title: bur1as/ctk1Δ_Sth1_Myc_SC_1

description: Bological Replicate-1


title: ctk1Δ_Rpb3_SC_1

status: Public on Nov 24 2014

type: genomic

city: Rochester

first: Chhabi

last: Govind

state: mi

address: 333 Science and Engineering Building

department: Biological Sciences

country: USA

institute: Oakland University

description: Bological Replicate-1

hyb_protocol: The samples were lableled using BioPrime Array CGH Genomic Labeling Module kit and hybridized according to the Manufacturer's recommended protocol

scan_protocol: Agilent Technologies Scanner G2505B US45102973

data_processing: Data processed on R. Median normalization carried out.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

label_protocol: manufacturer's recommended protocol was followed

growth_protocol: Chromatin immunoprecipitation experiments were performed as described previously (Govind et al., 2012). Briefly, 100 ml of cells (A600 = 0.6) were cross-linked with 1% formaldehyde for 15 minutes at ambient temperature and quenched with glycine. Chromatin was isolated and fragmented by sonication (Branson450) to an average size of 300-400 base pairs. The soluble fraction of chromatin was used for ChIP using the appropriate antibodies.

extract_protocol: The ChIP and Input DNA was extracted by Phenol:Chloform method after reverse-crosslinking at 65 degree C, and after proteinase K treatment. DNA was fragmented with DNase prior to labeling

treatment_protocol: The cells were either grown in SC or YPD. For inducing Gcn4, the cells were grown in SC and then treated with 0.65 µM of sulfometuron methyl (SM; Chemservice, cat# N-13254) for 20 minutes and processed for ChIP analysis. The kin28as/bur2Δ were treated with 1NA-PP1 and bur1as/ctk1Δ strains were treated with 3MB-PP1 before processing for cross-linking and chromatin preparation

tag: myc-tagged

tag: antibody

value: Rpb3 (Neoclone:W0012)

tag: sample type

value: ChIP DNA

tag: parent strain

tag: strain

value: input


title: 646 aa veh::1

type: RNA

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: gene expression in Ishikawa cells with AA ERa vehicle

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

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

molecule: total RNA

organism: Homo sapiens

source_name: Ishikawa cells with AA ERa vehicle

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

growth_protocol: None.

extract_protocol: RNA was prepared with Trizol and clean up was via the Qiagen Rneasy Kit

treatment_protocol: All Ishikawa stable ERa cell lines were starved in phenol-red free DMEM:F12 +10% stripped FBS and were treated with vehicle (0.01% DMSO) or Estradiol (E2- 10nM) for 4 or 24hrs

tag: cell type

value: endometrial cancer cells

tag: infected cell line

value: AA ERa

tag: treatment

value: vehicle


title: NLC#2 LENALIDOMIDE

city: Modena

first: Rossana

last: Maffei

state: Modena

address: Via del Pozzo 71

department: Dept of Hematology and Oncology

country: Italy

institute: University of Modena and Reggio Emilia

description: Gene expression data from NLCs generated from PBMCs of CLL patients in vitro with the addition of 0,5µM lenalidomide

hyb_protocol: Cy3-labeled cRNAs (1.65 ug) were fragmented to an average size of 50-100 nt by incubation at 60°C for 30 min using in situ Hybridization kit-plus (Agilent). Samples were hybridized for 17 hours at 65°C on 4x44K Whole Human Genome Microarray (Agilent).

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

data_processing: Fluorescence data were analyzed with Feature Extraction Software v.10.5 (Agilent Technologies) an QC Chart tool v.1.3 to obtain background subtracted, spatially detrended Processed Signal intensities and quality control analyses.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Peripheral blood, nurse-like cells from CLL patient 2 generated with the addition of lenalidomide

label_protocol: High quality RNAs were amplified and Cy3-labeled using Low Input Quick Amp Labeling kit (Agilent Technologies, Palo alto, CA, USA). Agilent RNA One-Color Spike-In was added in each sample to provide positive controls for monitoring the microarray workflow from sample amplification and labelling to microarray processing. It contains 10 in vitro synthesized, polyadenylated transcripts derived from the Adenovirus E1A transcriptome that are premixed at various ratios. All cRNA products were purified using RNeasy columns (QIAGEN). Dye incorporation and cRNA yield were checked with InfiniteM200 (Tecan).Samples had to contain at least 6 pmole of cyanine dye/ug of cRNA to be considered suitable for subsequent hybridization.

