title: UC7CONB

description: replicate 2

data_processing: Quantile normalization in the Linear Models for Microarray Data (LIMMA) package in the R language environment was used to normalize the data

source_name: urothelial cancer cell line

label_protocol: Biotinylated cRNA were prepared with Illumina RNA amplification kit

growth_protocol: UC14, Scaber and UC7 cell lines were obtained from MD Anderson Bladder SPORE Tissue Bank. Cell lines were cultured in 10% FBS modified Eagle's MEM with standard supplements at 37 °C in 5% CO2 incubator

extract_protocol: Total RNA was extracted by mirVANA miRNA Isolation Kit. Quality control was performed by NanoDrop ND-1000 and Agilent Bioanalyzer.

tag: sample type

value: control


title: m12_Ovarian

status: Public on Feb 10 2014

type: genomic

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: Normal colon mucosa from the same patient as the tumor was used as reference in the oaCGH experiments

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.

data_processing: The profiles were dewaved (van de wiel et al, Bioinformatics. 2009, median normalized and corrected for tumor cell percentage by using the R package CGHcall (van de Wiel et al, Bioinformatics. 2007)

molecule: genomic DNA

organism: Homo sapiens

source_name: Ovarian metastasis

label_protocol: DNA labeling protocol according to Enzo Life Sciences

extract_protocol: DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Brosens et al, J Pathol. 2010

tag: tissue

value: Ovarian metastasis (FFPE)

tag: patient

tag: type

value: metastasis

tag: site

value: Ovary

source_name: normal colorectum mucosa

value: normal colon mucosa obtained from the same patient as ch1


title: m15_Lung

source_name: Lung metastasis

value: Lung metastasis (FFPE)

value: Lung


title: m16_Liver

source_name: Liver metastasis

value: Liver metastasis (FFPE)

value: Liver


title: m11_Omental

source_name: Omental metastasis

value: Omental metastasis (FFPE)

value: Omentum


title: UC7CONC

type: RNA

city: Houston

first: Woonyoung

last: Choi

state: TX

address: 1515 Holcombe

country: USA

institute: Md Anderson Cancer center

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

label: biotin

molecule: total RNA

tag: cell line


title: UC7CONA

description: replicate 1


title: liver-tumor-ras-rep3

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

hyb_protocol: 10 µg of fragmented, biotinylated aRNA were hybridized for approximately 16 hrs at 45°C to the GeneChip® Mouse430_2 arrays. The arrays were then washed and stained with the GeneChip® Hybridization Wash and Stain kit (Affymetrix). The washing and staining steps were performed with GeneChip® Fluidics Workstation 450 (Affymetrix).

scan_protocol: Arrays were then scanned using a solid-state laser scanner (GeneArray® Scanner 3000 combined with the GeneChip® autoloader, Affymetrix). The Affymetrix GeneChip® Operating Software (GCOS) was used to generate the primary and secondary raw data files.

data_processing: The raw microarray data was normalized using the RMA method implemented in R (v.2.14.1)/Bioconductor (v.2.9).

organism: Mus musculus

source_name: Ha-ras-mutated liver tumor tissue

label_protocol: Processing of GeneChip® experiments was conducted as recommended by the manufacturer of the GeneChip® system (Affymetrix). For tissue samples, double stranded cDNA was synthesized with a starting amount of 0.1 µg total RNA. For RNA reverse transcription, the GeneChip® 3′ IVT Express Labelling Assay (lot ID 0904012, Affymetrix) was used in the presence of a T7-(dT)24 DNA oligonucleotide primer (Affymetrix). The cDNA was then transcribed in vitro in the presence of biotinylated ribonucleotides to form biotin-labelled amplified RNA (aRNA). The labelled aRNA was then purified and quantified by UV spectrophotometry at 260 nm and fragmented.

growth_protocol: 29-32 days old male C3H/HeJ mice were obtained from Charles River Laboratories (Germany). Animals were allowed to acclimatise for 5 days prior to being randomly divided into two treatment groups (n = 10).

extract_protocol: Frozen liver and kidney samples were homogenized in TRIzol reagent (Invitrogen) and subsequently purified on a silica-gel-based-membrane (RNeasy, Qiagen) according to the manufacturer's instructions. RNA quality was assessed by measuring the RIN (RNA Integrity Number) using an Agilent 2100 Bioanalyzer. RNA was stored at −80°C until GeneChip® experiment analysis.

treatment_protocol: Phenobarbital (Sigma 04710, 0.05% (w/v) in drinking water) was administered to one group through ad libitum access to drinking water for 28 days. Mice were checked daily for activity and behavior and sacrificed on the last day of dosing (day 28).

tag: strain

tag: gender

value: male

value: liver

tag: treated with

value: drinking water (control)

value: oral

value: ad libitum

value: 27 weeks


title: p23

source_name: Colorectal cancer

value: Colorectal cancer (FFPE)

value: primarytumor

value: Colorectum


title: m10_Liver

value: metastasis


title: liver-tumor-ras-rep1


title: m18_Omental

value: normal colon mucosa obtained from the same patient as ch1


title: UC7ROSIB

description: replicate 3

value: rosiglitazone treated (1μM, 24hours)


title: m7_LymphNode

source_name: Lymph node metastasis

value: Lymph node metastasis (FFPE)

value: Lymph node


title: liver-tumor-ras-rep2


title: m17_Omental


title: UC7ROSIA

description: replicate 1


title: m8_Ovarian

value: Ovarian metastasis (FFPE)

value: Ovary


title: m9_Omental

value: Omentalmetastasis (FFPE)

value: Omentum


title: Scaber_KDSTAT3C

description: replicate 3

value: Scaber

value: STAT3 siRNA


title: m5_Omental

value: Omental metastasis (FFPE)


title: Scaber_NTA

description: replicate 1

value: Non-targeting siRNA


title: liver-control-ctnnb1-rep6

source_name: Non-mutated liver control (non-tumor) tissue

value: male

value: liver

value: Phenobarbital in drinking water

value: oral

value: ad libitum

value: 27 weeks


title: liver-control-haras-rep3

value: drinking water (control)


title: liver-control-haras-rep1


title: Scaber_KDSTAT3B

description: replicate 2


title: Scaber_NTB

description: replicate 2


title: liver-tumor-ctnnb1-rep7

source_name: Ctnn1b-mutated liver tumor tissue


title: Scaber_KDSTAT3A

description: replicate 1


title: UC7ROSIC

description: replicate 2

value: rosiglitazone treated (1μM, 24hours)


title: liver-tumor-ctnnb1-rep5


title: m5_Ovarian

value: metastasis

value: normal colon mucosa obtained from the same patient as ch1


title: Ma.Mel79_TNF

city: Bonn

first: Michael

last: Holzel

address: Sigmund-Freud Str. 25

department: Institute of Clinical Chemistry and Clinical Pharmacology

country: Germany

institute: University Hospital Bonn

data_processing: Variance stabilization and normalisation using vsn package from bioconductor in R without background correction

source_name: melanoma culture_TNFalpha stimulated

label_protocol: 100ng RNA was converted to biotinylated cRNA using one round of amplification with Illumina Labelling Kit and one round of T7 polymerase

growth_protocol: Human melanoma cell lines were cultured in RPMI/10% FCS

extract_protocol: Total RNA was isolated using RLT buffer (Quiagen) and purified using spin columns. RNA quality was assayed using Agilent Bioanalyzer

treatment_protocol: Melanoma cell cultures were stimulated with 1000U/ml TNF-alpha for 72 hours or left untreated.

tag: cell type

value: human melanoma cells

tag: stimulated with

value: 1000U/ml TNF-alpha for 72 hrs

tag: braf

value: wild-type

tag: nras

value: mutated

tag: hras


title: liver-control-haras-rep2


title: UC14-KDP63B

description: replicate 2

value: p63 shRNA


title: m4_Omental

value: Omental metastasis (FFPE)

value: Omentum


title: liver-tumor-ctnnb1-rep6

value: male


title: liver-control-ctnnb1-rep5

value: liver


title: m14_Ovarian

value: Ovarian metastasis (FFPE)

value: Ovary


title: m6_LymphNode

value: Lymph node metastasis (FFPE)

value: Lymph node


title: liver-control-ctnnb1-rep4

value: Phenobarbital in drinking water

value: oral

value: ad libitum

value: 27 weeks


title: m2_Liver

value: Liver metastasis (FFPE)

value: metastasis

value: Liver

value: normal colon mucosa obtained from the same patient as ch1


title: m3_Ovarian


title: liver-tumor-ctnnb1-rep4


title: UC14-KDP63C

description: replicate 3

value: p63 shRNA


title: m1_Liver


title: Control 2 C58

city: Taian

first: Dong

last: Li

state: Shandong Province

address: No 2, Yingshengdonglu

department: Department of Public Health

country: China

institute: Taishan Medical College

description: plasma

hyb_protocol: The Hy3TM labeled sample was hybridized on a miRCURYTM LNA Array (v.18.0) (Exiqon, Denmark) according to array manual. The total 25 μl mixture from Hy3TM labeled sample was mixed with 25 μl hybridization buffer, denatured at 95°C for 2 mins, incubated on ice for 2 mins, and then hybridized to the miRCURYTM microarray for 16-20 hours at 56°C in a phalanTM hybridization bag

scan_protocol: A GenePix 4000B microarray scanner was used to scan the microarray and collect fluorescence intensity

data_processing: Genepix Pro 6.0 software (Axon) was used for image analysis. The original signal of each probe was corrected by subtracting that of the background. Probe intensities were corrected by subtracting background intensity and normalized using median array normalization, where each background-subtracted intensity was divided by the median intensity of non-control probes with corrected value ≥ 50 on the array.

source_name: fracture of clavicle

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used for miRNA labeling. Each sample was 3’-end-labeled with the Hy3TM fluorescent label using RNA ligase following the instructions of the labeling kit to obtain fluorescent probes for microarray hybridization

extract_protocol: The total RNA in 250 μl plasma was extracted following instructions of the TRIzol and miRNeasy mini kit (Qiagen, USA)

value: fracture of clavicle

tag: statue

value: Alive

tag: age

tag: Sex


title: Control 3 C82

description: plasma

source_name: radial head subluxation

value: radial head subluxation

value: female


title: Scaber_NTC

description: replicate 3

value: Scaber

tag: sample type

value: Non-targeting siRNA


title: liver-tumor-ctnnb1-rep3

value: male

tag: tissue

value: liver


title: UC14_NTC

description: replicate 3

value: Non-targeting shRNA


title: BCL vs B (female, HCV+)_Sample E

status: Public on Feb 09 2014

city: Kagoshima

first: Kyoko

last: Tsukiyama-Kohara

state: Kagoshima

department: Joint Faculty of Veterinary Medicine

country: Japan

institute: Kagoshima University

hyb_protocol: 0.825 µg of Cy3 or Cy5-labeled cRNA was fragmented using the Agilent Gene Expression Hybridization Kit protocol. Hybridizations were performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with a Laser Scanner GenePix 4000B (Molecular Devices) using a scan resolution of 5µm and appropriate gains on the photomultiplier (PMT) to obtain the highest intensity without saturation.

data_processing: Agilent Feature Extraction Software (v 9.5.1.1) was used for background subtraction and LOWESS normalization.

label_protocol: 150 ng of total RNA was amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer's protocol.

growth_protocol: SPF mouse

extract_protocol: RNA was extracted by Qiagen RNeasy kit and RNA integrity was assessed by Bioanalyzer.

treatment_protocol: Total RNA was from BCL or B cells.

