomotin knockout


title: NCI10423

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-243

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-238

value: Active;Stromal proportion_tertile1;Epithelial proportion_tertile2;Adipose proportion_tertile3


title: 59A PDR8-S288c - rep 1

description: Gene expression in sample 59A PDR8-S288c, biological rep 2


title: Angiomotin_knockout_replicate_2

description: Angiomotin knockout replicate 2


title: 59A PDR8-S288c - rep 3

description: Gene expression in sample 59A PDR8-S288c, biological rep 3


title: Wild_type_replicate_3

description: Wild type replicate 3

source_name: HEK293 cells

value: wild type


title: NCI10420

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-241

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-236


title: 59A PDR8-S288c - rep 2

description: Gene expression in sample 59A PDR8-S288c, biological rep 1


title: NCI10409

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-239

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-234


title: Angiomotin_knockout_replicate_1

description: Angiomotin knockout replicate 1


title: Hmeso MM line transfected with shCon, biological rep 1


title: Wild_type_replicate_1

description: Wild type replicate 1


title: Wild_type_replicate_2

description: Wild type replicate 2


title: L12_B7_29b

description: Gene expression in sample 29b

growth_protocol: Fermentations were done in a synthetic SM425 medium (with 425mg/L of assimilate nitrogen pH3.3 and previously describe as SM300, Bely et al, 1990) which mimics natural grape must. This medium was supplemented by 1mg/L of p-aminobenzoic acid and 14.5mg/L of iron(III) chloride. Cells sample for RNA extraction was performed at 66gCO2/L release (70% of fermentation advancement) in stationary phase.

value: segregate 29b


title: Yap_knockout_replicate_3

description: Yap knockout replicate 3


title: NCI10410

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-240

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-235

value: Inactive;Stromal proportion_tertile2;Epithelial proportion_tertile2;Adipose proportion_tertile3


title: NCI10408

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-238

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-233

value: Inactive;Stromal proportion_tertile2;Epithelial proportion_tertile3;Adipose proportion_tertile2


title: L12_B8_26c

description: Gene expression in sample 26c

value: segregate 26c


title: MDA-MB-231-Drosha-sh_2

city: Memphis

first: Meiyun

last: Fan

address: 19 S. Manassas Street

institute: University of Tennessee

description:
8508853001_F
Replicate 2 of 2.

hyb_protocol: Biotinylated cRNA were hybridized to the Illumina array per manufacturer's instructions.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Illumina GenomeStudio software was used for data processing: background subtraction and quantile normalization.

source_name: DROSHA-sh

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol.

growth_protocol: Cells were maintained in MEM medium (Invitrogen, Carlsbad, CA, USA) supplemented with 10% FBS and 100 units/ml penicillin.

extract_protocol: Total RNA in cell lysates was prepared using Trizol according to the manufacturer's instructions.

treatment_protocol: Cells were untreated.

value: basal-like breast cancer cells

tag: shRNA expression

value: DROSHA


title: MDA-MB-231-DROSHA-sh_1

description:
8508853001_E
Replicate 1 of 2.


title: MB23-DICER1-sh_2

description:
8508853001_D
Replicate 2 of 2.


title: MB23-DICER1-sh_1

description:
8508853001_C
Replicate 1 of 2.


title: L12_B3_31b

description: Gene expression in sample 31b

value: segregate 31b


title: L12_B5_5c

description: Gene expression in sample 5c

value: segregate 5c


title: L12_B4_S288Cs5

description: Gene expression in sample S288C, biological rep 2, technical rep 3

value: parent S288C


title: MDA-MB-231_2

description:
8508853001_B
Replicate 2 of 2.