growth_protocol: Blood samples from untreated patients that matched standard diagnostic criteria for CLL were obtained from the Hematology Unit of Modena Hospital, Italy with a protocol approved by the Institutional Review Board. All patients provided written informed consent in accordance with the declaration of Helsinki. Peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll density gradient centrifugation and used fresh or cryopreserved in RPMI-1640 medium (Life Technologies, Carlsbad, CA, USA), 50% fetal bovine serum (FBS), and 10% dimethyl sulfoxide (DMSO) and stored in liquid nitrogen until use. PBMCs from CLL patients were cultured (10 milion/mL) in RPMI-1640 medium with 10% FBS, 50µg/mL gentamicin, 100U/mL penicillin, 100µg/mL streptomycin for 10 days.

extract_protocol: total RNAs were extracted from NLCs using RNeasy Midi kit Plus (QIAGEN, Valencia, CA, USA) following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion. RNAs were quantified using InfiniteM200 (Tecan)

treatment_protocol: NLCs were generated either in the presence or absence of lenalidomide at 0.5 µM, provided at set up and every 3 days. The cell culture medium was not changed during culture time.

value: Nurse-like cells from periferal blood mononuclear cells of CLL patient

tag: subject

value: patient 2

value: lenalidomide

tag: disease state

value: chronic lymphocytic leukemia


title: gcn5Δ/esa1ts_Rpb3_SC_2

description: Biological Replicate-2


title: bur1as/ctk1Δ_Sth1_Myc_SM_1

description: Bological Replicate-1

value: Sulfometuron methyl + 3MB-PP1


title: ctk1Δ_Sth1_Myc_SM_2

description: Biological Replicate-2

value: Sulfometuron methyl


title: NLC#4 CTRL

description: Gene expression data from NLCs generated in vitro from PBMCs of CLL patients

source_name: Peripheral blood, nurse-like cells from CLL patient 4

value: patient 4


title: NLC#4 LENALIDOMIDE

source_name: Peripheral blood, nurse-like cells from CLL patient 4 generated with the addition of lenalidomide


title: ctk1Δ_Rpb3_SC_2

description: Biological Replicate-2


title: NLC#2 CTRL

source_name: Peripheral blood, nurse-like cells from CLL patient 2


title: ctk1Δ_Rpb3_SM_1

description: Bological Replicate-1


title: gcn5Δ/esa1ts_Rpb3_SM_1

description: Bological Replicate-1


title: bur1as/ctk1Δ_Rpb3_SM_1

description: Bological Replicate-1


title: NLC#3 CTRL

source_name: Peripheral blood, nurse-like cells from CLL patient 3

value: patient 3


title: NLC#3 LENALIDOMIDE

source_name: Peripheral blood, nurse-like cells from CLL patient 3 generated with the addition of lenalidomide


title: gcn5Δ/esa1ts_Sth1_Myc_SC_1

description: Bological Replicate-1


title: ctk1Δ_Sth1_Myc_SC_1

description: Bological Replicate-1


title: ctk1Δ_Rpb3_SM_2

description: Biological Replicate-2


title: gcn5Δ/esa1ts_Rpb3_SM_2

description: Biological Replicate-2


title: bur1as/ctk1Δ_Rpb3_SM_2

description: Biological Replicate-2


title: ctk1Δ_Sth1_Myc_SC_2

description: Biological Replicate-2


title: gcn5Δ/esa1ts_Sth1_Myc_SC_2

description: Biological Replicate-2


title: 646 h1 24hr::3

description: gene expression in Ishikawa cells with H1 ERa 24hr 10nM E2 treatment

value: H1 ERa

value: 24 hr with 10nM Estradiol


title: gcn5Δ/esa1ts_Rpb3_SC_1

description: Bological Replicate-1


title: NLC#1 CTRL

source_name: Peripheral blood, nurse-like cells from CLL patient 1

value: patient 1


title: NLC#1 LENALIDOMIDE

source_name: Peripheral blood, nurse-like cells from CLL patient 1 generated with the addition of lenalidomide


title: SFD 9

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

hyb_protocol: Samples were hybridized with GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) by A GeneChip Fluidics Station FS-400 and GeneChip Scanner 3000 7G

data_processing: Probe Logarithmic Intensity Error (PLIER) log2 normalized signal

label: biotin

organism: Mus musculus

source_name: mice fed saturated high fat diet

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: RNA was isolated using the RNeasy mini kit or the RNeasy Lipid tissue mini kit (QIAGEN), according to the manufacturer's instructions.