value: 129/sv, BALB/c, and C57BL/6J mixed background

value: BCL (tumor tissue)

tag: hcv status

value: HCV+

value: B cell


title: Patient 3 D64

description: plasma

source_name: Ventricular septal defect

value: Ventricular septal defect


title: Patient 2 D55

description: plasma


title: UC14_NTA

description: replicate 1


title: liver-tumor-ctnnb1-rep2

value: Phenobarbital in drinking water

value: oral

value: ad libitum

value: 27 weeks


title: UC14-KDP63A

description: replicate 1

value: p63 shRNA


title: Control 1 C56

description: plasma

value: radial head subluxation

value: Alive


title: Patient 1 D28

description: plasma


title: HCV- vs+（male B cell)_Sample D

value: HCV-


title: HCV+ vs - (male B cell) _Sample C


title: B vs BCL(male,HCV+)_Sample B


title: liver-tumor-ctnnb1-rep1


title: BCL vs B (male,HCV+)_Sample A


title: HCV+vs - (female B cell) _Sample G

value: female


title: B vs BCL(female, HCV+)_Sample F


title: UC14_NTB

description: replicate 2


title: HCV- vs+（female B cell)_Sample H


title: MURA150 R11-technical replicate 2

city: RENNES

first: rogue

last: alexandra

address: 2 av du professeur leon bernard

country: France

institute: inserm

description: Gene expression after 24h-treatment with muraglitazar 150µM  in HepaRG cells

hyb_protocol: 825 ng of Cy3-RNAs and 825 ng of Cy5-RNAswere hybridized using the Hybridisation Kit Plus (Agilent) onto 4×44K Whole Human Genome Microarrays (G4112F, Agilent). 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 two color scan setting for 4x44k array slides

data_processing: Agilent Feature Extraction Software (10.1) was used for background subtraction and LOWESS normalization.

source_name: HepaRG cells

label_protocol: Five hundred ng of total RNA from each cell culture were reverse-transcribed into double-strand cDNAs and amplified for 2 h at 40°C using the Quick Amp Labeling Kit (Agilent). cDNAs were transcribed into antisense cRNA and labeled with CTP-Cy3 fluorescent dye for 2 h at 40°C following the manufacturer's protocol. Cyanine-labeled cRNAs were purified using RNeasy minikit (Qiagen, Inc., Valencia, CA).

growth_protocol: HepaRG cells were seeded at a density of 2.6x104 cells/cm2 in Williams’ E medium supplemented with 10% FCS, 100 units/mL penicillin, 100 μg/mL streptomycin, 5 μg/mL insulin, 2 mM glutamine and 5x10−5 M hydrocortisone hemisuccinate. After two weeks they were shifted to the same culture medium supplemented with 2% DMSO for two more weeks. At that time HepaRG cells were well differentiated and used for treatments by chemicals. Human hepatocytes undergoing resection for primary and secondary tumors were obtained by collagenase perfusion of histologically normal liver fragments and used for the preparation of RNA samples and primary cultures. Hepatocyte cultures were obtained by seeding 170,000 cells/cm² in 6-well plates in a Williams’ E medium supplemented with 10% FCS, 100 units/µl penicillin, 100 µg/ml streptomycin, 1 µg/ml insulin, 2 mM glutamine, and 1 µg/ml bovine serum albumin. The medium was discarded 12 h after seeding, and cells were thereafter maintained in serum-free medium supplemented with 5 x 10-5 M hydrocortisone hemisuccinate. HH were used 24 h after seeding.

extract_protocol: Cells were harvested in lysis buffer (RLT buffer and β-mercaptoethanol). Total RNA was isolated using the RNeasy mini kit (Qiagen). RNA quantity and purity were assessed with a Nanodrop ND-1000 spectrophotometer (Nyxor Biotech, Paris, France) and RNA integrity was checked with a Bioanalyzer 2100 (Agilent Technologies, Massy, France).

treatment_protocol: TRO, ROSI, MURA and TESA were dissolved in DMSO and treatments were performed in a FCS-free medium. All control and treated cultures received 0.1% DMSO as the vehicle final concentration.

value: HepaRG cells

tag: treatment

value: 24h-treatment with 0.1% DMSO

value: 24h-treatment with muraglitazar 150µM


title: TESA300 R10-technical replicate 2

description: Gene expression after 24h-treatment with tesaglitazar 300µM  in HepaRG cells

value: 24h-treatment with tesaglitazar 300µM


title: TESA300 R9-technical replicate 2


title: TESA300 R11-technical replicate 2


title: TESA300 R10-technical replicate 1


title: MURA150 R11-technical replicate 1


title: MURA100 R9-technical replicate 1

description: Gene expression after 24h-treatment with muraglitazar 100µM  in HepaRG cells

value: 24h-treatment with muraglitazar 100µM


title: MURA50 R11-technical replicate 1

description: Gene expression after 24h-treatment with muraglitazar 50µM  in HepaRG cells

value: 24h-treatment with muraglitazar 50µM


title: MURA150 R9-technical replicate 1


title: MURA100 R11-technical replicate 1


title: MURA150 R10-technical replicate 1


title: MURA50 R10-technical replicate 2


title: TESA300 R11-technical replicate 1


title: MURA100 R9-technical replicate 2


title: MURA100 R11-technical replicate 2


title: TESA300 R9-technical replicate 1


title: MURA50 R11-technical replicate 2


title: MURA100 R10-technical replicate 1


title: MURA150 R10-technical replicate 2


title: MURA100 R10-technical replicate 2


title: MURA150 R9-technical replicate 2


title: MURA50 R9-technical replicate 1


title: MURA20 R10-technical replicate 2

description: Gene expression after 24h-treatment with muraglitazar 20µM  in HepaRG cells

value: 24h-treatment with muraglitazar 20µM


title: MURA50 R10-technical replicate 1


title: ROSI150 R11-technical replicate 2

description: Gene expression after 24h-treatment with rosiglitazone 150µM  in HepaRG cells

value: 24h-treatment with rosiglitazone 150µM


title: MURA20 R9-technical replicate 2


title: MURA20 R10-technical replicate 1


title: MURA50 R9-technical replicate 2


title: ROSI150 R11-technical replicate 1


title: ROSI150 R9-technical replicate 2


title: ROSI100 R10-technical replicate 2

description: Gene expression after 24h-treatment with rosiglitazone 100µM  in HepaRG cells

value: 24h-treatment with rosiglitazone 100µM


title: ROSI150 R10-technical replicate 1


title: ROSI100 R9-technical replicate 1


title: MURA20 R9-technical replicate 1


title: ROSI100 R10-technical replicate 1


title: ROSI50 R10-technical replicate 2

description: Gene expression after 24h-treatment with rosiglitazone 50µM  in HepaRG cells

value: 24h-treatment with rosiglitazone 50µM


title: ROSI100 R11-technical replicate 1


title: ROSI50 R11-technical replicate 2


title: ROSI20 R11-technical replicate 2

description: Gene expression after 24h-treatment with rosiglitazone 20µM  in HepaRG cells

value: 24h-treatment with rosiglitazone 20µM


title: ROSI50 R9-technical replicate 2


title: ROSI50 R9-technical replicate 1


title: ROSI150 R9-technical replicate 1


title: ROSI100 R11-technical replicate 2


title: ROSI50 R11-technical replicate 1


title: ROSI150 R10-technical replicate 2


title: ROSI50 R10-technical replicate 1


title: TRO40 R11-technical replicate 1

description: Gene expression after 24h-treatment with troglitazone 40µM  in HepaRG cells

value: 24h-treatment with troglitazone 40µM


title: ROSI20 R11-technical replicate 1


title: TRO40 R11-technical replicate 2


title: ROSI20 R10-technical replicate 2


title: ROSI20 R9-technical replicate 1


title: ROSI100 R9-technical replicate 2


title: ROSI20 R10-technical replicate 1


title: TRO40 R10-technical replicate 1


title: TRO40 R10-technical replicate 2


title: TRO40 R9-technical replicate 2


title: ROSI20 R9-technical replicate 2


title: TRO20 R11-technical replicate 2

description: Gene expression after 24h-treatment with troglitazone 20µM  in HepaRG cells

value: 24h-treatment with troglitazone 20µM


title: TRO40 R9-technical replicate 1


title: TRO20 R9-technical replicate 2


title: TRO20 R10-technical replicate 1


title: TRO20 R11-technical replicate 1


title: TRO5 R11-technical replicate 1

description: Gene expression after 24h-treatment with troglitazone 5µM  in HepaRG cells

value: 24h-treatment with troglitazone 5µM


title: TRO20 R10-technical replicate 2


title: TRO5 R11-technical replicate 2


title: TRO5 R9-technical replicate 2


title: HH1_TESA300

description: Gene expression after 24h-treatment with TESA 300µM in human hepatocytes

hyb_protocol: 1650 ng of Cy3-RNAs were hybridized using the Hybridisation Kit Plus (Agilent) onto 4×44K Whole Human Genome Microarrays (G4112F, Agilent). 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 4x44k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014850_D_F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HH1_TESA300 replicate 1

growth_protocol: Human hepatocytes undergoing resection for primary and secondary tumors were obtained by collagenase perfusion of histologically normal liver fragments and used for the preparation of RNA samples and primary cultures. Hepatocyte cultures were obtained by seeding 170,000 cells/cm² in 6-well plates in a Williams’ E medium supplemented with 10% FCS, 100 units/µl penicillin, 100 µg/ml streptomycin, 1 µg/ml insulin, 2 mM glutamine, and 1 µg/ml bovine serum albumin. The medium was discarded 12 h after seeding, and cells were thereafter maintained in serum-free medium supplemented with 5 x 10-5 M hydrocortisone hemisuccinate. HH were used 24 h after seeding.

value: human hepatocytes

tag: donor number

value: donor 1

value: 24h-treatment with TESA 300µM


title: HH2_TESA300

source_name: HH2_TESA300 replicate 1

value: donor 2


title: HH4_TESA300

source_name: HH4_TESA300 replicate 1

value: donor 4


title: TRO20 R9-technical replicate 1

value: HepaRG cells

value: 24h-treatment with 0.1% DMSO


title: HH3_MURA150

description: Gene expression after 24h-treatment with MURA 150µM in human hepatocytes

source_name: HH3_MURA150 replicate 1

value: donor 3

value: 24h-treatment with MURA 150µM


title: HH4_MURA150

source_name: HH4_MURA150 replicate 1


title: TRO5 R10-technical replicate 1


title: HH3_TESA300

source_name: HH3_TESA300 replicate 1


title: HH2_MURA100

description: Gene expression after 24h-treatment with MURA 100µM in human hepatocytes

source_name: HH2_MURA100 replicate 1

value: 24h-treatment with MURA 100µM


title: HH2_MURA50

description: Gene expression after 24h-treatment with MURA 50µM in human hepatocytes

source_name: HH2_MURA50 replicate 1

value: 24h-treatment with MURA 50µM


title: HH4_ROSI150

description: Gene expression after 24h-treatment with ROSI 150µM in human hepatocytes

source_name: HH4_ROSI150 replicate 1

value: 24h-treatment with ROSI 150µM


title: HH3_MURA100

source_name: HH3_MURA100 replicate 1


title: TRO5 R10-technical replicate 2


title: HH2_MURA150

source_name: HH2_MURA150 replicate 1


title: HH3_MURA50

source_name: HH3_MURA50 replicate 1


title: HH4_MURA100

source_name: HH4_MURA100 replicate 1


title: HH1_MURA100

source_name: HH1_MURA100 replicate 1


title: HH1_MURA150

source_name: HH1_MURA150 replicate 1


title: TRO5 R9-technical replicate 1


title: HH4_MURA50

source_name: HH4_MURA50 replicate 1


title: HH2_ROSI150

source_name: HH2_ROSI150 replicate 1


title: HH4_ROSI100

description: Gene expression after 24h-treatment with ROSI 100µM in human hepatocytes

source_name: HH4_ROSI100 replicate 1

value: 24h-treatment with ROSI 100µM


title: HH3_ROSI100

source_name: HH3_ROSI100 replicate 1


title: HH3_ROSI150

source_name: HH3_ROSI150 replicate 1


title: HH1_MURA50

source_name: HH1_MURA50 replicate 1


title: HH4_ROSI50

description: Gene expression after 24h-treatment with ROSI 50µM in human hepatocytes

source_name: HH4_ROSI50 replicate 1

value: 24h-treatment with ROSI 50µM


title: HH3_TRO40

description: Gene expression after 24h-treatment with TRO 40µM in human hepatocytes