source_name: Control

value: control


title: L12_B2_28c

description: Gene expression in sample 28c

value: segregate 28c


title: NCI10406

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-237

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-232

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

value: Active;Stromal proportion_tertile1;Epithelial proportion_tertile1;Adipose proportion_tertile3


title: L12_B6_S288Cs1

description: Gene expression in sample S288C, biological rep 1, technical rep 3


title: NCI10404

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-236

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-231


title: NCI10402

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-235

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-230

value: Active;Stromal proportion_tertile1;Epithelial proportion_tertile3;Adipose proportion_tertile3


title: shRNA 691 R6 T5

city: Seattle

first: Nathan

last: Palpant

state: WA

address: 850 Republican St

institute: University of Washington

description: SAMPLE 3

data_processing: The complete set of microarray data was assessed for quality, followed by quantile normalization using the Bioconductor package lumi.  The dataset was initially filtered by flagging probes that were below a signal 'noise floor,' which was established using the 75th percentile of the negative control probe signals within each array.  We subsequently filtered the dataset by employing a variance filter using the 'shorth' function of the Bioconductor package genefilter.  Pair-wise statistical analyses was performed using Bioconductor v. 2.10, limma v.3.12.3, lumi v.2.8.0.

source_name: RUES2_shRNA TMEM88

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Cardiac differentiation of hES cells is as described by Laflamme et al Nature Biotechnology 2007

extract_protocol: Samples were isolated using Qiagen RNease kit

value: human embryonic stem cells

tag: transduced with

value: shRNA targeting TMEM88

tag: time point

value: Day 5 of cardiac differentiation; cardiovascular progenitor cell stage


title: NCI10394

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-234

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-229


title: MDA-MB-231_1

description:
8508853001_A
Replicate 1 of 2.


title: shRNA control R2 T5

description: SAMPLE 2

source_name: RUES2_shRNA control

value: control shRNA


title: Knockdown_day12_rep2

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

institute: National Institutes for Quantum and Radiological Science and Technology

description: Gene expression in 3D culture of knockdown cells at day 12

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >11.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing Agilent fragmentation buffer and Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 50 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014850_D_F_20110819) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Knockdown cells_day12_replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the One-Color Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were cultured in a 1:1 mix of DME and Ham’s F12 media supplemented with 2% equine serum, 10 ug/ml insulin, 5 ng/ml EGF, 100 ng/ml cholera toxin, 0.5 ug/ml hydrocortisone, and 2% reconstituted basement membrane (Matrigel; BD Bioscuences).

extract_protocol: RNA was prepared using the AllPrep DNA/RNA Mini kit (QIAGEN) following the manufacturer's recommendations.

value: BRIP1 knockdown

tag: day


title: L12_B1_29c

description: Gene expression in sample 29c

hyb_protocol: Agilent gene expression microarrays 8x15k was used for the micro array hybridization, with one-color method. Array design is based on ID 016322 completed with the 39 genes from the new region of EC1118 (Agilent Technologies, Santa Clara, CA, USA). A quantity of 600ng of labeled cRNA were hybridized for 17h in 65°C in a rotative hybridization oven (Corning) using the Expression Hybridization kit (Agilent Technologies, 5188-5242). Plate were washed with expression wash buffer kit (Agilent Technologies, 5188-5325 5188-5326).

label_protocol: Cy3-labeled cRNA was synthesized with the One color RNA Spike-In kit (Agilent Technologies) and purified with RNeasy kit (Qiagen). Quality and quantity of RNA were controlled at each step by spectrometry (NanoDrop 1000, Thermo Scientific)

value: segregate 29c


title: shRNA 94 R7 T5

description: SAMPLE 4

scan_protocol: Standard Illumina scanning protocol


title: NCI10392

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-233

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-228

value: Active


title: Knockdown_day8_rep3

description: Gene expression in 3D culture of nockdown cells at day 8

source_name: Knockdown cells_day8_replicate 3


title: Control_day12_rep1

description: Gene expression in 3D culture of control cells at day 12

source_name: Control_day12 cells_replicate 1

value: HMEC


title: Control_day12_rep2

source_name: Control_day12 cells_replicate 2


title: NCI10375

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-230

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-225

value: Inactive


title: Knockdown_day12_rep3

source_name: Knockdown cells_day12_replicate 3


title: NCI10370

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-229

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-224

value: Inactive;Stromal proportion_tertile3;Epithelial proportion_tertile1;Adipose proportion_tertile1