tag: gender

value: Male

tag: diet

value: SFD

tag: tissue

value: Bone Marrow


title: ctk1Δ_Sth1_Myc_SM_1

description: Bological Replicate-1

value: ChIP DNA

value: input


title: CSF-70years-Sample3

city: Clemson

first: David

middle: Matthew

last: Feliciano

state: South Carolina

address: 132 Long Hall

institute: Clemson University

hyb_protocol: Samples were hybridized to Affymetrix Genechip miRNA 3.0 arrays (Affymetrix, Santa Clara, CA) for 16 hours at 45°C, washed and stained with an Affymetrix fluidics station.

scan_protocol: Chips were scanned using a 16-bit Genechip scanner 3000 7G platform (Solid State 532 nm Diode-pumped Frequency Doubled neodymium-doped yttrium aluminum garnet green laser).

data_processing: Samples were analyzed using the Affymetrix GeneChip® Command Console software and TM4 microarray software suite using hierarchical clustering analysis.

label: Biotin

source_name: CSF Vesicles

label_protocol: Samples were subjected to analysis on an Agilent Technologies Bioanalyzer. 500 ng of RNA was subjected to Poly A tail labeling and ligation with the FlashTag Biotin Labeling kit (Affymetrix, Santa Clara, CA) and subjected to ELOSA QC analysis.

extract_protocol: Briefly, to isolate total RNA, Trizol was added to exosome pellets and vortexed for 15 seconds. Samples were incubated for 5 minutes at room temperature, chloroform added, manually agitated for 15 seconds, incubated for an additional 5 minutes at room temperature, and centrifuged for 15 minutes at 12,000 x g at 4°C. The aqueous phase was transferred to a fresh tube and isopropyl alcohol added the precipitate RNA. Samples were incubated overnight at -20oC then centrifuged for 10 minutes at 12,000 x g at 4°C. Supernatant was discarded and pellets were washed with 70% ethanol, vortexed, and centrifuged for 5 minutes at 12,000x g at 4°C. The previous step was repeated and samples dried and rehydrated in RNase/DNase free DEPC treated water.

value: CSF vesicles

tag: age

value: > 70 years


title: CSF-70years-Sample2


title: PFD 6

source_name: mice fed polyunsaturated high fat diet

value: PFD


title: CSF-70years-Sample1


title: LFD 4

source_name: mice fed low fat diet

value: LFD


title: PFD 8


title: gcn5Δ/esa1ts_Sth1_Myc_SM_1

description: Bological Replicate-1

source_name: WT


title: WT_Rpb3_YPD_1

description: Bological Replicate-1

value: Rpb3 (Neoclone:W0012)


title: gcn5Δ/esa1ts_Sth1_Myc_SM_2

description: Biological Replicate-2


title: WT_Rpb3_YPD_2

description: Biological Replicate-2


title: WT_Rpb3_SC_2

description: Biological Replicate-2


title: LFD 2


title: PFD 7


title: WT_Sth1-Myc_YPD_1

description: Bological Replicate-1


title: LFD 3


title: CSF-2years-Sample3

value: < 2 years


title: PFD 5


title: WT_Rpb3_SM_1

description: Bological Replicate-1

value: Sulfometuron methyl


title: WT_Rpb3_SC_1

description: Bological Replicate-1


title: WT_Sth1-Myc_SC_2

description: Biological Replicate-2


title: WT_Rpb3_SM_2

description: Biological Replicate-2


title: SFD 12


title: CSF-2years-Sample2


title: SFD 11


title: WT_Sth1-Myc_YPD_2

description: Biological Replicate-2


title: LFD 1


title: WT_Sth1-Myc_SC_1

description: Bological Replicate-1


title: CSF-2years-Sample1


title: WT_Sth1-Myc_SM_2

description: Biological Replicate-2


title: WT_Sth1-Myc_SM_1

description: Bological Replicate-1


title: MSCs from MM patient cultured in solitary_37mscSoPa_1605

status: Public on Nov 23 2014

city: Salamanca

first: Javier

last: De Las Rivas

address: Campus Miguel de Unamuno

department: CSIC and University of Salamanca

country: Spain

institute: Cancer Research Center (CiC-IBMCC)

description:
Gene expression data from human clinical samples
37mscSoPa_1605

hyb_protocol: Hybridized to the Affymetrix GeneChip HG-U133 Plus 2.0 oligonucleotide microarray, after quality checking on GeneChips Test Arrays.