source_name: HH3_TRO40 replicate 1

value: 24h-treatment with TRO 40µM


title: HH2_ROSI100

source_name: HH2_ROSI100 replicate 1


title: HH1_ROSI150

source_name: HH1_ROSI150 replicate 1


title: HH3_TRO20

description: Gene expression after 24h-treatment with TRO 20µM in human hepatocytes

source_name: HH3_TRO20 replicate 1

value: 24h-treatment with TRO 20µM


title: HH4_TRO40

source_name: HH4_TRO40 replicate 1


title: HH4_TRO20

source_name: HH4_TRO20 replicate 1


title: HH1_ROSI100

source_name: HH1_ROSI100 replicate 1


title: HH2_TRO20

source_name: HH2_TRO20 replicate 1


title: HH3_control

description: Gene expression after 24h-treatment with 0.1% DMSO in human hepatocytes

source_name: HH3_control replicate 1


title: HH1_TRO5

description: Gene expression after 24h-treatment with TRO 5µM in human hepatocytes

source_name: HH1_TRO5 replicate 1

value: 24h-treatment with TRO 5µM


title: HH1_TRO20

source_name: HH1_TRO20 replicate 1

value: human hepatocytes


title: HH2_control

source_name: HH2_control replicate 1


title: HH1_control rep2

source_name: HH1_control replicate 2

value: donor 1


title: HH3_TRO5

source_name: HH3_TRO5 replicate 1


title: HH2_ROSI50

source_name: HH2_ROSI50 replicate 1


title: HH4_control rep2

source_name: HH4_control replicate2


title: HH1_control

source_name: HH1_control replicate 1


title: HH2_TRO5

source_name: HH2_TRO5 replicate 1


title: HH3_control rep2

source_name: HH3_control replicate2


title: HH4_TRO5

source_name: HH4_TRO5 replicate 1


title: HH1_ROSI50

source_name: HH1_ROSI50 replicate 1


title: HH4_control

source_name: HH4_control replicate 1


title: HH3_ROSI50

source_name: HH3_ROSI50 replicate 1


title: HH2_control rep2

source_name: HH2_control replicate2


title: SMMC-7721_control_rep2

status: Public on Feb 08 2014

city: shanghai

first: shu-han

last: sun

address: 800 Xiang-Yin Road

institute: Second Military Medical University

hyb_protocol: Using the Phalanx hybridization system.

scan_protocol: Data extraction using GenePix™  4100 from Molecular Devices.

data_processing: GPR files were loaded into Rosetta Resolver® System (Rosetta Biosoftware) to process data analysis.

source_name: control SMMC-7721

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method.

extract_protocol: The total RNA was extracted from the differnent stable SMMC-7721 cells using TRIzol reagent (ambion).

value: hepatocellular carcinoma

tag: cell line


title: 7966

city: New York

first: Jing

last: Shen

address: 650 W. 168th St. Black Building Rm.1608

institute: Columbia University

description: Tumor

data_processing:
For the normalization it uses the average of the endogenous control: U6 snRNA
Target miRNA signals normalized to the control; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_Controls)]
ABI DataAssist TM software automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports HCC tumor /non-tumor tissue ratios.

label: FAM

source_name: Liver tissue

extract_protocol:
Total RNA, including miRNAs was isolated from frozen tissue samples using RNeasy Microarray Tissue Mini Kits (Qiagen, Frederick, MA) according to the manufacturer’s protocol.
TaqMan Low Density Arrays (TLDA, Applied Biosystems, Foster City, CA), examining 733 miRNAs profiles (670 unique human mature miRNAs ), were used to generate genome-wide miRNA profiles for 10 paired HCC tumor and adjacent non-tumor tissues. A two-step process was performed involving a reverse transcription (RT) reaction followed by a quantitative real-time PCR (qRT-PCR). The RT reaction was carried out according to the manufacturer's instructions including 1mM dNTPs (including TTP), 50U MultiScribe Reverse Transcriptase, 3.8U RNase inhibitor, and 1×Reverse Transcription buffer. Input RNA of 750 ng was used for each RT reaction. TaqMan stem-loop primers for 733 unique human miRNAs, 1 endogenous controls (U6 snRNA) and 1 negative control (ath-miR-159a) were used in the RT reaction. Conditions for the RT reaction were as follows: 16°C for 30 min, 42°C for 30 min, 85°C for 5 min, then hold at 4°C. The RT products were then diluted (10x) by 0.1xTE (pH 8.0) prior to adding TaqMan 2× Universal PCR Master Mix (No AmpErase UNG). The entire mixture was added to individual ports of the TaqMan Human MicroRNA Array v3. The array were centrifuged at 1,200 rpm for 1 min, and then run on 7900HT Fast Real-Time PCR system for 95°C, 10 min followed by 40 cycles of 95°C for 15 s, 60°C for 1 min. Cycle threshold (Ct) values were calculated using the SDS2.2.2. Normalized expression was reported as 2−ΔΔCt, where Ct was the threshold cycle to detect fluorescence. Ct value greater than 40 was considered as below the detection threshold of the array.

value: Female

value: tumor


title: 7980

description: Tumor

value: Male


title: 7965

description: Non-tumor

value: adjacent non-tumor


title: 7529

description: Non-tumor


title: 7530

description: Tumor


title: 7670

description: Non-tumor


title: 7669

description: Tumor


title: SMMC-7721_control_rep3


title: 7979

description: Non-tumor


title: 7527

description: Non-tumor


title: 7528

description: Tumor


title: 7526

description: Tumor


title: 7525

description: Non-tumor


title: 7517

description: Non-tumor


title: 7518

description: Tumor


title: 7523

description: Non-tumor


title: SMMC-7721_control_rep1


title: 7515

description: Non-tumor


title: 7516

description: Tumor


title: 7524

description: Tumor


title: 7514

description: Tumor


title: 7513

description: Non-tumor


title: SMMC-7721_lncRNA-ATB_overexpression_rep2

source_name: SMMC-7721 stably overexpress lncRNA-ATB


title: TGF-β_untreated_rep3

hyb_protocol: 1 μg of each labeled cRNA was  fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505B).

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies).

extract_protocol: The total RNA was extracted from above mentioned treated or untreated SMMC-7721 cells, and then mRNA was purified from 1 μg total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).


title: SMMC-7721_lncRNA-ATB_overexpression_rep1


title: SMMC-7721_lncRNA-ATB_overexpression_rep3


title: gamma-catenin WT, biological replicate 3

city: Epalinges

first: Werner

last: Held

address: Chemin des Boveresses 155

department: Ludwig Center for Cancer Research

institute: University of Lausanne

hyb_protocol: Affymetrix Mouse Gene 1.0 ST arrays (Affymetrix, Santa Clara, CA, USA) were hybridized with 2.3 μg of fragmented target at 45°C for 16 hours, and washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix) and raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package (Affymetrix).

data_processing: Expression data was background corrected, normalized and summarized on probe set level using the RMA algorithm implemented in Affymetrix Expression Console version 1.1.

source_name: Day 21 after BCR-ABL1 transduction and transplantation, WT

label_protocol: For each sample, 100 ng of total RNA was amplified using the Ambion® WT Expression Kit (4411973, Life Technologies) kit. 5.5 μg of the cDNA was fragmented and labeled with GeneChip® WT Terminal Labeling kit (901525, Affymetrix).

extract_protocol: Trizol (Invitrogen) extraction of total RNA and RNA clean up using RNeasy mini kit (Qiagen) were performed according to the manufacturers' instructions.

treatment_protocol: C57BL/6 (B6) mice (CD45.1+) were reconstituted with fetal liver cells from embryos expressing or lacking gamma-catenin (CD45.2+). At least 8 weeks later, total bone marrow cells from chimeric mice were transduced with BCR-ABL1+ IRES GFP retrovirus and transplanted into lethally irradiated B6 recipients (CD45.1+). Three weeks later, GFP+ (BCR-ABL1+) B220+ BP-1+ CD45.2+ B cells were flow sorted.

tag: strain/background

tag: genotype/variation

value: Jup+/+

value: bone marrow

value: BCR-ABL1+ BP1+ B cells


title: TGF-β_treated_rep2

source_name: SMMC-7721 continuously treated with 10 ng/ml of recombinant TGF-β1 for 21 days


title: TGF-β_untreated_rep1


title: TGF-β_treated_rep3


title: TGF-β_treated_rep1


title: gamma-catenin WT, biological replicate 2


title: gamma-catenin KO, biological replicate 1

source_name: Day 21 after BCR-ABL1 transduction and transplantation, gamma-catenin KO

value: Jup-/-


title: HDAC2 KO mice colon rep 2

city: Sherbrooke

first: Martin

last: Lessard

state: Qc

address: 2000 College

department: Sherbrooke Research Centre

country: Canada

institute: Agriculture and AgriFood Canada

description: gene expression data in colon epitelial cells from HDAC1/2 KO mice

hyb_protocol: Hybridized target cRNA is stained with streptavidin phycoerythrin

scan_protocol: arrays are scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the GeneChip® array.

data_processing: Data analysis, normalization average difference and expression measurements were subsequently completed with Flexarray software version 1.6.1.  Background correction and normalization were assessed with a multi-array average (RMA) algorithm. Significant statistical differences were calculated with the Student’s t test, with the cut-off for statistical significance set to a p value of 0.05 or below.

source_name: epithelium from colon of HDAC2 KO mouse no.2

label_protocol: Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization

growth_protocol: HDAC2 conditionally mutated mice were provided by Dr EN Olson (University of Texas Southwestern Medical Center, Dallas, TX) (Montgomery et al., 2007). Floxed HDAC2 mice were crossed with villin-Cre transgenic mice to insure specific intestinal epithelial cell gene deletion (Madison et al., 2002). Genomic DNA was recovered with the Spin Doctor genomic DNA kit (Gerard Biotech, Oxford, OH). Mouse genotypes were determined with already published RT-PCR protocols (Montgomery et al., 2007). Mice were fed a normal diet in a transgenic mouse facility.

extract_protocol: Total RNAs from the colon of three control and three HDAC2 IEC-specific knockout mice were isolated with the Rneasy kit (Qiagen, Mississauga, ON, Canada). cDNA preparation and microarray assay were performed at the Microarray platform of the McGill University and Génome Quebec Innovation Centre

treatment_protocol: no treatment was given to mice

value: colon

value: HDAC2 KO


title: TGF-β_untreated_rep2


title: gamma-catenin KO, biological replicate 2


title: gamma-catenin KO, biological replicate 3


title: control mice colon rep 3

description: gene expression data in colon epitelial cells from normal mice

source_name: epithelium from colon of control mouse no.3

value: control


title: HDAC2 KO mice colon rep 3

source_name: epithelium from colon of HDAC2 KO mouse no.3


title: P. falciparum K1 HDTAB treated

city: Kuala Lumpur

first: Mohd Ridzuan

last: Mohd Abd Razak

address: Jalan Pahang

country: Malaysia

institute: Institute for Medical Research

description: Gene expression data after parasite incubation for 72 hours

hyb_protocol: Biotinylated cRNA was purified using GeneChip®  Sample Cleanup Module kit and 20 µg were fragmented by incubating with fragmenting buffer at 94 oC for 35 min, then mixed with hybridization cocktail (50 pM control oligonucleotide B2, 1X eukaryotic hybridization controls (bioB, bioC, bioD, cre), 1X hybridization mix and 10% DMSO) prior to hybridization onto GeneChip® Plasmodium/Anopheles Genome Array (Affymetrix).

scan_protocol: The hybridized gene chip was scanned by Affymetric GeneChip Scanner 3000 equipped with GeneChip® Operating Software (GCOS) and GeneChip Fluidics Station 450

data_processing: The DNA microarray data were analysed using Affymetrix expression console software

organism: Plasmodium falciparum

source_name: Parasite trophozoites with HDTAB treatment incubated for 72 hours

label_protocol: RNA was spiked with eukaryotic poly-A RNA as positive labelling control and was then converted to cDNA using GeneChip® Expression 3’-Amplification Reagent One-Cycle cDNA synthesis kit (Affymetrix, USA). cDNA was purified using the GeneChip sample cleanup kit and then converted to cRNA and biotinylated by incubating with the IVT reaction master mix (1X IVT labelling buffer, IVT labelling NTP mix and IVT labelling enzyme mix) (GeneChip® Expression 3’-Ampification Reagent for IVT labelling kit; Affymetrix). at 37 oC for 16 hours.