title: L11_B7_28b

description: Gene expression in sample 28b

value: segregate 28b


title: NCI10377

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-231

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-226

value: Active;Stromal proportion_tertile3;Epithelial proportion_tertile3;Adipose proportion_tertile1


title: Control_day12_rep3

source_name: Control_day12 cells_replicate 3


title: Knockdown_day12_rep1

source_name: Knockdown cells_day12_replicate 1


title: L11_B8_S288Cs5

description: Gene expression in sample S288C, biological rep 2, technical rep 2

value: parent S288C


title: L11_B6_24a

description: Gene expression in sample 24a

value: segregate 24a


title: NCI10365

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-226

source_name: Human Reference B

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-221

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

source_name: Normal Tissue Adjacent to Breast Tumor


title: NCI10362

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-225

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-220

value: Inactive;Stromal proportion_tertile2;Epithelial proportion_tertile2;Adipose proportion_tertile2


title: L11_B5_25a

description: Gene expression in sample 25a

value: segregate 25a


title: Control_day8_rep3

description: Gene expression in 3D culture of control cells at day 8

source_name: Control cells_day8_replicate 3


title: Knockdown_day8_rep2

description: Gene expression in 3D culture of knockdown cells at day 8

source_name: Knockdown cells_day8_replicate 2


title: Knockdown_day8_rep1

source_name: Knockdown cells_day8_replicate 1


title: L11_B4_23b

description: Gene expression in sample 23b

value: segregate 23b


title: L11_B3_23c

description: Gene expression in sample 23c

value: segregate 23c


title: NCI10352

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-224

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-219

value: Inactive;Stromal proportion_tertile3;Epithelial proportion_tertile2;Adipose proportion_tertile2


title: Control_day8_rep2

source_name: Control cells_day8_replicate 2


title: L11_B2_22c

description: Gene expression in sample 22c

value: segregate 22c


title: Control_day8_rep1

source_name: Control cells_day8_replicate 1


title: Control_day4_rep3

description: Gene expression in 3D culture of control cells at day 4

source_name: Control cells_day4_replicate 3


title: Knockdown_day4_rep1

description: Gene expression in 3D culture of knockdown cells at day 4

source_name: Knockdown cells_day4_replicate 1

value: BRIP1 knockdown


title: Knockdown_day4_rep3

source_name: Knockdown cells_day4_replicate 3


title: L11_B1_22d

description: Gene expression in sample 22d

value: segregate 22d


title: NCI10351

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-223

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-218

value: Inactive;Stromal proportion_tertile3;Epithelial proportion_tertile2;Adipose proportion_tertile1


title: Knockdown_day4_rep2

source_name: Knockdown cells_day4_replicate 2


title: Control_day4_rep2

source_name: Control cells_day4_replicate 2

value: HMEC


title: NCI10329

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-218

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-213

value: Inactive;Stromal proportion_tertile2;Epithelial proportion_tertile3;Adipose proportion_tertile2


title: NCI10340

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-221

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-216

value: Active;Stromal proportion_tertile3;Epithelial proportion_tertile1;Adipose proportion_tertile1


title: NCI10349

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-222

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-217


title: L10_B7_59As5

description: Gene expression in sample 59A, biological rep 2, technical rep 3

value: parent 59A


title: Oct4mGS#2, biological rep1

city: Kyoto

first: Seiji

last: Takashima

address: 53 Kawahara-cho, Shogoin, Sakyo

department: Department of Molecular Genetics

institute: Kyoto University

description: Gene expression data from mGS cells induced from GS cells by lentivirus-mediated transfection of Oct4 in combination with knock-down of p53.

