title: Sensitive_6

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

description:
11_4973
Healthy adult blood donor from NLGIP (Israel).
Thiopurine-sensitive lymphoblastoid cell line gene expression data.

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on Affymetrix Human Gene 2.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix).

data_processing: The data were preprocessed and analyzed using Partek Genomics Suite.

source_name: Lymphoblastoid cell line, sensitive to thiopurine

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from total RNA (following the GeneChip Whole Transcript (WT) Sense Target Labelling Assay kit, Affymetrix).

growth_protocol: Human LCLs were obtained from the National Laboratory for the Genetics of Israeli Populations (NLGIP), a human diversity biobank at Tel-Aviv University, Tel Aviv, Israel. The cell lines in the NLGIP collection were generated from lymphocytes isolated from blood samples donated for this purpose by consenting healthy adults (health status, age and ethnicity were self-reported by donors). All cell lines were prepared with EBV generated from the same source of B-95-8 marmoset cell line as described. LCLs were cultured in RPMI medium supplemented with 10% fetal calf serum, antibiotics (100 U/ml penicillin; 100 μg/ml streptomycin), and 2 mM extra l-glutamine (final concentration of 4 mM l-glutamine). Cells were incubated at a temperature of 37°C in a humidified CO2 incubator (6% CO2; 100% humidity) in upright-standing T-75 flasks. The volume was adjusted three-times per week by adding fresh medium to maintain concentrations of between 1 and 2 million cells per ml. Under these growth conditions, cultured LCLs can be maintained continuously for several months in the same flask. Experiments were carried out within 6 months of thawing new vials of each cell line.

extract_protocol: Nucleic acid extractions were performed from cells incubated under optimal growth conditions and with no added drugs. Total RNA extractions from cell pellets was performed with the miRNeasy® miniKit (Qiagen, Netherlands) according to the manufacturer's instructions. RNA quality and quantification were assessed using the 2100-Bioanalyzer (Agilent Technologies, CA, USA).

treatment_protocol: Drug concentrations for assessing growth inhibition were 2μM of 6-MP or 5μM of azathioprine, as these concentrations were closed to the mean IC50 and allowed to classify at best the LCLs. Cells were diluted to 200,000 cells/mL and incubated in 96-well plates (Falcon, NY, USA) in a volume of 200μL (40,000 cells/well) for 3 days, with drug working solutions added as needed in three replicates, and six replicates for the controls (cells treated with 20μL PBS). After 72 h, a tetrazolium derivative, MTS reagent (CellTiter 96® AQueous One Solution Cell Proliferation Assay [Promega, WI, USA]), was added (volume 40μL) to each well, including blank wells containing only PBS solution. After further incubation for 4 h, the absorption at 490nm was measured using a microplate reader spectrophotometer (Safir™ [Tecan, Switzerland]), which is reliable to the living cells present in the medium. Growth inhibition relative to control was assessed for each cell line at least two times on two different batches, i.e., different cell vials thawed from liquid nitrogen stock. Reproducibility for repeated thawing was high, as previously reported.

value: lymphoblastoid cell line

tag: phenotype

value: sensitive to thiopurine

tag: donor

value: healthy adult


title: blood_lun_012

status: Public on Mar 09 2015

type: genomic

city: Hannover

first: Ottmar

last: Distl

address: Buenteweg 17 p

department: Institute for Animal Breeding and Genetics

country: Germany

institute: University of Veterinary Medicine Hannover

description: Sample name: TIHO-Lundehund_012

hyb_protocol: Standard Illumina protocol for Infinium HD Beadchip

scan_protocol: Illumina iScan with Dual-Scanner Autoloader

data_processing: Illumina GenomeStudio Version 2011.1 with Genotyping Module 1.9.4

label: biotin

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: blood

extract_protocol: Genomic DNA was extracted from the blood samples through a standard ethanol fractionation with concentrated sodiumchloride (6 M NaCl) and sodium dodecyl sulphate (10% SDS).

tag: breed

value: Lundehund

tag: gender

value: female

tag: tissue

value: blood


title: blood_lun_010

description: Sample name: TIHO-Lundehund_010

label_protocol: Standard Illumina protocol for Infinium HD Beadchip

value: male


title: blood_lun_011

description: Sample name: TIHO-Lundehund_011


title: blood_lun_009

description: Sample name: TIHO-Lundehund_009


title: blood_lun_006

description: Sample name: TIHO-Lundehund_006


title: VC-053

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

hyb_protocol: 7.5ug of Cy5-labeled sample was combined with 7.5ug of Cy3-labeled male reference, and samples were hybridized and washed by following Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol v7.2 on on Agilent SurePrint G3 Human Catalog CGH 8x60K (Design ID 021924)

scan_protocol: Scanned at a 3um scan resolution and 20 bit tiff file setting on the Agilent DNA Microarray Scanner G2505C

data_processing:
Quantified signal intensities and pre-processed data with Agilent Feature Extraction 11.0.1.1
FE files loaded into Nexus Copy Number Software v.7.5.1  (Biodiscovery Inc.) for analysis.

organism: Homo sapiens

source_name: plasma cell-free DNA

label_protocol: 50ng gDNA (or as much as possible if yield was less) was whole genome amplified with Sigma WGA2 kit.  2.5ug WGA product was labeled by following NimbleGen Arrays User’s Guide: CGH Analysis v5.0, which included a 2 min 95C heat step and labeling with Cy-labeled random nanomers (TriLink Biotechnologies) and Klenow 3'-5'exo-(New England Biolabs).

extract_protocol: Genomic DNA extracted with QIAamp Circulating Nucleic Acid Kit (Cat No 55114)

tag: disease state

value: Castrate resistant prostate cancer

tag: sample type

value: plasma

source_name: male reference DNA (Promega Corp)

value: male reference DNA (Promega Corp)


title: Resistant_3

type: RNA

country: France

description:
9_5452
Healthy adult blood donor from NLGIP (Israel).
Thiopurine-resistant lymphoblastoid cell line gene expression data.

label: Biotin

molecule: total RNA

source_name: Lymphoblastoid cell line, resistant to thiopurine

tag: cell type

value: resistant to thiopurine


title: Sensitive_5

description:
8_1112
Healthy adult blood donor from NLGIP (Israel).
Thiopurine-sensitive lymphoblastoid cell line gene expression data.


title: VC-052


title: PAO1_fabF1-depleted_60min_rep2

city: Worcester

first: Donald

middle: T

last: Moir

state: Massachusetts

address: 1 Innovation Dr.

department: Anti-infectives

country: USA

institute: Microbiotix, Inc.

description:
This sample is of ∆fabF1 ∆fabF2 Pseudomonas aeruginosa ATCC47085 grown in the absence of IPTG. It is the second of two biological replicates used in this experiment, each from separate cultures.
Pseudomonas aeruginosa PAO1-LAC (ATCC47085)

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

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

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

organism: Pseudomonas aeruginosa PAO1

source_name: Pseudomonas aeruginosa PAO1-LAC (ATCC47085) ∆fabF1 ∆fabF2::tet/pUCP24GW-lacIQ-lacPO-Paer-fabF1 (strain MDM1345)

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

growth_protocol:
Pseudomonas aeruginosa PAO1-LAC strains carrying lac-regulated complemented deletions of FASII genes were grown overnight aerobically in LB broth with 30 mcg/ml gentamicin at 37°C  and diluted 100-fold into 7 ml Vogel-Bonner minmal medium (VBMM) +30 mcg/ml gentamicin with excess (1 mM) or limiting (≤0.06 mM) inducer (IPTG) and grown at 37°C until growth slowed in the limiting inducer cultures.
Cells were harvested by centrifugation about 120 minutes after detectable effects on growth were observed in the limiting IPTG cultures.  Cells were resuspended in a 2:1 mixture of RNA Protect Bacteria Reagent:VBMM and stored at -70°C until used for RNA isolation.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by gel electrophoretic analysis of glyoxylated RNA samples.

tag: genotype

value: ∆fabF1 ∆fabF2 complemented by lac-regulated fabF1 on pUCP24 plasmid

value: normal

tag: accession


title: PAO1_fabF1-excess_60min_rep2

description:
This sample is of ∆fabF1 ∆fabF2 Pseudomonas aeruginosa ATCC47085 grown in excess IPTG (1 mM). It is the second of two biological replicates used in this experiment, each from separate cultures.
Pseudomonas aeruginosa PAO1-LAC (ATCC47085)


title: VC-051


title: blood_lun_016

description: Sample name: TIHO-Lundehund_016


title: VC-048


title: Sensitive_4

description:
7_1369
Healthy adult blood donor from NLGIP (Israel).
Thiopurine-sensitive lymphoblastoid cell line gene expression data.


title: VC-047


title: VC-049


title: blood_lun_007

description: Sample name: TIHO-Lundehund_007


title: Sensitive_1

description:
6_1747
Healthy adult blood donor from NLGIP (Israel).
Thiopurine-sensitive lymphoblastoid cell line gene expression data.


title: VC-050


title: blood_lun_015

description: Sample name: TIHO-Lundehund_015


title: Sensitive_2

description:
5_1585
Healthy adult blood donor from NLGIP (Israel).
Thiopurine-sensitive lymphoblastoid cell line gene expression data.


title: blood_lun_005

description: Sample name: TIHO-Lundehund_005


title: Resistant_5

description:
4_5519
Healthy adult blood donor from NLGIP (Israel).
Thiopurine-resistant lymphoblastoid cell line gene expression data.


title: PAO1_fabG-depleted_60min_rep2

description:
This sample is of ∆fabG Pseudomonas aeruginosa ATCC47085 grown in limiting IPTG (0.06 mM). It is the second of two biological replicates used in this experiment, each from separate cultures.
Pseudomonas aeruginosa PAO1-LAC (ATCC47085)

source_name: Pseudomonas aeruginosa PAO1-LAC (ATCC47085) ∆fabG::tet/pUCP24GW-lacIQ-lacPO-Paer-fabG (strain MDM1284)

value: ∆fabG complemented by lac-regulated fabG on pUCP24 plasmid


title: Resistant_2

description:
2_1823
Healthy adult blood donor from NLGIP (Israel).
Thiopurine-resistant lymphoblastoid cell line gene expression data.


title: blood_lun_003

description: Sample name: TIHO-Lundehund_003


title: VC-045


title: blood_lun_008

description: Sample name: TIHO-Lundehund_008


title: PAO1_fabG-excess_60min_rep2

description:
This sample is of ∆fabG Pseudomonas aeruginosa ATCC47085 grown in excess IPTG (1 mM). It is the second of two biological replicates used in this experiment, each from separate cultures.
Pseudomonas aeruginosa PAO1-LAC (ATCC47085)


title: Resistant_4

description:
3_1976
Healthy adult blood donor from NLGIP (Israel).
Thiopurine-resistant lymphoblastoid cell line gene expression data.


title: Resistant_1

description:
1_1801
Healthy adult blood donor from NLGIP (Israel).
Thiopurine-resistant lymphoblastoid cell line gene expression data.


title: blood_lun_002

description: Sample name: TIHO-Lundehund_002


title: PAO1_accD-excess_60min_rep2

description:
This sample is of ∆accD Pseudomonas aeruginosa ATCC47085 grown in excess IPTG (1 mM). It is the second of two biological replicates used in this experiment, each from separate cultures.
Pseudomonas aeruginosa PAO1-LAC (ATCC47085)

source_name: Pseudomonas aeruginosa PAO1-LAC (ATCC47085) ∆accD::tet/pUCP24GW-lacIQ-lacPO-Paer-accD (strain MDM1325)

value: ∆accD complemented by lac-regulated accD on pUCP24 plasmid


title: PAO1_fabF1-depleted_60min_rep1

description:
This sample is of ∆fabF1 ∆fabF2 Pseudomonas aeruginosa ATCC47085 grown in the absence of IPTG. It is the first of two biological replicates used in this experiment, each from separate cultures.
Pseudomonas aeruginosa PAO1-LAC (ATCC47085)


title: PAO1_accD-depleted_60min_rep2

description:
This sample is of ∆accD Pseudomonas aeruginosa ATCC47085 grown in limiting IPTG (0.02 mM). It is the second of two biological replicates used in this experiment, each from separate cultures.
Pseudomonas aeruginosa PAO1-LAC (ATCC47085)


title: Sensitive_3

description:
10_1363
Healthy adult blood donor from NLGIP (Israel).
Thiopurine-sensitive lymphoblastoid cell line gene expression data.


title: PAO1_fabF1-excess_60min_rep1

description:
This sample is of ∆fabF1 ∆fabF2 Pseudomonas aeruginosa ATCC47085 grown in excess IPTG (1 mM). It is the first of two biological replicates used in this experiment, each from separate cultures.
Pseudomonas aeruginosa PAO1-LAC (ATCC47085)


title: blood_lun_001

description: Sample name: TIHO-Lundehund_001


title: KO_LPS_3

city: Singapore

first: Michael

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

hyb_protocol: According to beadchip array manufacturer's protocol

data_processing: Array data were extracted at the probe level with no background correction using Illumina's BeadStudio software. These raw data were quantile normalized. Statistical analysis and differential gene expression were carried out using the limma package in R 2.15.2/Bioconductor. Resulting p-values were corrected for multiple testing using the Benjamini-Hochberg false discovery rate.

