title: reference: SKCO1 cells transfected  bcatsiRNA , test:  SKCO1 cells transfected  TNFR1 siRNA5 experiment 1

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 1


title: reference: SKCO1 cells transfected  bcatsiRNA , test:  SKCO1 cells transfected  TNFR1 siRNA6 experiment 1

status: Public on Oct 02 2014

type: RNA

city: Halifax

first: Kirill

last: Rosen

state: NS

address: ARC, CRC, 5849 University Ave

country: Canada

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 siRNA6 (test sample). Experiment 1

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.

molecule: total RNA

organism: Homo sapiens

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-siRNA6


title: TE-5 [gene]

status: Public on Sep 20 2014

city: Sakai

first: OSAMU

last: ISHIBASHI

address: 1-1 Gakuen-cho, Naka-ku

department: Grad Sch Life & Environmental Sciences

country: Japan

institute: Osaka Prefecture University

hyb_protocol: cRNA (600 ng) was applied for hybridization using the Gene Expression Hybridization Kit (Agilent) according to the manufacturer's instructions.

scan_protocol: Fluorescent signals were detected using a SureScan Microarray Scanner G4900DA (Agilent).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to generate quantized raw data. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. A global mean normalization method was used.

source_name: Esophageal squamous cell carcinoma-derived cell line

label_protocol: Total RNAs (100 ng) were Cy3-labeled using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions.

growth_protocol: TE-1, TE-5, and TE-8 were cultured in RPMI-1640 supplemented with 10% fetal bovine serum. Het-1A was cultured using the BEGM kit (Lonza, Basel, Switzerland).

extract_protocol: AGPC method

treatment_protocol: The cells underwent no treatment during culture.

tag: cell line

tag: cell type

value: esophageal squamous cell carcinoma-derived cell line

tag: gender of donor

value: female

tag: age of donor

tag: stage of escc

value: IV

tag: differentiation of escc

value: poor


title: TE-8 [gene]

value: male

value: III

value: moderate


title: C5 vs. S5

status: Public on Aug 27 2014

city: Seongnam-si

first: Ah-Young

last: Kwon

state: Gyeonggi-do

address: 351 Yatap-dong, Bundang-gu

department: Department of Pathology

country: South Korea

institute: College of Medicine, CHA University

description: Ovarian serous carcinoma_no5_Spheroid-forming cell vs. Corresponding primary cancer cell

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.

label_protocol: 0.2ug of total RNA was labeled using Low Input Quick Amp Labeling Kit, Two-Color (Agilent Technology) as following manufacturer's instructions.

growth_protocol: Serum-free DMEM/F12 medium supplemented with 20 ng/ml epidermal growth factor,10 ng/ml basic fibroblast growth factor, 0.4% bovine serum albumin, and 5 µg/mL insulin.

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

value: primary cancer cell of ovarian serous carcinoma

value: Isolated spheroid-forming cell of ovarian serous carcinoma


title: control 7 vs. sample 7

description: Ovarian serous carcinoma_no7_Spheroid-forming cell vs. Corresponding primary cancer cell

source_name: control 7

source_name: sample 7


title: TE-1 [gene]

value: II

value: well


title: control 3-1 vs. S3

description: Ovarian serous carcinoma_no3_Spheroid-forming cell vs. Corresponding primary cancer cell

source_name: control 3-1


title: DU145_ALDH-_rep1

status: Public on Jul 15 2014

city: Dresden

first: Vasyl

last: Lukiyanchuk

address: Handelallee 26

country: Germany

institute: OncoRay

description: Gene expression in ALDH-negative parental DU145 cells

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 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 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 at 37°C wit 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 scan protocol Agilent G3_GX_1_color for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using protocol GE1_107_Sep09 and Grid: 039494_D_F_20120628 to obtain background subtracted and spatially detrended Processed Signal intensities

source_name: DU145 parental, ALDH- population, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Standard tissue culture at 37 ºC in a humidified incubator with 5% CO2, in DMEM supplemented with 10% FBS, 10mM HEPES, and 1x Pen/Strep

extract_protocol: RNA was isolated with RNeasy mini kit (Qiagen) following the manufacturer's recommendations

treatment_protocol: Radioresistant sub-line was generated from original (parental) DU145 cell line by multiple X-ray irradiations, 4Gy/dose, 1 week recovery between doses. Prior to RNA isolation cells were stained with Aldefluor kit (Stem Cell Technologies) and sorted by FACS

value: ALDH- population

value: DU145 parental


title: C4 vs. S4

description: Ovarian serous carcinoma_no4_Spheroid-forming cell vs. Corresponding primary cancer cell


title: DU145_ALDH+_rep2

description: Gene expression in ALDH-positive parental DU145 cells

source_name: DU145 parental, ALDH+ population, replicate 2

value: ALDH+ population


title: DU145radioresistant_total_rep2

description: Gene expression in non-sorted radioresistant DU145 cells

source_name: DU145 radioresistant, non-sorted, replicate 2

value: non-sorted

value: DU145 radioresistant


title: DU145radioresistant_ALDH+_rep3

description: Gene expression in ALDH-positive radioresistant DU145 cells

source_name: DU145 radioresistant, ALDH+ population, replicate 3


title: DU145_ALDH+_rep1

source_name: DU145 parental, ALDH+ population, replicate 1


title: DU145_ALDH+_rep3

source_name: DU145 parental, ALDH+ population, replicate 3


title: DU145radioresistant_ALDH+_rep1

source_name: DU145 radioresistant, ALDH+ population, replicate 1


title: DU145_ALDH-_rep3

source_name: DU145 parental, ALDH- population, replicate 3


title: DU145radioresistant_ALDH-_rep3

description: Gene expression in ALDH-negative radioresistant DU145 cells

source_name: DU145 radioresistant, ALDH- population, replicate 3


title: DU145radioresistant_total_rep1

source_name: DU145 radioresistant, non-sorted, replicate 1


title: DU145_total_rep1

description: Gene expression in non-sorted parental DU145 cells

source_name: DU145 parental, non-sorted, replicate 1


title: DU145radioresistant_total_rep3

source_name: DU145 radioresistant, non-sorted, replicate 3


title: DU145_total_rep3

source_name: DU145 parental, non-sorted, replicate 3


title: DU145radioresistant_ALDH+_rep2

source_name: DU145 radioresistant, ALDH+ population, replicate 2


title: DU145_total_rep2

source_name: DU145 parental, non-sorted, replicate 2


title: DU145radioresistant_ALDH-_rep1

source_name: DU145 radioresistant, ALDH- population, replicate 1


title: DU145radioresistant_ALDH-_rep2

source_name: DU145 radioresistant, ALDH- population, replicate 2


title: DU145_ALDH-_rep2

source_name: DU145 parental, ALDH- population, replicate 2


title: BreastCancer_LuminalA_C320

status: Public on May 08 2014

city: Gainesville

first: Xin

last: Qi

state: FL

address: 1600 SW Archer Rd

department: Medicinal Chemistry

country: USA

institute: University of Florida

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity > 8 pmol Cy3/ug 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 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 Whole Human Genome Oligo Microarrays (GPL17077) 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 using Agilent stabilization and drying solution.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x60k array slides (Scan Area 61X21 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The data were analyzed by GeneSpring GX (Agilent) using one parameter of subtype, whose values are Luminal A, Luminal B, Triple Negative and normal. Genes were filtered with one-way ANOVA (p<0.05) and fold change >= 2.0.

source_name: Breast tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA using the One-Color Low Input Quick Amp labeling kit (Agilent, Valencia, CA) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen, Valencia, CA) purification.  Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer (NanoDrop Technologies, Inc).

