title: ZC-53

status: Public on Apr 25 2016

city: Hangzhou

first: jianfie

last: fu

address: 88 Jiefang Road,

department: Cancer Institute

institute: The Second Affiliated Hospital of Zhejiang University School of Medicine

description: Gene expression of human primary tumor tissue in lymph node negative subgroup in the resectable stage IV colorectal cancer.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 52.8ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G2600D) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 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 (G2600D) 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 10.5 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: primary tumor, lymphnode negative subgroup, replicate 1

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.

extract_protocol: Total RNA isolation was done with TRIzol (Invitrogen, Carlsbad, CA) according to the instructions of the manufacturer. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: In our center, 15 patients with resectable mCRC were analyzed, with 7 patients in lymph node negative subgroup and 8 patients in lymph node positive subgroup. Fresh-frozen tissue samples of primary colorectal cancer were obtained. All tissue samples were collected and immediately snap-frozen in liquid nitrogen, and stored at -80˚C until RNA extraction. Written informed consent from each patient was obtained according to the institutional regulations.

tag: diagnosis

value: stage IV colorectal cancer

value: primary tumor

tag: subgroup

value: lymph node negative


title: DD.R3_alveolar structures_expression

status: Public on Apr 29 2016

type: RNA

city: Tomsk

first: Aleksei

middle: A

last: Sleptcov

state: Tomskaya oblasty

address: 10 Naberejnaya Ushaiki

country: Russia

institute: Research Institute of Medical Genetics

description:
gene expression of laser-microdissected breast tumor cells composing alveolar structures
Agilent DNA Microarray Scanner G2600D

hyb_protocol: 3.5 μg of the labeled cDNA were hybridized to SurePrint G3 Human GE v2, 8x60K microarrays (G4851B) for 24 h at 65°C in a rotating Agilent hybridization oven. The cDNA was not fragmented before hybridization. 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 G2600D using one color scan setting for 8x60k array slides. Images were quantified using Agilent Feature Extraction Software (version v. 10.7.3.1). Slides were scanned immediately after washing on the GenePix 4100A Scanner using one color scan setting for 8x60k array slides. Images were quantified using GenePix Pro 5.0 software.

data_processing: Agilent Feature Extraction Software (v. 10.7.3.1) was used for background subtraction and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Homo sapiens

source_name: breast tumor from the patient DD

label_protocol: 2 μg of cDNA samples was Cy3-labeled using the SureTag DNA labeling kit (Agilent Technologies, Inc., USA), followed by RNAeasy MinElute column purification (Qiagen, USA). Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol:
laser microdissection protocol: Different morphological structures were isolated from 5 um hematoxylin&eosin stained sections of three different frozen breast tumor samples using PALM MicroBeam laser capture microdissection (Carl Zeiss, Germany). Each breast tumor was used for obtaining 90-120 samples (~900-1200 cells) of tubular, alveolar, and trabecular structures, 50-60 samples (up to 5000 cells) of solid structures, and 300-350 samples (~400-600 cells) of discrete groups of tumor cells. In addition, histologically normal ducts were microdissected from samples of tumor-adjacent normal breast tissue.
WTA protocol: RNA samples (a total of 18 samples) were amplified using the Ovation PicoSL WTA System V2 kit (NuGEN Technologies, Inc., USA). Amplified products (cDNA) were purified using QIAquick PCR Purification Kit (Qiagen, USA), had concentration ranging from 60 to 130 ng/ul, and stored at -80°C until gene expression microarray analysis.
Total RNA was extracted by RNeasy Plus Micro Kit (Qiagen, USA). Ribolock RNase inhibitor (Fermentas, Lithuania) was added to the isolated RNA. RNA quality was assessed by RIN using 2200 TapeStation Instrument and High Sensitivity R6K ScreenTape (Agilent Technologies, Inc., Santa Clara, USA). RIN varied from 4 to 8.

tag: tissue

value: breast tumor

tag: tumor structure

value: alveolar structures

tag: patient id

value: DD

tag: gender

value: female

tag: age

tag: histological type

value: invasive carcinoma of no special type

tag: molecular subtype

value: luminal B

tag: tnm stage

tag: therapy

value: without preoperative therapy


title: ZC-59

country: China

value: male


title: ZC-12


title: ZC-52


title: ZC-45

description: Gene expression of human primary tumor tissue in lymph node positive subgroup in the resectable stage IV colorectal cancer.

source_name: primary tumor, lymphnode  postive subgroup, replicate 1

value: lymph node positive


title: ZC-28


title: ZC-55


title: ZC-39


title: ZC-37


title: ZC-62


title: ZC-03


title: ZC-08


title: ZC-14


title: ZC-58


title: Differentially expressed genes by knocking down of TMEM184B in HSC3

status: Public on Apr 13 2016

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

country: Japan

institute: Chiba University

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution. Images were quantified using Agilent Feature Extraction software version 10.7.3.1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: control miRNA transfected cell line

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Normal cell culture medium RPMI 1640 or DMEM.

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

treatment_protocol: microRNA or siRNA transfection using Lipofectamine RNAiMAX (Invitrogen).

tag: cell line

tag: cell type

value: oral squamous cell carcinoma

tag: transfection

value: control

source_name: si-TMEM184B transfected cell line


title: Differentially expressed genes by knocking down of CORO1C-2 in EBC-1

source_name: mock transfected cell line

value: lung squamous cell carcinoma

value: no transfection

source_name: si-CORO1C-2 transfected cell line


title: Identification of miR-222 target genes in PC3

value: prostate cancer

source_name: miR-222 transfected cell line


title: ZC-15

value: stage IV colorectal cancer


title: Differentially expressed genes by knocking down of LOXL2-2 in A-498

value: renal cell carcinoma

source_name: si-LOXL2-2 transfected cell line


title: Identification of miR-223 target genes in PC3M

source_name: miR-223 transfected cell line


title: Differentially expressed genes by knocking down of CORO1C-1 in EBC-1

source_name: si-CORO1C-1 transfected cell line


title: Differentially expressed genes by knocking down of TMEM184B in SAS

value: SAS


title: Differentially expressed genes by knocking down of LOXL2-3 in 786-O

source_name: si-LOXL2-3 transfected cell line


title: Identification of miR-223 target genes in PC3


title: Identification of miR-221 target genes in PC3

source_name: miR-221 transfected cell line


title: Identification of miR-145-5p target genes in BOY

value: BOY

value: bladder cancer

source_name: miR-145-5p transfected cell line


title: Identification of miR-145-5p target genes in T24


title: Identification of miR-210 target genes in 786-O (48hours after reverse transfection)

source_name: miR-210 transfected cell line

tag: time

value: 48 hours after transfection with microRNAs


title: Identification of miR-23b cluster target genes in 786-O

source_name: control plasmid vector transfected cell line

source_name: miR-23b cluster plasmid transfected cell line

value: miR-23b cluster


title: Identification of miR-145-3p target genes in BOY

source_name: miR-145-3p transfected cell line


title: Differentially expressed genes by knocking down of HMBG3-2 in PC3

source_name: si-HMBG3-2 transfected cell line


title: Differentially expressed genes by knocking down of GOLM1-3 in PC3

source_name: control siRNA transfected cell line

source_name: si-GOLM1-3 transfected cell line


title: Differentially expressed genes by knocking down of LOXL2-2 in 786-O


title: Identification of miR-144-5p target genes in T24

source_name: miR-144-5p transfected cell line


title: Differentially expressed genes by knocking down of CENPF-3 in PC3

source_name: mock transfected cell line

source_name: si-CENPF-3 transfected cell line


title: Differentially expressed genes by knocking down of CENPF-1 in PC3

source_name: si-CENPF-1 transfected cell line


title: Identification of miR-144-3p target genes in T24

source_name: miR-144-3p transfected cell line


title: Identification of miR-210 target genes in 786-O (24hours after reverse transfection)

value: 24 hours after transfection with microRNAs


title: Identification of miR-29a target genes in A-498

source_name: miR-29a transfected cell line


title: Differentially expressed genes by knocking down of HMBG3-1 in PC3

source_name: si-HMBG3-1 transfected cell line


title: Identification of miR-451 target genes in T24

source_name: miR-451 transfected cell line


title: Identification of miR-205 target genes in C4-2

source_name: miR-205 transfected cell line


title: Differentially expressed genes by knocking down of GOLM1-1 in PC3

source_name: si-GOLM1-1 transfected cell line


title: Identification of miR-29a target genes in 786-O


title: Identification of miR-205 target genes in PC3


title: Identification of miR-205 target genes in DU145


title: Differentially expressed genes by knocking down of FOXM1 in BOY

data_processing: Agilent Feature Extraction Software version 10.7.3.1 was used for background subtraction and LOWESS normalization.

source_name: si-FOXM1 transfected cell line


title: Identification of miR-133a target genes in SK-MES-1

source_name: control miRNA transfected cell line

source_name: miR-133a transfected cell line


title: Identification of miR-452 target genes in PC3

source_name: miR-452 transfected cell line


title: Identification of miR-1 target genes in EBC-1

source_name: miR-1 transfected cell line


title: Identification of miR-1 target genes in SK-MES-1


title: Identification of miR-452 target genes in DU145


title: Differentially expressed genes by knocking down of FOXM1 in T24

source_name: control siRNA transfected cell line


title: Identification of miR-221 target genes in LNCaP

value: LNCap

source_name: miR-221 transfected cell line


title: Identification of miR-451 target genes in FaDu

source_name: mock

value: FaDu

value: hypopharyngeal cancer


title: Identification of miR-224 target genes in PC3

source_name: miR-224 transfected cell line


title: Identification of miR-221 target genes in DU145


title: Identification of miR-221 target genes in PC3


title: Identification of miR-24 target genes in BOY-GFP

value: BOY-GFP

source_name: miR-24 transfected cell line


title: Identification of miR-218 target genes in PC3

source_name: miR-218 transfected cell line


title: Identification of miR-224 target genes in DU145


title: Identification of miR-222 target genes in DU145

source_name: miR-222 transfected cell line


title: Identification of miR-222 target genes in PC3


title: Identification of miR-144 target genes in FaDu

source_name: miR-144 transfected cell line


title: Identification of miR-218 target genes in BOY-GFP


title: Differentially expressed genes by knocking down of LASP1 in PC3

source_name: si-LASP1 transfected cell line


title: Identification of miR-24 target genes in T24


title: Identification of miR-222 target genes in LNCaP


title: Identification of miR-133a target genes in EBC-1


title: Tumor_Fibroblasts_1,25(OH)2D3_Patient_44

status: Public on Apr 07 2016

city: Madrid

first: Maria Jesus

last: Larriba

state: Madrid

address: Arturo Duperier 4

department: Cancer Biology

country: Spain

institute: Instituto de Investigaciones Biomedicas "Alberto Sols"

description: Gene expression profile of colon tumor fibroblast primary culture established from patient 44 and treated with 1,25(OH)2D3 for 48 h

hyb_protocol: Microarray: Human Gene Expression G3 v2 60K (Agilent microarray design ID 039494, P/N G4851B). Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: 600 ng. Volume: 50 µl. Temperature (ºC): 65. Duration: 17 h.