organism: Mus musculus

source_name: Bone Marrow derived DC cells

label_protocol: Total RNA samples were amplified and biotinylated using the Illumina TotalPrep RNA amplification Kit (Ambion, Austin, TX).

growth_protocol: Bone marrow cells were harvested from Ezh2f/f mice and Ezh2f/f; Mx-cre mice using standard protocols before being cultured in RPMI 1640 (Gibco-BRL) complete medium supplemented with 20ng/ml GM-CSF and 10ng/ml IL-4 (Prospec Tany). On day 2 of culture, the cells were gently washed and the medium replaced with fresh complete medium supplemented with 10ng/ml GM-CSF. Cells were cultured for 6 or 7 days and medium was added or refreshed as necessary.

extract_protocol: Cells were lyzed in Trizol and RNA was isolated as described manifactures manual.

treatment_protocol: To generate mature DCs, the immature cells were stimulated overnight in the presence of 100ng/ml LPS (Sigma Aldrich). In some experiments, mature DC were starved for 6h in serum-free medium prior to analysis.

tag: strain

tag: genotype/variation

value: EZH2 KO

tag: tissue type

value: dendritic cells

tag: dc stage

value: mature

tag: treatment

value: LPS treated


title: KO_NT_3

scan_protocol: According to beadchip array manufacturer's protocol

value: immature

value: untreated


title: VC-044


title: WN_LPS_3

value: wild type


title: VC-041


title: PLN_NOD_12w_7

city: Stanford

first: Keiichi

last: Kodama

state: CA

address: 269 Campus Drive, Room 2225

department: Department of Medicine, Division of Immunology & Rheumatology

institute: Stanford Univeristy School of Medicine

description: Sample name: B7-12wk NOD PLN-7.txt:cy5ByCy3Signal(normalized)

hyb_protocol: Using the Agilent Two-Color Microarray-Based Gene Expression Analysis protocol, the fragmentation mix consisting of 750ng of cyanine 3 labeled amplified cRNA, 750ng of cyanine 5 labeled amplified cRNA, 50μ of 10X blocking agent (Gene Expression Hybridization Kit; Agilent Technologies), 10μl of 25X fragmentation buffer (Agilent Technologies) and nuclease free water to a total volume of 250μl, was incubated for 30 minutes at 60 degree Celsius and then 250 μl of 2X hybridization buffer was added to stop the fragmentation reaction.  The 500μl solution was then pipetted onto the microarray and incubated in an oven rotator at 60 degree Celsius for 17 hours.

scan_protocol: The arrays were then scanned using an Agilent Microarray Scanner laser based detection system.  Background subtracted signal data (BGSub Signal: raw spot signal – background signal) and processed signal were obtained from images using the Agilent Feature Extraction software version 8.5.

data_processing: Data were processed with Feature Extraction Software (Agilent Technologies), and gene expression data were processed (cy5: NOD, cy3: pooled NOD.B10) and presented as normalized expression ratios: Log2 (NOD processed signal / NOD.B10 processed signal) using GeneSpring GX 11.5 (Agilent Technologies).

source_name: Pancreatic lymph nodes_NOD

label_protocol: cRNA amplification and fluorescence labeling was performed using the Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). The cRNA synthesis involved a single amplification for two-color labeling, to create ample cyanine 5 (cy5; NOD) and cyanine 3 (cy3; NOD.B10) labeled cRN.. In this technique a primer that contains poly dT, and a T7 polymerase promoter is annealed to the poly A+ RNA (mRNA).  Reverse transcriptase is added to the reaction to synthesize the first and second strands of cDNA (to create double stranded DNA).  Fluorescence labeled anti-sense cRNA is next synthesized with T7 Polymerase, which simultaneously incorporates cy3- or cy5-labeled cytidine triphosphate (CTP).

extract_protocol: Total RNA was extracted using Trizol reagent and the Qiagen RNeasy mini kit.

value: NOD

tag: age

value: 12 weeks old

value: female

value: PLN

source_name: Pooled_pancreatic lymph nodes_NOD.B10


title: VC-040

value: Castrate resistant prostate cancer

value: plasma

value: male reference DNA (Promega Corp)


title: VC-043


title: VC-042


title: WT_NT_3


title: PLN_NOD_12w_6

description: Sample name: B6-12wk NOD PLN-6.txt:cy5ByCy3Signal(normalized)


title: blood_lun_004

description: Sample name: TIHO-Lundehund_004

value: Lundehund

value: blood


title: VC-039


title: PAO1_accD-depleted_60min_rep1

description:
This sample is of ∆accD Pseudomonas aeruginosa ATCC47085 grown in limiting IPTG (0.02 mM). It is the first of two biological replicates used in this experiment, each from separate cultures.
Pseudomonas aeruginosa PAO1-LAC (ATCC47085)

value: ∆accD complemented by lac-regulated accD on pUCP24 plasmid

value: normal


title: KO_NT_2

value: EZH2 KO

value: dendritic cells


title: PAO1_fabG-excess_60min_rep1

description:
This sample is of ∆fabG Pseudomonas aeruginosa ATCC47085 grown in excess IPTG (1 mM). It is the first of two biological replicates used in this experiment, each from separate cultures.
Pseudomonas aeruginosa PAO1-LAC (ATCC47085)

value: ∆fabG complemented by lac-regulated fabG on pUCP24 plasmid


title: VC-037


title: PAO1_accD-excess_60min_rep1

description:
This sample is of ∆accD Pseudomonas aeruginosa ATCC47085 grown in excess IPTG (1 mM). It is the first of two biological replicates used in this experiment, each from separate cultures.
Pseudomonas aeruginosa PAO1-LAC (ATCC47085)


title: VC-046


title: PLN_NOD_12w_1

description: Sample name: B1-12wk NOD PLN-1.txt:cy5ByCy3Signal(normalized)


title: PLN_NOD_12w_4

description: Sample name: B4-12wk NOD PLN-4.txt:cy5ByCy3Signal(normalized)


title: PLN_NOD_12w_3

description: Sample name: B3-12wk NOD PLN-3.txt:cy5ByCy3Signal(normalized)


title: VC-038


title: PLN_NOD_4w_7

description: Sample name: A7-4wk NOD PLN-7.txt:cy5ByCy3Signal(normalized)

value: 4 weeks old


title: PAO1_fabG-depleted_60min_rep1

description:
This sample is of ∆fabG Pseudomonas aeruginosa ATCC47085 grown in limiting IPTG (0.06 mM). It is the first of two biological replicates used in this experiment, each from separate cultures.
Pseudomonas aeruginosa PAO1-LAC (ATCC47085)


title: VC-035


title: WT_NT_2

value: immature

value: untreated


title: VC-036


title: PLN_NOD_4w_6

description: Sample name: A6-4wk NOD PLN-6.txt:cy5ByCy3Signal(normalized)

value: NOD


title: PH110_Hal010081

city: Rochester

first: Marc

middle: A

last: Becker

state: MN

address: 200 First St SW

department: Medical Oncology

institute: Mayo Clinic

description: total RNA

hyb_protocol: Following fragmentation, hybridization, washing and staining was performed using Affymetrix GeneTitan® Multi-Channel (MC) Instrument per the manufacturer instructions.

scan_protocol: GeneChips were scanned the Affymetrix GeneTitan® Multi-Channel (MC) Instrument per the manufacturer instructions.

data_processing: Base-2 logarithm transformed intensity data from the two batches of samples were normalized within each batch using frozen robust multi-array analysis (frozen RMA).

source_name: Carcinoma of ovary, fallopian tube or peritoneum

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: Primary ovarian cancer tumorgrafts derived from fresh tumor tissue of women undergoing surgical resection for primary peritoneal, fallopian and/or ovarian cancer were injected intraperitoneally into SCID Beige mice and upon engraftment confirmation, tumor tissue was harvested and RNA extracted for subsequent gene expression analysis.

extract_protocol: Total RNA was extracted from cells using the RNeasy mini RNA isolation kit (Qiagen, Valencia, CA). The integrity of RNA samples was verified using an Agilent 2100 Bioanalyzer (1.8-2.0; Agilent Technologies, Palo Alto, CA).

treatment_protocol: Frozen tissue stored at -80°C taken after surgery.

tag: histology

value: Serous

tag: Stage

value: IIIC

tag: surgery timing

value: Primary

tag: debulking category

value: Optimal

tag: primary treatment

tag: platinum

tag: taxane

tag: other chemo

tag: vital status

value: Alive


title: WN_LPS_2

value: wild type

value: mature

value: LPS treated


title: VC-034

tag: disease state

value: Castrate resistant prostate cancer

tag: sample type

value: plasma

value: male reference DNA (Promega Corp)


title: PH095_Hal010306

description: total RNA

value: IV

value: Chemo

value: Yes

value: No

value: Dead


title: PH115_Hal010092

description: total RNA


title: KO_NT_1

tag: strain

value: EZH2 KO

value: dendritic cells

value: immature

value: untreated


title: PLN_NOD_4w_5

description: Sample name: A5-4wk NOD PLN-5.txt:cy5ByCy3Signal(normalized)

value: NOD

value: 4 weeks old

tag: gender

value: female

tag: tissue

value: PLN


title: PH087_Hal010256

description: total RNA

value: Serous

value: IIIC

value: Primary

value: Optimal

value: Alive


title: VC-032

value: Castrate resistant prostate cancer

value: plasma

value: male reference DNA (Promega Corp)


title: KO_LPS_2

tag: genotype/variation

tag: tissue type

tag: dc stage

value: mature

value: LPS treated


title: PH085_Hal010090

description: total RNA

tag: histology

value: Chemo

value: Yes

value: Dead


title: KO_LPS_1

value: EZH2 KO

value: dendritic cells

tag: treatment


title: VC-033


title: WN_LPS_1

value: wild type


title: PLN_NOD_4w_1

description: Sample name: A1-4wk NOD PLN-1.txt:cy5ByCy3Signal(normalized)

value: NOD

tag: age

value: 4 weeks old

value: female

value: PLN


title: PLN_NOD_4w_3

description: Sample name: A3-4wk NOD PLN-3.txt:cy5ByCy3Signal(normalized)


title: PH080_Hal010323

description: total RNA

value: Serous

tag: Stage

value: IC

tag: surgery timing

value: Primary

tag: debulking category

value: Optimal

value: No


title: PLN_NOD_4w_4

description: Sample name: A4-4wk NOD PLN-4.txt:cy5ByCy3Signal(normalized)


title: PLN_NOD_10d_3

description: Sample name: 10d PLN-3.txt:cy5ByCy3Signal(normalized)

value: 10 days old


title: VC-027

value: Castrate resistant prostate cancer

value: plasma

value: male reference DNA (Promega Corp)


title: VC-028


title: Bovine raw milk whey supernatant after ultracentrifugation

city: Zama-City

first: Hirohisa

last: Izumi

state: Kanagawa-Pref.

address: 1-83, 5-Chome, Higashihara

department: Nutrition Research Department

country: Japan

institute: Morinaga Milk Industry Co., Ltd.

hyb_protocol: Cy3 labelled RNA samples were hybridized to Bovine Oligo DNA microarrays ver. 2.0 (4X44K) (Agilent Technologies) at 65 ºC for 17 hr with a Gene Expression Hybridyzation Kit (Agilent Technologies). After hybridyzation, the microarray slides were washed and dried according to the manufacture's instruction.

scan_protocol: The microarray slides were scanned on an Agilent DNA Microarray Scanner (Agilent Technologies).

data_processing: Fluorescent signal intensities were extracted from the images with the Feature Extraction Software (v.10.7.3.1) (Agilent Technologies). The raw signal values were not normalized when importing the Feature Extraction files into GeneSpring GX 11.5.1.

organism: Bos taurus

label_protocol: Total purified RNA from 3 samples were mixed equally. And cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low RNA Input Quick Amp Labeling Kit (Agilent) according to the manufacture's instruction, followed by miRNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted and purified using an miRNeasy Serum/Plasma Kit (Qiagen, Hilden, Germany). Briefly, exosome and supernatant samples were diluted with five volumes of QIAzol Lysis Reagent, mixed thoroughly by vortexing and incubated for 5 min. Then chloroform (equal volume to sample) was added to homogenate, mixed thoroughly by vortexingand incubated for 3 min. The homogenate were centrifuged (12,000 x g, 4 ºC, 15 min). The resulting aqueous phase was mixed thoroughly with 1.5 volumes of 100 % ethanol and passed through an miRNeasy column. The column was washed according to the manufacture's protocol, and RNA was eluted in nuclease free water. The quanity and integrity of the RNA were assessed using RNA 6000 Pico Kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)

treatment_protocol: Whey samples from raw milk were ultracentrifuged (10,000 g, 4 °C, 90 min). Resulted supernatant was carefully collected avoiding contamination of pelleted exosome. Pelleted exosome was resuspended in PBS and ultracentrifuged (10,000 g, 4 °C, 90 min) to wash. This wash step was done totally twice.