scan_protocol: Labeling and hybridization were performed according to protocols from Affymetrix. Briefly, 100 ng of total RNA was amplified and labeled using the GeneChip two-cycle cDNA synthesis kit and GeneChip IVT labeling kit (Affymetrix Inc.).

data_processing: The justRMA() function provided by the package Affy from R/Bioconductor was applied to the raw expression data. The probes were mapped to GENE LOCi by the CDF built by GATExplorer, which can be found at http://bioinfow.dep.usal.es/xgate/mapping/mapping.php

source_name: MSCs from MM patient cultured in solitary (i.e. no cocultured)

growth_protocol: Primary MSCs from bone marrow (BM) samples of healthy donors (n=8) and multiple myeloma (MM) patients (n=13) were generated as described by Garayoa et al. 2009 (PMID:19357701). Ficoll-Paque density gradient separation medium was used to isolate mononuclear cells from BM aspirates. MSCs were selected by adherence to plastic and subsequently expanded until passage 2 when they were used for co-culture.

extract_protocol: RNA isolation, labelling and microarray hybridization was done following the manufacturer’s protocols for the GeneChip platform: HG-U133 Plus 2.0 oligonucleotide arrays (Affymetrix).

treatment_protocol: For the MSC-MM.1S co-cultures we used a 6-well format transwell system with 1 µm pore size membrane. Briefly, 2 X 104 MSCs were first cultured attached to the lower side of the membrane, and when reached ≈ 85% confluence 1 X 106 MM.1S cells were seeded on the upper side. After 24 h co-culture in RPMI 1640 medium supplemented with 10% FBS and antibiotics, MSCs were recovered by trypsinization, washed once in PBS and stored at -80°C in RLT buffer (Qiagen) until RNA extraction. Absence of MM.1S cells in the recovered MSC population was assessed in selected samples by flow cytometry analysis.

tag: tissue source

value: multiple myeloma (MM) patient

value: bone marrow

value: primary Mesenchymal Stromal Cells (MSC)

tag: culture condition


title: MSCs from MM patient cultured in solitary_36mscSoPa_1301

description:
Gene expression data from human clinical samples
36mscSoPa_1301

label_protocol: Labeling and hybridization were performed according to protocols from Affymetrix. Briefly, 100 ng of total RNA was amplified and labeled using the GeneChip two-cycle cDNA synthesis kit and GeneChip IVT labeling kit (Affymetrix Inc.).

value: cultured in solitary (i.e. no cocultured)


title: MSCs from MM patient cultured in solitary_34mscSoPa_1605

description:
Gene expression data from human clinical samples
34mscSoPa_1605


title: MSCs from MM patient cultured in solitary_32mscSoPa_UGA

description:
Gene expression data from human clinical samples
32mscSoPa_UGA


title: MSCs from healthy donor cultured in solitary_23mscSoD_0015

description:
Gene expression data from human clinical samples
23mscSoD_0015

source_name: MSCs from healthy Donor cultured in solitary (i.e. no cocultured)