scan_protocol: Scanned on an G2505C DNA microarray scanner (Agilent). Images were analysed by Agilent Feature Extraction Software (ver. 11.5), which performed feature quantitation and additive detrend correction. Normexp background subtraction was performed.

data_processing: Quantile normalization was performed using limma package available at Bioconductor

source_name: Colon tumor fibroblasts, 1,25(OH)2D3-treated, patient 44

label_protocol: Amount of nucleic acid labeled: 100 ng. Commercial One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit following manufacturer's instructions. Agilent manual G4140-90040 of May 2010. Amplification: by RNA polymerases. Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of Cy3-CTP fluorophore. Labeled samples are purified with silica-based spin columns.

growth_protocol: Primary cultures of colon normal and tumor fibroblasts were established following the explant outgrowth technique from fresh surgical specimens of normal colon mucosa and colon primary tumor resected from colorectal cancer patients.

extract_protocol: Total RNA was extracted using the NucleoSpin miRNA extraction kit (Macherey-Nagel, Düren, Germany) following manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Primary human colon normal and tumor fibroblasts cultured in Fibroblast Growth Medium 2 (Lonza, Basel, Switzerland) were treated with 1,25(OH)2D3 (Sigma-Aldrich, San Louis, MO) or vehicle (ethanol) and incubated for 48 h at 37 ºC in a humidified incubator with 5% CO2.

tag: treatment

value: Colon tumor fibroblasts

tag: patient

value: Patient 44


title: Tumor_Fibroblasts_Vehicle_Patient_44

description: Gene expression profile of colon tumor fibroblast primary culture established from patient 44 and treated with vehicle for 48 h

source_name: Colon tumor fibroblasts, vehicle-treated, patient 44

value: Vehicle


title: Differentially expressed genes between BOY-GFP and its parental cell

source_name: parental cell

value: parental cell

source_name: GFP expressing cell line

value: GFP


title: Tumor_Fibroblasts_1,25(OH)2D3_Patient_38

description: Gene expression profile of colon tumor fibroblast primary culture established from patient 38 and treated with 1,25(OH)2D3 for 48 h

source_name: Colon tumor fibroblasts, 1,25(OH)2D3-treated, patient 38

value: Patient 38


title: Tumor_Fibroblasts_1,25(OH)2D3_Patient_43

description: Gene expression profile of colon tumor fibroblast primary culture established from patient 43 and treated with 1,25(OH)2D3 for 48 h

source_name: Colon tumor fibroblasts, 1,25(OH)2D3-treated, patient 43

value: Patient 43


title: Tumor_Fibroblasts_1,25(OH)2D3_Patient_16

description: Gene expression profile of colon tumor fibroblast primary culture established from patient 16 and treated with 1,25(OH)2D3 for 48 h

source_name: Colon tumor fibroblasts, 1,25(OH)2D3-treated, patient 16

value: Patient 16


title: Tumor_Fibroblasts_Vehicle_Patient_27

description: Gene expression profile of colon tumor fibroblast primary culture established from patient 27 and treated with vehicle for 48 h

source_name: Colon tumor fibroblasts, vehicle-treated, patient 27

value: Patient 27


title: Tumor_Fibroblasts_1,25(OH)2D3_Patient_11

description: Gene expression profile of colon tumor fibroblast primary culture established from patient 11 and treated with 1,25(OH)2D3 for 48 h

source_name: Colon tumor fibroblasts, 1,25(OH)2D3-treated, patient 11

value: Patient 11


title: Tumor_Fibroblasts_Vehicle_Patient_45

description: Gene expression profile of colon tumor fibroblast primary culture established from patient 45 and treated with vehicle for 48 h

source_name: Colon tumor fibroblasts, vehicle-treated, patient 45

value: Patient 45


title: Tumor_Fibroblasts_Vehicle_Patient_43

description: Gene expression profile of colon tumor fibroblast primary culture established from patient 43 and treated with vehicle for 48 h

source_name: Colon tumor fibroblasts, vehicle-treated, patient 43


title: Tumor_Fibroblasts_1,25(OH)2D3_Patient_27

description: Gene expression profile of colon tumor fibroblast primary culture established from patient 27 and treated with 1,25(OH)2D3 for 48 h

source_name: Colon tumor fibroblasts, 1,25(OH)2D3-treated, patient 27


title: Tumor_Fibroblasts_1,25(OH)2D3_Patient_45

description: Gene expression profile of colon tumor fibroblast primary culture established from patient 45 and treated with 1,25(OH)2D3 for 48 h

source_name: Colon tumor fibroblasts, 1,25(OH)2D3-treated, patient 45


title: Tumor_Fibroblasts_Vehicle_Patient_38

description: Gene expression profile of colon tumor fibroblast primary culture established from patient 38 and treated with vehicle for 48 h

source_name: Colon tumor fibroblasts, vehicle-treated, patient 38


title: TFK-1 cell-without TSA-rep2

status: Public on Mar 15 2016

city: wuhan

first: wei

last: yao

address: NO.1095 of jiefang stree

institute: Tongji hospital

description: Gene expression after without TSA treated in TFK-1 cell

hyb_protocol: 0.6 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 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to OE Human lncRNA Microarray V4.0 (Agilent) 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 (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: TFK-1 cell, without TSA, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 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: TFK-1 Cells were cultured in RPMI-1640 containing 10% fetal calf serum

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions

treatment_protocol: TFK-1 cells treated by TSA in indicated concentration (IC50) 48 hours as the experiment sample and no TSA as the control sample.

value: cholangiocarcinoma


title: Tumor_Fibroblasts_Vehicle_Patient_11

description: Gene expression profile of colon tumor fibroblast primary culture established from patient 11 and treated with vehicle for 48 h

source_name: Colon tumor fibroblasts, vehicle-treated, patient 11


title: TFK-1 cell-without TSA-rep3

source_name: TFK-1 cell, without TSA, replicate 3


title: TFK-1 cell-TSA-rep1

description: Gene expression after TSA treated in TFK-1 cell

source_name: TFK-1 cell, TSA, replicate 1


title: hiPSCs 2

status: Public on Mar 09 2016

city: Suita

first: Ryuhei

last: Hayashi

state: Osaka

address: 2-2 Yamadaoka

institute: Osaka University Graduate School of Medicine

hyb_protocol: standard Agilent protocol

scan_protocol: Microarrays were scanned with SureScan Microarray Scanner G2600D (Agilent).

data_processing: The scanned images were analyzed with Feature Extraction Software (ver. 11.5.1.1, Agilent) according to the Agilent instruction. The obtained data was normalized by global normalization method.

source_name: hiPSCs

label_protocol: Labeling was performed using Low Input Quick Amp Labeling Kit, One-Color (Agilent technologies, Palo Alto, CA). Hybridization and washing were performed using Gene Expression Hybridization Kit and Gene Expression Wash Buffers Kit (Agilent). Each procedure was conducted according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted by the QIAZol reagent (Qiagen, Valencia, CA)

value: undifferentiated hiPSCs

tag: source

value: 201B7 hiPSCs purchased from RIKEN


title: Tumor_Fibroblasts_Vehicle_Patient_16

description: Gene expression profile of colon tumor fibroblast primary culture established from patient 16 and treated with vehicle for 48 h

source_name: Colon tumor fibroblasts, vehicle-treated, patient 16


title: Tomato_HS294T_2

status: Public on Mar 01 2016

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description:
US11263921_253949430778_S01_GE2_1105_Oct12_1_4.txt
HS294T cells with Tomato virus

hyb_protocol: cRNAs were hybridized to the Agilent 2-color 60-mer oligo arrays (Agilent SurePrint G3 Human GE 8x60K).

scan_protocol: The slides were scanned with Agilent Microarray Scanner G2505C (Agilent Technologies) and the raw intensity values were obtained with the Feature Extraction software, version 11.0.1.1 (Agilent Technologies). Raw data was quality checked according to the Agilent standard procedures.

data_processing:
Data pre-processing and differential expression analysis of the gene expression data were done in R. First, the probe profile expression data were normalized using quantile normalization and corrected for batch processing effects using ComBat. Next, after mapping from probsets to Ensemble gene IDs, the differentially expressed genes (DE genes) between pre- and post-treatment samples were identified using limma. Finally, functional categorization of DE genes was performed using a novel R-based package namely BACA.  It queries the DAVID knowledgebase and build a charts showing multiple enrichment analysis results across different conditions/treatments.
For the analysis using the limma package, genes were defined as being differentially expressed after satisfying a minimum fold-change of ±1.5 and a maximum Benjamini-Hochberg adjusted p-value of 0.01.

source_name: HS294T (HTB-140) Tomato virus

label_protocol: Independent pools of two RNA samples each (total of 600 ng) were labeled using T7 RNA polymerase amplification method (Low Input Quick Amp Labeling Kit, Agilent Technologies, Inc., Santa Clara, CA, USA), according to the instructions of the manufacturer. cRNAs were then labeled with Cy3 and Cy5 dyes (Agilent Technologies)

growth_protocol: HS294T cells were cultured on 6-well plates 1,5x10^6 cells/well in 10% DMEM (with 1% L-glutmanine and 1% Pen-Strep) over night. THP-1 cells were cultured in T75 flasks in 10% RPMI-1640 (with 1% L-glutmanine, 1% Pen-Strep and 0,05 mM 2-Mercaptoethanol).

extract_protocol: Total RNA was purified with RNeasy Plus Mini kit (Qiagen, Venlo, NL) according to manufacturer´s instructions.

treatment_protocol: Cells were infected with 0.1 pfu/cell of virus (vvdd-tdTomato control virus or vvdd-tdTomato-hDAI virus) for 16 hours. Mock samples were treated with PBS only. 2% growth medium was used as treatment medium.