extract_protocol: Total RNAs were extracted using Qiagen RNeasy Mini Kit, QIAshredder kit and RNase-Free DNase Set kit (Qiagen, Valencia, CA) following manufacturer's recommendations. The protocol includes homogenization of tissue by grinding in mortor with liquid nitrogen and binding to the RNeasy Mini spin column, then DNase were used to get rid of trace amount of DNA. RNAs were quantified using a NanoDrop-2000 spectrophotometer and their qualities were monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: tissue type

value: breast cancer

tag: cancer subtype

value: Luminal A


title: BreastCancer_TripleNegative_C934

value: Triple Negative


title: BreastCancer_LuminalA_C156


title: MM231-D3H2LN-GFP-CD44+BM2 cells

status: Public on Jul 03 2014

city: Tokyo

first: Yusuke

last: Yoshioka

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

department: Division of Molecular and Cellular Medicine

institute: National Cancer Center Research Institute

description: Gene expression of the cells metastatic to bone marrow with expression of cancer stem cell marker, CD44

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

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

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 background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: metastatic breast cancer cell line to bone marrow sorted by FACS

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

growth_protocol: To track metastasis and establish a bone marrow-metastatic cell line, lentiviral infection of MDA-MB-231-luc-D3H2LN cells, was performed with the pGreenPuro Scramble Hairpin Control (construct MZIP000-PA-1, System Biosciences) to establish breast cancer cells that stably expressed both firefly luciferase and a GFP cloned from copepod Pontellina plumata (cop-GFP, also known as ppluGFP2). These cells, which we called MDA-MB-231-luc-D3H2LN-GFP, were cultured in RPMI containing 10% heat-inactivated fetal bovine serum (FBS) and penicillin with 100 units/mL, streptomycin with 100 µg/mL, and amphotericin B with 0.25µg/mL at 37°C in 5% CO2. The left heart ventricle of eight-week-old female C.B-17/Icr-scid/scidJc1 mice were injected with 1 × 105 MDA-MB-231-luc-D3H2LN-GFP cells suspended in 100 μl of PBS. The subsequent development of metastasis was monitored by injecting luciferin into the mice and measuring bioluminescence using an IVIS imaging system and Living Image 2.50 analysis software. On day 10, bioluminescence was detected in the bilateral legs of a mouse that had received an intracardiac injection. The mouse was sacrificed, and bone marrow was extracted from the legs, cultured in RPMI as described for the parental MDA-MB-231-luc-D3H2LN-GFP cell line above, and microscopically analyzed for GFP-positive cells. An MDA-MB-231-luc-D3H2LN-GFP cell was isolated and cultured under zeocin selection to establish clones, which we called MM231-D3H2LN-GFP-BM2 cells, cultured in RPMI as described above for the parental line.

extract_protocol: Total RNA was extracted from cultured cells using the QIAzol reagent and the miRNeasy Mini Kit (Qiagen) following the manufacturer's recommendations.

treatment_protocol: We sorted MM231-D3H2LN-GFP-BM2 cells co-cultured with BM-MSCs into CD44- and CD44+ populations.

value: MM231-D3H2LN-GFP-CD44+BM2 cells


title: BreastCancer_LuminalA_C935


title: MM231-D3H2LN-GFP-CD44-BM2 cells

description: Gene expression of the cells metastatic to bone marrow without expression of cancer stem cell marker, CD44

value: MM231-D3H2LN-GFP-CD44-BM2 cells


title: BreastCancer_LuminalA_C098


title: MM231-D3H2LN-GFP-BM2 cells

description: Gene expression of the cells metastatic to bone marrow

source_name: metastatic breast cancer cell line to bone marrow

value: MM231-D3H2LN-GFP-BM2 cells


title: BreastCancer_LuminalB_C734

value: Luminal B


title: BreastCancer_LuminalA_C943b


title: MM231-D3H2LN-GFP cells

description: Gene expression of the parental cells

source_name: breast cancer cell line

value: MM231-D3H2LN-GFP cells


title: BreastCancer_LuminalA_C878


title: BreastCancer_LuminalA_C579b


title: BreastCancer_LuminalA_C533b


title: BreastCancer_LuminalA_C968a


title: BreastCancer_LuminalA_xC557a


title: BreastCancer_LuminalA_C722a


title: BreastCancer_LuminalA_D419b


title: BreastCancer_LuminalA_C939a


title: BreastCancer_LuminalA_C660a


title: BreastCancer_LuminalA_C472a


title: BreastCancer_TripleNegative_C421c


title: BreastCancer_LuminalA_C501c


title: BreastCancer_LuminalB_C737a


title: BreastCancer_LuminalA_C449a


title: BreastCancer_TripleNegative_C313a


title: BreastCancer_LuminalA_C282a


title: BreastCancer_LuminalA_C629a


title: BreastCancer_LuminalB_C242a


title: Analysis 8: HPV Negative - Biological replicate 8

status: Public on Mar 05 2014

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

institute: University of South Carolina

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_1_3 sample in analysis 1, 2, 3, 4, 6

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.6 pmol Cy3/ug 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 instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to  Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray (G4858A-039494) 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 immersed in acetonitrile and dried immediately by slowly removing the slide.

scan_protocol: Slides were scanned immediately after washing on an Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green at 20 bit).

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 background subtracted and spatially detrended Processed Signal intensities.  Data was uploaded into Genespring version 11.5.1 where it was log2 transformed, quantile normalized and base line transformed using the median of all samples. Data was filted by flags in a way that at least 75% of the samples in any of the experimental groups had DETECTED flags. Then, differentially expressed genes were determined.

source_name: HPV Negative - Oropharyngeal squamous cell carcinoma

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with a NanoDrop 2000c Spectrophotometer.

extract_protocol: Total RNA was isolated from fresh frozen tumor samples or normal tissue using a miniaturized mortar and pestle system (CryoGrinder™, CryoCooler™, OPS diagnostics LLC) and TRIzol® Reagent (Ambion®, by Life Technologies).

tag: gender

value: Female

tag: race

value: European American


title: Analysis 8: HPV Negative - Biological replicate 6

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_2_3 sample in analysis 1, 2, 3, 4, 6

value: Male


title: Analysis 8: HPV Negative - Biological replicate 4

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_2_1 sample in analysis 1, 2, 3, 4, 6


title: Analysis 6: HPV Negative - Biological replicate 15

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_1_3 sample in analysis 1, 2, 3, 4, 8


title: Analysis 8: HPV Negative - Biological replicate 3

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_3 sample in analysis 1, 2, 3, 4, 6


title: Analysis 8: HPV Negative - Biological replicate 5

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_1_1 sample in analysis 1, 2, 3, 4, 6


title: Analysis 7: Normal - Biological replicate 4

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_2_2 sample in analysis 5, 6, 8

source_name: Normal - Benign uvula, tonsil


title: Analysis 6: HPV Negative - Biological replicate 16

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_3 sample in analysis 1, 2, 3, 4, 8


title: Analysis 7: Normal - Biological replicate 3

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_2_4 sample in analysis 5, 6, 8


title: Analysis 6: HPV Negative - Biological replicate 12

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_1_4 sample in analysis 1, 2, 4

value: African American


title: Analysis 8: HPV Negative - Biological replicate 1

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_1 sample in analysis 1, 2, 3, 4, 6


title: Analysis 7: Normal - Biological replicate 2

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_2_1 sample in analysis 5, 6, 8


title: Analysis 6: HPV Negative - Biological replicate 9

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_1_3 sample in analysis 1, 2, 4


title: Analysis 8: HPV Negative - Biological replicate 2

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_2 sample in analysis 1, 2, 3, 4, 6


title: Analysis 6: HPV Negative - Biological replicate 10

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_2_3 sample in analysis 1, 2, 3, 4, 8


title: Analysis 8: HPV Negative - Biological replicate 7

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_2_3 sample in analysis 1, 2, 3, 4, 6


title: Analysis 6: HPV Negative - Biological replicate 7

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_2_4 sample in analysis 1, 2, 4


title: Analysis 6: HPV Negative - Biological replicate 13

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_2_1 sample in analysis 1, 2, 4


title: Analysis 6: HPV Negative - Biological replicate 14

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_2_3 sample in analysis 1, 2, 3, 4, 8


title: Analysis 6: HPV Negative - Biological replicate 4

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_2_1 sample in analysis 1, 2, 3, 4, 8


title: Analysis 7: Normal - Biological replicate 1

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_1_2 sample in analysis 5, 6, 8


title: Analysis 6: HPV Negative - Biological replicate 5

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_2_2 sample in analysis 1, 2, 4


title: Analysis 6: HPV Negative - Biological replicate 3

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_4 sample in analysis 1, 2, 4


title: Analysis 6: HPV Negative - Biological replicate 6

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_2_3 sample in analysis 1, 2, 4


title: Analysis 5: HPV Active - Biological replicate 12

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_1_1 sample in analysis 1, 3

source_name: HPV Active - Oropharyngeal squamous cell carcinoma

extract_protocol: Total RNA was isolated from fresh frozen tumor samples using a miniaturized mortar and pestle system (CryoGrinder™, CryoCooler™, OPS diagnostics LLC) and TRIzol® Reagent (Ambion®, by Life Technologies).