tag: breed

value: Holstein


title: PH070_Hal010302

description: total RNA

value: IV

tag: primary treatment

value: Chemo

tag: platinum

value: Yes

tag: taxane

tag: other chemo

value: Dead


title: PLN_NOD_10d_5

description: Sample name: 10d PLN-5.txt:cy5ByCy3Signal(normalized)

tag: strain

value: NOD


title: PLN_NOD_10d_4

description: Sample name: 10d PLN-4.txt:cy5ByCy3Signal(normalized)

tag: gender

value: female


title: Bovine raw milk whey-derived exosome

source_name: Bovine raw milk whey-derived exosome


title: PH077_Hal010303

description: total RNA

tag: vital status


title: PH069_Hal010301

description: total RNA

value: Mixed


title: VC-031

tag: disease state

tag: sample type


title: WT_NT_1

tag: genotype/variation

value: wild type

tag: tissue type

value: dendritic cells

tag: dc stage

value: immature

value: untreated


title: PLN_NOD_10d_6

description: Sample name: 10d PLN-6.txt:cy5ByCy3Signal(normalized)

tag: age

tag: tissue

value: PLN


title: VC-026


title: PLN_NOD_10d_1

description: Sample name: 10d PLN-1.txt:cy5ByCy3Signal(normalized)

value: 10 days old


title: VC-025

value: Castrate resistant prostate cancer


title: VC-030

value: plasma


title: PH055_Hal010057

description: total RNA

tag: histology

value: Serous

tag: Stage

tag: surgery timing

value: Primary

value: Optimal

value: No


title: PH058_Hal010058

description: total RNA

value: IC

tag: debulking category

tag: primary treatment

value: Chemo

value: Yes

value: Alive


title: PH054_Hal010031

description: total RNA

value: IIIC

tag: platinum

tag: taxane


title: Seedling_brm clf_rep2

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

country: China

institute: shenzhen university

description: brm clf2

hyb_protocol: Affymetrix ATH1 arrays were hybridized in three biological replicates according to the manufacturer’s instructions.

scan_protocol: Standard Affymetrix protocol.

data_processing: The microarray data were analyzed using the R package affy (affy_1.34.0) from BioConductor. The MAS5 method was used.

organism: Arabidopsis thaliana

source_name: 14-day-old seedling

label_protocol: Standard Affymetrix protocol.

growth_protocol: All plants were grown at 22°C under 16h light/8h dark

extract_protocol: RNAs were isolated from wild-type and brm-1, clf-29 and brm-1 clf-29 seedlings. Seedlings were ground and extracted with RNeasy Plant Mini kit (Qiagen) .

tag: ecotype

value: Columbia (Col)

value: brm-1 clf-29

value: whole seedling

tag: developmental stage


title: PH063_Hal010033

description: total RNA

tag: other chemo

tag: vital status


title: VC-023

tag: disease state

tag: sample type

value: male reference DNA (Promega Corp)


title: VC-022


title: PH052_Hal010056

description: total RNA

value: IIIB


title: PLN_NOD_10d_2

description: Sample name: 10d PLN-2.txt:cy5ByCy3Signal(normalized)

tag: strain

value: NOD

value: 10 days old

tag: gender

value: female

value: PLN


title: VC-024

value: Castrate resistant prostate cancer

value: plasma


title: Seedling_brm clf_rep1

description: brm clf1

tag: genotype/variation


title: Seedling_clf_rep3

tag: tissue


title: VC-021


title: VC-029


title: Seedling_clf_rep2


title: Seedling_clf_rep1


title: Seedling_brm_rep3


title: PH051_Hal010055

description: total RNA

tag: histology

value: Serous

value: Primary

value: Optimal


title: PH045_Hal010029

description: total RNA

tag: Stage

value: Unstaged

value: Chemo

value: Yes

value: No

value: Dead


title: VC-018


title: VC-017


title: VC-019


title: PH048_Hal010322

description: total RNA

value: IIIC

tag: surgery timing


title: PH046_Hal010054

description: total RNA

value: IV

tag: debulking category


title: PH044_Hal010053

description: total RNA

tag: primary treatment


title: PH053_Hal010300

description: total RNA

tag: platinum


title: Seedling_brm_rep1

value: Columbia (Col)

value: whole seedling


title: Seedling_Col_rep3

value: wild-type


title: VC-020

value: male reference DNA (Promega Corp)


title: PH042_Hal010043

description: total RNA

tag: taxane


title: VC-014


title: Seedling_brm_rep2

tag: ecotype


title: VC-015


title: Seedling_Col_rep1

tag: developmental stage


title: PH039_Hal010298

description: total RNA

value: Sub-optimal

tag: other chemo


title: VC-012

value: Castrate resistant prostate cancer


title: PH038_Hal010321

description: total RNA

tag: vital status


title: Seedling_Col_rep2


title: VC-016

tag: disease state

value: plasma


title: VC-010

tag: sample type


title: PH041_Hal010028

description: total RNA

value: Serous


title: VC-008


title: VC-013


title: PH040_Hal010052

description: total RNA

value: Primary


title: VC-011


title: PH034_Hal010050

description: total RNA

value: Undifferentiated

value: Optimal


title: VC-007


title: VC-009


title: PH026_Hal010045

description: total RNA

value: Chemo


title: VC-006


title: PH029_Hal010047

description: total RNA

value: Mixed

value: IC

value: Yes


title: PH037_Hal010319

description: total RNA

value: Clear Cell

value: No

value: Alive


title: PH036_Hal010026

description: total RNA

value: IIIC

value: Dead


title: VC-005

value: male reference DNA (Promega Corp)


title: VC-004


title: PH018_Hal010044

description: total RNA

value: IV


title: Seedling_brm clf_rep3

description: brm clf3

value: Columbia (Col)

value: brm-1 clf-29

value: whole seedling


title: VC-002

value: Castrate resistant prostate cancer

value: plasma


title: PH013_Hal010294

description: total RNA

value: Serous

value: IIA

value: Primary

value: Optimal


title: VC-001


title: PH006_Hal010018

description: total RNA

value: Carcinosarcoma

value: Chemo

value: Yes


title: PH015_Hal010022

description: total RNA

value: Endometrioid

value: IIC

value: No

value: Alive


title: VC-003

value: male reference DNA (Promega Corp)


title: G. arboreum wild and wax mutant swap tech rep1

status: Public on Mar 08 2015

city: Lahore

first: Muhammad

middle: Younas

last: khan

state: Punjab

address: Thokar Niaz Baig

department: Molecular biology

country: Pakistan

institute: National centre of Excellence in Molecular biology

description: Un-sequenced PCR amplified DNAs from Clones were spotted in duplicate. The differentially expressed genes were after hybridization and data analysis sequenced.

hyb_protocol: Equal concentrations of Cy3 and Cy5 labelled cDNAs in terms of dye pmoles were taken and mixed in the 2X hybridization buffer. The target was heated to 95oC for three minutes and then immediately put on ice. Slide was placed in chamber of hybstation (Genomic Solutions®) with array side up. Target was injected to slide in chamber at 65oC and then slide was incubated at 42oC for 24 hours. Slide was removed from hybstation and washed in solution containing 1X SSC, 0.2% SDS at 42oC for 2 min with agitation. Then, slide was shifted to second wash solution containing 0.1X SSC, 0.2% SDS at room temperature and incubated for 2 min with agitation. After 2 min slide was moved to third wash solution containing 0.1X SSC and kept for 2 min with agitation. Slide was spin dried immediately by keeping slide in 50 ml tube with kimwipe stuffed in the bottom in a swing bucket rotor at 2000rpm for 1min and preceded for slide scan.

scan_protocol: Slide was scanned in Cy3 and Cy5 channels with the help of scanner UC 4X4 (Genomic solution®). The scanned slide was initially analyzed with the help of GENE INTEGRATOR software of GeneTAC™ UC4 (Genomic solution®) and raw data were generated.

data_processing: The data in the VALUE column were normalized with the help of house keeping genes and lowess normalization through MIDAS provided by TM4.

organism: Gossypium arboreum

source_name: G. arboreum epicuticular wax mutant (Gawm3)

label_protocol: For the aminoallyl labeling of cDNA, 45 µg of total RNA, DNA free, was taken and 2 µg of OligodT18 primer was added to it and final volume was made up to 18.0 µL with RNase-free water. The contents were mixed well and incubated at 70oC for 10 minutes. After incubation the mixture was placed on ice for 30 seconds, centrifuged and following contents were added: 5X First Strand buffer 6.0 µL 0.1 M DTT 3.0 µL 50X aminoallyl-dNTP mix 0.5 µL SuperScript III RT (200U/µL) 2.0 µL RNAse inhibitor 0.5 µL The contents were mixed well, centrifuged briefly and incubated at 42oC for 3 hours. Then to hydrolyze RNA, 2U of RNAse H were added, mixed and incubated at 37oC for 15 minutes. Added 25µL of 1M Tris (pH 6.8) to nutrilize pH. Unincorporated aa-dUTP and free amines were removed through (Qiagen pcr purification kit). Dry cDNA was dissolved in 5µl 0.1M sodium carbonate (pH 9.0) and 5 µl Cy3 dye was added to sample and mixed. The reaction was incubated for 1 hour in the dark at room temperature.

extract_protocol: Jaakola et al. (2001), CTAB and PVP method was used for total RNA extraction.

tag: organ

value: Leaf

source_name: G. arboreum wild plant


title: G. arboreum wild and wax mutant reg bio rep

scan_protocol: Slide was scanned in Cy3 and Cy5 channels with the help of scanner UC 4X4 (Genomic solution®). The scanned slide was initially analyzed with the help of TIGER SPOTFINDER software available freely on line from the TM4 website.


title: activated CD103neg ICOSpos, biological rep2

city: Campus de Cantoblanco

first: Alberto

last: Pascual-Montano

state: Madrid

address: Darwin 3

country: Spain

institute: National Center for Biotecnology

description: Gene expression data from sorted and activated CD103neg ICOSpos Treg isolated from pooled cervical, axillary, brachial, inguinal, mesenteric and para-aortic lymph nodes of adult wild type mice

hyb_protocol: 85µl cocktail (23.5ng/µl labeled DNA) were loaded on Mouse Gene 1.0 ST Array (Affymetrix) and hybridized for 17 hours (45°C, 60rpm) in Hybridization oven 645 (Affymetrix). The arrays were washed and stained on Fluidics Stations 450 (Affymetrix) by using the Hybridization Wash and Stain Kit (Affymetrix) under FS450_0007 protocol.

scan_protocol: The GeneChips were scanned with an Affymetrix GeneChip Scanner 3000 7G. DAT images and CEL files of the microarrays were generated using Affymetrix GeneChip Command Control (Affymetrix).

data_processing: Raw intensities were background corrected, summarized and normalized by RMA using Affy package of Bioconductor.

source_name: CD103neg ICOSpos Treg activated for 3 days by an in vitro suppression assay

label_protocol: 270 ng of total RNA was subjected to target synthesis using the WT Expression kit (Ambion). Fragmentation and labeling of amplified cDNA was performed using the WT Terminal Labeling Kit (Affymetrix). Synthesis reactions was carried out using a PCR machine (TProfessionnal, Biometra) in 0.2ml tubes (Starlab).

growth_protocol: Treg were isolated from 8 -12 week old female mice and sorted by flow cytometry into subsets defined by CD103 and ICOS expression. RNA was isolated from individual subsets directly or after a 3 day activation period in vitro in a Treg suppression assay

extract_protocol: RNA was isolated using the RNeasy Micro kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: In vitro suppression assays were performed for 3 days in 12 well Falcon plates containing 1'000'000 Ly5.1 congenic naive CD4 cells, 2'000'000 irradiated Rag2-/- splenocytes and 200'000 Treg of the specified subset in the presence of soluble anti CD3 mAb (0.5ug/ml). After 3 days, cultures were stained for CD4, CD25 and Ly5.1 and Treg were sorted as Ly5.1neg CD4pos CD25pos

tag: age

value: 8 -12 week old

tag: gender

value: female

tag: strain

value: lymph nodes


title: G. arboreum wild and wax mutant swap tech rep2

tag: ogan


title: PH003_Hal010247

description: total RNA

tag: histology

tag: Stage

value: IIIC

value: Dead


title: G. arboreum wild and wax mutant reg tech rep2

value: leaf


title: G. arboreum wild and wax mutant reg tech rep1

data_processing: The data in the VALUE column were normalized with the help of house keeping genes and lowess nornmalization through MIDAS provided by TM4.