tag: virus

value: vvdd-tdTomato


title: hDAI_THP1_3

description:
US11263921_253949430778_S01_GE2_1105_Oct12_2_3.txt
THP1 cells with Tomato-hDAI virus

source_name: THP-1 (TIB-202) Tomato-hDAI virus

value: vvdd-tdTomato-hDAI


title: TFK-1 cell-TSA-rep3

source_name: TFK-1 cell, TSA, replicate 3


title: TFK-1 cell-TSA-rep2

source_name: TFK-1 cell, TSA, replicate 2


title: Tomato_HS294T_3

description:
US11263921_253949430778_S01_GE2_1105_Oct12_1_3.txt
HS294T cells with Tomato virus


title: MOCK_THP1_2

description:
US11263921_253949430778_S01_GE2_1105_Oct12_1_4.txt
THP1 cells untreated

source_name: THP-1 (TIB-202) MOCK

value: no virus, only PBS


title: Tomato_HS294T_1

description:
US11263921_253949430778_S01_GE2_1105_Oct12_1_2.txt
HS294T cells with Tomato virus


title: hiPSCs 3

tag: tissue


title: Tomato_THP1_2

description:
US11263921_253949430778_S01_GE2_1105_Oct12_2_4.txt
THP1 cells with Tomato virus

source_name: THP-1 (TIB-202) Tomato virus


title: hiPSCs 1


title: TFK-1 cell-without TSA-rep1

source_name: TFK-1 cell, without TSA, replicate 1


title: HDAI_HS294T_1

description:
US11263921_253949430778_S01_GE2_1105_Oct12_1_3.txt
HS294T cells with Tomato-hDAI virus

source_name: HS294T (HTB-140) Tomato-hDAI virus


title: Tomato_THP1_1

description:
US11263921_253949430778_S01_GE2_1105_Oct12_2_1.txt
THP1 cells with Tomato virus


title: Tomato_THP1_3

description:
US11263921_253949430778_S01_GE2_1105_Oct12_2_2.txt
THP1 cells with Tomato virus


title: Identification of miR-145-3p target genes in T24

source_name: mock transfected cell line

value: bladder cancer

value: no transfection

source_name: miR-145-3p transfected cell line


title: MOCK_HS294T_2

description:
US11263921_253949430778_S01_GE2_1105_Oct12_2_4.txt
HS294T cells untreated

source_name: HS294T (HTB-140) MOCK


title: C4-2B-shctrl

status: Public on Mar 03 2016

city: Shanghai

first: Mingang

last: Hao

address: NO. 280 South Chongqing Road

department: Department of Biochemistry and Molecular & Cell Biology

institute: Shanghai Jiao Tong University School of Medicine

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression Microarrays (G2505C) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then scan slides immediately to minimize the impact of environmental oxidants on signal intensities..

scan_protocol: Slides were scanned immediately after washing on the Agilent Human Gene Expression Microarrays (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100% (Hi) and 10% (Lo)).

data_processing: The scanned images were analyzed with Agilent Feature Extraction (FE) software using default parameters and set FE Project Properties to export data to txt.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-2305) 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: C4-2B cells were cultured in RPMI 1640 medium supplemented with 10% FBS (Invitrogen Corp, Carlsbad, CA). DU145 cells was cultured in DMEM medium with 10% FBS.

extract_protocol: Total RNA were extracted using Trizol (Invitrogen)  following the manufacturer's recommendations.  Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

value: control


title: C4-2B-shHIC1

value: HIC1 silencing


title: HDAI_HS294T_3

description:
US11263921_253949430778_S01_GE2_1105_Oct12_2_3.txt
HS294T cells with Tomato-hDAI virus


title: hDAI_THP1_1

description:
US11263921_253949430778_S01_GE2_1105_Oct12_1_1.txt
THP1 cells with Tomato-hDAI virus


title: HDAI_HS294T_2

description:
US11263921_253949430778_S01_GE2_1105_Oct12_2_1.txt
HS294T cells with Tomato-hDAI virus


title: DU145-shHIC1


title: MOCK_HS294T_1

description:
US11263921_253949430778_S01_GE2_1105_Oct12_2_2.txt
HS294T cells untreated


title: DU145-shctrl


title: HDAI_THP1_2

description:
US11263921_253949430778_S01_GE2_1105_Oct12_1_2.txt
THP1 cells with Tomato-hDAI virus


title: MOCK_THP1_1

description:
US11263921_253949430778_S01_GE2_1105_Oct12_1_1.txt
THP1 cells untreated


title: TRAIL REPLICATE 4

status: Public on Feb 01 2016

city: RENNES

first: Nathalie

last: THERET

address: 2 avenue Pr Leon Bernard

department: INSERM U1085

country: France

institute: University of Rennes 1

description: Sample name: 253949410823_2_4

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing:
The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolverâ gene expression data analysis system (Rosetta Biosoftware).
the signal intensities from the single-experiment raw data lists are normalized by dividing the intensity values by their median.

source_name: Cell treated with TRAIL

label_protocol: To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

growth_protocol: The HT29 human colon adenocarcinoma cell line was obtained from ATCC (American Type Culture Collection, Rockville, MD, USA) and cultured at 37°C under a humidified atmosphere of 5 % CO2 in DMEM medium (GlutaMAXTM, high glucose, Life Technologies, St Aubin, France) supplemented with 10 % heat inactivated-fetal calf serum (FCS)

extract_protocol: standard RNA extraction protocols (NucleoSpin® RNA II).

treatment_protocol: 6 h treatment combining TRAIL (100 ng/ml + 2 µg/ml anti-Flag M2 antibody) with propionibacterial culture supernatant (SN diluted to 1/2) or a mixture of propionate (30 mM) and acetate (15 mM) (C3/C2, the major metabolites used in the amounts present in the diluted SN).

value: colon adenocarcinoma

tag: agent

value: TRAIL


title: TRAIL REPLICATE 1

description: Sample name: 253949410823_2_1


title: SN REPLICATE 1

description: Sample name: 253949410823_1_1

source_name: Cell treated with SN

value: SN


title: T+C3/C2 REPLICATE 3

description: Sample name: 253949410824_1_3

source_name: Cell treated with TRAIL + C3/C2

value: TRAIL + C3/C2


title: C3/C2 REPLICATE 1

description: Sample name: 253949411079_2_4

source_name: Cell treated with C3/C2


title: NT REPLICATE 3

description: Sample name: 253949410822_1_3

source_name: non treated cell

value: untreated


title: NT REPLICATE 4

description: Sample name: 253949410822_1_4


title: T+SN REPLICATE 4

description: Sample name: 253949410824_2_4

source_name: Cell treated with TRAIL + SN

value: TRAIL + SN


title: T+C3/C2 REPLICATE 1

description: Sample name: 253949410824_1_1


title: SN REPLICATE 2

description: Sample name: 253949410823_1_2


title: C3/C2 REPLICATE 3

description: Sample name: 253949410822_2_3


title: C3/C2 REPLICATE 2

description: Sample name: 253949410822_2_2


title: TRAIL REPLICATE 2

description: Sample name: 253949410823_2_2


title: T+SN REPLICATE 2

description: Sample name: 253949410824_2_2


title: SN REPLICATE 4

description: Sample name: 253949410823_1_4


title: NT REPLICATE 2

description: Sample name: 253949410822_1_2


title: T+SN REPLICATE 1

description: Sample name: 253949410824_2_1


title: NT REPLICATE 1

description: Sample name: 253949411079_1_4


title: T+C3/C2 REPLICATE 4

description: Sample name: 253949410824_1_4


title: C3/C2 REPLICATE 4

description: Sample name: 253949410822_2_4


title: SN REPLICATE 3

description: Sample name: 253949410823_1_3


title: T+C3/C2 REPLICATE 2

description: Sample name: 253949410824_1_2


title: DMSO_Control_1

status: Public on Jan 03 2016

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

hyb_protocol: As per manufacturer recommended protocol

data_processing:
Raw data analyzed by GeneSpring Gx v 12.0
gProcessed Signal was normalized to 50th Percentile and median to all samples using GeneSpring GX v 12.0

label_protocol: Agilent mRNA Complete Labeling and Hybridization Kit

growth_protocol: Cal27 cells were grown in standard culture conditions

extract_protocol: Trizol method

treatment_protocol: Cal27 cells were treated with luteolin with DMSO as control for 24 hours

value: HNSCC cell line Cal27

value: Control


title: Luteolin_Treated_Test_25um_1

scan_protocol: As per manufacturer recommended protocol

value: Luteolin

tag: dose


title: Luteolin_Treated_Test_10um_1


title: DMSO_Control_2


title: Luteolin_Treated_Test_25um_2


title: Luteolin_Treated_Test_10um_2


title: T+SN REPLICATE 3

description: Sample name: 253949410824_2_3


title: SOC-20, differentiated

status: Public on Dec 31 2015

city: Chuo-ku

first: koji

last: okamoto

state: Tokyo

address: 5-1-1 Tsukiji

department: Division of Cancer Differentiation

institute: National Cancer Center Research Institute

description:
Gene expression after differentiation
SAMPLE 8

hyb_protocol: 0.6 ug of labelled cRNA was fd hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851B, Agilent) for 17 hours at 65C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (Agilent).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1(Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F/20120628).

label_protocol: 100ng of total RNA was Cy3-labeled according to the manufacturer's protocol of On-Color Microarray-Based Gene Expression Analyses (Low Input Quick Amp Labeling), ver 6.5.

growth_protocol: Undifferentiated ovarian cancer stem cells were grown in grown in STEMPRO hESC SFM (Gibco) supplemented with 8 ng/ml bFGF (Invitrogen), penicillin/streptomycin, and in the presence or absence of 20 μM Y27632 (Wako) and/or 10 μg/ml insulin on ultra-low-attachment culture dishes (Corning).

extract_protocol: Total RNAs were extracted using miRNeasy mini kit (QIAGEN) according to the manufacturer’s protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer. RNA quality control was performed in 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).

treatment_protocol: Differentiation of spheroid cells were induced by cultivating dissociated spheroid cells on standard culture dishes in the presence of 10% fetal bovine serum for 14 days.


title: SOC-5, undifferentiated

description:
Gene expression before differentiation
SAMPLE 5

value: undifferentiated ovarian cancer stem cells


title: SOC-20, undifferentiated

description:
Gene expression before differentiation
SAMPLE 7


title: SOC-5, differentiated

description:
Gene expression after differentiation
SAMPLE 6

value: differentiated ovarian cancer stem cells


title: SOC-2, undifferentiated

description:
Gene expression before differentiation
SAMPLE 3


title: SOC-2, differentiated

description:
Gene expression after differentiation
SAMPLE 4


title: SOC-4, differentiated

description:
Gene expression after differentiation
SAMPLE 2


title: liver_patient_7_HCC_rep1 (mRNA)

status: Public on Dec 21 2015

city: Tokyo

first: Y-H.