title: Analysis 6: HPV Negative - Biological replicate 2

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_2 sample in analysis 1, 2, 3, 4, 8


title: Analysis 6: HPV Negative - Biological replicate 8

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_1_1 sample in analysis 1, 2, 3, 4, 8


title: Analysis 6: HPV Negative - Biological replicate 1

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_1 sample in analysis 1, 2, 3, 4, 8


title: Analysis 6: HPV Negative - Biological replicate 11

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_1_3 sample in analysis 1, 2, 4


title: Analysis 5: HPV Active - Biological replicate 2

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_2_4 sample in analysis 1, 3


title: Analysis 5: HPV Active - Biological replicate 9

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_2_2 sample in analysis 1, 3


title: Analysis 5: HPV Active - Biological replicate 10

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_2_2 sample in analysis 1, 3


title: Analysis 4: EA - HPV Negative - Biological replicate 8

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_1_3 sample in analysis 1, 2, 3, 6, 8

source_name: EA - HPV Negative - Oropharyngeal squamous cell carcinoma


title: Analysis 5: HPV Active - Biological replicate 1

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_2_3 sample in analysis 1, 3


title: Analysis 5: HPV Active - Biological replicate 7

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_1_4 sample in analysis 1, 3


title: Analysis 5: HPV Active - Biological replicate 11

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_2_3 sample in analysis 1, 3


title: Analysis 5: HPV Active - Biological replicate 5

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_1_3 sample in analysis 1, 3


title: Analysis 4: EA - HPV Negative - Biological replicate 4

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_2_1 sample in analysis 1, 2, 3, 6, 8


title: Analysis 4: EA - HPV Negative - Biological replicate 3

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_3 sample in analysis 1, 2, 3, 6, 8


title: Analysis 4: EA - HPV Negative - Biological replicate 1

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_1 sample in analysis 1, 2, 3, 6, 8


title: Analysis 5: HPV Active - Biological replicate 3

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_1_1 sample in analysis 1


title: Analysis 4: EA - HPV Negative - Biological replicate 5

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_1_1 sample in analysis 1, 2, 3, 6, 8


title: Analysis 4: EA - HPV Inactive - Biological replicate 2

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_1_4 sample in analysis 1, 3, 7

source_name: EA - HPV Inactive - Oropharyngeal squamous cell carcinoma


title: Analysis 5: HPV Active - Biological replicate 4

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_2_4 sample in analysis 1, 3


title: Analysis 5: HPV Active - Biological replicate 8

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_2_4 sample in analysis 1, 3


title: Analysis 4: EA - HPV Negative - Biological replicate 2

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_2 sample in analysis 1, 2, 3, 6, 8


title: Analysis 4: EA - HPV Negative - Biological replicate 6

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_2_3 sample in analysis 1, 2, 3, 6, 8


title: Analysis 4: EA - HPV Inactive - Biological replicate 4

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_1_4 sample in analysis 1, 3, 7


title: Analysis 4: AA - HPV Negative - Biological replicate 7

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_1_4 sample in analysis 1, 2, 6

source_name: AA - HPV Negative - Oropharyngeal squamous cell carcinoma


title: Analysis 4: EA - HPV Inactive - Biological replicate 1

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_1_2 sample in analysis 1, 3, 7


title: Analysis 5: HPV Active - Biological replicate 6

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_2_1 sample in analysis 1, 3


title: Analysis 4: EA - HPV Inactive - Biological replicate 3

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_2_1 sample in analysis 1, 3, 7


title: Analysis 4: AA - HPV Negative - Biological replicate 5

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_1_3 sample in analysis 1, 2, 6


title: Analysis 4: AA - HPV Negative - Biological replicate 8

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_2_1 sample in analysis 1, 2, 6


title: Analysis 4: AA - HPV Negative - Biological replicate 2

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_2_2 sample in analysis 1, 2, 6


title: Analysis 4: AA - HPV Negative - Biological replicate 3

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_2_3 sample in analysis 1, 2, 6


title: Analysis 4: AA - HPV Negative - Biological replicate 6

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_1_3 sample in analysis 1, 2, 6


title: Analysis 4: AA - HPV Negative - Biological replicate 1

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_4 sample in analysis 1, 2, 6


title: Analysis 4: AA - HPV Inactive - Biological replicate 2

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_1_1 sample in analysis 1

source_name: AA - HPV Inactive - Oropharyngeal squamous cell carcinoma


title: Analysis 4: AA - HPV Inactive - Biological replicate 4

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_1_2 sample in analysis 1


title: Analysis 3: HPV Negative - Biological replicate 4

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_2 sample in analysis 1, 2, 4, 6, 8


title: Analysis 4: AA - HPV Inactive - Biological replicate 1

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_2_2 sample in analysis 1


title: Analysis 3: HPV Negative - Biological replicate 3

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_3 sample in analysis 1, 2, 4, 6, 8


title: Analysis 3: HPV Negative - Biological replicate 5

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_2_3 sample in analysis 1, 2, 4, 6, 8


title: Analysis 4: AA - HPV Negative - Biological replicate 4

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_2_4 sample in analysis 1, 2, 6


title: Analysis 4: AA - HPV Inactive - Biological replicate 3

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_1_2 sample in analysis 1


title: Analysis 3: HPV Inactive - Biological replicate 3

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_1_4 sample in analysis 1, 4, 7

source_name: HPV Inactive - Oropharyngeal squamous cell carcinoma


title: Analysis 3: HPV Negative - Biological replicate 7

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_1 sample in analysis 1, 2, 4, 6, 8


title: Analysis 3: HPV Negative - Biological replicate 8

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_1_3 sample in analysis 1, 2, 4, 6, 8


title: Analysis 3: HPV Inactive - Biological replicate 2

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_1_2 sample in analysis 1, 4, 7


title: Analysis 3: HPV Negative - Biological replicate 2

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_1_1 sample in analysis 1, 2, 4, 6, 8


title: Analysis 3: HPV Active - Biological replicate 10

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_2_2 sample in analysis 1, 5


title: Analysis 3: HPV Negative - Biological replicate 6

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_2_1 sample in analysis 1, 2, 4, 6, 8


title: Analysis 3: HPV Inactive - Biological replicate 4

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_1_4 sample in analysis 1, 4, 7


title: Analysis 3: HPV Active - Biological replicate 11

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_1_3 sample in analysis 1, 5


title: Analysis 3: HPV Negative - Biological replicate 1

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_2_3 sample in analysis 1, 2, 4, 6, 8


title: Analysis 3: HPV Inactive - Biological replicate 1

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_2_1 sample in analysis 1, 4, 7


title: Analysis 3: HPV Active - Biological replicate 8

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_2_3 sample in analysis 1, 5


title: Analysis 3: HPV Active - Biological replicate 9

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_2_4 sample in analysis 1, 5


title: Analysis 3: HPV Active - Biological replicate 1

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_1_1 sample in analysis 1, 5


title: Analysis 3: HPV Active - Biological replicate 5

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_2_1 sample in analysis 1, 5


title: Analysis 3: HPV Active - Biological replicate 4

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_1_4 sample in analysis 1, 5


title: Analysis 3: HPV Active - Biological replicate 6

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_2_3 sample in analysis 1, 5


title: Analysis 3: HPV Active - Biological replicate 2

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_2_4 sample in analysis 1, 5


title: Analysis 3: HPV Active - Biological replicate 3

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_2_2 sample in analysis 1, 5


title: Analysis 3: HPV Active - Biological replicate 7

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_2_4 sample in analysis 1, 5


title: LPS SAMPLE 12

status: Public on Feb 10 2014

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 3

hyb_protocol: Hybridization and washing were performed according to the Illumina Manual Direct Hybridization Assay Guide

scan_protocol: Scanning was performed on the Illumina iScan (Illumina, Inc., San Diego, CA, U.S.A.).