growth_protocol: Continuous cultivation of malaria parasite, P. falciparum in vitro was maintained according to the candle jar method of Trager and Jensen (1976)  in complete culture medium containing  RPMI 1640 (Gibco, USA), 0.2% sodium bicarbonate, 25 mM HEPES,  40 µg/L gentamicin and 10% human serum.

extract_protocol: the RNA was extracted using Trizol reagent (Invitrogen, USA) followed by purification using Purelink Micro to Midi kit (Invitrogen, USA) and DNase treatment to the manufacturer’s instructions.

treatment_protocol: P. falciparum was exposed to HDTAB at IC50 value (2 µM) for 72 hours

tag: strain

value: hexadecyltrimethylammonium bromide


title: 35S:CDO1 normoxia 3

status: Public on Feb 07 2014

city: Pisa

first: Francesco

last: Licausi

address: Via Mariscoglio 34

department: Institute of Life Sciences

country: Italy

institute: Scuola Superiore Sant'Anna

description: PCO1 N3

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: RMA algorithm using RobinA software (PMID:22684630)

organism: Arabidopsis thaliana

source_name: 35S:CDO1 normoxia

label_protocol: Affymetrix standard labeling protocol

growth_protocol: Seeds were sown in 6-cm diameter pots containing moisted Arabidopsis soil. The seeds were stratified at 4°C in the dark for 2 days and then the pots were moved in a growth chamber at short photoperiodic conditions (8h light 16 h darkness) with 18°C in the night and 22°C in the day.

extract_protocol: Total RNA was extracted from whole 5-week old plants using the RNeasy kit (Qiagen). RNA quality was assessed by agarose gel electrophoresis and spectrophotometry. RNA was processed for use on Affymetrix Arabidopsis Genome GeneChip arrays.

treatment_protocol: Plants were harvested at 10am in the morning, 2h after the start of the day.

value: 35S:PCO1 transgenic (overexpression of Plant Cysteine Oxidase (PCO1))

value: 4 wks

value: normoxia

value: whole rosette


title: wild type hypoxia 3

description: WT H3

source_name: wild type hypoxia

treatment_protocol: Plants were treated in the darkness at 5% O2 v/v in air for 4h at 10am in the morning, 2h after the start of the day

value: wild type

tag: subjected to

value: 4h hypoxia (5% O2 v/v in air)


title: gamma-catenin WT, biological replicate 1

tag: cell type


title: 35S:PCO1 hypoxia 1

description: CDO1 H1

source_name: 35S:PCO1 hypoxia


title: 35S:PCO1 hypoxia 3

description: CDO1 H3


title: 35S:PCO1 hypoxia 2

description: CDO1 H2


title: 35S:CDO1 normoxia 2

description: PCO1 N2


title: wild type hypoxia 2

description: WT H2


title: 35S:CDO1 normoxia 1

description: PCO1 N1


title: wild type normoxia 3

description: WT N3

source_name: wild type normoxia


title: wild type hypoxia 1

description: WT H1


title: P. falciparum K1 untreated

source_name: Parasite trophozoites without treatment incubated for 72 hours


title: control mice colon rep 2

source_name: epithelium from colon of control mouse no.2


title: Rapa Female 21 [chronic]

city: Saint Louis

first: Wilson

middle: Chun Yim

last: Fok

state: MO

address: 660 S Euclid Ave

department: Hematology

institute: Washington University in St. Louis

description: RF 21; Rapa F649

data_processing: Data was processed in matlab by log2 transformation and  quantile normalization

source_name: Rapa female liver

label_protocol: Biotinylated cRNA were prepared using Ambion kit- Illumina TotalPrep RNA Amplification Kit

extract_protocol: Total RNA was extracted from 25 mg of liver in each sample using Qiagen Rneasy kit following manufacturer’s protocol.  RNA quantity was assessed by Nanodrop and RNA quality was assessed by Agilent Bioanalyzer.

value: 25 months

tag: gender

value: female

tag: treatment group

value: Rapamycin

value: liver


title: HDAC2 KO mice colon rep 1

source_name: epithelium from colon of HDAC2 KO mouse no.1


title: Rapa Female 11 [chronic]

description: RF 11; Rapa F639


title: Rapa Female 15 [chronic]

description: RF 15; Rapa F643


title: Rapa Female 17 [chronic]

description: RF 17; Rapa F645


title: control mice colon rep 1

source_name: epithelium from colon of control mouse no.1


title: Rapa Female 9 [chronic]

description: RF 9; Rapa F636


title: Rapa Female 19 [chronic]

description: RF 19; Rapa F647


title: Rapa Female 13 [chronic]

description: RF 13; Rapa F641


title: Rapa Female 3 [chronic]

description: RF 3; Rapa F628


title: wild type normoxia 2

description: WT N2


title: Rapa Female 8 [chronic]

description: RF 8; Rapa F635


title: Rapa Female 14 [chronic]

description: RF 14; Rapa F642


title: Rapa Female 7 [chronic]

description: RF 7; Rapa F633


title: wild type normoxia 1

description: WT N1


title: Rapa Female 20 [chronic]

description: RF 20; Rapa F648


title: Rapa Female 10 [chronic]

description: RF 10; Rapa F637


title: Rapa Female 4 [chronic]

description: RF 4; Rapa F630


title: Rapa Female 5 [chronic]

description: RF 5; Rapa F631


title: Rapa Female 6 [chronic]

description: RF 6; Rapa F632


title: Rapa Female 1 [chronic]

description: RF 1; Rapa F626


title: Control Female 16 [chronic]

description: CF 16; Ctrl F695

source_name: control female liver

value: Control


title: Rapa Female 16 [chronic]

description: RF 16; Rapa F644


title: Control Female 15 [chronic]

description: CF 15; Ctrl F694


title: Rapa Female 18 [chronic]

description: RF 18; Rapa F646


title: Rapa Female 12 [chronic]

description: RF 12; Rapa F640


title: Rapa Female 2 [chronic]

description: RF 2; Rapa F627


title: Control Female 10 [chronic]

description: CF 10; Ctrl F686


title: Control Female 11 [chronic]

description: CF 11; Ctrl F687


title: Control Female 5 [chronic]

description: CF 5; Ctrl F656


title: Control Female 9 [chronic]

description: CF 9; Ctrl F683


title: Control Female 3 [chronic]

description: CF 3; Ctrl F653


title: Control Female 12 [chronic]

description: CF 12; Ctrl F689


title: Control Female 6 [chronic]

description: CF 6; Ctrl F658


title: Rapa-2 Male 6 [chronic]

description: R2M 6; Rapa M365

source_name: Rapa male liver

value: male


title: Rapa-2 Male 5 [chronic]

description: R2M 5; Rapa M364


title: Control Female 4 [chronic]

description: CF 4; Ctrl F655


title: Control Female 7 [chronic]

description: CF 7; Ctrl F659


title: Rapa-2 Male 4 [chronic]

description: R2M 4; Rapa M360


title: Control Female 1 [chronic]

description: CF 1; Ctrl F651


title: Rapa-2 Male 2 [chronic]

description: R2M 2; Rapa M355


title: Rapa-2 Male 3 [chronic]

description: R2M 3; Rapa M359


title: Control Female 2 [chronic]

description: CF 2; Ctrl F652


title: Control Female 14 [chronic]

description: CF 14; Ctrl F693


title: Control Female 8 [chronic]

description: CF 8; Ctrl F682


title: Rapa-2 Male 1 [chronic]

description: R2M 1; Rapa M354


title: Rapa-1 Male 6 [chronic]

description: R1M 6; Rapa M350


title: Rapa-1 Male 3 [chronic]

description: R1M 3; Rapa M344


title: Control Male 16 [chronic]

description: CM 16; Ctrl M726

source_name: control male liver


title: Rapa-1 Male 7 [chronic]

description: R1M 7; Rapa M352


title: Rapa-1 Male 4 [chronic]

description: R1M 4; Rapa M345


title: Control Male 13 [chronic]

description: CM 13; Ctrl M723


title: Control Male 15 [chronic]

description: CM 15; Ctrl M725


title: Rapa-1 Male 5 [chronic]

description: R1M 5; Rapa M348


title: Control Male 12 [chronic]

description: CM 12; Ctrl M722


title: Rapa-1 Male 1 [chronic]

description: R1M 1; Rapa M341


title: Control Male 14 [chronic]

description: CM 14; Ctrl M724


title: Control Male 9 [chronic]

description: CM 9; Ctrl M718


title: Control Male 7 [chronic]

description: CM 7; Ctrl M374


title: Control Male 10 [chronic]

description: CM 10; Ctrl M719


title: Control Male 19 [chronic]

description: CM 19; Ctrl M730


title: Control Male 11 [chronic]

description: CM 11; Ctrl M721


title: Rapa-1 Male 2 [chronic]

description: R1M 2; Rapa M342


title: Control Male 18 [chronic]

description: CM 18; Ctrl M729


title: Control Male 3 [chronic]

description: CM 3; Ctrl M368


title: Control Male 5 [chronic]

description: CM 5; Ctrl M372


title: Control Male 1 [chronic]

description: CM 1; Ctrl M366


title: Control Male 17 [chronic]

description: CM 17; Ctrl M728


title: Control Male 8 [chronic]

description: CM 8; Ctrl M716


title: Rapa Female 11

description: RF 11; Rapa F1060

data_processing: Data was processed in matlab by log2 transformation and quantile normalization. Please note that the normalized data was processed with detection p-value <0.05 and also normalized as a large dataset with other arrays that were not included in this Series, resulting a reduced data set of 17,082 data rows.


title: Control Male 6 [chronic]

description: CM 6; Ctrl M373


title: Control Male 4 [chronic]

description: CM 4; Ctrl M371


title: Control Male 2 [chronic]

description: CM 2; Ctrl M367


title: Rapa Female 10

description: RF 10; Rapa F1030


title: Rapa Female 9

description: RF 9; Rapa F1029


title: Control Female 13 [chronic]

description: CF 13; Ctrl F692


title: Rapa Female 8

description: RF 8; Rapa F1028


title: Rapa Female 7

description: RF 7; Rapa F1017


title: Rapa Female 5

description: RF 5; Rapa F984


title: Rapa Female 6

description: RF 6; Rapa F1016


title: Control Female 9

description: CF 9; Ctrl F1127


title: Rapa Female 4

description: RF 4; Rapa F954


title: Rapa Female 2

description: RF 2; Rapa F952


title: Rapa Female 1

description: RF 1; Rapa F951


title: Control Female 1

description: CF 1; Ctrl F939


title: Control Female 2

description: CF 2; Ctrl F940


title: Rapa Male 12

description: RM 12; Rapa M871


title: Control Female 6

description: CF 6; Ctrl F1000


title: Control Female 8

description: CF 8; Ctrl F1126


title: Rapa Male 11

description: RM 11; Rapa M835


title: Control Female 5

description: CF 5; Ctrl F999


title: Rapa Male 9

description: RM 9; Rapa M833


title: Control Female 3

description: CF 3; Ctrl F996


title: Rapa Female 3

description: RF 3; Rapa F953


title: Rapa Male 5

description: RM 5; Rapa M755


title: Control Female 7

description: CF 7; Ctrl F1012


title: Rapa Male 10

description: RM 10; Rapa M834


title: Control Female 4

description: CF 4; Ctrl F997


title: Rapa Male 7

description: RM 7; Rapa M782


title: Control Male 10

description: CM 10; Ctrl M847


title: Control Male 9

description: CM 9; Ctrl M820


title: Rapa Male 6

description: RM 6; Rapa M781


title: Rapa Male 1

description: RM 1; Rapa M751


title: Rapa Male 4

description: RM 4; Rapa M754


title: Rapa Male 2

description: RM 2; Rapa M752


title: Rapa Male 8

description: RM 8; Rapa M783


title: sun-exposed pre-auricular skin 21A

city: Beijing

first: lili

last: zhang

address: No.7 Beitucheng West Road, Chaoyang District

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

description:
hybridized on  Illumina HUMANWG-6 v3.0 BeadChip
sun-exposed pre-auricular skin

data_processing: With Aglient GeneSpring GX 10.0,raw data of the common probes (37,352) in the two versions of BeadChip (Illumina HUMANWG-6 v2.0 and v3.0 BeadChips) was preprocessed using the default parameters and then normalized by a quantile algorithm. Next, the normalized data was filtered based on their flag values. Only entities having the present and marginal flags (correspond to detection p-value <0.05) and at least 60% of samples in one of the two groups met the above criteria were determined as the expressed probes. The processed data for the common probes are on the Series record. The Probe IDs of the common probes were not the same so we used Illumina HUMANWG-6 v3.0 BeadChip probe IDs as the IDs for the combined data.