last: Taguchi

state: Non-US/Canada

address: 1-13-27 Kasuga,Bukyo-ku

department: Physics

institute: Chuo University

description:
HCC
mRNA_13

hyb_protocol: For miRNA microarray, 100 ng of RNA was labeled and hybridized using the Human microRNA Microarray Kit (Rel 14.0) (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microRNA microarrays Version 1.0.For mRNA micaroarray, 100 ng of RNA was labeled and hybridized using the SurePrint G3 Human GE microarray kit (G4851B) (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microarrays.

scan_protocol: For miRNA microarray, hybridization signals were detected with Agilent DNA microarray scanner G2539B and the scanned images were analyzed using Agilent feature extraction software (v10.10.1.1). For mRNA microarray, hybridization signals were detected with Agilent DNA microarray scanner G2539A and the scanned images were analyzed using Agilent feature extraction software (v10.10.1.1).

data_processing: For miRNA and mRNA microarray, gProcessedSignal was extracted and normalized so as to have zero mean and variance of 1.

source_name: liver mRNA HCC tumor part

extract_protocol: RNA was prepared using the mirVana miRNA isolation kit (Life Technologies, CA, USA) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Surgically resected hepatocellular carcinoma (HCC) samples and surrounded non-tumor samples, and cholangiocarcinoma (CCC) samples and surrounded non-tumor samples

value: patient 7

tag: disease state

value: HCC

value: liver_HCC tumor part

tag: gender

value: male

tag: histol information

value: Moderately

tag: date of birth

tag: afp

tag: pivka-ii

tag: cea

tag: tumor size

tag: hospotal id


title: liver_patient_15_CCC_rep1 (mRNA)

description:
CCC
mRNA_29

source_name: liver mRNA CCC tumor part

label_protocol: For miRNA microarray, 100 ng of RNA was labeled and hybridized using the Human microRNA Microarray Kit (Rel 14.0) (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microRNA microarrays Version 1.0.For mRNA micaroarray, 100 ng of RNA was labeled and hybridized using the SurePrint G3 Human GE microarray kit (G4851B) (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microarrays.

value: patient 15

value: CCC

value: liver_CCC tumor part

value: female

tag: age


title: liver_patient_16_CCC_rep1 (mRNA)

description:
CCC
mRNA_31

value: patient 16


title: liver_patient_14_CCC_rep1 (mRNA)

description:
CCC
mRNA_27

value: patient 14


title: liver_patient_13_CCC_rep1 (mRNA)

description:
CCC
mRNA_25

value: patient 13


title: liver_patient_8_HCC_rep1 (mRNA)

description:
HCC
mRNA_15

value: patient 8


title: Control siRNA-treated HCC1937 cells

status: Public on Nov 30 2015

city: Fukuoka

first: Hideya

last: Onishi

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Cancer Therapy and Research

institute: Graduate School of Medical Sciences, Kyushu University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (Agilent-039494 SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

source_name: HCC1937 cells, control siRNA

label_protocol: cRNA was amplified and labelled using a Low Input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: The culture condition for CD24-siRNA-treated HCC1937 cells was as following: RPMI1640 medium supplemented with 10% FCS, L-Gln and penicillin-streptomycin, 5% CO2/air.

extract_protocol: Total RNA was isolated and purified from CD24-treated HCC1937 cells using High Pure RNA Isolation Kit (Roche, #11 828 665 001).

treatment_protocol: Following overnight attachment to a 6-well plate, 3.0 x 10^5 cells per well were transfected for 48 hours using Lipofectamine® RNAiMAX Reagent (Invitrogen by Life Technologies) according to the manufacturer's protocol. Sixteen hours after the medium change, siRNA-transfected cells were used for further experiments.

tag: cell line

tag: cell type

value: breast cancer cell line

tag: sirna

value: control


title: SOC-4, undifferentiated

description:
Gene expression before differentiation
SAMPLE 1

value: undifferentiated ovarian cancer stem cells


title: liver_patient_12_CCC_rep1 (mRNA)

description:
CCC
mRNA_23

tag: patient

value: patient 12


title: liver_patient_6_HCC_rep1 (mRNA)

description:
HCC
mRNA_10

value: patient 6

tag: tissue

value: Poorly


title: 18740_FD-pCDH.txt:gProcessedSignal(normalized)

status: Public on Dec 01 2015

city: Taipei

first: Tsai-Tsen

last: Liao

state: State...

address: No.201, Sec.2, Shih-Pai Rd. Peitou, Taipei, Taiwan, 11221, R.O.C

country: Taiwan

institute: Institute of Clinical Medicine

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Human V2 GE 8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3

data_processing:
Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.
Normalized signal is generated from gProcessedSignal after normalized by quantile
There are three kinds of flags for the data quality of the feature (gFEFlags):
Detected: the data quality of the feature is good enough. In general, the signal of the feature is well above background, uniform, not saturated, and not a population outlier.
Compromise: the data quality of the feature is also good but the signal is too weak because of the low expression level of the gene. Generally, the signal of the feature is uniform, not saturated not a population outlier, but not well above background.
not Detected: the data quality of the feature Generally not good enough. the signal of the feature maybe not uniform, or saturated or a population outlier.

source_name: FaDu_pCDH vector

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process. 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.

growth_protocol: cultivated in RPMI + 10% fetal bovine serum

extract_protocol: Cells were lysed by adding 2 ml of trizol reagent (Invitrogen) and homogenized by passing through a syringe with a needle (26G). RNA was picked up in the aqueous phase following phase separation by chloroform. The RNA was then precipitate with isopropanol, washed with ethanol (75%), dissolved in DEPC-treated RNAse/DNAse free water and quantified by spectrophotometry.

treatment_protocol: FaDu cells were infection with pCDH-ARID3B or empty vector control.

value: FaDu

value: Head and neck cell line

tag: transfected with

value: pCDH vector (control)


title: liver_patient_2_CCC_rep1 (mRNA)

description:
CCC
mRNA_3

value: patient 2

value: male


title: liver_patient_1_CCC_rep1 (mRNA)

description:
CCC
mRNA_1

value: patient 1

value: CCC

value: liver_CCC tumor part

value: moderate tubular


title: liver_patient_9_HCC_rep1 (mRNA)

description:
HCC
mRNA_17

value: patient 9

value: HCC

value: liver_HCC tumor part

value: Moderately


title: liver_patient_10_HCC_rep1 (mRNA)

description:
HCC
mRNA_19

value: patient 10


title: CD24 siRNA-treated HCC1937 cells

source_name: HCC1937 cells, CD24 siRNA

value: breast cancer cell line


title: liver_patient_5_CCC_rep1 (mRNA)

description:
CCC
mRNA_9

value: patient 5


title: liver_patient_11_CCC_rep1 (mRNA)

description:
CCC
mRNA_21

value: patient 11

value: female


title: Control siRNA-treated MCF-7 cells

source_name: MCF-7 cells, control siRNA

growth_protocol: The culture condition for CD24-siRNA-treated MCF-7 cells was as following: RPMI1640 medium supplemented with 10% FCS, L-Gln and penicillin-streptomycin, 5% CO2/air.

extract_protocol: Total RNA was isolated and purified from CD24-treated MCF-7 cells using High Pure RNA Isolation Kit (Roche, #11 828 665 001).

value: control


title: liver_patient_4_CCC_rep1 (mRNA)

description:
CCC
mRNA_7

value: patient 4


title: liver_patient_3_CCC_rep1 (mRNA)

description:
CCC
mRNA_5

value: patient 3


title: 18738_FD-3B-1.txt:gProcessedSignal(normalized)

value: FaDu

value: Head and neck cell line


title: CD24 siRNA-treated MCF-7 cells

source_name: MCF-7 cells, CD24 siRNA


title: HCT116 cells transfected with a ZNF582-AS1 expression vector 2

status: Public on Nov 13 2015

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

institute: Sapporo Medical University

description: gene expression in HCT116 cells transfected with a ZNF582-AS1 expression vector (replicate 2)

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: The microarray data were analyzed using GeneSpring GX version 13

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: HCT116 cells were cultured in McCoy's 5A Medium supplemented with 10% heat-inactivated fetal bovine serum.  The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using a RNeasy Mini Kit (QIAGEN).

treatment_protocol: HCT116 cells were transfected with a ZNF582-AS1 expression vector or an empty vector. Seventy-two hours after transfection, total RNA was extracted

tag: vector


title: HCT116 cells transfected with an empty vector 2

description: gene expression in HCT116 cells transfected with an empty vector (replicate 2)

value: empty


title: HCT116 cells transfected with a ZNF582-AS1 expression vector 1

description: gene expression in HCT116 cells transfected with a ZNF582-AS1 expression vector (replicate 1)


title: NCI-N417_Scramble8

status: Public on Oct 07 2015

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

description: NCI-N417 cell line transfected with Scramble 8 (short hairpin RNA number 8 doubly mutated)

hyb_protocol: Microarray: Human Gene Expression G3 v2 60K (Agilent microarray design ID 039494, P/N G4851B). Microarray sequences and annotations are listed in sheet '039494_hg19_20120628'. Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: 600 ng. Volume: 50 µL. Temperature (ºC): 65. Duration: 17 hours.

scan_protocol: Scanned on an G2505C DNA microarray scanner (Agilent).

data_processing: Images were analysed by Agilent Feature Extraction Software (ver. 11.5), which performed feature quantitation and additive detrend correction. No background subtraction was performed.

source_name: Small Cell Lung Cancer (SCLC)

label_protocol: Amount of nucleic acid labeled: 100ng. Commercial One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit by following manufacturer instructions. Agilent manual G4140-90040 of May 2010. Amplification: by RNA polymerases. Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of Cy3-CTP fluorophore. Labeled samples are purified with silica-based spin columns.

growth_protocol: Cells where growth on RPMI media with 10% FBS, 1% PS

extract_protocol: Total mRNA was extrated using Trizol Reagent.