data_processing: Image analysis and extraction of raw expression data was performed with Illumina GenomeStudio v2011.1 Gene Expression software with default settings (no background substraction and no normalization)

label: Biotin

source_name: monocyte-derived macrophages

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc., Austin, TX, U.S.A.) according to the manufacturers specifications with an input of 200 ng total RNA.

growth_protocol: Monocytes were isolated from buffy coats of healthy blood donors (Sanquin, Amsterdam, The Netherlands) by lymphoprep (Axis-Shield, Oslo, Norway) density gradient centrifugation followed by plastic adherence and culture in IMDM (Lonza, Basel, Switzerland) containing 10% human pool serum, 1% penicillin/streptomycin (Invitrogen, San Diego, CA), and 0.25% ciproxin (Bayer, Leverkusen, Germany).

extract_protocol: Macherey-Nagel Total RNA isolation Nucleospin RNAII

treatment_protocol: Fluticasone propionate (FP, 100 nM), Lipopolysacharide (LPS, 10 ng/ml)

value: monocyte-derived macrophages

tag: culture condition

value: Untreated (7d) + LPS (6h)


title: INF SAMPLE 5

description: Replicate 1

label: biotin

treatment_protocol: Fluticasone propionate (FP, 100 nM), Interferon gamma (IFNy, 12,5 ng/ml)

value: FP (5d) --> FP+IFNy (2d)


title: INF SAMPLE 3

description: Replicate 1

value: FP (7d)


title: LPS SAMPLE 2

description: Replicate 2

value: Untreated (7d)


title: LPS SAMPLE 9

description: Replicate 3

value: FP (7d) + LPS (6h)


title: LPS SAMPLE 3

description: Replicate 3


title: LPS SAMPLE 7

description: Replicate 1


title: INF SAMPLE 8

description: Replicate 2

value: FP+IFNy (7d)


title: INF SAMPLE 4

description: Replicate 2


title: LPS SAMPLE 1

description: Replicate 1


title: INF SAMPLE 7

description: Replicate 1


title: INF SAMPLE 6

description: Replicate 2


title: INF SAMPLE 11

description: Replicate 1

value: IFNy (7d)


title: INF SAMPLE 10

description: Replicate 2

value: IFNy (5d) --> FP+IFNy (2d)


title: LPS SAMPLE 6

description: Replicate 3


title: LPS SAMPLE 11

description: Replicate 2


title: INF SAMPLE 1

description: Replicate 1


title: INF SAMPLE 2

description: Replicate 2


title: LPS SAMPLE 8

description: Replicate 2


title: LPS SAMPLE 4

description: Replicate 1


title: INF SAMPLE 9

description: Replicate 1


title: LPS SAMPLE 10

description: Replicate 1


title: LPS SAMPLE 5

description: Replicate 2


title: INF SAMPLE 12

description: Replicate 2


title: LPS 10 ng/ml

status: Public on Jan 03 2014

description: 1% autologous serum macrophages

hyb_protocol: Hybridization and washing were performed according to the Illumina Manual “Direct Hybridization Assay Guide”

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc., Austin,  TX, U.S.A.) according to the manufacturer’s specifications with an input of 200 ng total RNA.

growth_protocol: Monocytes were isolated from buffy coats of healthy blood donors by Ficoll and percoll density gradientsand culture in X Vivo-10 supplemented with 1% Autologous serum for 7 days.

extract_protocol: Rneasy Total RNA isolation

treatment_protocol: At day 7 cells were treated for 24 hours with  Dexamethasone 100nM, LPS 10 ng/ml, IL-10 20 ng/ml, IL-13 20 ng/ml, IL-4 20 ng/ml or  IFNy 20 ng/ml

value: LPS 10 ng/ml


title: IL-13 20 ng/ml

description: 1% autologous serum macrophages

value: IL-13 20 ng/ml


title: IFNy 20 ng/ml

description: 1% autologous serum macrophages

value: IFNy 20 ng/ml


title: IL-4 20 ng/ml

description: 1% autologous serum macrophages

value: IL-4 20 ng/ml


title: IL-10 20 ng/ml

description: 1% autologous serum macrophages

value: IL-10 20 ng/ml


title: Dexamethasone 100nM

description: 1% autologous serum macrophages

value: Dexamethasone 100nM


title: Untreated

description: 1% autologous serum macrophages

value: Untreated


title: sh2_shTEAD4

status: Public on Jan 01 2014

city: Shanghai

first: Chen-Ying

last: Liu

address: 1665 Kong Jiang Road

country: China

institute: Xinhua Hospital, Shanghai Jiao Tong University

description: Gene expression of LoVo cells expressing sh2_shTEAD4

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 Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 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 8x60k 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 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

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: LoVo stable cells were cultured in the RPMI 1640 medium supplemented with 10% FBS.

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

value: LoVo colorectal cancer cells

tag: genotype/variation

value: expressing sh1_shTEAD4


title: pLKO.1 control

description: Gene expression of LoVo cells expressing pLKO.1 vector

source_name: LoVo_pLKO.1 vector

value: expressing pLKO.1 vector


title: 16-2_Th1

status: Public on Dec 31 2013

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: 1.6 µg labeled cRNA was hybridized to microarrays for 16h at 68°C and scanned using the Agilent DNA Microarray Scanner.

scan_protocol: Microarrays were scanned using the Agilent Scanner System. Data extractions were performed using Feature Extraction Software 10.7.1 (Agilent) with default patrameters of the GE1_107_Sep09 extraction protocol

data_processing: log2 transformed, median normalized to all samples, signal intensity expressed as relative to median signal intensity of all samples

organism: Mus musculus

source_name: Th1 supernatant

label_protocol: 500ng of total RNA were applied for Cy3-labelling reaction using the one color Quick Amp Labeling protocol (Agilent Technologies; Waldbronn, Germany).

extract_protocol: RNAeasy

treatment_protocol: Th1 supernatant

tag: treatment

value: Th1 supernatant

value: microglia


title: 14-3_Th17

source_name: Th17 supernatant

treatment_protocol: Th17 supernatant

value: Th17 supernatant


title: 786-O_knockdown 3_rep3

status: Public on Nov 25 2013

city: Beijing

first: xu

last: zhang

address: Fuxing road

institute: PLA general hospital

description:
Sample name: SH3
Total 1399 different expression genes (DEGs) including 880 up-regulated and 519 down regulated genes were found in overexpression S100A6 and vector control group.

hyb_protocol: The labeled cRNAs were hybridized onto the microarray according to the manufacturer’s standard protocols.

scan_protocol: After washing,  the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array  images  to get  raw data. Genesrping were employed  to  finish  the basic analysis  with  the  raw  data.  To  begin  with,  the  raw  data  was  normalized  with  the quantile algorithm. The probes that at least 1 out of all samples have flags in Detected were  chosen  for  further  data  analysis.  Differentially  expressed  genes  were  then identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05.   expression pattern among samples.

source_name: clear renal cell carcinoma cell line 786-O, stable transfection with knockdown of S100A6

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed  to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

growth_protocol: The 786-O cells were cultured in RPMI 1640 medium (HyClone), and the culture medium was supplemented with 10% fatal bovin serum (FBS, Gibco). The cells were maintained at 37℃ with 5% CO2.

extract_protocol: Total RNA from each sample was extracted using TRK1001（LC Sciences, Cat. TRK-1001, Total RNA Purification Kit）according to the manufacturer’s instructions. Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: The 786-O cells were stable transfection with overexpression and knockdown of S100A6, each treatment had a vector transfection control. The final purity of stable transfection is 99%.