source_name: pre-auricular skin

label_protocol: Biotinylated cRNA samples were prepared with the  Illumina TotalPrep Amplification Kit from Ambion

extract_protocol: RNA was extracted with Trizol reagent

treatment_protocol: Fat tissues were removed within 5 minutes of obtaining the skin samples

tag: site

value: pre-auricular


title: Control Male 7

description: CM 7; Ctrl M799


title: sun-protected post-auricular skin 20B

description:
hybridized on  Illumina HUMANWG-6 v3.0 BeadChip
sun-protected post-auricular skin

source_name: post-auricular skin

value: post-auricular


title: Control Male 8

description: CM 8; Ctrl M819


title: Control Male 4

description: CM 4; Ctrl M739


title: sun-exposed pre-auricular skin 20A


title: sun-protected post-auricular skin 21B


title: sun-exposed pre-auricular skin 19A


title: Control Male 3

description: CM 3; Ctrl M738


title: Control Male 6

description: CM 6; Ctrl M798


title: Rapa Male 3

description: RM 3; Rapa M753


title: Control Male 5

description: CM 5; Ctrl M796


title: sun-protected post-auricular skin 19B


title: sun-protected post-auricular skin 18B


title: MEP_rep3 [methylation]

city: Bronx

first: Boris

last: Bartholdy

state: NY

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

hyb_protocol: Labeling and DNA hybridization onto a human hg17 custom designed oligonucleotide array (50mers) was carried out by Roche/NimbleGen (Madison, WI). The 2006-10-26_HG17_HELP_Promoter array covers 25,626 HpaII amplifiable fragments (HAF). EpiTyper by MassArray (Sequenom, CA) was used to confirm methylation of selected loci. Uniformity of hybridization was evaluated by adapting a published algorithm for the NimbleGen platform. Hybridizations with strong regional artifacts were discarded and repeated. Normalized signal intensities from each array were compared with a 20% trimmed mean of signal intensities across all arrays in that experiment. Arrays with significant intensity bias that could not be explained by the biology of the sample were excluded. (Sequenom, CA) was used to confirm methylation of selected loci as previously described.

scan_protocol: See manufacturer's web site www.nimblegen.com.

data_processing: Signal intensities at each HAF were calculated as 25% trimmed mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity (equaling 2.5 mean-absolute-difference, MAD) above the median of random probe signals were regarded failed. These failed loci represent the population of fragments that did not amplify by PCR. Loci were designated methylated when the level of HpaII signal intensity was indistinguishable from background as described for MspI. Fragments successfully amplified by PCR, i.e. distinguishable above background, were subjected to normalization. For this, an intra-array quantile approach was used: HpaII/MspI ratios are aligned across density-dependent sliding windows of fragment size-sorted data. The log2(HpaII/MspI) was used as a representative for methylation and analyzed as a continuous variable. If the centered log2(HpaII/MspI) ratio was <0, the corresponding fragment was considered methylated. It was considered hypomethylated in cases where log2(HpaII/MspI) was >0.

source_name: sorted MEP from human bone marrow, MspI-digested DNA

label_protocol: Labeling was carried out by Roche/Nimblegen (Madison, WI). For details, see manufacturer's web site www.nimblegen.com.

growth_protocol: Uncultured primary cells.

extract_protocol: Cells were sorted into RLT buffer (Qiagen, Valencia, CA), homogenized by passing five times through a needle. Simultaneous harvest of RNA and genomic DNA was achieved with the AllPrep kit (Qiagen, Valencia, CA) following the instructions of the manufacturer. Integrity of genomic DNA of high molecular weight was assured by electrophoresis for all samples used. HpaII or MspI (NEB, Ipswich, MA) digestions of genomic DNA were performed overnight prior to overnight ligation of the HpaII adapter with T4 ligase. PCR amplified adapter-ligated HpaII or MspI fragments were submitted to Roche-NimbleGen, Inc. (Madison, WI) and labeled according to protocol (see manufacturer's web site www.nimblegen.com).

treatment_protocol: No treatment.

value: Lin (CD2, CD3, CD4, CD7, CD10, CD11b, CD14, CD15, CD19, CD20, CD56, and Glycophorin A )-, CD34+, CD38+, CD123-, CD45RA- cells

tag: disease status

value: healthy

tag: restriction enzyme

value: MspI

source_name: sorted MEP from human bone marrow, HpaII-digested DNA

value: HpaII


title: MEP_rep1 [methylation]


title: sun-exposed pre-auricular skin 18A

tag: age


title: MEP_rep2 [methylation]


title: sun-protected post-auricular skin 17B


title: ST-HSC_rep3 [methylation]

source_name: sorted ST-HSC from human bone marrow, MspI-digested DNA

value: Lin (CD2, CD3, CD4, CD7, CD10, CD11b, CD14, CD15, CD19, CD20, CD56, and Glycophorin A )-, CD34+, CD38-, CD90- cells

source_name: sorted ST-HSC from human bone marrow, HpaII-digested DNA


title: Control Male 2

description: CM 2; Ctrl M737


title: sun-exposed pre-auricular skin 17A


title: Control Male 1

description: CM 1; Ctrl M736


title: LT-HSC_rep2 [methylation]

source_name: sorted LT-HSC from human bone marrow, MspI-digested DNA

value: Lin (CD2, CD3, CD4, CD7, CD10, CD11b, CD14, CD15, CD19, CD20, CD56, and Glycophorin A )-, CD34+, CD38-, CD90+ cells

source_name: sorted LT-HSC from human bone marrow, HpaII-digested DNA


title: CMP_rep1 [methylation]

source_name: sorted CMP from human bone marrow, MspI-digested DNA

value: Lin (CD2, CD3, CD4, CD7, CD10, CD11b, CD14, CD15, CD19, CD20, CD56, and Glycophorin A )-, CD34+, CD38+, CD123+, CD45RA- cells

source_name: sorted CMP from human bone marrow, HpaII-digested DNA


title: CMP_rep3 [methylation]


title: LT-HSC_rep3 [methylation]


title: sun-protected post-auricular skin 16B


title: sun-exposed pre-auricular skin 16A


title: ST-HSC_rep2 [methylation]


title: CMP_rep2 [methylation]


title: ST-HSC_rep1 [methylation]


title: CC.SJS

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

description: To export to gene expression data based on unique gene, we use Illumina BeadStudio software.

hyb_protocol: Labeled, amplified material (1,500 ng per array) was hybridized to a ver. 2 of the Illumina Human-6 BeadChip (48K) according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA). Array signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the BeadChip manual.

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions.

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformation.

source_name: humancholangiocarcinoma

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina’s recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina® TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using RiboGreen were measured (Quant-iTTM RiboGreen® RNA assay kit; Invitrogen-Molecular Probes, ON, Canada) by the Victor3 spectrophotometer (PerkinElmer, CT) and cRNA quality was checked on a 1% agarose gel.

extract_protocol: Total RNA was isolated from tissues with TRIzol (Life Technologies, NY) reagent according to the manufacturer’s protocol. RNA quality and integrity were confirmed by electrophoresis on agarose gel stained with ethidium bromide and examined under ultraviolet light.

value: humancholangiocarcinoma (CC.SJS)


title: sun-protected post-auricular skin 15B


title: CC.LYO

value: humancholangiocarcinoma (CC.LYO)


title: CC.LHG

value: humancholangiocarcinoma (CC.LHG)


title: LT-HSC_rep1 [methylation]


title: CC.LMS

value: humancholangiocarcinoma (CC.LMS)


title: sun-exposed pre-auricular skin 15A


title: CC.LJS

value: humancholangiocarcinoma (CC.LJS)


title: CC.LSH

value: humancholangiocarcinoma (CC.LSH)


title: sun-protected post-auricular skin 14B


title: CC.KHC

value: humancholangiocarcinoma (CC.KHC)


title: sun-exposed pre-auricular skin 14A


title: CC.YCU

value: humancholangiocarcinoma (CC.YCU)


title: sun-protected post-auricular skin 13B


title: CC.HDS

value: humancholangiocarcinoma (CC.HDS)


title: sun-exposed pre-auricular skin 13A

value: pre-auricular


title: CC.HSR

value: humancholangiocarcinoma (CC.HSR)


title: CC.KJA

value: humancholangiocarcinoma (CC.KJA)


title: sun-protected post-auricular skin 12B

value: post-auricular


title: CC.KHS

value: humancholangiocarcinoma (CC.KHS)


title: sun-exposed pre-auricular skin 12A


title: CC.GHS

value: humancholangiocarcinoma (CC.GHS)


title: CC.HSW

value: humancholangiocarcinoma (CC.HSW)


title: CC.GMG

value: humancholangiocarcinoma (CC.GMG)


title: CC.JSJ

value: humancholangiocarcinoma (CC.JSJ)


title: CC.BSD

value: humancholangiocarcinoma (CC.BSD)


title: sun-protected post-auricular skin 11B


title: CC.CYS

value: humancholangiocarcinoma (CC.CYS)


title: ND.3

source_name: normal cell

value: cultured biliary epithelial cells (ND.3)


title: ND.2

value: cultured biliary epithelial cells (ND.2)


title: CC.CSB

value: humancholangiocarcinoma (CC.CSB)


title: CK.L2.3

source_name: cholangiocarcinoma cell lines

value: cholangiocarcinoma cells


title: CK.Y1.2


title: CC.BJP

value: humancholangiocarcinoma (CC.BJP)


title: H69.1

source_name: Immortalixed Chonangiocyte

value: Immortalixed Chonangiocyte (H69)


title: sun-protected post-auricular skin 10B


title: sun-exposed pre-auricular skin 11A

value: pre-auricular


title: sun-exposed pre-auricular skin 10A


title: CK.L1.3


title: ND.4

value: cultured biliary epithelial cells (ND.4)


title: sun-protected post-auricular skin 9B

description:
hybridized on  Illumina HUMANWG-6 v2.0 BeadChip
sun-protected post-auricular skin


title: CK.K1.1


title: sun-exposed pre-auricular skin 9A

description:
hybridized on  Illumina HUMANWG-6 v2.0 BeadChip
sun-exposed pre-auricular skin


title: CK.P1.2


title: sun-protected post-auricular skin 8B


title: CK.P2.1


title: sun-exposed pre-auricular skin 8A


title: S.CK.PT.3

source_name: SCK cholangiocarcinoma cells treated with parthenolide

value: SCK cholangiocarcinoma cells

value: parthenolide


title: S.CK.1

source_name: sarcomatoid cholangiocarcinoma cell

value: sarcomatoid cholangiocarcinoma cell


title: Cho.PK.6

source_name: Cho-CK cholangiocarcinoma cells treated with parthenolide

value: Cho-CK cholangiocarcinoma cells


title: ND.1

value: cultured biliary epithelial cells (ND.1)