treatment_protocol: Not special  additional treatment

tag: shRNA


title: NCI-N417_shRNA8

description: NCI-N417 cell line transfected with short hairpin RNA number 8, against KAT6B gene


title: HCC33_shRNA8

description: HCC33 cell line transfected with short hairpin RNA number 8, against KAT6B gene


title: NCI-N417_Scramble5

description: NCI-N417 cell line transfected with Scramble 5 (short hairpin RNA number 5 doubly mutated)


title: HCC33_Scramble5

description: HCC33 cell line transfected with Scramble 5 (short hairpin RNA number 5 doubly mutated)


title: HCC33_shRNA5

description: HCC33 cell line transfected with short hairpin RNA number 5, against KAT6B gene


title: HCC33_Scramble8

description: HCC33 cell line transfected with Scramble 8 (short hairpin RNA number 8 doubly mutated)


title: NCI-N417_shRNA5

description: NCI-N417 cell line transfected with short hairpin RNA number 5, against KAT6B gene


title: HCT116 cells transfected with an empty vector 1

description: gene expression in HCT116 cells transfected with an empty vector (replicate 1)


title: Lung_Squamous_Carcinoma_Patient62

status: Public on Sep 25 2015

city: Beijing

first: Ning

last: An

address: NO.17 Pan Jiayuan Nan Li, Chao Yang District

institute: Chinese academy of medical sciences

description: Gene expression of lung squamous carcinoma precancerous and cancer tissue

hyb_protocol: 600 ng of CTP-Cy3-labelled cRNA (specific activity > 10.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 min in a reaction volume of 25 µl containing 25 x Agilent fragmentation buffer and 10 x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2 x Agilent hybridization buffer were added to the fragmentation mixture and hybridized to SurePrint G3 Human GE v2 8x60K (Agilent) for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1 (Agilent) and 1 min with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief passage in acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides: scan area was 61x21.6 mm, scan resolution 3 µm, dye channel was set to Green, Tiff file dynamic range was 20 bits and Green PMT was set to 100 %.

data_processing: Normalized expression data were extracted with R package “limma” using cyclic loess method, and the ComBat algorithm was utilized to eliminate potential batch effects

source_name: Lung Squamous Carcinoma Tissue

label_protocol: CTP-cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Microarray-Based Gene Expression Analysis (Agilent, version 6.6) according to manufacturer's instructions, followed by RNeasy column purification (RNeasy Mini kit, QIAGEN). Dye incorporation and cRNA yield and quality were checked by spectrophotometry (Nanodrop ND1000, Labtech) and with the Agilent 2100 Bioanalyser.

extract_protocol: Total RNA was extracted from frozen tissues using the TRIzol RNA isolation reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s specifications. RNA integrity was evaluated using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). If the RNA integrity number was greater than or equal to 6.5, the total RNA was purified using the RNeasy Mini Kit (Cat No.74106, Qiagen, Germany). The RNA concentration was determined with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, USA).

value: Cancer tissue obtained from bronchoscopy

tag: status

value: Stage IV


title: Lung_Squamous_Carcinoma_Patient61


title: DLD/FR1 FR(-)

status: Public on Sep 30 2015

city: Nishinomiya

first: Tomoki

last: Yamano

state: Hyogo

address: 1-1 Mukogawa-cho

department: Department of Surgery

institute: Hyogo College of Medicine

description: Gene expression without drug treatment

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K v2 Microarrays 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.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: DLD/FR1 cells without FR

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Colon cancer cell lines were cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum.

extract_protocol: RNA was extracted using TRIzol and TRIzol RNA Purification kit (Invitrogen) following the manufacture's instructions.

treatment_protocol: Colon cancer cells were seeded at a density of one million cells in P10 plate. The next day, medium was changed to fresh medium with or without 10 ng/ml of FR901464. The cells were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: colon cancer cells


title: HCT/FR1 FR10

description: Gene expression with drug treatment

source_name: HCT/FR1 cells with 10ng/ml FR


title: Lung_Squamous_Carcinoma_Patient54

value: Stage III


title: HCT116 FR(-)

description: Gene expression without drug treatment

source_name: HCT116 cells without FR


title: Lung_Squamous_Carcinoma_Patient60


title: Lung_Squamous_Carcinoma_Patient53


title: Lung_Squamous_Carcinoma_Patient59


title: HCT116 FR10

description: Gene expression with drug treatment

source_name: HCT116 cells with 10ng/ml of FR


title: Lung_Squamous_Carcinoma_Patient58


title: DLD/FR1 FR10

description: Gene expression with drug treatment

source_name: DLD/FR1 cells with 10ng/ml FR


title: DLD1 FR10

description: Gene expression with drug treatment

source_name: DLD1 cells with 10ng/ml of  FR


title: DLD1 FR(-)

description: Gene expression without drug treatment

source_name: DLD1 cells without FR


title: Lung_Squamous_Carcinoma_Patient57


title: Lung_Squamous_Carcinoma_Patient56


title: HCT/FR1 FR(-)

description: Gene expression without drug treatment

source_name: HCT/FR1 cells without FR


title: Lung_Squamous_Carcinoma_Patient55


title: Lung_Squamous_Carcinoma_Patient46

value: Stage II


title: Lung_Squamous_Carcinoma_Patient44


title: Lung_Squamous_Carcinoma_Patient45


title: Lung_Squamous_Carcinoma_Patient51


title: Lung_Squamous_Carcinoma_Patient43


title: Lung_Squamous_Carcinoma_Patient48


title: Lung_Squamous_Carcinoma_Patient52


title: Lung_Squamous_Carcinoma_Patient31

value: Stage I


title: Lung_Squamous_Carcinoma_Patient38


title: Lung_Squamous_Carcinoma_Patient41


title: Lung_Squamous_Carcinoma_Patient32


title: Lung_Squamous_Carcinoma_Patient37


title: Lung_Squamous_Carcinoma_Patient29


title: Lung_Squamous_Carcinoma_Patient40


title: Lung_Squamous_Carcinoma_Patient30


title: Lung_Squamous_Carcinoma_Patient33


title: Lung_Squamous_Carcinoma_Patient25


title: Lung_Squamous_Carcinoma_Patient27


title: Lung_Squamous_Carcinoma_Patient34


title: Lung_Squamous_Carcinoma_Patient39


title: Lung_Squamous_Carcinoma_Patient22

value: Carcinoma in situ


title: Lung_Squamous_Carcinoma_Patient28


title: Lung_Squamous_Carcinoma_Patient35


title: Lung_Squamous_Carcinoma_Patient36


title: Lung_Squamous_Carcinoma_Patient18


title: Lung_Squamous_Carcinoma_Patient20


title: Lung_Squamous_Carcinoma_Patient19


title: Lung_Squamous_Carcinoma_Patient23


title: Lung_Squamous_Carcinoma_Patient21


title: Lung_Squamous_Carcinoma_Patient24


title: Lung_Squamous_Carcinoma_Patient17


title: Lung_Squamous_Carcinoma_Patient26


title: Lung_Squamous_Carcinoma_Patient16


title: Lung_Squamous_Carcinoma_Patient12


title: Lung_Squamous_Carcinoma_Patient10


title: Lung_Squamous_Carcinoma_Patient5

value: Mild-moderate dysplasia


title: Lung_Squamous_Carcinoma_Patient1


title: Lung_Squamous_Carcinoma_Patient14


title: Lung_Squamous_Carcinoma_Patient8


title: Lung_Squamous_Carcinoma_Patient3


title: Lung_Squamous_Carcinoma_Patient15


title: Lung_Squamous_Carcinoma_Patient4


title: Lung_Squamous_Carcinoma_Patient11


title: Lung_Squamous_Carcinoma_Patient9


title: Lung_Squamous_Carcinoma_Patient13


title: Lung_Squamous_Carcinoma_Patient7


title: Lung_Squamous_Carcinoma_Patient6


title: Lung_Squamous_Carcinoma_Patient2


title: siRNA-mideiated ARID1A down-regulated

status: Public on Sep 03 2015

city: Gifu

first: Tamotsu

last: Takeuchi

address: Yanagido

department: Pathology and Translational Research

institute: Gifu University School of Medcine

description: MOK indicates control siRNA treated cells, while A indicates siRNA-mideiated ARID1A down-regulated cells.

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: scanned by Agilent Technologies Micorarrray Scanner and calculated using Agilent Feature 10.7.3.1.

data_processing: import to GeneSpring GX

source_name: human invasive breast cancer cells MDA-MB-157 cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 600ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions.

extract_protocol: total RNAs were extracted using Rneasy mini kit (Qiagen) accoring to the the manufacturer's recommendations.


title: control siRNA treated cells

value: human invasive breast cancer cells MDA-MB-157 cells


title: IL-10treatedMacrophages_CCR5usingHIV-1_NonReplicating_rep1

status: Public on Aug 01 2015

city: Guildford

first: Fernando

middle: O

last: Martinez Estrada

state: Surrey

address: Stag Hill

department: Faculty of Health & Medical Sciences

country: United Kingdom

institute: University of Surrey

description:
Replicate 1
MDM+IL10_R5HI_1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Background-subtracted data were normalised by Quantiles in R/Bioconductor.

label: biotin

source_name: Monocyte-derived macrophages polarized with IL-10 for 5 days

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

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from buffy coats using Lymphoprep density gradient centrifugation. Monocytes were isolated by adherence to plastic and cultured in Iscove’s modified Dulbecco’s medium supplemented with 10% [v/v] heat-inactivated human pooled serum (HPS), penicillin (100 U/ml), streptomycin (100 µg/ml) and ciproxin (5 mg/ml) at 37oC in a humidified atmosphere supplemented with 5% CO2.

extract_protocol: Total RNA was isolated using TriPure Isolation Reagent and RNA samples were cleaned with RNeasy Mini Spin columns.

treatment_protocol: Monocytes were incubated for 5 days in the presence of different cytokines: IFN-gamma (250 U/ml) in combination with TNF-alpha (12.5 ng/ml) (M1), IL-4 (50 ng/ml) (M2a), IL-10 (50 ng/ml) (M2c) or medium alone. At day 5, stimulated and untimulated cells were inoclated at an MOI or 0.075 with CCR5-using HIV-1 (NL4-3 Ba-L strain), CXCR4-using HIV-1 (NL4-3 strain), CCR5-using HIV-1 non-replicating virus (obtianed by heat-inactivation), CXCR4-using HIV-1 non-replicating virus, or mock treated.