value: clear cell renal cell carcinoma cell line 786-O

value: knockdown of S100A6


title: 786-O_knockdown control 3_rep3

description:
Sample name: SHC3
Total 1399 different expression genes (DEGs) including 880 up-regulated and 519 down regulated genes were found in overexpression S100A6 and vector control group.

source_name: clear renal cell carcinoma cell line 786-O, stable transfection with knockdown control of S100A6

value: knockdown control of S100A6


title: 16-3_Th17


title: 12-1_IMDM

source_name: untreated

treatment_protocol: untreated

value: untreated


title: 13-3_Th17


title: 16-1_IMDM


title: 786-O_knockdown control 2_rep3

description:
Sample name: SHC2
Total 1399 different expression genes (DEGs) including 880 up-regulated and 519 down regulated genes were found in overexpression S100A6 and vector control group.


title: 12-3_Th17


title: 13-1_IMDM


title: 786-O_overexpression control 3_rep3

description:
Sample name: OEC3
Total 344 different expression genes (DEGs) including 191 up-regulated and 153 down regulated genes were found in overexpression S100A6 and vector control group.

source_name: clear renal cell carcinoma cell line 786-O, stable transfection with overexpression control of S100A6

value: overexpression control of S100A6


title: 14-2_Th1


title: 14-1_IMDM


title: 786-O_knockdown control 1_rep3

description:
Sample name: SHC1
Total 1399 different expression genes (DEGs) including 880 up-regulated and 519 down regulated genes were found in overexpression S100A6 and vector control group.


title: 786-O_knockdown 2_rep3

description:
Sample name: SH2
Total 1399 different expression genes (DEGs) including 880 up-regulated and 519 down regulated genes were found in overexpression S100A6 and vector control group.


title: 786-O_overexpression control 2_rep3

description:
Sample name: OEC2
Total 344 different expression genes (DEGs) including 191 up-regulated and 153 down regulated genes were found in overexpression S100A6 and vector control group.


title: 13-2_Th1


title: 786-O_overexpression 3_rep3

description:
Sample name: OE3
Total 344 different expression genes (DEGs) including 191 up-regulated and 153 down regulated genes were found in overexpression S100A6 and vector control group.

source_name: clear cell renal cell carcinoma cell line 786-O, stable transfection with overexpression of S100A6

value: overexpression of S100A6


title: 786-O_knockdown 1_rep3

description:
Sample name: SH1
Total 1399 different expression genes (DEGs) including 880 up-regulated and 519 down regulated genes were found in overexpression S100A6 and vector control group.


title: sh1_shTEAD4

description: Gene expression of LoVo cells expressing sh1_shTEAD4


title: 12-2_Th1


title: 786-O_overexpression control 1_rep3

description:
Sample name: OEC1
Total 344 different expression genes (DEGs) including 191 up-regulated and 153 down regulated genes were found in overexpression S100A6 and vector control group.


title: 786-O_overexpression 1_rep3

description:
Sample name: OE1
Total 344 different expression genes (DEGs) including 191 up-regulated and 153 down regulated genes were found in overexpression S100A6 and vector control group.


title: 786-O_overexpression 2_rep3

description:
Sample name: OE2
Total 344 different expression genes (DEGs) including 191 up-regulated and 153 down regulated genes were found in overexpression S100A6 and vector control group.


title: DMS273-DyeSwap

status: Public on Nov 15 2013

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

country: Spain

institute: IDIBELL

description: Pooled clone 21-30-31 DMS-273

hyb_protocol: Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 300 ng. Volume: 50 uL. Temperature (ºC): 65. Duration: 17 hours.

scan_protocol: Scanned on an G2505C DNA microarray scanner (Agilent). Images were analysed by Agilent Feature Extraction Software (ver. 10.7), which performed feature quantitation and additive detrend correction. No background subtraction was performed.

data_processing: Data from hybridised microarray images were quantitated, corrected by additive detrending and submitted to dye bias normalisation after bias detection by linear and Lowess curve fitting methods (Agilent FeatureExtraction (FE) Software).Raw data signals are thresholded to 1, and replicated probe signals for the individual channels (Cy5 and Cy3) are summarized by computing their geometric mean. Normalised signal values are obtained by Cy5/Cy3 ratio computing and Log base2 transformation. These manipulations are done with GeneSpring GX12 software.

source_name: DMS-273 Control

label_protocol: Amount of nucleic acid labeled: 100ng. Commercial Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit by following manufacturer instructions. Agilent manual G4140-90050 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 either Cy3-CTP or Cy5-CTP fluorophores. Labeled samples are purified with silica-based RNeasy spin columns (Qiagen).

growth_protocol: Total RNA fraction. RNA Integrity Numbers were in the range 9.3 to 10.0 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer.

extract_protocol: Trizol

value: scrambled

value: DMS-273 SCLC

tag: tissue

value: Lung

source_name: Pooled clone 21-30-31 DMS-273

value: SETDB1 KD


title: NCI-H1437-DyeSwap

description: Pooled clone 56A-56B NCI-H1437

source_name: NCI-H1437 Control

value: NCI-H1437 NSCLC

source_name: Pooled clone 56A-56B NCI-H1437


title: NCI-H1437 rep1

description: NCI-H1437 Control

source_name: Pooled clone 56A NCI-H1437


title: NCI-H1437 rep2

description: NCI-H1437 Control

source_name: Pooled clone 56B NCI-H1437


title: DMS-273 rep3

description: DMS-273 Control

source_name: Pooled clone 31 DMS-271


title: DMS-273 rep2

description: DMS-273 Control

source_name: Pooled clone 30 DMS-272


title: Identification of miR-143 target genes in DU145

status: Public on Sep 25 2013

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

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

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).

value: prostate cancer

tag: transfection or treatment

value: control

source_name: miR-143 transfected cell line


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

source_name: control siRNA transfected cell line

source_name: si-GOLM1 transfected cell line


title: Identification of miR-143 target genes in PC3


title: Medium (SAMPLE 4)

status: Public on Jul 26 2013

description: Replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalized

source_name: monocyte-derived macrophages, Medium

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

growth_protocol: Monocytes were isolated from buffy coats of healthy blood donors by lymphoprep density gradient centrifugation followed by plastic adherence and culture in IMDM containing 10% human pool serum, 1% penicillin/streptomycin (Invitrogen, San Diego, CA), and 0.25% ciproxin (Bayer, Leverkusen, Germany).

extract_protocol: Tripure isolation reagent ( roche) + Rneasy cleanup

treatment_protocol: cells were stimulated with indicated cytokines for 5 days.

value: monocyte-derived macrophages

value: 10% Human serum


title: HBL100_shHIC1_sample

status: Public on Aug 22 2013

first: Gang

last: Xiao

address: 227 South Chongqing Road

institute: Shanghai Jiao-Tong University School of Medicine

description:
CGCD_KD
Gene expression in HBL100 cell line, H1C1 konck-downed

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit. Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm, Gene Spring Software 12.0 (Agilent technologies, Santa Clara, CA, US).

source_name: HBL100_HIC1 knockdown

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Human breast cancer cell lines MDA-MB-231 and the immortalized epithelial cells HBL-100 were maintained in DMEM (Hyclone), supplement with 10% FBS (GIBCO) and 1% penicillin/streptomycin. Cells were cultured at 37℃ water-saturated 5% CO2 atmosphere.

extract_protocol: Total RNA was checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: For restoring expression of HIC1 in MDA-MB-231 cells, human full-length HIC1 cDNA was inserted into lentivirus vector pHR-SIN-CSIGW. For the production of lentivirus, lenti-x cells were transfected with the PMD2.G, PSPAX2 and HIC1 expression vector using the lipofectamine 2000 (Invitrogen). After 48 hours, culture supernatants were collected and passed through 0.45µm filters, mixed with fresh media (1:1) and polybrene (8μg/ml) to infect target cells. For generation of a stable HIC1 knockdown cell line, GV248 lentiviral vectors expressing short hairpin RNAs targeting HIC1 were purchased from GeneChem Company (China, Shanghai). Lentiviruses were produced as described above and infected cells were selected by puromycin treatment at 1μg/ml.