title: activated CD103neg ICOSneg, biological rep2

description: Gene expression data from sorted and activated CD103neg ICOSneg Treg isolated from pooled cervical, axillary, brachial, inguinal, mesenteric and para-aortic lymph nodes of adult wild type mice

source_name: CD103neg ICOSneg Treg activated for 3 days by an in vitro suppression assay

tag: tissue


title: activated CD103pos ICOSpos, biological rep2

description: Gene expression data from sorted and activated CD103pos ICOSpos Treg isolated from pooled cervical, axillary, brachial, inguinal, mesenteric and para-aortic lymph nodes of adult wild type mice

source_name: CD103pos ICOSpos Treg activated for 3 days by an in vitro suppression assay


title: activated CD103pos ICOSpos, biological rep1


title: activated CD103pos ICOSneg, biological rep1

description: Gene expression data from sorted and activated CD103pos ICOSneg Treg isolated from pooled cervical, axillary, brachial, inguinal, mesenteric and para-aortic lymph nodes of adult wild type mice

source_name: CD103pos ICOSneg Treg activated for 3 days by an in vitro suppression assay


title: activated CD103neg ICOSneg, biological rep1


title: PH027_Hal010046

description: total RNA

value: Serous

tag: surgery timing

value: Primary

tag: debulking category

tag: primary treatment


title: CD103neg ICOSpos, biological rep1

description: Gene expression data from sorted CD103neg ICOSpos Treg isolated from pooled cervical, axillary, brachial, inguinal, mesenteric and para-aortic lymph nodes of adult wild type mice

source_name: freshly sorted ex vivo CD103neg ICOSpos Treg


title: CD103neg ICOSneg, biological rep2

description: Gene expression data from sorted CD103neg ICOSneg Treg isolated from pooled cervical, axillary, brachial, inguinal, mesenteric and para-aortic lymph nodes of adult wild type mice

source_name: freshly sorted ex vivo CD103neg ICOSneg Treg


title: CD103neg ICOSneg, biological rep1


title: activated CD103neg ICOSpos, biological rep1


title: CD103pos ICOSpos, biological rep1

description: Gene expression data from sorted CD103pos ICOSpos Treg isolated from pooled cervical, axillary, brachial, inguinal, mesenteric and para-aortic lymph nodes of adult wild type mice

source_name: freshly sorted ex vivo CD103pos ICOSpos Treg


title: CD103pos ICOSneg, biological rep1

description: Gene expression data from sorted CD103pos ICOSneg Treg isolated from pooled cervical, axillary, brachial, inguinal, mesenteric and para-aortic lymph nodes of adult wild type mice

source_name: freshly sorted ex vivo CD103pos ICOSneg Treg


title: CD103pos ICOSpos, biological rep2


title: activated CD103pos ICOSneg, biological rep2


title: CD103neg ICOSpos, biological rep2


title: CD103pos ICOSneg, biological rep2


title: fibroblast-derived induced pluripotent stem cells, replicate b

status: Public on Mar 07 2015

city: Duesseldorf

first: Ulf

last: Tiemann

address: Moorenstrasse 5

department: Institute for Stem Cell Research and Regenerative Medicine

institute: Heinrich Heine University Duesseldorf

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data was processed by mapping bead intensities using BeadStudio 3.2 (Illumina), performing background correction using the Robust Multiarray Analysis (Affymetrix), normalizing gene expression using the lumi package of R‑Bioconductor, and performing variance stabilization by log2 scaling.

label_protocol: Biotinylated cRNA was prepared using the TotalPrep RNA Amplification Kit (Ambion)

extract_protocol: RNA was extracted using the RNeasy Mini Kit (Qiagen)

tag: strain background

tag: cell type

value: fibroblast-derived induced pluripotent stem cells (Fib-iPSCs)


title: fibroblasts, replicate a

source_name: fibroblasts

value: fibroblasts


title: embryonic stem cells, replicate b

source_name: embryonic stem cells

value: embryonic stem cells (ESCs)


title: fibroblast-derived induced pluripotent stem cells, replicate a


title: pluripotent stem cell line 4, replicate b

source_name: pluripotent stem cell line

value: germline-derived pluripotent stem cells (gPSCs)


title: G. arboreum wild and wax mutant swap bio rep


title: pluripotent stem cell line 1, replicate b


title: pluripotent stem cell line 4, replicate a


title: pluripotent stem cell line 3, replicate b


title: embryonic stem cells, replicate a


title: pluripotent stem cell line 1, replicate a


title: pluripotent stem cell line 2, replicate b


title: pluripotent stem cell line 2, replicate a


title: pluripotent stem cell line 3, replicate a


title: induced pluripotent stem cell line 4, replicate b

source_name: induced pluripotent stem cell line

value: GSC-derived induced pluripotent stem cells (iPSCs)


title: induced pluripotent stem cell line 3, replicate a


title: induced pluripotent stem cell line 4, replicate a


title: induced pluripotent stem cell line 2, replicate b


title: induced pluripotent stem cell line 2, replicate a


title: induced pluripotent stem cell line 3, replicate b


title: germline stem cell line 2, replicate b

source_name: germline stem cell line

value: germline stem cells (GSCs)


title: induced pluripotent stem cell line 1, replicate b


title: germline stem cell line 2, replicate a


title: germline stem cell line 1, replicate b


title: induced pluripotent stem cell line 1, replicate a


title: Lamin A DamID in dKO mESC (rep 1)

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

hyb_protocol: The labeled MePCR DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, 80 μg per sample was combined into 33.6 μl water, and mixed with 2.4 μl Alignment oligo, 24 μl hybridization component A, and 60 μl 2x Hybridization Buffer. The entire 120 μl was used for hybridization in Tecan hybridization stations for 16-18 h at 42C. Arrays were then washed in 42 °C Nimblegen washbuffer1, and room temperature Nimblegen washbuffer 2 and 3. All buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Microarrays were scanned in a Agilent Scanner (Model G2505C, Serial number US22502518), which uses Scan Control software (Version A.8.1.3). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were double-pass scanned at maximum PMT for each channel, at a 2 um per pixel resolution.

data_processing: Arrays were quantified with NimbleScan 2.5. Raw .pair files were read with the Ringo package for R and the loess normalized. Subsequently, single channel data was obtained and subjected to quantile-quantile normalisation over all available cell types and replicates, with the exception of sample 1

source_name: Dam-Lamin A in dKO mESC (rep 1)

label_protocol: 1.5 µg MePCR DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3/Cy5 nonamers following manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html). Labeling time was extended to 12 hours to increase yield.

extract_protocol: mESC cells were infected with lenti-virus expressing either Dam-Emerin, Dam-lamin A or Dam-only. After 48 hours gDNA was isolated with the Qiagen Blood and Tissue kit following the manufacturer's protocol. 0,5 μg of gDNA was digested with DpnI (New England Biolabs), adapters were ligated with T4 ligase (New England Biolabs), and the ligation reaction was subsequently digested with DpnII (New England Biolabs). 100 ng of the DpnII digested material was used as input for a PCR amplification of methylated fragments (MePCR), see Vogel et al., 2008, Nature Protocols for details. MePCR fragments were purified by Qiaquick Spin columns (Qiagen).

value: mESC

tag: dam status

value: Dam-lamin A

value: Dam-only

source_name: Dam-only in dKO mESC (rep 1)


title: Lamin A DamID in wt mESC (rep 1)

source_name: Dam-Lamin A in wt mESC (rep 1)

source_name: Dam-only in wt mESC (rep 1)


title: Emerin DamID in tKO mESC (rep 2)

source_name: Dam-only in tKO mESC (rep 2)

value: Dam-Emerin

source_name: Dam-Emerin in tKO mESC (rep 2)


title: Emerin DamID in tKO mESC (rep 1)

source_name: Dam-Emerin in tKO mESC (rep 1)

source_name: Dam-only in tKO mESC (rep 1)


title: germline stem cell line 1, replicate a


title: Lamin A DamID in dKO mESC (rep 2)

source_name: Dam-only in dKO mESC (rep 2)

source_name: Dam-Lamin A in dKO mESC (rep 2)


title: Lamin A DamID in wt mESC (rep 2)

source_name: Dam-only in wt mESC (rep 2)

source_name: Dam-Lamin A in wt mESC (rep 2)


title: fibroblasts, replicate b

source_name: fibroblasts


title: Osl_rep3_exp1 vs. Control_rep3_exp1

city: Gent

first: Jana

last: Asselman

address: Coupure Links 653 (Building F, 2nd floor)

country: Belgium

institute: Ghent University

description: Expression Analysis

hyb_protocol: Labeled products were pooled and served as a final Master Mix for the array, The products were dried in a speedvac then resuspended in water prior to hybridization, which was performed with the NimbleGen hybridization kit. A single hybridization master for a given source and biological replicate.

scan_protocol: Axon GenePix 4200 Professional, 5 micron resolution.

data_processing: Raw signal intensity extract with NimbleScan 2.4 Software (Roche NimbleGen) in PAIR files. Quantile normalization to convert raw to processed data.

organism: Daphnia pulex

source_name: Control rep3 exp1

label_protocol: cDNA labeling using 1 O.D. Cy-labeled random nonomer primer and 100U Klenow fragment (3>5 exo) per 1 μg double-stranded cDNA.

growth_protocol: 4 day old animals were isolated from synchronized cultures of brood mothers. Mothers were fed a control diet of the non toxic green algae at an optimal diet ratio under constat light and temperature conditions

extract_protocol: Tissue was homogenized  and extracted RNA was purified using the Qiagen RNeasy protocol with on-column DNase treatment from specific tissues. Total RNA amplified using MessageAmp II aRNA Kit (Ambion). aRNA converted to ds cDNA using SuperScript cDNA Synthesis Kit (Invitrogen).

treatment_protocol: Animals were exposed for 10 days to a control diet or a diet containing 50% of one of the five cyanobacteria. Animals were fed daily and experimental jars were changed out three times a week. After 10 days RNA was extracted.

tag: Sex

value: female

tag: developmental stage

value: adult

value: whole body

source_name: Osl rep3 exp1


title: Emerin DamID in wt mESC for comparison with lamin B1 DamID. Single array

source_name: Dam-Emerin in wt mESC

source_name: Dam-only in wt mESC


title: Emerin DamID in dKO mESC (rep 2)

source_name: Dam-Emerin in dKO mESC (rep 2)


title: Osl_rep1_exp1 vs. Control_rep1_exp1

description: Expression Analysis

source_name: Control rep1 exp1

source_name: Osl rep1 exp1


title: Control_rep2_exp1 vs. Osl_rep2_exp1

description: Expression Analysis

source_name: Osl rep2 exp1

source_name: Control rep2 exp1


title: Emerin DamID in wtmESC (rep 2)

source_name: Dam-Emerin in wt mESC (rep 2)


title: Emerin DamID in dKO mESC (rep 1)

source_name: Dam-Emerin in dKO mESC (rep 1)

source_name: Dam-only in dKO mESC (rep 1)


title: Osl_rep1_exp2 vs. Control_rep1_exp1

description: Expression Analysis

source_name: Control rep1 exp2

source_name: Osl rep1 exp2


title: Nod_rep3_exp2 vs. Control_rep3_exp2

description: Expression Analysis

source_name: Control rep3 exp2

source_name: Nod rep3 exp2


title: Nod_rep3_exp1 vs. Control_rep3_exp1

description: Expression Analysis

source_name: Nod rep3 exp1


title: Control_rep4_exp1 vs. Osl_rep4_exp1

description: Expression Analysis

source_name: Osl rep4 exp1

source_name: Control rep4 exp1


title: Control_rep2_exp2 vs. Osl_rep2_exp2

description: Expression Analysis

source_name: Osl rep2 exp2

source_name: Control rep2 exp2


title: Cyl_rep3_exp2 vs. Control_rep3_exp2

description: Expression Analysis

source_name: Cyl rep3 exp2


title: Control_rep4_exp1 vs. Nod_rep4_exp1

description: Expression Analysis

source_name: Nod rep4 exp1


title: Nod_rep1_exp2 vs. Control_rep1_exp1

description: Expression Analysis

source_name: Nod rep1 exp2


title: Control_rep4_exp2 vs. Nod_rep4_exp2

description: Expression Analysis

source_name: Nod rep4 exp2

source_name: Control rep4 exp2


title: Cyl_rep1_exp1 vs. Control_rep1_exp1

description: Expression Analysis

source_name: Control rep1 exp1

source_name: Cyl rep1 exp1


title: Control_rep2_exp2 vs. Nod_rep2_exp2

description: Expression Analysis

source_name: Nod rep2 exp2


title: Osl_rep3_exp2 vs. Control_rep3_exp2

description: Expression Analysis

source_name: Osl rep3 exp2


title: Control_rep2_exp1 vs. Nod_rep2_exp1

description: Expression Analysis

source_name: Nod rep2 exp1

source_name: Control rep2 exp1


title: Control_rep4_exp1 vs. Cyl_rep4_exp1

description: Expression Analysis

source_name: Cyl rep4 exp1


title: Control_rep4_exp2 vs. Osl_rep4_exp2

description: Expression Analysis

source_name: Osl rep4 exp2


title: Aph_rep3_exp2 vs. Control_rep3_exp2

description: Expression Analysis

source_name: Control rep3 exp2

source_name: Aph rep3 exp2


title: Control_rep2_exp2 vs. Cyl_rep2_exp2

description: Expression Analysis

source_name: Cyl rep2 exp2


title: Control_rep4_exp2 vs. Aph_rep4_exp2

description: Expression Analysis

source_name: Aph rep4 exp2


title: Nod_rep1_exp1 vs. Control_rep1_exp1

description: Expression Analysis

source_name: Nod rep1 exp1


title: Cyl_rep1_exp2 vs. Control_rep1_exp1

description: Expression Analysis

source_name: Control rep1 exp2

source_name: Cyl rep1 exp2


title: Cyl_rep3_exp1 vs. Control_rep3_exp1

description: Expression Analysis

source_name: Control rep3 exp1

source_name: Cyl rep3 exp1


title: liver Wrn mutant vitamin C #3 / liver WT #3

city: Quebec

first: Michel

last: Lebel

state: Qc

address: 2705 Laurier Blvd, Local T-2-04

department: Centre Hospitalier de l’Université Laval (CHUL)

institute: Centre de Recherche du CHU de Québec

description: Biological Wrn vitamin C  replicate 3 of 4. Biological WT replicate 3 of 4.