tag: infection

value: CCR5-using HIV-1 non replicating inoculated


title: IL-10treatedMacrophages_CCR5usingHIV-1_rep2

description:
Replicate 2
MDM+IL10_R5_2

value: CCR5-using HIV-1 inoculated

value: Monocyte-derived macrophages polarized with IL-10 for 5 days


title: IL-10treatedMacrophages_mock_rep2

description:
Replicate 2
MDM+IL10_Mock_2

value: Uninfected


title: IL-10treatedMacrophages_CCR5usingHIV-1_NonReplicating_rep3

description:
Replicate 3
MDM+IL10_R5HI_3


title: IL-10treatedMacrophages_mock_rep3

description:
Replicate 3
MDM+IL10_Mock_3


title: IFNgTNFaTreatedMacrophages_CCR5usingHIV-1_NonReplicating_rep6

description:
Replicate 3
MDM_IFNgTNFa_R5HI_3

source_name: Monocyte-derived macrophages polarized with IFNgTNFa for 5 days


title: IFNgTNFaTreatedMacrophages_CCR5usingHIV-1_rep3

description:
Replicate 3
MDM+IFNgTNFa_R5_3

value: Monocyte-derived macrophages polarized with IFNgTNFa for 5 days


title: IL-10treatedMacrophages_CCR5usingHIV-1_rep1

description:
Replicate 1
MDM+IL10_R5_1


title: IFNgTNFaTreatedMacrophages_CCR5usingHIV-1_NonReplicating_rep5

description:
Replicate 2
MDM_IFNgTNFa_R5HI_2


title: IFNgTNFaTreatedMacrophages_CCR5usingHIV-1_rep1

description:
Replicate 1
MDM+IFNgTNFa_R5_1


title: IL-10treatedMacrophages_CCR5usingHIV-1_NonReplicating_rep2

description:
Replicate 2
MDM+IL10_R5HI_2


title: IL-10treatedMacrophages_CCR5usingHIV-1_rep3

description:
Replicate 3
MDM+IL10_R5_3


title: Lung_Squamous_Carcinoma_Patient50


title: IFNgTNFaTreatedMacrophages_mock_rep3

description:
Replicate 3
MDM+IFNgTNFa_Mock_3


title: IFNgTNFaTreatedMacrophages_CCR5usingHIV-1_NonReplicating_rep4

description:
Replicate 1
MDM_IFNgTNFa_R5HI_1


title: IFNgTNFaTreatedMacrophages_CCR5usingHIV-1_rep2

description:
Replicate 2
MDM+IFNgTNFa_R5_2


title: IL-4treatedMacrophages_CXCR4usingHIV-1_NonReplicating_rep2

description:
Replicate 2
MDM+IL4_X4HI_2

source_name: Monocyte-derived macrophages polarized with IL-4 for 5 days

value: CXCR4-using HIV-1 non replicating inoculated


title: Lung_Squamous_Carcinoma_Patient47


title: IL-4treatedMacrophages_CXCR4usingHIV-1_NonReplicating_rep3

description:
Replicate 3
MDM+IL4_X4HI_3

value: Monocyte-derived macrophages polarized with IL-4 for 5 days


title: IFNgTNFaTreatedMacrophages_mock_rep2

description:
Replicate 2
MDM+IFNgTNFa_Mock_2


title: IL-4treatedMacrophages_CXCR4usingHIV-1_NonReplicating_rep1

description:
Replicate 1
MDM+IL4_X4HI_1


title: IL-4treatedMacrophages_CXCR4usingHIV-1_rep2

description:
Replicate 2
MDM+IL4_X4_2

value: CXCR4-using HIV-1 inoculated


title: IL-4treatedMacrophages_CXCR4usingHIV-1_rep3

description:
Replicate 3
MDM+IL4_X4_3


title: IFNgTNFaTreatedMacrophages_mock_rep1

description:
Replicate 1
MDM+IFNgTNFa_Mock_1


title: IL-4treatedMacrophages_CCR5usingHIV-1_NonReplicating_rep1

description:
Replicate 1
MDM+IL4_R5HI_1


title: IL-4treatedMacrophages_CXCR4usingHIV-1_rep1

description:
Replicate 1
MDM+IL4_X4_1


title: IL-10treatedMacrophages_mock_rep1

description:
Replicate 1
MDM+IL10_Mock_1


title: IL-4treatedMacrophages_CCR5usingHIV-1_NonReplicating_rep3

description:
Replicate 3
MDM+IL4_R5HI_3


title: IL-4treatedMacrophages_CCR5usingHIV-1_NonReplicating_rep2

description:
Replicate 2
MDM+IL4_R5HI_2


title: IL-4treatedMacrophages_mock_rep3

description:
Replicate 3
MDM+IL4_Mock_3


title: macrophages_CXCR4usingHIV-1_rep2

description:
Replicate 2
MDM_X4_2

source_name: Monocyte-derived macrophages

value: Monocyte-derived macrophages


title: IL-4treatedMacrophages_CCR5usingHIV-1_rep1

description:
Replicate 1
MDM+IL4_R5_1


title: macrophages_CXCR4usingHIV-1-NonReplicating_rep3

description:
Replicate 3
MDM_X4HI_3


title: IL-4treatedMacrophages_CCR5usingHIV-1_rep2

description:
Replicate 2
MDM+IL4_R5_2


title: IL-4treatedMacrophages_mock_rep2

description:
Replicate 2
MDM+IL4_Mock_2


title: IL-4treatedMacrophages_mock_rep1

description:
Replicate 1
MDM+IL4_Mock_1


title: Macrophages_mock_rep3

description:
Replicate 3
MDM_Mock_3


title: IL-4treatedMacrophages_CCR5usingHIV-1_rep3

description:
Replicate 3
MDM+IL4_R5_3


title: macrophages_CXCR4usingHIV-1-NonReplicating_rep2

description:
Replicate 2
MDM_X4HI_2


title: macrophages_CCR5usingHIV-1_rep2

description:
Replicate 2
MDM_R5_2


title: Macrophages_mock_rep2

description:
Replicate 2
MDM_Mock_2


title: macrophages_CCR5usingHIV-1-NonReplicating_rep3

description:
Replicate 3
MDM_R5HI_3


title: macrophages_CCR5usingHIV-1-NonReplicating_rep2

description:
Replicate 2
MDM_R5HI_2


title: macrophages_CCR5usingHIV-1_rep3

description:
Replicate 3
MDM_R5_3


title: Lung_Squamous_Carcinoma_Patient42

value: Cancer tissue obtained from bronchoscopy


title: macrophages_CXCR4usingHIV-1_rep3

description:
Replicate 3
MDM_X4_3


title: macrophages_CCR5usingHIV-1_rep1

description:
Replicate 1
MDM_R5_1


title: macrophages_CXCR4usingHIV-1_rep1

description:
Replicate 1
MDM_X4_1


title: MCF7-luc anti-miR-27b-1

status: Public on Jun 18 2015

first: Ryou-u

last: Takahashi

address: 1-1, Tsukiji 5-chome, Chuo-ku

department: Division of Molecular and Cellular Medicine

description: Luminal-type breast cancer cells

hyb_protocol: The slides were hybridized for 17 h at 65°C, washed with Gene Expression Wash Buffer 1 (Agilent Technologies) for 1 min at room temperature, washed with Gene Expression Wash Buffer 2 (Agilent Technologies) for 1 min at 37 °C, and then air-dried.

scan_protocol: The arrays from three independent experiments were analysed using microarray scanner (Agilent Technologies).

data_processing: Gene expression levels were calculated using Feature Extraction version 10.7.3.1 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: miR-27b knockdown MCF7-luc cell line

label_protocol: Total RNAs (50 ng) from MCF7-luc derivatives were labelled and amplified using the Low Input Quick Amp labelling kit (Agilent Technologies).

growth_protocol: The cells were cultured with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.

extract_protocol: Total RNA and miRNA were isolated from cells and tumour tissues using the miRNeasy Mini Kit (QIAGEN).

treatment_protocol: Overexpression or knockdown of miR-27b using lentivirus vectors.

tag: treatment

value: miR-27b knockdown MCF7-luc cell line

value: Luminal-type breast cancer cells

tag: gender

value: female


title: MCF7-luc anti-NC-2

description: Luminal-type breast cancer cells

source_name: Control cell line

value: Control cell line


title: MCF7-luc anti-miR-27b-3

description: Luminal-type breast cancer cells


title: MCF7-luc miR-27b o.e-3

description: Luminal-type breast cancer cells

source_name: miR-27b overexpressing MCF7-luc cell line


title: MCF7-luc anti-NC-3

description: Luminal-type breast cancer cells


title: MCF7-luc miR-27b o.e-1

description: Luminal-type breast cancer cells

value: miR-27b overexpressing MCF7-luc cell line


title: MCF7-luc miR-27b o.e-2

description: Luminal-type breast cancer cells


title: MCF7-luc anti-miR-27b-2

description: Luminal-type breast cancer cells


title: macrophages_CCR5usingHIV-1-NonReplicating_rep1

description:
Replicate 1
MDM_R5HI_1


title: macrophages_CXCR4usingHIV-1-NonReplicating_rep1

description:
Replicate 1
MDM_X4HI_1


title: Macrophages_mock_rep1

description:
Replicate 1
MDM_Mock_1


title: MA-346

status: Public on Jan 31 2015

city: Kyoto

first: Megumu

last: Saito

address: 53, Shogoin-Kawahara

institute: Kyoto University

hyb_protocol: Labelled cDNA was fragmented with Gene Expression Hybridization Kit (Agilent Technologies), followed by hybridization at 65˚C for 17 hrs.

scan_protocol: Images were acquired by DNA Microarray Scanner (Agilent Technologies)

data_processing: Raw data were processed with FeatureExtraction version 10.7.3.1. Normalization among samples were performed by GeneSpring GX 12.6.1.  Signal were normalized to 75% percentile.

source_name: iPSC

label_protocol: 100 ng of total RNA was first amplified with WT-OvationTM Pico System (Nugen). The RNA was labelled with Cy3 using Genomic DNA Enzymatic Labeling Kit (Agilent Technologies).

growth_protocol: Episomal vectors encoding reprogramming factors (OCT3/4, SOX2, KLF4, L-MYC, LIN28 and p53 shRNA) were transduced into fibroblasts on day 0 as described previously (Okita et al., 2011). The transfected cells were reseeded onto feeder layers on day 7, and maintained in embryonic stem cell medium (ReproCELL). Around day 30, the iPSC colonies were picked up and expanded. Cell culture was performed under 37°C , with 5% CO2 and 21% O2.

extract_protocol: Total RNA was extracted and purified using RNA mini kit (QIAGEN) according to manufacturer’s instruction.

treatment_protocol: No treatment applied.

value: iPSC


title: MA-345


title: MCF7LacZ

status: Public on Apr 28 2015

city: Nagakute

first: Kenji

last: Kasai

state: Aichi

address: 1-1 Yazakokarimata

department: Department of Pathology

institute: Aichi Medical University School of Medicine

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 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 SurePrint G3 Human GE v2 8x60K Microarray (G4851B) 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 (G2505B) using one color scan setting for 8x60k 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 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: MCF-7 expressing LacZ.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Quick Amplification 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 ND-1000 Spectrophotometer.

extract_protocol: Not provided.

tag: genotype/variation

value: expressing LacZ


title: MCF7-luc anti-NC-1

description: Luminal-type breast cancer cells


title: MCF7GLI1

source_name: MCF-7 expressing GLI1.

value: expressing GLI1


title: MA-342


title: HOC124_pt

status: Public on Jan 07 2015

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

country: Italy

institute: Fondo Edo Tempia

hyb_protocol: Hybridization was carried out for 17 hours at 65°C by rotating at 10 rpm. Microarray slides were washed in GE Wash Buffer-1 for 2 minutes and pre-warmed GE Wash Buffer-2 for 2 minutes at room temperature.