value: human breast cancer cells

value: HIC1 knockdown


title: M-CSF (SAMPLE 6)

description: Replicate 2

source_name: monocyte-derived macrophages, M-CSF

value: 10% Human serum+50 ng/ml of M-CSF


title: Monocytes (SAMPLE 2)

description: Replicate 2

source_name: monocytes

value: monocytes

value: Monocytes directly after isolation


title: M-CSF (SAMPLE 5)

description: Replicate 1


title: Identification of miR-27b target genes in A498

value: renal cell carcinoma

source_name: miR-27b transfected cell line


title: Medium (SAMPLE 3)

description: Replicate 1


title: IL-4 (SAMPLE 9)

description: Replicate 1

source_name: monocyte-derived macrophages, IL-4

value: 10% Human serum+50 ng/ml of IL-10


title: IL-10 (SAMPLE 7)

description: Replicate 1

source_name: monocyte-derived macrophages, IL-10

value: 10% Human serum+50 ng/ml of IL-4


title: IL-4 (SAMPLE 10)

description: Replicate 2


title: Differentially expressed genes 12h after CXCL10 treatment in 786O

source_name: non treatment cell line

value: no treatment

source_name: CXCL10 12h

value: CXCL10 12h


title: IL-10 (SAMPLE 8)

description: Replicate 2


title: Monocytes (SAMPLE 1)

description: Replicate 1


title: HBL100_shCtrl_sample

description:
CGCC_KD
Gene expression in HBL100 cell line, control

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 12.0 (Agilent technologies, Santa Clara, CA, US).


title: Identification of miR-27b target genes in 786O


title: IFN-y (SAMPLE 12)

description: Replicate 2

source_name: monocyte-derived macrophages, IFN-y

value: 10% Human serum+50 U/ml of IFN-γ plus 12.5 ng/ml of TNF-α


title: IFN-y (SAMPLE 11)

description: Replicate 1


title: tumoral sample 171

status: Public on May 23 2013

city: Nantes

first: Boris

last: HALGAND

address: 1, rue Gaston Veil

country: France

institute: INSERM

description:
T_171_10296_2_1
raw data file: US82400123_253949410296_S01_GE2_107_Sep09_2_1.txt

scan_protocol: Scanner Agilent G2565CA Feature extraction 10.7

data_processing: Feature extraction 10.7 with protocol GE_107_sep09 and grid 039494_G2_D_F_20120628. Both positive and negative control probes were excluded from data normalization and data was filtered by the average of the median of the samples (79.1490322580645).  The features which at least 50% of the samples have values above the cut were included (resulting in 28,782 data rows in the sample data table).

source_name: sample of human liver from resection and transplantation

label_protocol: labelling protocol  was agilent protocol 'G4140-90050_GeneExpression_Two_Color_v6.5-mai 2010' and the labelling was pseudo mono color (1/2 of the sample with Cy3 and 1/2 of the sample with Cy5)

extract_protocol:
liver from human biospies and transplantation
Total RNA was extracted using Mirvana extraction kit following manufacturer protocol

tag: patient id

value: liver

tag: tissue subtype

value: tumoral


title: tumoral sample 209

description:
T_209_10296_2_3
raw data file: US82400123_253949410296_S01_GE2_107_Sep09_2_3.txt


title: tumoral sample 81

description:
T_81_10294_2_4
raw data file: US82400123_253949410294_S01_GE2_107_Sep09_2_4.txt


title: tumoral sample 197

description:
T_197_10296_2_4
raw data file: US82400123_253949410296_S01_GE2_107_Sep09_2_4.txt


title: tumoral sample 155

description:
T_155_10296_1_3
raw data file: US82400123_253949410296_S01_GE2_107_Sep09_1_3.txt


title: Differentially expressed genes by knocking down of GOLM1 in DU145

tag: cell line

value: prostate cancer


title: tumoral sample 223

description:
T_223_10294_2_3
raw data file: US82400123_253949410294_S01_GE2_107_Sep09_2_3.txt


title: tumoral sample 59

description:
T_59_10294_1_3
raw data file: US82400123_253949410294_S01_GE2_107_Sep09_1_3.txt


title: tumoral sample 69

description:
T_69_10295_1_2
raw data file: US82400123_253949410295_S01_GE2_107_Sep09_1_2.txt


title: tumoral sample 187

description:
T_187_10293_2_4
raw data file: US82400123_253949410293_S01_GE2_107_Sep09_2_4.txt


title: tumoral sample 165

description:
T_165_10293_1_4
raw data file: US82400123_253949410293_S01_GE2_107_Sep09_1_4.txt


title: tumoral sample 103

description:
T_103_10293_1_2
raw data file: US82400123_253949410293_S01_GE2_107_Sep09_1_2.txt


title: tumoral sample 31

description:
T_31_10292_1_1
raw data file: US82400123_253949410292_S01_GE2_107_Sep09_1_1.txt


title: tumoral sample 115

description:
T_115_10292_1_4
raw data file: US82400123_253949410292_S01_GE2_107_Sep09_1_4.txt


title: tumoral sample 183

description:
T_183_10292_2_2
raw data file: US82400123_253949410292_S01_GE2_107_Sep09_2_2.txt


title: tumoral sample 145

description:
T_145_10292_2_1
raw data file: US82400123_253949410292_S01_GE2_107_Sep09_2_1.txt


title: tumoral sample 191

description:
T_191_10292_2_4
raw data file: US82400123_253949410292_S01_GE2_107_Sep09_2_4.txt


title: tumoral sample 39

description:
T_39_10291_1_1
raw data file: US82400123_253949410291_S01_GE2_107_Sep09_1_1.txt


title: tumoral sample 49

description:
T_49_10291_1_2
raw data file: US82400123_253949410291_S01_GE2_107_Sep09_1_2.txt


title: tumoral sample 201

description:
T_201_10291_2_3
raw data file: US82400123_253949410291_S01_GE2_107_Sep09_2_3.txt


title: tumoral sample 43

description:
T_43_10292_1_2
raw data file: US82400123_253949410292_S01_GE2_107_Sep09_1_2.txt


title: tumoral sample 131

description:
T_131_10291_1_4
raw data file: US82400123_253949410291_S01_GE2_107_Sep09_1_4.txt


title: tumoral sample 161

description:
T_161_10291_2_2
raw data file: US82400123_253949410291_S01_GE2_107_Sep09_2_2.txt


title: tumoral sample 95

description:
T_95_10292_1_3
raw data file: US82400123_253949410292_S01_GE2_107_Sep09_1_3.txt


title: tumoral sample 141

description:
T_141_10268_2_1
raw data file: US82400123_253949410268_S01_GE2_107_Sep09_2_1.txt


title: tumoral sample 135

description:
T_135_10291_2_1
raw data file: US82400123_253949410291_S01_GE2_107_Sep09_2_1.txt


title: tumoral sample 177

description:
T_177_10296_1_2
raw data file: US82400123_253949410296_S01_GE2_107_Sep09_1_2.txt


title: tumoral sample 139

description:
T_139_10296_1_3
raw data file: US82400123_253949410296_S01_GE2_107_Sep09_1_3.txt


title: tumoral sample 77

description:
T_77_10268_1_2
raw data file: US82400123_253949410268_S01_GE2_107_Sep09_1_2.txt


title: tumoral sample 75

description:
T_75_10296_1_4
raw data file: US82400123_253949410296_S01_GE2_107_Sep09_1_4.txt


title: tumoral sample 205

description:
T_205_10293_2_2
raw data file: US82400123_253949410293_S01_GE2_107_Sep09_2_2.txt


title: tumoral sample 213

description:
T_213_10267_1_3
raw data file: US82400123_253949410267_S01_GE2_107_Sep09_1_3.txt


title: tumoral sample 203

description:
T_203_10296_2_3
raw data file: US82400123_253949410296_S01_GE2_107_Sep09_2_3.txt