hyb_protocol: Resultant labeled-cDNA were hybridized for 17 hr at 45C on Mouse Gene 1.0 ST Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning was performed with GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Plier normalization. Data analyses were performed using GeneSpring 12.0 software (Agilent Technologies, Inc., Santa Clara, CA). The probeset signals were calculated with the Plier algorithm. The annotation is based on na32 (mm9). The probesets that had low signals (less than 100) in all samples were excluded from the analysis. Statistical analysis was performed by one-way analysis of variance (ANOVA) with a Benjamini and Hochberg false discovery rate (BH-FDR = 0.05). The 12085 probes that showed more than 2-fold expression change in at least one pair of samples were subjected to hierarchical clustering (Distance metric: Pearson Centered, Linkage method: Average).

source_name: Oct4 mGS cells

label_protocol: For generating whole transcript sense target with label, purified total RNA were converted to sense strand cDNA using The Ambion WT Expression Kit for Affymetrix GeneChip Whole Transcript (WT) Expression Arrays (Applied Biosystems). Resultant cDNA samples were labeled using GeneChip WT terminal Labeling Kit (Affymetrix, Santa Clara, CA).

growth_protocol: All pluripotent cell lines were maintained on MEFs in Dulbecco modified Eagle medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 1000 U/ml LIF (ESGRO; Merck Millipore, Billerica, MA), non-essential amino acid mixture (Invitrogen, Carlsbad, CA), and 0.1 mM 2-mercaptoethanol (ME). GS cells were maintained on MMC-treated MEF feeder with StemPro-34 SFM (Invitrogen) supplemented with StemPro supplement (Invitrogen), 25 µg/ml insulin, 100 µg/ml transferrin, 60 µM putrescine, 30 nM sodium selenite, 6 mg/ml D-(+)-glucose, 30 µg/ml pyruvic acid, 1 µl/ml DL-lactic acid (Sigma, St Louis, MO), 5 mg/ml bovine albumin (ICN Biomedicals, Irvine, CA), 2 mM L-glutamine, 5 x 10-5 M 2-mercaptoethanol, minimal essential medium (MEM) vitamin solution (Invitrogen), MEM nonessential amino acid solution (Invitrogen), 10-4 M ascorbic acid, 10 µg/ml d-biotin, 30 ng/ml beta-estradiol, 60 ng/ml progesterone (Sigma), 10 ng/ml human basic fibroblast growth factor, 10 ng/ml recombinant rat glial cell line-derived neurotrophic factor (Peprotech, London, UK) and 1% fetal calf serum (JRH Biosciences, Lenexa, KS).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by purification with Rneasy Plus Mini kit (Qiagen).

treatment_protocol: Cultured cells were collected by trypsin-EDTA and incubated on 0.1% gelatin-coated dish for 30min to remove feeder cells. Resultant samples were pelletted and susupended in Trizol reagent (Invitrogen).

value: DBA/2; GFP Tg

value: Oct4 mGS cells

tag: treatment


title: Oct4mGS#3, biological rep2

value: lentivirus-mediated transfection of Oct4 in combination with knock-down of p53


title: Oct4mGS#3, biological rep1


title: L10_B6_21c

description: Gene expression in sample 21c

value: segregate 21c


title: L10_B5_22a

description: Gene expression in sample 22a

value: segregate 22a


title: L10_B8_22b

description: Gene expression in sample 22b

value: segregate 22b


title: L10_B4_20b

description: Gene expression in sample 20b

value: segregate 20b


title: NCI10331

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-219

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-214

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: Oct4mGS#2, biological rep2


title: NCI10320

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-216

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-211

value: Active;Stromal proportion_tertile1;Epithelial proportion_tertile1;Adipose proportion_tertile3


title: Oct4mGS#1, biological rep2


title: Sox2mGS#3, biological rep2

description: Gene expression data from mGS cells induced from GS cells by lentivirus-mediated transfection of Sox2 in combination with knock-down of p53.

source_name: Sox2 mGS cells

value: Sox2 mGS cells


title: Control_day4_rep1

source_name: Control cells_day4_replicate 1


title: NCI10327

description: Normal Tissue Adjacent to Breast Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-217

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-212

value: Inactive


title: Oct4mGS#1, biological rep1