hyb_protocol: Hybridization and washing was performed using the in situ Hybridization Plus kit (Agilent) and following the manufacturer's instructions.

scan_protocol: Arrays were scanned on an Axon GenePix® 4000B. Data were extracted from images using GenePix® version 6.0 with local background estimation.

data_processing:
Data were processed using limma in BioConductor (www.bioconductor.org). The data were background subtracted using normexp and also normalized using the loess method.
lowess normalized log2 ratio (intensity liver Wrn+vitamin C / intensity liver WT) in ALL.1.5.001.vitc.vs.wt.txt

source_name: Liver tissue

label_protocol: Protocol from Agilent

growth_protocol: Mice were maintained on a reversed 12:12-h light-dark cycle with controlled temperature (21 ± 1°C) and humidity. Food and water were provided ad libitum.

extract_protocol: Extraction of total RNA protocol described in Sambrook et al., 1989. Molecular cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press.

treatment_protocol: Wrn mutant mice were treated with 0.4% vitamin C in drinking water since weaning. WT mice were the untreated  controls.

value: liver

value: male

tag: genotype

value: Wrn mutant

tag: treatment

value: treated with vitamin C since weaning

value: 3 months of age

value: wild type


title: liver Wrn mutant vitamin C #1 / liver WT #1

description: Biological Wrn vitamin C  replicate 1 of 4. Biological WT replicate 1 of 4.

tag: age


title: liver Wrn mutant vitamin C #4 / liver WT #4

description: Biological Wrn vitamin C  replicate 4 of 4. Biological WT replicate 4 of 4.


title: Control_rep2_exp1 vs. Aph_rep2_exp1

description: Expression Analysis

source_name: Aph rep2 exp1


title: Control_rep2_exp1 vs. Cyl_rep2_exp1

description: Expression Analysis

source_name: Cyl rep2 exp1


title: Control_rep2_exp2 vs. Aph_rep2_exp2

description: Expression Analysis

source_name: Aph rep2 exp2

source_name: Control rep2 exp2


title: Aph_rep1_exp2 vs. Control_rep1_exp1

description: Expression Analysis

source_name: Aph rep1 exp2


title: T+high BPA_1

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

description: Gene expression data from lateral prostate of  rat treated with testosterone + high dose of Bisphenol A

hyb_protocol: Used Affymetrix GeneChip hybridization and stain kit following the manufacturer's instruction

scan_protocol: The GeneChips are scanned with Affymetrix GeneChip Scanner 3000 7G Plus using Affymetrix GeneChip Command Console 3.2.3.1515 software and Affymetrix present settings

data_processing: Microarray data was preprocessed using RMA implemented in R with BrainArray custom CDF

organism: Rattus norvegicus

source_name: lateral prostate_treated with Testosterone + high dose Bisphenol A

label_protocol: Ovation Pico WTA System (NuGen, San Carlos, CA) following the manufacturer's instruction

growth_protocol: Protocols of animal usage were approved by the University of Cincinnati Medical School Animal Care and Usage Committee. NBL rats were purchased from Charles River Laboratories (Kingston, NY), and kept under standard conditions.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA)

treatment_protocol: Control rats were implanted subcutaneously with empty capsules. Treated rats were surgically implanted with Silastic capsules containing hormones/BPA for 32 weeks.

value: Noble

value: lateral prostate

tag: gender

value: Male

value: Testosterone (30 mg) + Bisphenol A (320 mg)


title: Control_rep4_exp2 vs. Cyl_rep4_exp2

description: Expression Analysis

source_name: Cyl rep4 exp2

source_name: Control rep4 exp2


title: T+high BPA_2

tag: strain


title: liver Wrn mutant vitamin C #2 / liver WT #2

description: Biological Wrn vitamin C  replicate 2 of 4. Biological WT replicate 2 of 4.


title: T+low BPA_3

description: Gene expression data from lateral prostate of  rat treated with testosterone + low dose of Bisphenol A

source_name: lateral prostate_treated with Testosterone + low dose Bisphenol A

value: Testosterone (30 mg) + Bisphenol A (15 mg)


title: T+E2_2

description: Gene expression data from lateral prostate of  rat treated with testosterone + estradiol

source_name: lateral prostate_treated with Testosterone + Estradiol

value: Testosterone (30 mg) + Estradiol (15 mg)


title: T+E2_3


title: Emerin DamID in wtmESC (rep 1)

source_name: Dam-Emerin in wt mESC (rep 1)

value: mESC

value: Dam-only

source_name: Dam-only in wt mESC (rep 1)


title: T+E2_4


title: Aph_rep3_exp1 vs. Control_rep3_exp1

description: Expression Analysis

value: female

source_name: Aph rep3 exp1


title: Control_4

description: Gene expression data from lateral prostate of untreated control rat

source_name: lateral prostate_untreated

value: untreated


title: Ana_rep1_exp2 vs. Control_rep1_exp1

description: Expression Analysis

source_name: Control rep1 exp2

value: adult

value: whole body

source_name: Ana rep1 exp2


title: T+low BPA_1


title: Control_rep2_exp1 vs. Ana_rep2_exp1

description: Expression Analysis

source_name: Ana rep2 exp1

source_name: Control rep2 exp1


title: Control_rep4_exp2 vs. Ana_rep4_exp2

description: Expression Analysis

source_name: Ana rep4 exp2


title: Control_rep4_exp1 vs. Ana_rep4_exp1

description: Expression Analysis

source_name: Ana rep4 exp1

source_name: Control rep4 exp1


title: Control_rep2_exp2 vs. Ana_rep2_exp2

description: Expression Analysis

source_name: Ana rep2 exp2

source_name: Control rep2 exp2


title: Control_rep4_exp1 vs. Aph_rep4_exp1

description: Expression Analysis

source_name: Aph rep4 exp1


title: Aph_rep1_exp1 vs. Control_rep1_exp1

description: Expression Analysis

source_name: Control rep1 exp1

source_name: Aph rep1 exp1


title: T+low BPA_2

source_name: lateral prostate_treated with Testosterone + low dose Bisphenol A


title: Control_1


title: Control_3


title: T+high BPA_3

source_name: lateral prostate_treated with Testosterone + high dose Bisphenol A


title: Control_2


title: hepatocellular carcinoma [M807_plate4_F11]

city: New York

first: Augusto

last: Villanueva

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: Following fragmentation, 1 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: Array quality in mice studies was assessed with the arrayQualityMetrics package of Bioconductor (http://www.bioconductor.org). Data were normalized and logged-2 transformed using the RMA algorithm.

source_name: hepatocellular carcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Samples collected within 1 hour of surgical resection and fresh-frozen. Stored at -80ºC.

extract_protocol: Trizol according to manufacturer

treatment_protocol: Samples didn't receive any treatment

tag: subject

value: hepatocellular carcinoma patient

value: male

tag: age (yrs)

tag: tumor stage

value: bclcA

value: liver

tag: tissue subtype

value: primary hepatocellular carcinoma

tag: sample type

value: fresh frozen tissue


title: cirrhosis [M804_plate4_F10]

source_name: cirrhosis

tag: tissue

value: non-tumor cirrhosis


title: cirrhosis [M802_plate4_F08]


title: cirrhosis [M808_plate4_F12]


title: hepatocellular carcinoma [M803_plate4_F09]


title: hepatocellular carcinoma [M787_plate4_E05]


title: cirrhosis [M792_plate4_E10]


title: hepatocellular carcinoma [M793_plate4_E11]


title: hepatocellular carcinoma [M805_plate1_H07]


title: cirrhosis [M790_plate4_E08]


title: cirrhosis [M794_plate4_E12]


title: hepatocellular carcinoma [M801_plate4_F07]


title: hepatocellular carcinoma [M795_plate4_F01]

value: bclcB


title: cirrhosis [M788_plate4_E06]


title: cirrhosis [M796_plate4_F02]


title: hepatocellular carcinoma [M789_plate4_E07]


title: hepatocellular carcinoma [M797_plate4_F03]


title: cirrhosis [M798_plate4_F04]


title: cirrhosis [M800_plate4_F06]


title: cirrhosis [M784_plate4_E04]


title: hepatocellular carcinoma [M791_plate4_E09]


title: hepatocellular carcinoma [M799_plate4_F05]


title: hepatocellular carcinoma [M785_placa96_2_H07]


title: hepatocellular carcinoma [M777_placa96-3_H07]


title: cirrhosis [M780_plate4_D12]


title: cirrhosis [M774_plate4_D10]


title: Ana_rep1_exp1 vs. Control_rep1_exp1

description: Expression Analysis

source_name: Ana rep1 exp1


title: cirrhosis [M782_plate4_E02]


title: Ana_rep3_exp1 vs. Control_rep3_exp1

description: Expression Analysis

source_name: Control rep3 exp1

source_name: Ana rep3 exp1


title: cirrhosis [M760_plate4_C12]


title: hepatocellular carcinoma [M761_placa96-3_H06]


title: hepatocellular carcinoma [M781_plate4_E01_2]

value: bclcC


title: T+E2_1

source_name: lateral prostate_treated with Testosterone + Estradiol

value: Noble

value: lateral prostate

value: Male


title: hepatocellular carcinoma [M769_plate4_D05]


title: hepatocellular carcinoma [M765_plate4_D03]


title: cirrhosis [M764_plate4_D02]


title: hepatocellular carcinoma [M771_plate4_D07_2]


title: hepatocellular carcinoma [M759_plate4_C11]


title: hepatocellular carcinoma [M773_plate4_D09]


title: cirrhosis [M752_plate4_C10]


title: cirrhosis [M766_plate4_D04]


title: hepatocellular carcinoma [M783_plate4_E03]


title: hepatocellular carcinoma [M749_plate24_1_E09]


title: hepatocellular carcinoma [M751_plate4_C09]


title: hepatocellular carcinoma [M757_plate24_1_G09]


title: cirrhosis [M748_plate4_C08]


title: hepatocellular carcinoma [M763_plate4_D01]


title: hepatocellular carcinoma [M755_plate24_1_F09]


title: hepatocellular carcinoma [M779_plate4_D11]


title: cirrhosis [M746_plate4_C06]


title: hepatocellular carcinoma [M747_plate4_C07]


title: Ana_rep3_exp2 vs. Control_rep3_exp2

description: Expression Analysis

source_name: Control rep3 exp2

source_name: Ana rep3 exp2


title: hepatocellular carcinoma [M745_plate4_C05]


title: hepatocellular carcinoma [M743_plate4_C03]


title: hepatocellular carcinoma [M723_plate4_B07]


title: cirrhosis [M740_plate4_C02]


title: hepatocellular carcinoma [M725_plate24_1_A09]


title: cirrhosis [M744_plate4_C04]


title: hepatocellular carcinoma [M741_plate24_1_D09]


title: hepatocellular carcinoma [M735_plate24_1_C09]


title: hepatocellular carcinoma [M733_plate4_B11]


title: hepatocellular carcinoma [M729_plate4_B09]


title: cirrhosis [M730_plate4_B10]


title: cirrhosis [M720_plate4_B06]


title: cirrhosis [M734_plate4_B12]


title: hepatocellular carcinoma [M711_plate4_A11]


title: hepatocellular carcinoma [M719_plate4_B05]


title: hepatocellular carcinoma [M727_plate24_1_B09]


title: cirrhosis [M716_plate4_B04]


title: cirrhosis [M712_plate4_A12]


title: hepatocellular carcinoma [M739_plate4_C01]


title: cirrhosis [M724_plate4_B08]


title: cirrhosis [M708_plate4_A10]


title: cirrhosis [M704_plate4_A08]


title: hepatocellular carcinoma [M709_plate1_G01]


title: hepatocellular carcinoma [M707_plate4_A09]


title: hepatocellular carcinoma [M713_plate4_B01]