scan_protocol: Microarray slides were scanned in an Agilent Scanner version C (G2505C, Agilent Technologies).

data_processing: Images were analyzed using the Feature Extraction software v10.7. Raw data elaboration was carried out with Bioconductor (www.bioconductor.org), using R statistical language. Background correction was performed with the normexp method with an offset of 50 and quantile was used for between-array normalization. The LIMMA (LInear Models for Microarray Analysis) package was then used to identify differentially expressed genes in EOC-xenografts versus their corresponding patient tumors. The empirical Bayes method was used to compute a moderated t-statistics. Transcripts with a log base two fold change (logFC) greater than 1 or lower than -1 and p-value less than 0.01 were considered as differentially expressed.

source_name: Ovarian cancer from patient

label_protocol: Labeled cRNA target was prepared starting from100 ng of input RNA [RNA integrity number (RIN) > 7.0] by Low Input Quick Amp Labelling Kit and One-Color Spike-In Kit (Agilent Technologies) and purified with RNeasy Mini Kit (Qiagen) according to the manufacturer’s recommendation and protocols. Cyanine3CTP-labelled cRNA was quantified on a NanoDrop ND1000 Spectrophotometer using Microarray/RNA-40 measurement and the specific activity of cyanine 3 was calculated for each reaction. We set the minimum threshold of 2 μg for yield and 7 pmol/μg for the specific activity. Labeled cRNA (600ng) was fragmented by incubation with 5μl of 10× blocking reagent and 1μl of 25× fragmentation buffer in a 25μl reaction volume for 30 minutes at 60°C. Twentyfive microliters of 2× GE Hybridization Buffer Hi-RPM was added to fragmented cRNA;  40 μl of this  “hybridization mix” were placed onto the  SurePrint G3 Human GE V2 8x60K microarrays (50,599 Biological Features/array; Agilent Technologies).

growth_protocol: EOC-xenografts Subcutis models (s.c.). Tumors were dissected free of necrotic tissue repeatedly rinsed in HBSS and 2-4 mm of tissue was implanted subcutaneously  in the flank of nude mice.  Tumor growth was measured with a Vernier caliper, and tumor weights (mg = mm3) were calculated as follows: (length [mm] × width2 [mm2]) / 2.  Intraperitoneal models (i.p.). Ascites was centrifuged, washed repeatedly, resuspended in HBSS and implanted intraperitoneally in nude mice at a concentration of 10-20 ×10e6. Criteria for growing tumors were abdominal distension and palpable tumor masses in the peritoneal cavity. Mice were killed when they presented signs of discomfort (survival), ascites was harvested and the volume recorded.  Intrabursal transplantation (i.b.). Ovarian cancer cells from enzymatic digestion or ascites (1×10e6 cell suspension) were injected orthotopically under the bursa of the mouse ovary, as detailed in Supplementary data. At necroscopy, the ovary image was acquired with a macrodigital imaging system (MacroPATH; Milestone S.r.l, Sorisole, Italy); the two diameters were determined, the mean calculated and taken as measure of tumor mass. Ascites was harvested and the volume recorded.  Clinical specimens (primary ovarian tumors, metastasis, ascitic fluid) were obtained from patients undergoing surgery for ovarian tumor by laparotomy or paracentesis and in nude mice within 24hr. Established EOC-xenografts were cryopreserved frozen in DMSO and passed serially in nude mice for further studies (i.e. EOC-xenograft sample were immediately snap frozen for gene expression analysis).

extract_protocol: RNA isolation and assessment of human and mouse proportion. Qiazol and the miRNeasy Mini Kit together with a DNase I digestion step (Qiagen) were used according to the manufacturer’s recommendations to isolate total RNA from EOC-xenografts and patient tumor specimens. Total RNA quality was checked for integrity using RNA Nano Chips on Agilent Bioanalyzer 2100 (Agilent Technologies). Xenograft tumors are composed of a mixture of human- and mouse-derived cells; to assess their respective amount, total RNA was evaluated by way of species-specific TaqMan Prime Time qPCR assays for beta actin (ACTB). Briefly, 200ng tot RNA were reverse transcribed with random hexamers in a 20 microliters reaction by the High Capacity cDNA Reverse Transcription kit (Applied Biosystems); cDNA (2 microliters of the 1:20 dilution) was PCR amplified in 10 μl reaction, in presence of 500nM primers, 250nM probe (Hs PT39a22214847, MmPT53a.31778008, IDT) and the TaqMan gene expression master mix 1x (Applied Biosystem) on the Applied Biosystems 7900HT Fast Real Time PCR system (40 cycles at 94°C for 15 s, 60°C for 60s). Standard curves, generated with the following formula: [CtmouseACTB – CthumanACTB = (m-h Ct)] using known using known human and mouse tot RNA mixtures (100%, 95, 90 ,80, 75, 70, 60, 50%), were used to determine the proportions of human and mouse ACTB RNA in EOC-xenograft. The value (m-h Ct) obtained for each sample (analyzed in triplicate) was plotted against the standard curve to extrapolate the percentage of human RNA. Only samples with a human RNA content > 75%  were considered further.

treatment_protocol: EOC-xenografts collected from subcutis (sc), abdominal masses (am) and ascitic fluid (A) of mice engrafted with tumors at different passages (62 xenograft samples representing 29 EOC-xenograft models) and from 9 patient specimens, underwent one-color microarray-based gene expression profiling by way of SurePrint G3 Human GE V2 8x60K microarrays (50,599 Biological Features/array; Agilent Technologies) .

value: Epithelial Ovarian Cancer (EOC)

value: patient-derived tumor


title: MA-344


title: HOC230_pt


title: HOC218_pt


title: MA-343


title: HOC212_pt


title: HOC154_pt


title: HOC182_pt


title: HOC164_pt


title: HOC244_pt


title: Gene expression in MDA-MB-231

status: Public on Dec 31 2014

city: Shinagawa-ku

first: Hideyuki

last: Takeshima

department: Institute for Advanced Life Sciences

institute: Hoshi University

description: Untreated cells

hyb_protocol: 600 ng of labeled cRNA was hybridized to SurePrint G3 Human GE v2 8x60K Microarray for 17 hours at 65℃ and 10 rpm rotation. Microarrays was washed according to Agilent protocol.

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

data_processing: Scanned data was analyzed with Feature Extraction Ver.9.1 and analyzed using GeneSpring Ver.12.5 software (Agilent Technologies).

source_name: Breast cancer cell line, MDA-MB-231

label_protocol: From 200 ng of total RNA, Cy3-labeled cRNA was synthesized using Low Input Quick Amp Labeling Kit (Agilent technologies).

growth_protocol: Du145, PC3, MCF7, and MDA-MB-231 were maintained in RPMI1640 medium.  RWPE1 was maintained in keratinocyte-SFM.  HMEC was maintained in mammary epithelial cell serum-free growth medium.

extract_protocol: Total RNA was extracted from cancer cell lines and normal cells using ISOGEN (Nippon Gene, Tokyo, Japan).


title: HOC135_pt


title: Gene expression in Du145

description: Untreated cells

source_name: Prostate cancer cell line, Du145


title: Gene expression in PC3

description: Untreated cells

source_name: Prostate cancer cell line, PC3


title: Gene expression in MCF7

description: Untreated cells

source_name: Breast cancer cell line, MCF7


title: KP-MRT-RY_negative

status: Public on Nov 01 2014

first: Seishiro

last: Nodomi

address: 54 Kawahara-cho, Shogoin, Sakyo-ku

department: Pediatrics

institute: Graduate School of Medicine, Kyoto University

hyb_protocol: 3.0 ug of Cy3-labelled cDNA (specific activity >25.0 pmol Cy3/ug cDNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer 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 SurePrint G3 Human GE v2 8×60K Microarray 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 (Scan Area 71x21.6 mm, Scan resolution 10um).

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

source_name: Cell line

label_protocol: cDNA was generated from 2.0 ng RNA using Ribo-SPIA technology (NuGEN Technologies). Cyanine-3 (Cy3) labeled cDNA was generated using the Genomic DNA Enzymatic Labeling Kit (Agilent) according to the manufacturer's instructions.  Quality of labeled cDNA was checked by 2100 Bioanalyzer. Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: All cell lines were cultured in RPMI-1640 medium containing penicillin, streptomycin, L-glutamine, and 10% heat-inactivated fetal bovine serum (FBS) at 37 °C, and 5% CO2 humidified incubator.

extract_protocol: RNA was prepared using the RNeasy mini kit (Qiagen) following the manufacturer's recommendations.

treatment_protocol: Purified cells were sorted by FACSAriaⅡusing anti-human CD146 antibody (Miltenyi)

value: KP-MRT-RY

tag: mcam

value: negative


title: KP-MRT-NS_negative

value: KP-MRT-NS


title: HepG2

status: Public on Nov 12 2014

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays (8x60K v2, Design ID 039494) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: HepG2, passage15

label_protocol: 100 ng total RNA from all samples was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

extract_protocol: RNA was extracted using RNeasy Mini Kit.

treatment_protocol: For each human iPSC line for hepatocyte differentiation, all differentiated cells are constantly removed by manually picking up. Before the initiation of hepatocyte differentiation, human iPSCs were dissociated into clumps by using dispase (Roche) and plated onto BD Matrigel Basement Membrane Matrix Growth Factor Reduced (BD Biosciences). These cells were cultured in the MEF-conditioned medium for 3-4 days.  The differentiation protocol for the induction of definitive endoderm cells, hepatoblasts, and hepatocytes was based on our previous reports with some modifications.  Briefly, in the definitive endoderm differentiation, human iPSCs were cultured for 4 days in the L-Wnt3A-expressing cell (ATCC, CRL2647)-conditioned RPMI1640 medium (Sigma) which contains 100 ng/ml Activin A (R&D Systems), 4 mM L-Glutamine, 0.2% FBS (PAA Laboratories), and 1×B27 Supplement Minus Vitamin A (Life Technologies).  For the induction of HBCs, the definitive endoderm cells were cultured for 5 days in RPMI1640 medium (Sigma) which contains 30 ng/ml bone morphogenetic protein 4 (BMP4) (R&D Systems) and 20 ng/ml FGF4 (R&D Systems), 4 mM L-Glutamine, and 1×B27 Supplement Minus Vitamin A.  The protocol for HBC proliferation using human recombinant laminin-111 (BioLamina) was based on our previous report with some modifications. Briefly, the hPSC-derived HBCs were first purified from the hPSC-derived cells (day 9) by selecting attached cells on a human recombinant LN111-coated dish (final coating concentration was 1.0 μg/cm2) at 15 min after plating.  The hPSC-derived HBCs were cultured on a human LN111-coated dish (2.5 × 104 cells/cm2) in maintenance DMEM/F12 medium (DMEM/F12 medium (Invitrogen) was supplemented with 10% FBS (PAA laboratories), 1×insulin/transferrin/selenium, 10 mM nicotinamide, 10-7 M Dexamethasone (DEX) (Sigma), 20 mM HEPES, 25 mM NaHCO3, 1×GlutaMAX, 40 ng/ml hepatocyte growth factor (HGF) (R&D Systems) and 20 ng/ml epidermal growth factors (EGF) (R&D Systems)). The medium was refreshed every day. The HBCs were dissociated with Accutase (Millipore) into single cells, and subcultured every 6 or 7 days.  To perform the hepatocyte differentiation, the HBCs were cultured for 5 days in RPMI1640 medium (Sigma) which contains 20 ng/ml HGF, 4 mM L-Glutamine, and 1×B27 Supplement Minus Vitamin A.  And then, the cells were cultured for 11 days in Hepatocyte Culture Medium (HCM, Lonza) without EGF but with 20 ng/ml oncostatin M (OsM). Unlike our previous reports, the current differentiation method could omit the use of adenovirus-mediated overexpression of hepatic transcription factors.