title: tumoral sample 35

description:
T_35_10294_1_3
raw data file: US82400123_253949410294_S01_GE2_107_Sep09_1_3.txt


title: tumoral sample 159

description:
T_159_10293_2_1
raw data file: US82400123_253949410293_S01_GE2_107_Sep09_2_1.txt


title: tumoral sample 199

description:
T_199_10295_1_1
raw data file: US82400123_253949410295_S01_GE2_107_Sep09_1_1.txt


title: tumoral sample 113

description:
T_113_10295_1_3
raw data file: US82400123_253949410295_S01_GE2_107_Sep09_1_3.txt


title: tumoral sample 99

description:
T_99_10295_2_1
raw data file: US82400123_253949410295_S01_GE2_107_Sep09_2_1.txt


title: tumoral sample 195

description:
T_195_10293_1_3
raw data file: US82400123_253949410293_S01_GE2_107_Sep09_1_3.txt


title: tumoral sample 143

description:
T_143_10294_2_1
raw data file: US82400123_253949410294_S01_GE2_107_Sep09_2_1.txt


title: tumoral sample 79

description:
T_79_10292_2_3
raw data file: US82400123_253949410292_S01_GE2_107_Sep09_2_3.txt


title: tumoral sample 207

description:
T_207_10292_1_1
raw data file: US82400123_253949410292_S01_GE2_107_Sep09_1_1.txt


title: tumoral sample 221

description:
T_221_10296_1_1
raw data file: US82400123_253949410296_S01_GE2_107_Sep09_1_1.txt


title: tumoral sample 217

description:
T_217_10267_1_2
raw data file: US82400123_253949410267_S01_GE2_107_Sep09_1_2.txt


title: tumoral sample 169

description:
T_169_10292_1_3
raw data file: US82400123_253949410292_S01_GE2_107_Sep09_1_3.txt


title: tumoral sample 41

description:
T_41_10293_2_4
raw data file: US82400123_253949410293_S01_GE2_107_Sep09_2_4.txt


title: tumoral sample 215

description:
T_215_10291_1_3
raw data file: US82400123_253949410291_S01_GE2_107_Sep09_1_3.txt


title: tumoral sample 47

description:
T_47_10291_2_4
raw data file: US82400123_253949410291_S01_GE2_107_Sep09_2_4.txt


title: tumoral sample 93

description:
T_93_10291_2_2
raw data file: US82400123_253949410291_S01_GE2_107_Sep09_2_2.txt


title: tumoral sample 149

description:
T_149_10291_2_1
raw data file: US82400123_253949410291_S01_GE2_107_Sep09_2_1.txt


title: tumoral sample 189

description:
T_189_10268_2_4
raw data file: US82400123_253949410268_S01_GE2_107_Sep09_2_4.txt


title: tumoral sample 211

description:
T_211_10268_2_3
raw data file: US82400123_253949410268_S01_GE2_107_Sep09_2_3.txt


title: tumoral sample 133

description:
T_133_10268_1_4
raw data file: US82400123_253949410268_S01_GE2_107_Sep09_1_4.txt


title: Tumoral sample 51

description:
T_51_10268_1_1
raw data file: US82400123_253949410268_S01_GE2_107_Sep09_1_1.txt

value: Tumoral


title: tumoral sample 67

description:
T_67_10267_1_3
raw data file: US82400123_253949410267_S01_GE2_107_Sep09_1_3.txt


title: tumoral sample 83

description:
T_83_10268_1_2
raw data file: US82400123_253949410268_S01_GE2_107_Sep09_1_2.txt


title: tumoral sample 185

description:
T_185_10268_2_1
raw data file: US82400123_253949410268_S01_GE2_107_Sep09_2_1.txt


title: Differentially expressed genes 24h after CXCL10 treatment in 786O

tag: cell type

source_name: CXCL10 24h

value: CXCL10 24h


title: IL-4 treated macrophages M2 BMMF-1

status: Public on Sep 29 2012

description: Replicate 1

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: RMA in Affy R bioconductor

source_name: Bone Marrow derived macrophages

label_protocol: Affymetrix standard protocol

growth_protocol: Mouse bone marrow derived macrophages were prepared by culturing bone marrow extracts for 7 days in RPMI 1640 supplemented with MCSF ( 15 % of L-cell conditioned medium).

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were treated for 18 hours with 20 ng/ml of mIL-4.

tag: strain

value: macrophages

value: 18 hours with 20 ng/ml of mIL-4

tag: replicate


title: tumoral sample 129

description:
T_129_10267_1_2
raw data file: US82400123_253949410267_S01_GE2_107_Sep09_1_2.txt


title: Thio TCP M2

description: Replicate 1

source_name: thioglycolate-elicited murine peritoneal macrophages, incubated in OptiMEM-10 + IL-4 (supernatant from IL-4 producing cell line) for 24 hrs on tissue culture plastic

growth_protocol: Mouse thioglycollate  and Biogel elicited macrophages were isolated by adhesion and cultured on Pemanox or Tissue culture plastic, in RPMI 1640 .

treatment_protocol: Cells were treated for 24 hours with IL-4 (supernatant of mIL-4 cDNA transfected X63Ag8-653 plasmcytoma cell line).


title: IL-4 treated macrophages MF-3

description: replicates: Donor 3

data_processing: The data were normalised using quantile normalisation in Lumi (R Bioconductor).

source_name: monocyte derived macrophages

growth_protocol: Human ciculating monocytes were isolated using a double gradient of Ficall and Percoll, followed by an additional step with the monocyte isolation Kit II of Miltenyi. Cells were cultured in bacteriological plastic for 7 days in X-Viv0 10 medium supplemented with 1% autologous serum.

treatment_protocol: At day 7 cells were treated with IL-4 for 48 hours with 10 ng/ml of IL-4.

tag: sample type

value: Random Healthy donors

value: 48 hours with 10 ng/ml of IL-4

value: Donor 3


title: Biogel M0

description: Replicate 2

source_name: biogel-elicited murine peritoneal macrophages, incubated in OptiMEM-10 for 24 hrs on tissue culture plastic


title: IL-4 treated macrophages MF-1

description: replicates: Donor 1

value: Donor 1


title: DMS-273 rep1

description: DMS-273 Control

source_name: Pooled clone 21 DMS-273

value: SETDB1 KD

value: DMS-273 SCLC

value: Lung

source_name: DMS-273 Control

value: scrambled


title: Thio TCP M0

description: Replicate 3

source_name: thioglycolate-elicited murine peritoneal macrophages, incubated in OptiMEM-10 for 24 hrs on tissue culture plastic


title: Resting Macrophages MF-2

description: replicates: Donor 2

value: Donor 2


title: Resting Macrophages MF-3

description: replicates: Donor 3


title: Biogel M2

description: Replicate 3

source_name: biogel-elicited murine peritoneal macrophages, incubated in OptiMEM-10 + IL-4 (supernatant from IL-4 producing cell line) for 24 hrs on tissue culture plastic


title: Resting Macrophages M0 BMMF-1

description: Replicate 1


title: IL-4 treated macrophages-2

description: replicates: Donor 2

growth_protocol: Human ciculating monocytes were isolated using a double gradient of Ficall and Percoll, followed by an additional step with the monocyte isolation Kit II of Miltenyi. Cells were cultured in tissue culture plastic for 7 days in X-Viv0 10 medium supplemented with 1% autologous serum.

treatment_protocol: At day 7 cells were treated with IL-4 for 48 hours with 20 ng/ml of IL-4.