title: hepatocellular carcinoma [M715_plate4_B03]


title: cirrhosis [M714_plate4_B02]


title: cirrhosis [M702_plate4_A06]


title: hepatocellular carcinoma [M705_plate24 2_B09]


title: hepatocellular carcinoma [M701_plate4_A05]


title: hepatocellular carcinoma [M697_placa96_2_H06]


title: hepatocellular carcinoma [M703_plate4_A07]


title: cirrhosis [M688_placa96-3_E10]


title: hepatocellular carcinoma [M695_plate4_A03]


title: cirrhosis [M694_plate4_A02]


title: cirrhosis [M690_placa96-3_E12]


title: cirrhosis [M696_plate4_A04]


title: hepatocellular carcinoma [M679_placa96-3_E03]


title: cirrhosis [M680_placa96-3_E04]


title: cirrhosis [M686_placa96-3_E08]


title: hepatocellular carcinoma [M693_plate4_A01]


title: hepatocellular carcinoma [M683_plate4_H05]


title: hepatocellular carcinoma [M691_plate1_H06]


title: cirrhosis [M772_plate4_D08]


title: hepatocellular carcinoma [M685_placa96-3_E07]


title: hepatocellular carcinoma [M681_placa96-3_E05]


title: hepatocellular carcinoma [M689_placa96-3_E11]


title: hepatocellular carcinoma [M677_placa96-3_E01]


title: hepatocellular carcinoma [M687_placa96-3_E09]


title: hepatocellular carcinoma [M673_placa96-3_D09]


title: hepatocellular carcinoma [M671_placa96-3_D07]


title: cirrhosis [M672_placa96-3_D08]


title: cirrhosis [M682_placa96-3_E06]


title: cirrhosis [M674_placa96-3_D10]


title: hepatocellular carcinoma [M675_placa96-3_D11]


title: hepatocellular carcinoma [M669_placa96-3_D05]


title: cirrhosis [M678_placa96-3_E02]


title: cirrhosis [M676_placa96-3_D12]


title: cirrhosis [M666_placa96-3_D04]


title: hepatocellular carcinoma [M665_placa96-3_D03]


title: cirrhosis [M670_placa96-3_D06]


title: hepatocellular carcinoma [M667_plate4_H04]


title: hepatocellular carcinoma [M663_plate4_H03]


title: cirrhosis [M662_placa96-3_D02]


title: hepatocellular carcinoma [M661_placa96-3_D01]


title: cirrhosis [M654_placa96-3_C12]


title: cirrhosis [M652_placa96-3_C10]


title: hepatocellular carcinoma [M655_placa96-3_H05]


title: cirrhosis [M648_placa96-3_C08]


title: hepatocellular carcinoma [M657_plate4_H01]


title: hepatocellular carcinoma [M659_plate4_H02]


title: hepatocellular carcinoma [M647_placa96-3_C07]


title: hepatocellular carcinoma [M643_placa96-3_C05]


title: hepatocellular carcinoma [M653_placa96-3_C11]


title: hepatocellular carcinoma [M649_placa96-3_H04]


title: hepatocellular carcinoma [M651_placa96-3_C09]


title: hepatocellular carcinoma [M633_placa96-3_C03]


title: hepatocellular carcinoma [M631_placa96-3_C01_2]


title: cirrhosis [M644_placa96-3_C06]


title: cirrhosis [M632_placa96-3_C02]


title: hepatocellular carcinoma [M639_placa96-3_H02]


title: hepatocellular carcinoma [M645_placa96-3_H03]


title: hepatocellular carcinoma [M629_placa96-3_B11]


title: cirrhosis [M630_placa96-3_B12]


title: hepatocellular carcinoma [M635_placa96-3_H01]


title: cirrhosis [M626_placa96-3_B08]


title: cirrhosis [M628_placa96-3_B10]


title: cirrhosis [M624_placa96-3_B06]


title: cirrhosis [M770_plate4_D06]


title: hepatocellular carcinoma [M619_placa96-3_B01]


title: cirrhosis [M620_placa96-3_B02]


title: hepatocellular carcinoma [M625_placa96-3_B07]


title: hepatocellular carcinoma [M627_placa96-3_B09]


title: hepatocellular carcinoma [M623_placa96-3_B05]


title: cirrhosis [M634_placa96-3_C04]


title: hepatocellular carcinoma [M617_placa96-3_A11]


title: cirrhosis [M618_placa96-3_A12]


title: cirrhosis [M622_placa96-3_B04]


title: hepatocellular carcinoma [M621_placa96-3_B03]


title: cirrhosis [M614_placa96-3_A08]


title: cirrhosis [M616_placa96-3_A10]


title: hepatocellular carcinoma [M615_placa96-3_A09]


title: hepatocellular carcinoma [M613_placa96-3_A07]


title: hepatocellular carcinoma [M595_placa96-3_A03]


title: hepatocellular carcinoma [M593_placa96-3_A01]


title: hepatocellular carcinoma [M605_placa96_2_H03]


title: hepatocellular carcinoma [M601_placa96_2_H01]


title: hepatocellular carcinoma [M607_placa96_2_H04]


title: hepatocellular carcinoma [M599_placa96-3_A05]


title: hepatocellular carcinoma [M609_placa96_2_H05]


title: hepatocellular carcinoma [M587_placa96_2_F09]


title: cirrhosis [M594_placa96-3_A02]


title: cirrhosis [M582_placa96_2_F06_2]


title: hepatocellular carcinoma [M597_placa96_2_G12]


title: hepatocellular carcinoma [M603_placa96_2_H02]


title: hepatocellular carcinoma [M579_placa96_2_F03]


title: cirrhosis [M596_placa96-3_A04]


title: cirrhosis [M600_placa96-3_A06]


title: hepatocellular carcinoma [M581_placa96_2_F05]


title: cirrhosis [M590_placa96_2_F12]


title: hepatocellular carcinoma [M591_placa96_2_G11]


title: hepatocellular carcinoma [M589_placa96_2_F11]


title: cirrhosis [M586_placa96_2_F08]


title: cirrhosis [M588_placa96_2_F10]


title: cirrhosis [M578_placa96_2_F02]


title: hepatocellular carcinoma [M571_placa96_2_E09]


title: hepatocellular carcinoma [M577_placa96_2_F01]


title: cirrhosis [M570_placa96_2_E08]


title: cirrhosis [M580_placa96_2_F04]


title: cirrhosis [M572_placa96_2_E10]


title: cirrhosis [M574_placa96_2_E12]


title: hepatocellular carcinoma [M585_placa96_2_F07]


title: cirrhosis [M568_placa96_2_E06]


title: cirrhosis [M566_placa96_2_E04]


title: hepatocellular carcinoma [M561_placa96_2_G10]


title: hepatocellular carcinoma [M559_placa96_2_G09]


title: hepatocellular carcinoma [M569_placa96_2_E07]


title: hepatocellular carcinoma [M565_placa96_2_E03]


title: cirrhosis [M548_placa96_2_D10]


title: hepatocellular carcinoma [M543_placa96_2_G06]


title: hepatocellular carcinoma [M553_placa96_2_G07]


title: cirrhosis [M550_placa96_2_D12]


title: hepatocellular carcinoma [M557_placa96_2_G08]


title: cirrhosis [M552_placa96_2_E02]


title: cirrhosis [M540_placa96_2_D06]


title: hepatocellular carcinoma [M545_placa96_2_D07]


title: hepatocellular carcinoma [M551_placa96_2_E01]


title: hepatocellular carcinoma [M537_placa96_2_G05]


title: hepatocellular carcinoma [M549_placa96_2_D11]


title: hepatocellular carcinoma [M533_plate24 2_A09]


title: cirrhosis [M534_plate24 2_G09]


title: hepatocellular carcinoma [M529_placa96_2_D01]


title: cirrhosis [M532_placa96_2_D04]


title: hepatocellular carcinoma [M539_placa96_2_D05]


title: cirrhosis [M546_placa96_2_D08]


title: hepatocellular carcinoma [M535_placa96_2_G04]


title: hepatocellular carcinoma [M519_placa96_2_C09]


title: hepatocellular carcinoma [M531_placa96_2_D03]


title: hepatocellular carcinoma [M547_placa96_2_D09]


title: hepatocellular carcinoma [M505_placa96_2_C03]


title: cirrhosis [M506_placa96_2_C04]


title: hepatocellular carcinoma [M523_placa96_2_C11]


title: hepatocellular carcinoma [M517_placa96_2_G03]


title: cirrhosis [M530_placa96_2_D02]


title: cirrhosis [M520_placa96_2_C10]


title: cirrhosis [M524_placa96_2_C12]


title: cirrhosis [M516_placa96_2_C08]


title: cirrhosis [M504_placa96_2_C02]


title: hepatocellular carcinoma [M511_placa96_2_G02]


title: hepatocellular carcinoma [M503_placa96_2_C01]


title: hepatocellular carcinoma [M501_placa96_2_B11_2]


title: cirrhosis [M510_placa96_2_C06]


title: cirrhosis [M500_placa96_2_B10]


title: hepatocellular carcinoma [M497_placa96_2_G01]


title: cirrhosis [M502_placa96_2_B12]


title: cirrhosis [M468_placa96_2_A10]


title: hepatocellular carcinoma [M459_placa96_2_A07]


title: hepatocellular carcinoma [M573_placa96_2_E11]


title: hepatocellular carcinoma [M489_placa96_2_B05]


title: hepatocellular carcinoma [M483_placa96_2_B03]


title: hepatocellular carcinoma [M493_placa96_2_B07]


title: hepatocellular carcinoma [M499_placa96_2_B09]


title: hepatocellular carcinoma [M461_plate1_H04]


title: hepatocellular carcinoma [M477_placa96_2_A11]


title: cirrhosis [M494_placa96_2_B08]


title: cirrhosis [M484_placa96_2_B04]


title: cirrhosis [M480_placa96_2_B02]


title: hepatocellular carcinoma [M479_placa96_2_B01]


title: hepatocellular carcinoma [M455_placa96_2_A05]


title: hepatocellular carcinoma [M443_plate1_H02]


title: cirrhosis [M478_placa96_2_A12]


title: hepatocellular carcinoma [M467_placa96_2_A09]


title: hepatocellular carcinoma [M567_placa96_2_E05]


title: hepatocellular carcinoma [M439_placa96_2_A03]


title: hepatocellular carcinoma [M423_plate1_F09]


title: cirrhosis [M456_placa96_2_A06]


title: cirrhosis [M460_placa96_2_A08]


title: hepatocellular carcinoma [M473_plate1_H05]


title: hepatocellular carcinoma [M421_plate1_F07]


title: hepatocellular carcinoma [M425_plate1_F11]


title: hepatocellular carcinoma [M411_plate1_F05]


title: cirrhosis [M424_plate1_F10]


title: cirrhosis [M422_plate1_F08]


title: cirrhosis [M436_placa96_2_A02]


title: hepatocellular carcinoma [M407_plate1_H01]


title: cirrhosis [M412_plate1_F06]


title: cirrhosis [M440_placa96_2_A04]


title: hepatocellular carcinoma [M515_placa96_2_C07]


title: hepatocellular carcinoma [M435_placa96_2_A01]


title: cirrhosis [M392_plate1_E12]


title: hepatocellular carcinoma [M451_plate1_H03]


title: cirrhosis [M394_plate1_F02]


title: hepatocellular carcinoma [M379_plate1_E07]


title: hepatocellular carcinoma [M399_plate1_F03]


title: hepatocellular carcinoma [M393_plate1_F01]


title: cirrhosis [M400_plate1_F04]


title: hepatocellular carcinoma [M397_plate1_G12]


title: hepatocellular carcinoma [M385_plate1_E09]


title: hepatocellular carcinoma [M391_plate1_E11]


title: cirrhosis [M380_plate1_E08]


title: cirrhosis [M386_plate1_E10]


title: cirrhosis [M426_plate1_F12]


title: cirrhosis [M374_plate1_E06]


title: hepatocellular carcinoma [M375_plate1_G11]


title: cirrhosis [M372_plate1_E04]


title: hepatocellular carcinoma [M373_plate1_E05]


title: hepatocellular carcinoma [M371_plate1_E03]


title: hepatocellular carcinoma [M369_plate1_G10]


title: cirrhosis [M490_placa96_2_B06]


title: hepatocellular carcinoma [M363_plate1_E01]


title: cirrhosis [M346_plate1_D10]


title: cirrhosis [M364_plate1_E02]


title: cirrhosis [M320_plate1_D02]


title: hepatocellular carcinoma [M345_plate1_D09]


title: hepatocellular carcinoma [M329_plate1_G06]


title: cirrhosis [M358_plate1_D12]


title: hepatocellular carcinoma [M327_plate1_D05]


title: hepatocellular carcinoma [M339_plate1_D07]


title: cirrhosis [M340_plate1_D08]


title: cirrhosis [M328_plate1_D06]


title: cirrhosis [M312_plate1_C12]


title: hepatocellular carcinoma [M321_plate1_G05]


title: hepatocellular carcinoma [M325_plate1_D03_2]


title: hepatocellular carcinoma [M353_plate1_G09]


title: hepatocellular carcinoma [M357_plate1_D11]


title: hepatocellular carcinoma [M319_plate1_D01]


title: hepatocellular carcinoma [M335_plate1_G07]


title: hepatocellular carcinoma [M279_plate1_C07]


title: EBC1-R

city: Tokyo

first: Teppei

last: Sugano

address: Sendagi, Bunkyo-ku

institute: Graduate School of Medicine,

hyb_protocol: Following fragmentation, 5.5ug of single-strand cDNA were hybridized for 17 hr at 45℃ on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip®  Scanner 3000 7G.

data_processing: The data were analyzed with GeneSpring GX Version11.5.1 (RMA16) using Agilent Technologies default analysis settings and global scaling as normalization method. The trimmed mean was used with normalized data.

source_name: PHA-665752-resistant EBC1 cells, EBC1-R cell line

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip® WT Terminal  Labeling and Hybridization  User Manual  for use with the Ambion® WT  Expression Kit, 2009, Affymetrix).