title: S.CK.PT.1


title: S.CK.PT.4


title: Choi.PK.6

source_name: Choi-CK cholangiocarcinoma cells treated with parthenolide

value: Choi-CK cholangiocarcinoma cells


title: S.CK.3


title: S.CK.4


title: J.CK.6


title: sun-protected post-auricular skin 7B

source_name: post-auricular skin

value: post-auricular


title: Choi.CK.6


title: S.CK.PT.2


title: J.PK.4

source_name: JCK cholangiocarcinoma cells treated with parthenolide

value: JCK cholangiocarcinoma cells


title: S.CK.2


title: Cho.CK.5


title: J.PK.3


title: Choi.PK.5


title: sun-protected post-auricular skin 6B


title: J.CK.5


title: sun-exposed pre-auricular skin 7A

source_name: pre-auricular skin


title: Cho.CK.6


title: sun-protected post-auricular skin 5B


title: sun-protected post-auricular skin 4B


title: sun-exposed pre-auricular skin 5A


title: sun-exposed pre-auricular skin 4A


title: sun-exposed pre-auricular skin 6A


title: Cho.PK.4


title: Choi.CK.5


title: Cho.PK.5


title: J.PK.2


title: sun-protected post-auricular skin 3B


title: Choi.PK.4


title: Choi.CK.4


title: Cho.PK.3


title: sun-exposed pre-auricular skin 3A


title: Cho.CK.2


title: sun-protected post-auricular skin 2B


title: sun-protected post-auricular skin 1B


title: sun-exposed pre-auricular skin 2A


title: J.CK.4


title: Choi.PK.3


title: sun-exposed pre-auricular skin 1A


title: Cho.CK.1


title: J.PK.1


title: Choi.CK.3


title: J.CK.3


title: Control Morholino  (POOL4)

city: PADOVA

first: Enrico

last: Moro

address: Via U. Bassi 58/B

department: Molecular Medicine

institute: University of Padova

description: Fourty-eight hours post-morpholino injection fish were sacrificed and total RNA extracted for gene expression analysis

hyb_protocol: 1.65 μg of labeled aRNA was used in each reaction and hybridization was carried out at 65°C for 17 hours in a hybridization oven rotator (Agilent, Santa Clara, CA, USA). The arrays were washed using Agilent Gene expression washing buffers and Stabilization and Drying Solution, as suggested by the supplier.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) and Agilent Feature Extraction software version 10.5.1.1 was used for image analysis. Gene expression data were performed on three biological replicates for each condition.

data_processing: Inter-array normalization of expression levels (gProcessedSignal) was performed with quantile method to correct possible experimental distortions. Normalization function was applied to the expression data of all the experiments and the values for within-arrays replicate spots were then averaged (according the same ProbeName ID). Feature Extraction Software, which provided spot quality measures, was used to evaluate the quality and reliability of the hybridization. In particular, the flag “positive and significative” (set to 1 if the spot had an intensity value significantly different from the local background and to 0 when otherwise) was used to filter out unreliable probes: the flag equal to 0 was to be noted as “not available (NA)” the spot intensity and therfore not used in the average calculation. Probes with a high proportion of NA values were removed from the dataset in order to carry out a more solid and unbiased statistical analyses. Thirty-three percent of NA was used as the threshold in the filtering process. Differentially expressed genes identification (One-way ANOVA), hierarchical clustering analysis (Sperman Rank Correlation or Euclidean distance) using average linkage method were performed using the TMev suite. Gene Ontology analysis of differentially expressed genes was performed on web tool GeneCodis3. Cytoscape tool in association with the Agilent Literature Search plug-in (http://apps.cytoscape.org/apps/agilentliteraturesearch (accessed on 19 December)) was used to produce network of differentially expressed genes. Network was analyzed using Network Analyzer and CentiScaPe plug-in. Supervised pathway analysis was performed by GSEA  implemented in the Graphite web tool.

organism: Danio rerio

source_name: whole embryo

label_protocol: 1 μg of total RNA was labeled with “Agilent One-Color Microarray-Based Gene Expression protocol” according to the manufacturer's protocol. The synthesized cDNA was transcribed into aRNA and labeled with Cy3-dCTP. Labeled aRNA was purified with RNeasy Mini columns (Qiagen, Valecia, CA, USA). The quality of each aRNA sample was verified by total yield and specificity calculated with NanoDrop ND-1000 spectrophotometer measurements (Nanodrop, Wilmington, DE, USA).

extract_protocol: RNA was extracted by Trizol (Invitrogen, Italy) method according to manufacturer's instructions. DNAse digestion was performed to reduced genomic DNA contamination. All samples were quantitated using a NanoDrop ND-1000 RNA samples were checked for integrity by capillary electrophoresis (RNA 6000, NanoLabChip Analyzer Agilent Techologies).

treatment_protocol: Pools of one hundred one-cell stage embryos were microinjected with morpholino and control morpholino. Fish were grown for two days before RNA extraction.

value: GL and Tubingen

tag: sample type

value: 2 days old whole embryo lysate

tag: developmental stage

value: one-cell stage embryo

value: control


title: MEP_rep3 [expression]

hyb_protocol: Labeling and hybridization onto the NimbleGen Homo sapiens HG18 60mer expr (385k) was carried out by Roche/NimblGen (Madison, WI) according to the manufacturer's protocols (see manufacturer's website (www.nimblegen.com)).

scan_protocol: See manufacturer's web site (www.nimblegen.com).

data_processing: Gene expression profiling was performed on NimbleGen HG18 arrays (design name 2006-08-03_HG18_60mer_expr, Roche-NimbleGen Inc., Madison, WI). The raw data (.pair file) was analyzed by the NimbleScan software package (Roche NimbleGen, Inc.). The data was normalized using the RMA algorithm.

source_name: sorted MEP from human bone marrow

extract_protocol: Cells were sorted into RLT buffer (Qiagen, Valencia, CA), homogenized by passing five times through a needle. Simultaneous harvest of RNA and genomic DNA was achieved with the AllPrep kit (Qiagen, Valencia, CA) following the instructions of the manufacturer. Total RNA was linearly amplified and transcribed with the MessageAmp Kit AM1751 (Ambion/ Life Technologies, Carlsbad, CA) prior to microarray gene expression analysis following the NimbleGen Arrays User's Guide (NimbleGen, Madison, WI). Integrity of RNA and cDNA was verified at each step of amplification using the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA).

value: Lin (CD2, CD3, CD4, CD7, CD10, CD11b, CD14, CD15, CD19, CD20, CD56, and Glycophorin A )-, CD34+, CD38+, CD123-, CD45RA- cells

value: healthy


title: Control Morholino  (POOL1)


title: Morpholino injected (POOL4)

value: GBA1 morpholino


title: Control Morholino  (POOL2)


title: MEP_rep2 [expression]

label_protocol: See manufacturer's web site (www.nimblegen.com).


title: VAT_MetS+_5958031032_R03C01

city: Quebec

first: Frederic

last: Guenard

address: 2440, Hochelage blvd

institute: Laval University

hyb_protocol: Standard illumina protocol

scan_protocol: Standard illumina protocol

data_processing: The GenomeStudio® software version 2011.1 (Illumina Inc.) and the Methylation Module were used. Beta values were estimated and data correction (background subtraction and normalization) was applied using internal control probe pairs. CpG sites with a detection p-value > 0.05 were removed from analysis.

label_protocol: Standard illumina protocol

growth_protocol: Visceral adipose tissue was obtained during biliopancreatic diversion surgery

extract_protocol: Genomic DNA was extracted from the VAT using the DNeasy Blood & Tissue kit, as recommended by the manufacturer

treatment_protocol: Obese men with and without the metabolic syndrome

tag: disease state

value: MetS+

value: Male

tag: tissue

value: Visceral adipose tissue


title: VAT_MetS+_5958031032_R02C01


title: Control Morholino  (POOL3)

tag: treatment


title: Morpholino injected (POOL3)


title: MEP_rep1 [expression]


title: CMP_rep3 [expression]

source_name: sorted CMP from human bone marrow

value: Lin (CD2, CD3, CD4, CD7, CD10, CD11b, CD14, CD15, CD19, CD20, CD56, and Glycophorin A )-, CD34+, CD38+, CD123+, CD45RA- cells


title: Nodes_TMA_T5

city: Basel

first: Arne

last: Mueller

address: Klybeckstrasse 141

institute: Novartis Pharma

description:
Sample name: 69310505
MeDIP DNA from TMA treated lymph node cells

hyb_protocol: Labelled samples were applied commercially to a Nimblegen 2.1M Deluxe promoter array by Nimblegen, Iceland

scan_protocol: NimbleScan software version 2.6.0.0, by Nimblegen, Iceland

data_processing: Signals for each probe of the 5mC-enriched samples (Cy5 labelled) were compared to input samples (Cy3 labelled) to generate log2 (IP/Input) scores (fold changes). These log2 scores were then normalized by subtracting the weighted median log2 score from each array and scaling each array for the same median absolute deviation using the Limma package in R/Bioconductor (Smyth, G. K., and Speed, T. P. (2003). Normalization of cDNA microarray data. Methods 31, 265-273). Subsequent analyses were carried out in the Refiner Genome and Analyst modules of the Expressionist® software package (Version 7.0, Genedata AG, Basel). Using the Sliding-Window ANOVA Activity from Refiner Genome (Genedata Expressionist® Refiner Genome Reference Manual, Version 7.0), genomic ranges with a minimum length of 400bp and a higher than usual variance (threshold: p-value of at least 100 on the phred scale) were identified and then exported to Analyst for further analysis.

label_protocol: For each sample, 6 μg of amplified IP and Input material was sent to Roche Nimblegen (Reykjavík, Iceland) for Cy5 and Cy3 labelling and hybridization on 2.1M Deluxe mouse promoter tiling arrays (MeDIP-array).

extract_protocol: Genomic DNA from mouse LN tissue samples was extracted by overnight proteinase K digestion (Sigma) in lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM ethylenediamine tetra-acetic acid [EDTA] pH 8.0, 0.5% sodium dodecyl sulphate) prior to RNaseA digestion, phenol-chloroform extraction and ethanol precipitation. Genomic DNA was sonicated (Bioruptor, Diagenode, Liège, Belgium) to produce DNA fragments ranging in size from 300 to 1000 bp, with a mean fragment size of 500 bp. For each sample 6 μg of fragmented DNA (input) was denatured for 10 min at 95°C and immunoprecipitated for 3 h at 4°C with 15 μl mouse monoclonal antibody against 5-methylcytidine (Eurogentec, Seraing, Belgium) in a final volume of 500 μl immunoprecipitation  buffer (10 mM sodium phosphate (pH 7.0), 140 mM NaCl, 0.05% Triton X-100). This mixture was incubated with 60 μl of magnetic M-280 protein G Dynabeads (Invitrogen, Paisley, UK) for 2 h prior to washing all unbound fragments three times with 1 ml immunoprecipitation buffer. Washed beads were then resuspended in 250 μl of lysis buffer and incubated with proteinase K for 2 h at 50°C. The immunoprecipated methylated DNA was recovered by phenol-chloroform extraction and ethanol precipitation the resuspended in 20 μ Tris EDTA. For qPCR analysis, 10 μl aliquots of immunoprecipated (IP) DNA were taken and diluted to 100 μl in Tris EDTA with each qPCR reaction using 2 μl of diluted DNA. For the MeDIP-array, 50 ng of input DNA and 10 μl of IP DNA was subjected to whole genome amplification (WGA) using the WGA2:GenomePlex Complete Whole Genome Kit (Sigma) and tested for linear amplification by qPCR. Amplified DNA was then purified by passing through GenElute™ PCR Clean-Up columns (Sigma) and eluting into Tris EDTA.

treatment_protocol: 13 day chronic TMA treatment of 6-12 week old mice

value: Lymph node

value: Balb/c

tag: agent

value: TMA

tag: medip antibody

value: mouse monoclonal antibody against 5-methylcytidine (Eurogentec)

source_name: Input DNA from TMA treated lymph node cells


title: VAT_MetS+_5958091030_R03C01


title: CMP_rep2 [expression]


title: G-CSF treated Mouse 3_451071_2010-10-29_1sthyb_Cycle3

city: Atlanta

first: Liliana

last: Souza

state: GA

address: 1365 C Clifton RD, NE

department: Hematology/Oncology

institute: Emory University

description: Sample 3

hyb_protocol: Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed according to the manufacturer's protocols.  Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/support/dna-microarray-support.html)

scan_protocol: Arrays were scanned on an Roche MS 200 scanner per manufacturer's protocol (http://www.nimblegen.com/support/dna-microarray-support.html).