value: 48 hours with 20 ng/ml of IL-4


title: Thio permanox M0

description: Replicate 1

source_name: thioglycolate-elicited murine peritoneal macrophages, incubated in OptiMEM-10 for 24 hrs on Permanox plastic


title: Thio permanox M2

description: Replicate 2

source_name: thioglycolate-elicited murine peritoneal macrophages, incubated in OptiMEM-10 + IL-4 (supernatant from IL-4 producing cell line) for 24 hrs on Permanox plastic


title: IL-4 treated macrophages-3

description: replicates: Donor 3


title: Resting Macrophages MF-1

description: replicates: Donor 1


title: IL-4 treated macrophages M2 BMMF-3

description: Replicate 3


title: IL-4 treated macrophages M2 BMMF-2

description: Replicate 2


title: Resting Macrophages M0 BMMF-3

description: Replicate 3


title: Resting Macrophages M0 BMMF-2

description: Replicate 2


title: Resting Macrophages-3

description: replicates: Donor 3


title: IL-4 treated macrophages MF-2

description: replicates: Donor 2


title: IL-4 treated macrophages-1

description: replicates: Donor 1


title: tumoral sample 57

description:
T_57_10267_1_1
raw data file: US82400123_253949410267_S01_GE2_107_Sep09_1_1.txt

value: liver


title: Resting Macrophages-2

description: replicates: Donor 2


title: Resting Macrophages-1

description: replicates: Donor 1


title: Human Blood monocytes 3

status: Public on Apr 24 2009

description: Human Blood

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Signal values were generated using the Robust Multichip Average method with the Affymetrix Expression Console software. Statistical analysis and hierarchical clustering were done using the TM4 software.

source_name: Human Blood

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: HUES-2 ES cells were cultured at 37_C, 5% CO2 and atmospheric O2, and maintained on mitomycin C-inactivated mouse embryo fibroblasts (MEF) in 0.1% gelatin-coated six-well tissue culture plates containing 2 mL hES medium. hES medium consisted of knockout Dulbecco’s modified Eagle’s medium (Invitrogen GIBCO), 10% KO-Serum Replacement (Invitrogen GIBCO), 0.5% albumin (cat. no. 534021-4l; Sigma, St Louis, MO, USA), 2 mM Glutamax-I (Invitrogen GIBCO), 1% nonessential aminoacids (Invitrogen GIBCO), 100 U/mL penicillin and 100 mg/mL streptomycin (Invitrogen GIBCO), 0.055 mM b-mercaptoethanol, 10 ng/mL basic fibroblast growth factor (R&D). Medium was changed daily.   Differentiation of hES cells into monocytes: For embryoid body (EB) formation, hES cells were removed from feeder cells either mechanically by microdissecting hES colonies into 0.2-mm–diameter patches. Patches were transferred into six-well ultra-low adherence plates (Corning) in hES culture medium and cultured for 3 days at 37_C. For differentiation to monocytes, 50 to 100 EBs were transferred  into tissue culture T25 flasks containing 10 mL culture medium supplemented with M-CSF and IL-3. Medium was replaced every 5 to 7 days. Culture medium consisted of Advanced Dulbecco’s modified Eagle’s medium (Invitrogen GIBCO) and 10% fetal calf serum (Invitrogen GIBCO or Hyclone), supplemented with 50 ng/mL M-CSF (R&D), 25 ng/mL IL-3 (R&D), 2 mM L-glutamine (Invitrogen GIBCO), 100 U/mL penicillin and 100 mg/mL streptomycin (Invitrogen GIBCO), and 0.055 mM b-mercaptoethanol.   HUES2 Human ES cell-derived monocytes were differentiated into macrophages at a density of 1.5 _ 105 cells/cm2. Culture medium consisted of RPMI (Invitrogen GIBCO) and 10% fetal calf serum (Hyclone), supplemented with 100 ng/mL M-CSF (R&D), 2 mM L-glutamine (Invitrogen GIBCO), 100 U/mL penicillin and 100 mg/mL streptomycin (Invitrogen GIBCO). Medium was changed at day 3. Cells were harvested at day 7, by washing with PBS then lysing adherent cells in RNeasy lysis buffer (Qiagen).   Adult human blood was obtained from anonymous donors through the UK National Blood Bank Service, and tested negative for HIV-1, hepatitis B/C, and syphilis. Peripheral blood mononuclear cells were isolated by Ficoll-Hypaque (Pharmacia-Amersham) density gradient centrifugation from heparinized buffy coats. Monocytes  were isolated by CD14-positive selection using anti-CD14 magnetic beads (Miltenyi Biotec) by following manufacturer’s instructions.

extract_protocol: RNA was extracted with the RNeasy minikit (Qiagen).

value: Human Blood


title: tumoral sample 55

description:
T_55_10294_1_2
raw data file: US82400123_253949410294_S01_GE2_107_Sep09_1_2.txt

value: tumoral


title: Human embryonic cell-derived macrophages 1

description: HUES-2 human embryonic cell line (D. Melton, Harvard, http://www.mcb.harvard.edu/melton/HUES/HUES_manual.pdf), passage 16-38.

source_name: HUES-2 human embryonic cell line

value: HUES-2 human embryonic cell line


title: Human embryonic cell-derived macrophages 2


title: Human embryonic cell-derived monocytes 1


title: Human embryonic cell-derived macrophages 3


title: Human Blood monocytes 2

description: Human Blood


title: Human embryonic cell-derived monocytes 3


title: Human embryonic cell-derived monocytes 2


title: Human Blood monocytes 1

description: Human Blood


title: Macrophage at 7 days, biological rep1 HG-U133B

status: Public on Jul 10 2006

description: Monocytes

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HGU133 series. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with RNA using Bioconductor's R.

source_name: Blood

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

growth_protocol: RPMI 1640 20%FCS 100 ng/ml M-CSF

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

treatment_protocol: monocytes stimulated for 7 days with 100 ng/ml M-CSF

tag: Macrophage at 7 days, biological rep1


title: classical or M1 activated macrophages, biological rep2 HG-U133B

description: Monocytes

growth_protocol: mature macrophages supplemented with 20 ng/ml IFN-g+ 100 ng/ml LPS


title: Alternative or M2 activated macrophages, biological rep1 HG-U133B

description: Monocytes

treatment_protocol: mature macrophages supplemented with 20 ng/ml IL-4

tag: ALternative or M2 activated macrophages, biological rep1


title: Macrophage at 7 days, biological rep2 HG-U133B

description: Monocytes

tag: Macrophage at 7 days, biological rep2


title: Monocyteat 3 days, biological rep2 HG-U133B

description: Monocytes

treatment_protocol: monocytes stimulated for 3 days with 100 ng/ml M-CSF

tag: Monocyteat 3 days, biological rep2


title: Monocyte at 3 days, biological rep3 HG-U133B

description: Monocytes

tag: Monocyte at 3 days, biological rep3


title: classical or M1 activated macrophages, biological rep3 HG-U133B

description: Monocytes

treatment_protocol: mature macrophages supplemented with 20 ng/ml IFN-g+ 100 ng/ml LPS


title: Monocyte at T0, biological rep2 HG-U133B

description: Monocytes

growth_protocol: Cells were cultured in Petriperm dishes tomimic circulating conditions

treatment_protocol: freshly isolated monocytes

tag: Monocyte at T0, biological rep2


title: Alternative or M2 activated macrophages, biological rep3 HG-U133B

description: Monocytes

tag: ALternative or M2 activated macrophages, biological rep3


title: classical or M1 activated macrophages, biological rep1 HG-U133B

description: Monocytes


title: Ovary_Normal_UM-NO-3

status: Public on Apr 09 2007

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

description: Normal ovary

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Ann Arbor quantile-normalized trimmed-mean method

label_protocol: 3-5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: stage

tag: grade


title: Monocyte at T0, biological rep1 HG-U133B

description: Monocytes

tag: Monocyte at T0, biological rep1


title: Monocyte at T0, biological rep3 HG-U133B

description: Monocytes

tag: Monocyte at T0, biological rep3


title: Ovary_Normal_UM-NO-5

description: Normal ovary


title: Macrophage at 7 days, biological rep3 HG-U133B

description: Monocytes

tag: Macrophage at 7 days, biological rep3


title: Alternative or M2 activated macrophages, biological rep2 HG-U133B

description: Monocytes

tag: ALternative or M2 activated macrophages, biological rep2


title: Ovary_Normal_UM-NO-4

description: Normal ovary


title: Monocyte at 3 days, biological rep1 HG-U133B

description: Monocytes

tag: Monocyte at 3 days, biological rep1


title: Ovary_Normal_UM-NO-2

description: Normal ovary