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA) from frozen cells as previously described. High-density oligonucleotide array analysis was carried out using Affymetrix HG-U133A GeneChips (22,282 probe sets) as previously described.

treatment_protocol: These cell lines were maintained in RPMI 1640 medium (GIBCO) or minimum essential medium eagle supplemented with 10% fetal bovine serum (FBS) at 37◦C in a humidified incubator. EBC1 cells were incubated with increasing concentrations of MET inhibitor. Cells that survived incubation with the maximum concentration of MET inhibitor were stored for further analysis and referred to as MET inhibitor-resistant cells (EBC1-R). EBC1-R cells were maintained in medium containing 3 µM MET inhibitor.

tag: cell line


title: hepatocellular carcinoma [M337_plate1_G08]


title: cirrhosis [M326_plate1_D04]


title: cirrhosis [M280_plate1_C08]


title: hepatocellular carcinoma [M311_plate1_C11]


title: hepatocellular carcinoma [M305_plate1_C09]


title: cirrhosis [M306_plate1_C10]


title: Innate lymphoid cells of type 2

city: Solna

first: Joakim

middle: S

last: Dahlin

address: CMM, Visionsgatan 18

department: Department of Medicine, Solna

country: Sweden

institute: Karolinska Institutet

description: Sorted as lineage negative, c-kit negative/low, FcεRI negative, CD127 positive, CD25 positive ,T1/ST2 positive, CD16/32 negative peritoneal cells

hyb_protocol: GeneChip® Mouse Gene 2.0 ST Arrays were hybridized for 40 hours in a 45°C incubator during rotation at 60 rpm according to the standard protocols from Nugen Technologies Inc. (Ovation® One-Direct System M01312 v1 and Encore Biotin Module M01111 v5).

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G according to standard protocol from Affymetrix Inc. (GeneChip® Expression Wash, Stain and Scan Manual, PN 702731 Rev 3, Affymetrix Inc., Santa Clara, CA).

data_processing: The raw data were normalized using the robust multi-array average (RMA) method.

source_name: Innate lymphoid cells of type 2 from the peritoneal cavity of naïve mice

label_protocol: Biotinylated and amplified sense transcript cDNA was generated from the entire expressed genome according to the standard protocols from Nugen Technologies Inc. (Ovation® One-Direct System  M01312 v1 and Encore Biotin Module M01111 v5).

growth_protocol: Peritoneal cells were isolated from naïve female BALB/c mice. The mice were 10-11 weeks old.

extract_protocol: 100 cells of each population were sorted into 12 μl lysis buffer, provided with the Ovation® One-Direct System (Nugen Technologies Inc.).

treatment_protocol: PBS pH 7.4 containing 2 % heat-inactivated fetal calf serum was injected into the peritoneum of euthanized mice and the peritoneal cells were extracted and pooled from five mice. The peritoneal cells were stained with fluorescently labeled antibodies and doubly sorted using a FACS Aria III (BD Biosciences, Franklin Lakes, NJ).

value: Innate lymphoid cells of type 2

value: Peritoneal cells from naïve BALB/c mice

value: BALB/c


title: Mast cell progenitors

description: Sorted as lineage negative/low, c-kit high, FcεRI positive, CD127 negative, CD25 negative ,T1/ST2 positive, CD16/32 intermediate, side scatter low, integrin β7 high peritoneal cells

source_name: Mast cell progenitors from the peritoneal cavity of naïve mice

value: Mast cell progenitors


title: E2 GE

city: Toronto

first: Eric

middle: J

last: Chater-Diehl

state: ON

address: 686 Bay St.

institute: SickKids Research Institute

description: gene expression data from neonatal ethanol-injected 70 day old mouse hippocampus

hyb_protocol: One microgram of total RNA was labeled using the Flash Tag Biotin HSR kit from Genisphere (http://www.genisphere.com/array_detection_flashtag_biotin.html).  Samples were then hybridized to Affymetrix miRNA 2.0 arrays for 16 hours at 48°C.

scan_protocol: All washing steps were performed by a GeneChip Fluidics Station 450 and GeneChips were scanned with the GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA) using Command Console v1.1.

data_processing: Probe level (.CEL file) data was generated using Affymetrix Command Console v1.1.  Probes were summarized to the miRNA and gene level using RMA

source_name: Whole-hippocamal RNA

label_protocol: All sample labeling and GeneChip processing was performed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca). RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Single stranded complimentary DNA (sscDNA) was prepared from 200 ng of total RNA as per the Ambion WT Expression Kit for Affymetrix GeneChip Whole Transcript WT Expression Arrays (http://www.ambion.com/techlib/prot/fm_4411973.pdf, Applied Biosystems, Carlsbad, CA) and the Affymetrix GeneChip WT Terminal Labeling kit and Hybridization User Manual (http://media.affymetrix.com/support/downloads/manuals/wt_term_label_ambion_user_manual.pdf, Affymetrix, Santa Clara, CA).  Total RNA was first converted to cDNA, followed by in vitro transcription to make cRNA.  5.5 ug of single stranded cDNA was synthesized, end labeled

extract_protocol: Qiagen Allprep DNA RNA kit was used according to Qiagen protocol

treatment_protocol: All protocols were approved by the Animal Use Subcommittee (AUS) at the University of Western Ontario, London, Ontario, Canada. C57BL/6J (B6) mice were obtained from Jackson Laboratories (Bar Harbor, MA) and a population was subsequently maintained at the Animal Care Facility at the University of Western Ontario. Female mice 12-18 weeks of age were separated into individual cages and mated with males of approximately the same age. The day of birth was termed post-natal day (PD) zero.  Sex and weight-matched littermate pups were divided into two groups: ethanol-treated and saline control mice. Pups were given two subcutaneous dorsal injections at 9 am and 11 am on both PD4 and PD7. Ethanol-treated mice were injected with 2.5 g/kg of ethanol in 0.15 M NaCl. Pups were weaned on PD21 and housed in cages of two to four same-sex littermates. Male mice were used for all subsequent analyses (n=18). Mice were sacrificed on PD 70 via carbon dioxide asphyxiation. The hippocampus was dissected out, snap-frozen in liquid nitrogen, and stored at -80°C

value: hippocampus

value: ethanol


title: MCF7 tamoxifen resistant cell

city: Guangzhou

first: Junjun

last: Chu

state: Guangdong

address: 426 School of Life Sciences, Sun Yat-sen Univ. East Campus, Higher Education Mega Center

department: Breast Cancer Center

institute: SUN YAT-SEN UNIVERSITY

description: miRNA expression of MCF7 tamoxifen resistant cells

hyb_protocol: 1.0 ug of labeled RNA was hybridized for 16 hr at 48C on GeneChip miRNA 3.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix  GeneChip Scanner 3000

data_processing: The data were analyzed using expression console software version 1.2 using default analysis settings and RMA as normalization method.

source_name: MCF7 cells cultured in 1640 medium without phenol red 5% charcoal-stripped FBS (cFBS) with 1uM 4-hydroxytamoxifen for more than 1 year

label_protocol: 1.0 ug of total RNA was labeled using the Flash Tag Biotin RNA Labeling Kit for Affymetrix® GeneChip® miRNA Arrays  according to the manufacturer's instructions.

growth_protocol: MCF7-Pa cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 40U/ml insulin; MCF7-Re cells were cultured in 1640 medium without phenol red (Life Technologies, USA) supplemented with 5% charcoal-stripped FBS (cFBS) (HyClone, USA) and 1 uM 4-hydroxytamoxifen

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

treatment_protocol: MCF7-Pa and MCF7-Re cells were cultured in 1640 medium without phenol red supplemented with 5% charcoal-stripped FBS (cFBS) for 7days before RNA extraction.

tag: tamoxifen sensitive

value: No

value: Breast cancer


title: MCF7 parent cell

description: miRNA expression of MCF7 parent cells

source_name: MCF7 cells untreated

value: Yes

tag: cell type


title: cirrhosis [M276_plate1_C06]

value: hepatocellular carcinoma patient

value: liver


title: EBC1

source_name: EBC1 wild type cell line

growth_protocol: cell lines were maintained in RPMI 1640 medium (GIBCO) or minimum essential medium eagle supplemented with 10% fetal bovine serum (FBS) at 37◦C in a humidified incubator. EBC1 cells were incubated with increasing concentrations of MET inhibitor. Cells that survived incubation with the maximum concentration of MET inhibitor were stored for further analysis and referred to as MET inhibitor-resistant cells (EBC1-R). EBC1-R cells were maintained in medium containing 3 µM MET inhibitor.


title: Mature mast cells

description: Sorted as lineage negative/low, c-kit high, FcεRI positive, CD127 negative, CD25 negative ,T1/ST2 positive, CD16/32 intermediate, side scatter high, integrin β7 negative/low/intermediate peritoneal cells

source_name: Mature mast cells from the peritoneal cavity of naïve mice

value: Mature mast cells


title: hepatocellular carcinoma [M275_plate1_C05]

value: male

value: bclcA

value: primary hepatocellular carcinoma

value: fresh frozen tissue


title: C3 GE

description: gene expression data from neonatal saline-injected 70 day old mouse hippocampus

value: saline


title: E3 GE


title: C1 GE


title: E1 GE


title: E3 miRNA

description: miRNA expression data


title: hepatocellular carcinoma [M269_plate1_G03]


title: hepatocellular carcinoma [M267_plate1_C03]


title: cirrhosis [M262_plate1_C02]

value: non-tumor cirrhosis


title: hepatocellular carcinoma [M261_plate1_C01]


title: hepatocellular carcinoma [M271_plate1_G04]

value: female


title: cirrhosis [M268_plate1_C04]


title: E1 miRNA

description: miRNA expression data


title: C2 GE


title: E2 miRNA

description: miRNA expression data


title: C3 miRNA

description: miRNA expression data


title: hepatocellular carcinoma [M265_plate1_G02]


title: hepatocellular carcinoma [M257_plate24 2_G07]


title: C1 miRNA

description: miRNA expression data


title: hepatocellular carcinoma [M255_plate1_B11]


title: Freshly isolated monocyte (CD14+CD16+) from donor S6

city: Singapore

first: Wing-Cheong

last: Wong

address: 30 Biopolis Street #07-01

institute: Bioinformatics Institute, A*STAR

description:
replicate 2
S6-0-CD16

data_processing: See: Wong WC, Loh M, Eisenhaber F. On the necessity of different statistical treatment for Illumina BeadChip and Affymetrix GeneChip data and its significance for biological interpretation. Biol Direct. 2008 Jun 3;3:23. PubMed PMID: 18522715; PubMed Central PMCID: PMC2453111.

source_name: blood

label_protocol: Biotinylated aRNA were prepared with the TargetAmp 1-round Biotin-aRNA amplification kit for Illumina arrays

growth_protocol: Freshly isolated

extract_protocol: RNA was extracted with mirVana™ miRNA Isolation Kit. Quality control was performed with Agilent Bioanalyser.