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.6 CGH data extraction.
The *segMNT.txt files contain complete processed data and sample data table contains 'RATIO_CORRECTED' data.

source_name: Lin-Sca+ bone marrow_control

label_protocol: 1 µg  of Test and Reference DNA was directly labeled by Klenow random priming with Cy3/Cy5 nonamers per manufacturer's protocol (http://www.nimblegen.com/support/dna-microarray-support.html).

extract_protocol: Bone marrow cells were harvested from mice treated with diluents (samples called Cycle1, cycle2, cycle 3) or G-CSF for 4 months. Lin-Sca+ cells were isolated using the instructions provided by the manufacturer (Easy Sep 18756, 19756A, Stem Cell Technologies). Genomic DNA was extracted from Lin-Sca+ cells cells using the Qiagen DNeasy kit, and quantification and quality assessment were performed with picogreen, NanoDrop and a standard agarose gel. DNA was analyzed by array-comparative genomic hybridization (Array CGH) at the Florida State University NimbleGen Microarray Facility using NimbleGen 3×720K mouse whole-genome tiling arrays. Copy number abnormalities were identified using NimbleScan and BioDiscovery Nexus software. Aberrant segments were queried in the UCSC Genome Browser (GRCm38/mm10) for overlapping BAC alignments to be used for FISH validation of copy number loss and gain.

treatment_protocol: mice treated with diluent for 4 months

tag: treated with

value: G-CSF for 4 months

value: Lin-Sca+ Bone Marrow cells

source_name: Lin-Sca+ bone marrow_G-CSF treated

treatment_protocol: mice treated with G-CSF for 4 months

value: diluent for 4 months


title: Nodes_AOO_A5

description:
Sample name: 69310205
MeDIP DNA from AOO treated lymph node cells

treatment_protocol: 13 day chronic AOO treatment of 6-12 week old mice

tag: strain

value: AOO

source_name: Input DNA from AOO treated lymph node cells


title: Morpholino injected (POOL2)

value: GL and Tubingen

value: 2 days old whole embryo lysate

value: one-cell stage embryo


title: Morpholino injected (POOL1)


title: G-CSF treated Mouse 2_451071_2010-10-29_1sthyb_Cycle2

description: Sample 2


title: CMP_rep1 [expression]

value: healthy


title: Nodes_TMA_T4

description:
Sample name: 69322505
MeDIP DNA from TMA treated lymph node cells


title: G-CSF treated Mouse 1_451071_2010-10-29_1sthyb_Cycle1

description: Sample 1

treatment_protocol: mice treated with diluent for 4 months.

treatment_protocol: mice treated with G-CSF for 4 months.


title: ST-HSC_rep3 [expression]

source_name: sorted ST-HSC from human bone marrow

value: Lin (CD2, CD3, CD4, CD7, CD10, CD11b, CD14, CD15, CD19, CD20, CD56, and Glycophorin A )-, CD34+, CD38-, CD90- cells


title: Nodes_DNCB_D5

description:
Sample name: 69303805
MeDIP DNA from DNCB treated lymph node cells

treatment_protocol: 13 day chronic DNCB treatment of 6-12 week old mice

value: DNCB

source_name: Input DNA from DNCB treated lymph node cells


title: ST-HSC_rep2 [expression]


title: VAT_MetS+_5958091028_R06C02

value: MetS+

value: Male


title: LT-HSC_rep2 [expression]

source_name: sorted LT-HSC from human bone marrow

value: Lin (CD2, CD3, CD4, CD7, CD10, CD11b, CD14, CD15, CD19, CD20, CD56, and Glycophorin A )-, CD34+, CD38-, CD90+ cells


title: LT-HSC_rep3 [expression]


title: ST-HSC_rep1 [expression]


title: VAT_MetS+_5958091030_R02C01

value: Visceral adipose tissue


title: VAT_MetS+_5958091028_R02C01


title: VAT_MetS-_5958031032_R01C01

value: MetS-


title: Nodes_DNCB_D4

description:
Sample name: 69302605
MeDIP DNA from DNCB treated lymph node cells

value: Lymph node

value: Balb/c


title: Nodes_AOO_A1

description:
Sample name: 69303505
MeDIP DNA from AOO treated lymph node cells

value: mouse monoclonal antibody against 5-methylcytidine (Eurogentec)


title: Nodes_TMA_T1

description:
Sample name: 69277205
MeDIP DNA from TMA treated lymph node cells

value: TMA


title: VAT_MetS-_5958091030_R01C01


title: VAT_MetS-_5958031032_R05C02


title: Nodes_TMA_T3

description:
Sample name: 69302905
MeDIP DNA from TMA treated lymph node cells


title: VAT_MetS-_5958091028_R03C01


title: Nodes_DNCB_D1

description:
Sample name: 69277505
MeDIP DNA from DNCB treated lymph node cells


title: VAT_MetS+_5958091030_R06C02


title: Nodes_AOO_A2

description:
Sample name: 69276905
MeDIP DNA from AOO treated lymph node cells


title: Nodes_AOO_A3

description:
Sample name: 69309905
MeDIP DNA from AOO treated lymph node cells


title: Nodes_DNCB_D3

description:
Sample name: 69302305
MeDIP DNA from DNCB treated lymph node cells


title: VAT_MetS-_5958091029_R01C01


title: VAT_MetS-_5958091029_R06C02


title: B9188.2

status: Public on Feb 06 2014

city: Los Angeles

first: Fides

middle: D

last: Lay

state: CA

address: 615 Charles E Young Drive South, BSRB 457

department: MCDB

institute: UCLA

description: genomic DNA from normal peripheral blood 6

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation45 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: methylumi R package

label: Cy5 and Cy3

source_name: blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from urine samples using phenol-chloroform method

value: Female

tag: tissue type

value: blood

value: normal


title: Nodes_TMA_T2

description:
Sample name: 69275405
MeDIP DNA from TMA treated lymph node cells


title: Nodes_DNCB_D2

description:
Sample name: 69303205
MeDIP DNA from DNCB treated lymph node cells


title: B9295.2

description: genomic DNA from normal peripheral blood 5


title: Nodes_AOO_A4

description:
Sample name: 69275705
MeDIP DNA from AOO treated lymph node cells

value: AOO


title: B9413.2

description: genomic DNA from normal peripheral blood 3


title: LT-HSC_rep1 [expression]

tag: cell type


title: VAT_MetS-_5958091029_R03C01

tag: gender


title: SI9188.2

description: genomic DNA from normal small intestine 8

source_name: small intestine

value: small intestine


title: SI9295.2

description: genomic DNA from normal small intestine 7


title: U9188A.2

description: genomic DNA from neobladder urine 26

source_name: neobladder urine

value: neobladder urine


title: N5835

description: genomic DNA from normal urothelium 5

source_name: urothelium

value: urothelium


title: U9413B.2

description: genomic DNA from neobladder urine 23


title: N5757

description: genomic DNA from normal urothelium 2


title: SI9339.2

description: genomic DNA from normal small intestine 6


title: SI9413.2

description: genomic DNA from normal small intestine 5


title: B9333

description: genomic DNA from normal peripheral blood 2


title: U9295A.2

description: genomic DNA from neobladder urine 25


title: N5879

description: genomic DNA from normal urothelium 4


title: SI9333

description: genomic DNA from normal small intestine 4


title: B9339.2

description: genomic DNA from normal peripheral blood 4


title: N5776

description: genomic DNA from normal urothelium 3


title: B9307

description: genomic DNA from normal peripheral blood 1


title: U9333A

description: genomic DNA from neobladder urine 22


title: U9307A

description: genomic DNA from neobladder urine 21


title: U9000A

description: genomic DNA from neobladder urine 19


title: U9037A

description: genomic DNA from neobladder urine 20


title: X7905B

description: genomic DNA from neobladder urine 18


title: U9339A.2

description: genomic DNA from neobladder urine 24


title: X7277D

description: genomic DNA from neobladder urine 14


title: SI9307

description: genomic DNA from normal small intestine 3


title: X6861A

description: genomic DNA from neobladder urine 9


title: X7065C

description: genomic DNA from neobladder urine 12


title: SI9037

description: genomic DNA from normal small intestine 2


title: X7905A

description: genomic DNA from neobladder urine 17


title: X7464D

description: genomic DNA from neobladder urine 16


title: X6861B

description: genomic DNA from neobladder urine 10


title: X7464C

description: genomic DNA from neobladder urine 15


title: X7065B

description: genomic DNA from neobladder urine 11


title: N5740

description: genomic DNA from normal urothelium 1


title: SI9000

description: genomic DNA from normal small intestine 1


title: X6481B

description: genomic DNA from neobladder urine 5


title: X6534B

description: genomic DNA from neobladder urine 7


title: X7277C

description: genomic DNA from neobladder urine 13


title: X5789B

description: genomic DNA from neobladder urine 3


title: X4489B

description: genomic DNA from neobladder urine 1


title: X4489C

description: genomic DNA from neobladder urine 2


title: X6534C

description: genomic DNA from neobladder urine 8


title: X6481C

description: genomic DNA from neobladder urine 6


title: r2349_TAB

first: Pankaj

last: Chopra

address: 615 Michael St. NE, Ste. 375

department: Human Genetics

description: Sample name: r2349_TAB

hyb_protocol: Contained within the Illumina Infinium HumanMethylation450 BeadChips protocol

scan_protocol: Using an Illumina HiScan

data_processing:
raw signal intensities were quantile normalized separately and imputed values calculated for missing values. The beta value was calculated as: (signal b)/(signal a + signal b + 100)
Unmethylated and methylated signal intensities (see supplementary file linked to Series record)

label: Cy3, Cy5

organism: Macaca mulatta

source_name: Macaca mulatta, Brain

extract_protocol: Standard DNA extraction protocol

value: Brain

tag: methylation type


title: r2349_SB

description: Sample name: r2349_SB

label_protocol: Contained within the Illumina Infinium HumanMethylation450 BeadChips protocol


title: r04037_TAB_2

description: Sample name: r04037_TAB_2


title: r02089_SB

description: Sample name: r02089_SB


title: r02114_TAB_2

description: Sample name: r02114_TAB_2


title: r02089_TAB_2

description: Sample name: r02089_TAB_2


title: r04037_TAB_1

description: Sample name: r04037_TAB_1


title: r01099_TAB_2

description: Sample name: r01099_TAB_2


title: r02114_SB

description: Sample name: r02114_SB


title: r04037_SB

description: Sample name: r04037_SB


title: r02093_TAB

description: Sample name: r02093_TAB


title: r02093_SB

description: Sample name: r02093_SB


title: r00061_SB

description: Sample name: r00061_SB


title: r02114_TAB_1

description: Sample name: r02114_TAB_1


title: r00061_TAB

description: Sample name: r00061_TAB


title: r01099_SB

description: Sample name: r01099_SB


title: MB231 PIAS1 shRNA-SCM

first: BIN

last: LIU

address: 10833 Le Conte Avenue

description: Gene expression data from MDA-MB231 PIAS1 shRNA cells grown in SCM for 30 h.

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: MDA-MB231 PIAS1 shRNA cells

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

growth_protocol: MDA-MB231 Control shRNA and PIAS1 shRNA2 cells were cultured in DMEM plus 10% FBS (DMEM) or SCM for 30 h.