value: HepG2, passage15


title: KP-MRT-YM_positive

value: KP-MRT-YM

value: positive


title: KP-MRT-RY_positive


title: PHH-iPSCs

source_name: PHH-iPSCs, undifferentiated

value: PHH-iPSCs, undifferentiated


title: KP-MRT-YM_negative


title: LNCap, rep2 [set 2]

status: Public on Oct 17 2014

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

country: USA

institute: NIEHS

description:
LNCap-2
Gene expression in androgen sensitive prostate cancer cells

hyb_protocol: The fragmented and labeled aRNA (600ng) were hybridized onto Agilent’s 8x60k format Human LINC RNA array using Agilent Technologies Gene Hybridization protocol.

scan_protocol: The arrays were scanned using Agilent's C Scanner following the scan protocol

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20120628) to obtain mean signals which were background corrected, log transformed and normalized using using Limma package.

source_name: LNCaP prostate cancer cells

label_protocol: The samples were labeled using One Color Quick Amp Labeling kit following Manufacturer's (Agilent Technologies) protocol. The protocol incorporates Cyanine 3-CTP to the target (aRNA) material.

growth_protocol: Cells were grown in RPMI1640 medium supplemented with 10% fetal bovine serum. Cells were harvested at confluency 70%.

extract_protocol: Total RNAs were prepared using the RNeasy kit (QAIGEN, Valencia CA) following the manufacturer's recommendations. The prostate epithelial cell RNA was purchased from Biochain (Cat # R1234201-50, Newark CA).  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: After prostatectomy, the pathologist examined tumor part and adjacent normal part of prostate. Two biopsy needle amount tissues were obtained from 10 pair of samples and tissues were immersed in RNAlater (Ambion, Austin TX). After 24 hr at 4C, samples were stored at -80C.

value: LNCaP

value: Prostate Cancer cells


title: OMN54 P23-1

status: Public on Oct 23 2014

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

hyb_protocol: 600ng labeled cRNA was hybridized on Agilent SurePrint G3 Human GE 8x60K Microarray (Design ID 028004)

scan_protocol: Slides were scanned with the Agilent DNA Microarray Scanner at a 3um scan resolution using the one colour and 20 bit tiff file settings

data_processing: Image files were processed with Agilent Feature Extraction 11.0.1.1 to produce spatially detrended and background subtracted gProcessedSignal intensities. Processed green signal was quantile normalized with Agilent GeneSpring 12.0.

source_name: prostate tumor_OMN54

label_protocol: 100ng of total RNA was used as input for generation of Cyanine-3-labeled cRNA following Agilent’s One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.0.

growth_protocol: The LTL-313H transplantable, PTEN-deficient, metastatic and PSA-secreting, patient-derived prostate cancer tissue line (generation 13) was maintained as grafts under renal capsules of male NOD-SCID mice supplemented with testosterone as described in manuscript. For experiments, tumors were harvested 10 weeks after grafting and pieces of tumor tissue (2.5x2.5x1.25 mm3) were grafted under the renal capsules of 36 testosterone-supplemented male mice (6 groups; 6 mice/group; 4 grafts/mouse). The grafts had a 100% engraftment rate with an average tumor volume doubling time of 13-15 days. Increases in the plasma PSA levels of the mice were used as a measure of tumor growth.

extract_protocol: Total RNA was extracted from xenograft tissues using a mirVana™ miRNA Isolation Kit (Life Technologies, Burlington, ON, Canada) according to the manufacturer's instructions.

treatment_protocol: After about 6 weeks, when levels of ~12 ng PSA/ml plasma had been reached, i.e. equivalent to tumor volumes of 30-50 mm^3, the mice were randomly distributed into 6 groups and treated with docetaxel (ip; Q7d/3) and Aneustat (orally; Q1dX5/3) along the following schedule: (a) vehicle control, (b) docetaxel (5 mg/kg), (c) Aneustat (1652 mg/kg), (d) docetaxel (5 mg/kg) + Aneustat (413 mg/kg), (e) docetaxel (5 mg/kg) + Aneustat (826 mg/kg), and (f) docetaxel (5 mg/kg) + Aneustat (1652 mg/kg). Expression microarray data were obtained from LTL-313H xenografts treated under four different conditions: docetaxel (5 mg/kg), Aneustat (1652 mg/kg), docetaxel (5 mg/kg) + Aneustat (1652 mg/kg), and untreated controls.  Aneustat and docetaxel  were both dissolved in DMSO and added as single drugs or in various combinations. DMSO was used as the vehicle control.

tag: host strain

value: NOD-SCID mice

tag: host strain gender

value: male

tag: cell line source

tag: tissue type

value: patient-derived prostate cancer tissue xenograft

tag: treated with

value: OMN54 alone


title: OMN54 P22-1


title: Control 1B

source_name: prostate tumor_untreated

value: DMSO (untreated, vehicle control)


title: Combination P1P-2

source_name: prostate tumor_OMN54+Docetaxel

value: OMN54 + Docetaxel in combination


title: Docetaxel 1023-3A

source_name: prostate tumor_Docetaxel

value: Docetaxel alone


title: LNCap, rep1 [set 2]

description:
LNCap-1
Gene expression in androgen sensitive prostate cancer cells

tag: cell line

tag: cell type


title: Docetaxel 1024-4A


title: PC3, rep3 [set 2]

description:
PC3-3
Gene expression in androgen insensitive prostate cancer cells

source_name: PC3 prostate cancer cells


title: Pooled tumor, tech rep1 [set 2]

description:
Tumor-1
Gene expression in human prostate tumor tissues

source_name: Pool of 10 patient's prostate Tumor tissues

tag: tissue

tag: tumore stage

value: 5 T3a, 1 T4, 1 T2c, and 3 unknown


title: LNCap, rep3 [set 2]

description:
LNCap-3
Gene expression in androgen sensitive prostate cancer cells


title: PC3, rep1 [set 2]

description:
PC3-1
Gene expression in androgen insensitive prostate cancer cells


title: Control 3C


title: PC3, rep2 [set 2]

description:
PC3-2
Gene expression in androgen insensitive prostate cancer cells


title: KP-MRT-NS_positive


title: Pooled tumor,  tech rep2 [set 2]

description:
Tumor-2
Gene expression in human prostate tumor tissues

value: Pool of 10 patient's prostate Tumor tissues


title: Combination P18-2


title: reference: SKCO1 cells transfected  bcatsiRNA , test:  SKCO1 cells transfected  TNFR1 siRNA5 experiment 2

status: Public on Oct 02 2014

city: Halifax

first: Kirill

last: Rosen

state: NS

address: ARC, CRC, 5849 University Ave

institute: Dalhousie University

description: mRNA expression was compared in SKCO1 cells transfected with b-catenin siRNA (reference sample) to that transfected with b-catenin siRNA and TNFR1 siRNA5 (test sample). Experiment 2

hyb_protocol: Labeled aRNA samples (300ng of each dye component) were co-hybridized to each array on an Agilent SurePrint G3 Human (V2) Gene Expression 8x60K microarray slide and incubated for 17 hours at 65C and 10rpm.

scan_protocol: After washing, slides were scanned at 3um on an Agilent C scanner.

data_processing: Data was extracted using Agilent Feature Extraction v. 11.5.1 software. Agilent GeneSpring version 12.6.1. Replicate probes within an array were summarized by applying a geometric mean. Before log base 2 transformation, a thresholding step was applied to set probe intensities less than 1.0 to 1.0. Log base 2 transformation was followed by normalization by Percentile Shift to the 75 percentile for the array. Fold Change was calculated as the difference in log values.

source_name: SKCO1 human colon carcinoma cells

label_protocol: Total RNA was quantitated using a Nanodrop ND-2000c in pedestal mode.  Concentrations were determined by A260 values, with 260/280 ratios ranging from 1.8 - 2.0 and 260/230 ranging from 2.0 - 2.2.  All processing from labeling onward was carried out in an ozone regulated environment monitored at < 5ppb.  Transcript was amplified and labeled from 200ng of total RNA using Agilent Low-Input Quick Amp kit in the presence of Agilent Dual-Color Spike-In controls.  Yield and dye incorporation values were measured by Nanodrop.

growth_protocol: SKCO-1 cells were transfected or not transfectedwith a 100 nM cont RNA or 50 nM cont RNA together with 50 nM bcatsiRNA2 or 50 nM bcatsiRNA2 together with 50 nM TNFR1siRNA5 or 50 nM bcatsiRNA2 together with 50 nM TNFR1siRNA6

extract_protocol: Total RNA was isolated using a Qiagen RNeasy Mini Kit and protocol.  RNA samples were quantitated using a Nanodrop 2000c spectrophotmeter (A260/A280 ratio > 2.0) and quality assessed using an Agilent HP2100 Bioanalyzer and RNA Nano kit from Agilent.

tag: transfection

value: beta-catenin siRNA

value: beta-catenin and TNFR1-siRNA5


title: reference: SKCO1 cells transfected  bcatsiRNA , test:  SKCO1 cells transfected  TNFR1 siRNA6 experiment 2

description: mRNA expression was compared in SKCO1 cells transfected with b-catenin siRNA (reference sample) to that transfected with b-catenin siRNA and TNFR1 siRNA6 (test sample). Experiment 2

value: beta-catenin and TNFR1-siRNA6