tag: condition

value: healthy

tag: donor

value: Freshly isolated monocyte (CD14+CD16+)


title: Freshly isolated monocyte (CD14++CD16-) from donor S7

description:
replicate 3
S7-0-CD14

value: Freshly isolated monocyte (CD14++CD16-)


title: Freshly isolated monocyte (CD14+CD16+) from donor S7

description:
replicate 3
S7-0-CD16


title: C2 miRNA

description: miRNA expression data

value: hippocampus


title: Freshly isolated monocyte (CD14+CD16+) from donor S5

description:
replicate 1
S5-0-CD16


title: Freshly isolated monocyte (CD14++CD16-) from donor S6

description:
replicate 2
S6-0-CD14


title: Freshly isolated monocyte (CD14++CD16-) from donor S5

description:
replicate 1
S5-0-CD14


title: Freshly isolated monocyte (CD14+CD16+) from donor S8

description:
replicate 4
S8-0-CD16


title: P-Chk1-Ser280

type: protein

city: Paris

first: Leanne

last: de Koning

address: 26 rue d'Ulm

department: Department of translational research

institute: Institut Curie

hyb_protocol: After washes with TBST, arrays were probed with horseradish peroxidase-coupled secondary antibodies (Jackson ImmunoResearch Laboratories, Newmarket, UK) diluted in TBST-BSA for 1 h at RT. To amplify the signal, slides were incubated with Bio-Rad Amplification Reagent for 15 min at RT. The arrays were washed with TBST, probed with Cy5-Streptavidin (Jackson ImmunoResearch Laboratories) diluted in TBST-BSA for 1 h at RT and washed again in TBST. For staining of total protein, arrays were incubated 15 min in 7% acetic acid and 10% methanol, rinsed twice in water, incubated 5 min in Sypro Ruby (Invitrogen) and rinsed again. The processed slides were dried by centrifugation

scan_protocol: Arrays were scanned using a GenePix 4000B microarray scanner (Molecular Devices)

data_processing: Spot intensity was determined with MicroVigene software (VigeneTech Inc).  Raw data were subjected to quality control and all aberrent values, samples or antibodies were removed for further processing. For each sample, one relative protein expression level was determined from the technical replicates and the dilution series, using Normacurve software (Troncale et al., 2012). Bias due to the origin of the samples (NKI vs CAM) was removed using a median regression approach. In brief, data were scaled by array and the median for each sample across all arrays was computed. Then, linear regression was performed of scaled data on the median of proteins and residues were set as the final processed data. The entire normalisation process was done using all samples on the arrays, including cell lines and Triple-nagative breast cancer samples. Normalised data represent ILC samples only.

molecule: protein

source_name: Invasive lobular carcinoma (ILC)

label_protocol: Arrays were labeled with commercially available antibodies using an Autostainer Plus robot (Dako). Briefly, slides were incubated with avidin, biotin and peroxydase blocking reagents (Dako) before saturation with TBS containing 0.1% Tween-20 and 5% BSA (TBST-BSA). Slides were then probed overnight at 4°C with primary antibodies diluted in TBST-BSA.

extract_protocol: Three sections of fresh frozen tissue were lysed in hot Laemmli buffer (50 mM Tris pH =6.8, 2% SDS, 5% glycerol, 2 mM DTT, 2.5 mM EDTA, 2.5 mM EGTA, 1x HALT Phosphatase inhibitor (Perbio 78420), Protease inhibitor cocktail complete MINI EDTA-free (Roche 1836170, 1 tablet/10 mL), 2 mM Na3VO4 and 10 mM NaF) and boiled for 10 min at 100°C. Samples were sonicated in a waterbath for 1-2min to break the DNA and spinned for 10 min at 13000 rpm.  Supernatant was snapfrozen and protein concentration was measured (BCA reducing agents compatible kit, Pierce, Ref 23252).

tag: antibody vendor/catalog#

tag: source of antibody

value: Rabbit

tag: clonality

value: Polyclonal


title: TCF4

value: Monoclonal


title: Rad50


title: cirrhosis [M254_plate1_B10]

source_name: cirrhosis

value: hepatocellular carcinoma patient


title: cirrhosis [M256_plate1_B12]

value: liver


title: P-GSK3-alpha-beta-ser21-9


title: P-GSK3-alpha-beta-Tyr279-216

value: Epitomics 2309-1


title: hepatocellular carcinoma [M253_plate1_B09]

source_name: hepatocellular carcinoma


title: MSH2


title: cirrhosis [M244_plate1_B06]


title: P-Beta-Catenin-Ser675


title: hepatocellular carcinoma [M247_plate1_B07]

value: male


title: TAB2


title: P-Beta-Catenin-Ser552


title: hepatocellular carcinoma [M243_plate1_B05]

value: bclcA


title: cirrhosis [M248_plate1_B08]


title: P-Chk2-thr68


title: cirrhosis [M238_plate1_B04]


title: TCF3


title: P-progesterone-receptor

value: Epitomics 2258-1


title: FGFR4


title: Zap70-Syk

value: Epitomics 1688-1


title: VEGF-receptor1

value: Epitomics 1303-1


title: P-TSC2-Tuberin

value: Epitomics 1823-1


title: P-VEGF-receptor2-tyr1175


title: P-IRS1-Tyr632

value: Epitomics 3517-1


title: PTP1B

value: Epitomics 2066-1


title: cirrhosis [M236_plate1_B02]

value: non-tumor cirrhosis

value: fresh frozen tissue


title: hepatocellular carcinoma [M237_plate1_B03]

value: primary hepatocellular carcinoma


title: cirrhosis [M234_plate1_A12]


title: Src

value: Rabbit


title: P-VEGF-Receptor2-Tyr1214

value: Polyclonal


title: P-HSP27-Ser15

value: Epitomics 2231-1

value: Monoclonal


title: beta-catenin


title: P-MSK1-Ser376

value: Epitomics 1611-1


title: hepatocellular carcinoma [M235_plate1_B01]

value: hepatocellular carcinoma patient

value: female

value: liver


title: Rsk1-MAPKAPK1a-p90

value: Upstate (M06-668)


title: NAK-TBK1

value: Epitomics 3296-1


title: hepatocellular carcinoma [M229_plate1_A09]

value: bclcB


title: hepatocellular carcinoma [M223_plate1_A07]

value: male

value: bclcA


title: cirrhosis [M230_plate1_A10]


title: P-Stat1-Tyr701

value: Epitomics 2825-1


title: Tyk2

value: Upstate (M06-638)


title: P-Stat3-Tyr705


title: P-RSK2-Ser227


title: cirrhosis [M210_plate1_A04]

value: non-tumor cirrhosis

value: fresh frozen tissue


title: hepatocellular carcinoma [M233_plate1_A11]

value: primary hepatocellular carcinoma


title: Puma

value: Epitomics 1652-1

value: Rabbit


title: hepatocellular carcinoma [M213_plate1_A05]


title: P-Met-Tyr1349

value: Signalway 11238-1

value: Polyclonal


title: Cofilin_410


title: cirrhosis [M224_plate1_A08]

value: hepatocellular carcinoma patient


title: cirrhosis [M214_plate1_A06]


title: hepatocellular carcinoma [M209_plate1_A03]

value: female


title: P-Histone-H2AX-ser139

value: Abcam ab2893


title: Chk2

value: Mouse

value: Monoclonal


title: Freshly isolated monocyte (CD14++CD16-) from donor S8

description:
replicate 4
S8-0-CD14

value: healthy

value: Freshly isolated monocyte (CD14++CD16-)


title: Rad21

value: Upstate (M05-908)


title: RelB

value: Epitomics 1653-1


title: ROCK-II-ROK-alpha


title: Ki67


title: RSK2


title: GSK3-alpha-beta


title: hepatocellular carcinoma [B319_plate24 2_D07]

value: male

value: bclcC

value: liver


title: Cbl

value: Epitomics 1487-1


title: eIF4B


title: P-eEF2k-Ser366


title: eEF2k


title: cirrhosis [B324_plate24 2_E07]

value: non-tumor cirrhosis

value: fresh frozen tissue


title: B-Raf

value: Epitomics 1647-1

value: Rabbit


title: P-4EBP1

value: Epitomics 2250-1


title: P-Estrogen-receptor-alpha-Ser118

value: Epitomics 1091-1


title: P-GSK3-beta-Ser9


title: Paxillin


title: cirrhosis [M208_plate1_A02]

value: hepatocellular carcinoma patient


title: hepatocellular carcinoma [M207_plate1_A01]

value: female

value: primary hepatocellular carcinoma


title: hepatocellular carcinoma [B325_plate24 2_F07]

value: bclcA


title: fibronectin

value: Epitomics 1574-1

value: Monoclonal


title: cirrhosis [B316_plate24 2_A07]


title: hepatocellular carcinoma [B317_plate24 2_B07]


title: hepatocellular carcinoma [B307_plate24 2_H05]


title: Smad3

value: Epitomics 1735-1


title: P-YAP-65-Ser127

value: CST 4911S

value: Polyclonal


title: cirrhosis [B318_plate24 2_C07]

value: liver


title: cirrhosis [B306_plate24 2_G05]


title: YAP65

value: Epitomics 2060-1


title: Stat1


title: Smad2


title: P-Src-Tyr527


title: PYK2-CAK-beta


title: P-eIF4B-Ser422


title: Eostrogen-receptor-alpha


title: P-Smad2-Ser465-467-Smad3-Ser423-425


title: P-Her2-Tyr1139


title: Mst3


title: TSC2-tuberin

value: Epitomics 1613-1


title: P-PTP1B-Ser378

value: Epitomics 2163-1


title: hepatocellular carcinoma [B299_plate24_1_F07]

value: male

value: fresh frozen tissue


title: P-PDK1-Ser241

value: Rabbit


title: Mst1


title: Progesterone-receptor

value: Epitomics 1483-1


title: hepatocellular carcinoma [B301_plate24_1_H07]

value: hepatocellular carcinoma patient


title: Caseine-kinase-I-alpha


title: cirrhosis [B294_plate24_1_C07]

value: non-tumor cirrhosis


title: cirrhosis [B298_plate24_1_E07]


title: P-cofilin-Ser3


title: P-Her2


title: hepatocellular carcinoma [B265_plate24_1_B07]

value: female

value: primary hepatocellular carcinoma


title: IRS1

value: Upstate (M06-248)


title: IRAK1

value: Santa-Cruz sc-7883 (H-273)


title: Met

value: Santa-Cruz sc-10 (C-12)


title: MSK1

value: Monoclonal


title: Histone-H2AX

value: Abcam ab11175

value: Polyclonal


title: hepatocellular carcinoma [B247_plate24_1_H05]

value: bclcA

value: liver


title: cirrhosis [B264_plate24_1_A07]


title: P-Ezrin-Thr567-Radixin-Thr564-Moesin-Thr558


title: Her3

value: Santa-Cruz sc-285


title: FOXO3a


title: FAK


title: hepatocellular carcinoma [B243_plate24_1_F05]


title: P-Her3-Tyr1289


title: EphA2


title: cirrhosis [B242_plate24_1_E05]


title: hepatocellular carcinoma [B295_plate24_1_D07]

value: male


title: cirrhosis [B246_plate24_1_G05]

value: fresh frozen tissue


title: IKK-beta

value: Rabbit


title: P-EGFR-Tyr1173


title: EGFR_156

value: Santa-Cruz sc-03 (1005)


title: cirrhosis [B238_plate24_1_C05]

value: hepatocellular carcinoma patient


title: hepatocellular carcinoma [B239_plate24_1_D05]


title: cirrhosis [B300_plate24_1_G07]

value: non-tumor cirrhosis


title: hepatocellular carcinoma [B237_plate4_G12]


title: CaMKI

value: Epitomics 2202-1


title: cirrhosis [B236_plate4_G11]


title: AcK1


title: Mst4

value: Mouse


title: CD44

value: R&D BBA10


title: cirrhosis [B232_plate4_G09]


title: HER2

value: Lab Vision MS-432-P1 (Ab11)


title: RACK1


title: cirrhosis [B230_plate4_G07]


title: Hsp27


title: EGFR


title: Phospho-p53-Ser15


title: DNA-PK

value: Upstate (M05-907)


title: Rb

value: Monoclonal


title: hepatocellular carcinoma [B215_plate4_G06]

value: primary hepatocellular carcinoma


title: P-HER2-ErbB2-tyr1221-1222


title: caseine-kinaseI-epsilon


title: P-Rb-Thr356

value: Epitomics 2223-1


title: P-Rb-Ser807-811

value: Polyclonal


title: CrKL

value: Epitomics 1524-1


title: PLC-gamma1


title: PARP-uncleaved-p116

value: Epitomics 1077-1


title: Ras


title: hepatocellular carcinoma [B233_plate4_G10]

value: male

value: bclcA

value: liver


title: AlB1


title: cleaved-PARP-Asp214-p25

value: Epitomics 1051-1

value: Rabbit


title: p53_188


title: P-NDRG1-Thr346


title: PDGFR-alpha


title: hepatocellular carcinoma [B181_plate4_G04]

value: hepatocellular carcinoma patient

value: fresh frozen tissue


title: hepatocellular carcinoma [B209_plate4_H07]


title: cirrhosis [B180_plate4_G03]

value: non-tumor cirrhosis


title: hepatocellular carcinoma [B175_placa96-3_G12]


title: hepatocellular carcinoma [B179_plate4_G02]


title: hepatocellular carcinoma [B231_plate4_G08]


title: cirrhosis [B178_plate4_G01]


title: P-TAB2-ser372


title: cirrhosis [B214_plate4_G05]


title: P-p53-Ser392

value: Epitomics 2326-1


title: eEF2K

value: Epitomics 1718-1


title: Jak2


title: Stat3


title: Ezrin

value: Epitomics 2255-1


title: P-topoisomeraseIIa-thr1343

value: Epitomics 1871-1

value: Monoclonal


title: Gab1