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

tag: cell line

value: PIAS1 shRNA

tag: media

value: SCM


title: mC_TAB_2

description: Sample name: mC_TAB_2

source_name: Mus musculus, Brain


title: r01099_TAB_1

description: Sample name: r01099_TAB_1


title: X5789C

description: genomic DNA from neobladder urine 4

value: Male


title: mC_SB_2

description: Sample name: mC_SB_2


title: r02089_TAB_1

description: Sample name: r02089_TAB_1


title: mC_SB_1

description: Sample name: mC_SB_1


title: mC_TAB_1

description: Sample name: mC_TAB_1


title: MB231 PIAS1 shRNA-DMEM

description: Gene expression data from MDA-MB231 PIAS1 shRNA cells grown in DMEM for 30 h.

value: DMEM


title: MB231 con-SCM

description: Gene expression data from MDA-MB231 control shRNA cells grown in SCM for 30 h.

source_name: MDA-MB231 control shRNA cells

value: control shRNA


title: mA_TAB_1

description: Sample name: mA_TAB_1


title: HC11-ΔSAP_rep1

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

institute: FMI

description: cells grown in 0.03% FCS/RPMI without EGF, 48 h

hyb_protocol: 2ug of end-lageled cDNA was hybridized to Affymetrix Mouse Gene 1.0  ST arrays  following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidics protocol FS450_0007 was used for washing.

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.

data_processing: Probesets were summarized and probeset-level values normalized with justRMA() function from R (version 2.10.0) / Bioconductor (version 2.5) package affy using annotation from Netaffx (www.netaffx.com).

label_protocol: 200 ng total RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix (GeneChip Whole Transcription Sense Target Labeling technical manual, Rev. 2), labeling 10ug amplified cDNA.

growth_protocol: Cells were grown in 0.03% FCS/RPMI medium without epidermal growth factor (EGF) for 48 h before total RNA was extracted.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen).

value: mammary epithelial HC 11 cells originating from mid-pregnancy BALB/c mice (Danielson et al., 1984; Ball et al., 1988)

tag: genotype/variation

value: expressing Mkl1-RFP with a deletion of the SAP domain (HC11-ΔSAP)


title: HC11-ΔSAP_rep2


title: HC11-ΔSAP_rep3


title: mB_SB_2

description: Sample name: mB_SB_2


title: E06_45_TAB_2

description: Sample name: E06_45_TAB_2

source_name: Homo sapiens, Brain


title: mB_SB_1

description: Sample name: mB_SB_1


title: mB_TAB_2

description: Sample name: mB_TAB_2


title: HC11-mutB1_rep2

value: expressing Mkl1-RFP with a mutated SRF-interaction site (HC11-mutB1)


title: HC11-mutB1_rep3


title: HC11-mutB1_rep1


title: HC11-FL_rep3

value: expressing full length Mkl1-RFP (HC11-FL)


title: E06_45_TAB_1

description: Sample name: E06_45_TAB_1


title: HC11-FL_rep2


title: E06_45_SB

description: Sample name: E06_45_SB


title: IRAK1BP1-/-  + TNFα [MH02M014]

city: Indianapolis

first: Maureen

last: Harrington

address: 635 Barnhill Dr

department: Biochemistry & Mol Bio

institute: Indiana University

hyb_protocol: Standard Affymetrix hybridization protocol, hybridization for 17 hours.

scan_protocol: Arrays were scanned by Affymetrix 3000-7G scanner controlled by Affymetrix Genechip Command Console.

data_processing: CEL files were imported into Partek Genomics Suite (Partek, Inc., St. Louis, Mo). RMA signals were generated for the core probe sets using the RMA background correction, Quantile normalization and summarization by Median Polish.

source_name: embryonic fibroblast

label_protocol: Samples were labeled using Ambion WT expression kit followed by the Affymetrix WT terminal labeling kit.

growth_protocol: proliferating mouse embryonic fibroblasts

extract_protocol: manufacturer's conditions [Qiagen RNeasy® Mini Kit]

treatment_protocol: untreated or treated with recombinant human tumor necrosis factor-alpha (10 ng/ml) for 45 minutes

tag: genotype

value: IRAK1BP1 KO

value: TNFα


title: IRAK1BP1-/-  + TNFα [MH02M015]


title: HC11-FL_rep1


title: mB_TAB_1

description: Sample name: mB_TAB_1


title: E06_114_TAB_2

description: Sample name: E06_114_TAB_2


title: IRAK1BP1-/-  + TNFα [MH02M016]


title: E06_114_SB

description: Sample name: E06_114_SB


title: mA_TAB_2

description: Sample name: mA_TAB_2


title: IRAK1BP1-/-  + TNFα [MH02M013]


title: mA_SB_1

description: Sample name: mA_SB_1


title: r06015L

description: Sample name: r06015L

source_name: Macaca mulatta, Fetal Liver

value: Fetal Liver


title: mA_SB_2

description: Sample name: mA_SB_2


title: E06_114_TAB_1

description: Sample name: E06_114_TAB_1


title: r06013L

description: Sample name: r06013L


title: E06_113_TAB_1

description: Sample name: E06_113_TAB_1


title: IRAK1BP1-/-  control [MH02M012]


title: IRAK1BP1-/-  control [MH02M010]


title: WT + TNFα [MH02M007]

value: WT


title: IRAK1BP1-/-  control [MH02M011]


title: WT + TNFα [MH02M006]


title: r05072H

description: Sample name: r05072H

source_name: Macaca mulatta, Fetal Heart

value: Fetal Heart


title: E06_113_SB

description: Sample name: E06_113_SB


title: r06013P

description: Sample name: r06013P

source_name: Macaca mulatta, Placenta

value: Placenta


title: IRAK1BP1-/-  control [MH02M009]


title: WT + TNFα [MH02M005]


title: r03152P

description: Sample name: r03152P


title: E06_113_TAB_2

description: Sample name: E06_113_TAB_2


title: r06015H

description: Sample name: r06015H


title: WT + TNFα [MH02M008]


title: WT control [MH02M001]


title: r06013H

description: Sample name: r06013H


title: MB231 con-DMEM

description: Gene expression data from MDA-MB231 control shRNA cells grown in DMEM for 30 h.


title: Cannabis High T1, Sample66

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

institute: Health Canada

hyb_protocol: 825 ng of sample and reference cRNA were mixed and fragmented. cRNA was hybridized to whole mouse genome (4x44K) microarray slides (Agilent Technologies, Inc.) in stainless steel chambers. A block design was used with three samples and one control placed on each slide. Hybridization was carried out in a rotating hybridization oven in the dark at 65ºC and 10 rpm for 17 h. The slides were then washed for 1 min in each of Agilent's Gene Expression Wash Buffers 1 and 2.

scan_protocol: Arrays were scanned on an Agilent DNA Microarray Scanner using Agilent Scan Control software. Data were extracted using Agilent Feature Extraction 9.5 (protocol GE2-v5_95_Feb07).

data_processing: The median signal intensity of each microarray sample was used. Data was normalized using the Lowess approach using the R software. Technical replicates were averaged using the median.

source_name: Pulmonary epithelial cell line from Muta™Mouse, cannabis, high dose, 6hr + 4hr recovery

label_protocol: Fluorescently labelled cRNA was generated according to Agilent's Two-Color Microarray-Based Gene Expression Analysis protocol. 200 ng of sample RNA was labelled with Cy5 and 200ng of Universal Mouse Reference RNA was labelled with Cy3 using Agilent Low RNA Input Linear Amplification Kits.

growth_protocol: Cells (passage 12) were seeded at a density of 2-5 x 10e4 cells per 150mm plate, and cultured in DMEM F-12 supplemented with 2% v/v fetal bovine serum, 1% v/v penicillin/streptomycin, and 0.02% v/v murine epidermal growth factor. Cells were incubated at 37ºC in a 5% CO2 atmosphere for 2 days.

extract_protocol: RNA was extracted from the cells using TRIzol (Invitrogen), and cleaned-up using an RNeasy Mini Kit (Qiagen, Mississauga, ON, Canada) according to manufacturer's instructions. RNA quantity and quality were measured using a NanoDrop ND-1000 spectrophotometer.

treatment_protocol: Hand-rolled marijuana and tobacco cigarettes were smoked according to an ISO smoking regime with a puff volume of 35 mL, a puff duration of 2 seconds and a puff interval of 60 seconds. Particulate matter from mainstream smoke was collected on a 92mm glass fibre filter disc and subsequently dissolved in dimethyl sulfoxide. Murine epithelial lung cells were exposed to the tobacco smoke condensates (0, 25, 50, 90 μg/ml) or marijuana smoke condensates (0, 2.5, 5, 10 μg/ml) in serum-free medium for a six hour period. Following the six hour exposure, cells were either harvested immediately, or washed with phosphate-buffered saline and incubated in fresh serum-free medium for a four hour recovery period.

value: FEI

value: pulmonary epithelial cells

value: cannabis exposure

tag: treatment dosage

value: high dose D3 (10 ug/ml)

tag: time point

value: post exposure T1 = 6hr + 4hr recovery

source_name: Universal Mouse Reference Total RNA

extract_protocol: Universal Mouse Reference RNA (Agilent Technologies Canada, Inc., Mississauga, ON, CAN, catalogue #740100).

tag: sample type

value: reference


title: WT control [MH02M004]


title: RNF31 knocking down_2

city: Stockholm

first: Chunyan

last: Zhao

address: Hälsovägen 7-9

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

description:
72 hours of siRNA treatment
Cells were derived from a 69-year-old female.

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 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 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

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

source_name: MCF-7 cell line, total RNA, knocking down RNF31

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 RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: cells were cultured in DMEM red medium with 10% FBS

extract_protocol: RNA was prepared using the Versagene RNA Purification kit (Qiagen) following the 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: Control group and siRNF31 group were treated with 100uM siControl or 100uM siRNF31, respectively

value: epithelial cancer cells

tag: sirna

value: RNF31 siRNA


title: Cannabis Low T1, Sample65

source_name: Pulmonary epithelial cell line from Muta™Mouse, cannabis, low dose, 6hr + 4hr recovery

tag: treatment

value: low dose D1 (2.5 ug/ml)


title: r05072L

description: Sample name: r05072L

tag: tissue


title: WT control [MH02M003]


title: r03152L

description: Sample name: r03152L


title: RNF31 knocking down_3


title: Cannabis Control T1, Sample67

source_name: Pulmonary epithelial cell line from Muta™Mouse, cannabis, control, 6hr + 4hr recovery

value: control


title: RNF31 knocking down_4


title: r05072P

description: Sample name: r05072P


title: JC_Chimp

description: Sample name: JC_Chimp

organism: Pan troglodytes

source_name: Pan troglodytes, Blood

value: Blood


title: RNF31 knocking down_1


title: Cannabis Mid T1, Sample64

source_name: Pulmonary epithelial cell line from Muta™Mouse, cannabis, medium dose, 6hr + 4hr recovery

value: medium dose D2 (5 ug/ml)


title: Cannabis Low T2, Sample63

source_name: Pulmonary epithelial cell line from Muta™Mouse, cannabis, low dose, 6hr

value: post exposure T2 = 6hr


title: Knocking down control_1

source_name: MCF-7 cell line, total RNA, knocking down control

value: siControl


title: Cannabis Mid T1, Sample62


title: r03152H

description: Sample name: r03152H


title: Knocking down control_3


title: Cannabis High T1, Sample61


title: TGFBR3KD_rep3

city: Nashville

first: Harold

middle: L

last: Moses

state: TN

address: 2220 Pierece Ave

department: Cancer Biology

institute: Vanderbilt Univerisity

description: 3D culture D6

hyb_protocol: Following fragmentation, 10.5 ug of cRNA were hybridized for 16 hr at 40C.

scan_protocol: Scanned with Affymetrix using AGCC v. 3.2.4

data_processing: Analyzed in R 3.0.1 using the oligo package. Samples were normalized with the RMA algorithm, genes were annotated with the pd.hugene.1.0.st.v1 package, and differential gene expression analysis was conducted using the limma package.

source_name: SUM159 3D culture, TGFBR3KD

label_protocol: cRNA was prepared according to the standard Affymetrix protocol from 130 ug total RNA

growth_protocol: SUM159 grown in matrigel 3D cultures

extract_protocol: Aurum total RNA kit was used for RNA extraction

value: SUM159 breast cancer cell line