value: healthy donor


title: SFD 10

value: Male


title: MSCs from healthy donor cultured in solitary_25mscSoD_0017

description:
Gene expression data from human clinical samples
25mscSoD_0017


title: MSCs from healthy donor cultured in solitary_24mscSoD_0016

description:
Gene expression data from human clinical samples
24mscSoD_0016


title: MSCs from healthy donor cultured in solitary_21mscSoD_0013

description:
Gene expression data from human clinical samples
21mscSoD_0013


title: MSCs from healthy donor cultured in solitary_28mscSoD_8417

description:
Gene expression data from human clinical samples
28mscSoD_8417


title: MSCs from MM patient cocultured with MM.1S cells_20mscCoPa_ROGR

description:
Gene expression data from human clinical samples
20mscCoPa_ROGR

value: cocultured with MM.1S cells


title: MSCs from MM patient cultured in solitary_31mscSoPa_ND

description:
Gene expression data from human clinical samples
31mscSoPa_ND


title: MSCs from MM patient cocultured with MM.1S cells_19mscCoPa_1403

description:
Gene expression data from human clinical samples
19mscCoPa_1403


title: MSCs from MM patient cultured in solitary_29mscSoPa_1503

description:
Gene expression data from human clinical samples
29mscSoPa_1503


title: MSCs from MM patient cultured in solitary_35mscSoPa_EMG

description:
Gene expression data from human clinical samples
35mscSoPa_EMG


title: MSCs from MM patient cultured in solitary_30mscSoPa_AGV

description:
Gene expression data from human clinical samples
30mscSoPa_AGV


title: MSCs from healthy donor cultured in solitary_22mscSoD_0014

description:
Gene expression data from human clinical samples
22mscSoD_0014


title: MSCs from healthy donor cultured in solitary_27mscSoD_0019

description:
Gene expression data from human clinical samples
27mscSoD_0019


title: MSCs from healthy donor cultured in solitary_26mscSoD_0018

description:
Gene expression data from human clinical samples
26mscSoD_0018


title: MSCs from MM patient cocultured with MM.1S cells_18mscCoPa_1103

description:
Gene expression data from human clinical samples
18mscCoPa_1103


title: MSCs from MM patient cultured in solitary_33mscSoPa_FBH

description:
Gene expression data from human clinical samples
33mscSoPa_FBH


title: MSCs from MM patient cocultured with MM.1S cells_15mscCoPa_EMG

description:
Gene expression data from human clinical samples
15mscCoPa_EMG


title: MSCs from MM patient cocultured with MM.1S cells_14mscCoPa_1605

description:
Gene expression data from human clinical samples
14mscCoPa_1605


title: MSCs from MM patient cocultured with MM.1S cells_17mscCoPa_LMQ

description:
Gene expression data from human clinical samples
17mscCoPa_LMQ


title: MSCs from MM patient cocultured with MM.1S cells_13mscCoPa_FBH

description:
Gene expression data from human clinical samples
13mscCoPa_FBH


title: MSCs from MM patient cocultured with MM.1S cells_12mscCoPa_UGA

description:
Gene expression data from human clinical samples
12mscCoPa_UGA


title: MSCs from MM patient cocultured with MM.1S cells_11mscCoPa_ND

description:
Gene expression data from human clinical samples
11mscCoPa_ND


title: MSCs from MM patient cocultured with MM.1S cells_10mscCoPa_AGV

description:
Gene expression data from human clinical samples
10mscCoPa_AGV


title: MSCs from MM patient cocultured with MM.1S cells_09mscCoPa_1503

description:
Gene expression data from human clinical samples
09mscCoPa_1503


title: MSCs from MM patient cocultured with MM.1S cells_16mscCoPa_SCG

description:
Gene expression data from human clinical samples
16mscCoPa_SCG


title: MSCs from healthy donor cocultured with MM.1S cells_08mscCoD_8417

description:
Gene expression data from human clinical samples
08mscCoD_8417

source_name: MSCs from healthy Donor cocultured with MM.1S cells


title: MSCs from healthy donor cocultured with MM.1S cells_05mscCoD_0017

description:
Gene expression data from human clinical samples
05mscCoD_0017


title: DA3_alone rep2

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description:
C192_Mix(+)24h_Assay3_(MoGene-1_0-st-v1).CEL.pimg
gene expression data of DA3 cells alone

hyb_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

data_processing: Gene-level analyses was performed. RMA normalization, summarization by mean, all were done by Partek Genomics suite (version 6.5) Copyright ©

growth_protocol:
Two cell lines were used in this study: MBA-15, a pre-osteoblastic stromal cell line (Benayahu et al. 1989) and DA3, a mammary adenocarcinomal cell line, (Fu et al. 1990). Both cell lines were maintained in Dulbecco's Modified Essential Medium (DMEM) (Gibco, USA) with addition of 10% heat-inactivated fetal calf serum (FCS), supplemented with 1% glutamine and 1% penicillin/streptomycin in a humidified atmosphere of 5% CO2 at 37˚C.
cell coculture  protocol: MBA-15 cells were seeded at density of 2x10^4cells/cm2 and allowed to adhere overnight. The following day, DA3 mammary-adenocarcinoma cells were seeded on top of the MBA-15 monolayer at a density of 1.3x10^4 cells/cm2. In parallel, both cell types were cultured separately as controls. Cells were maintained in growth medium for 24 or 48h and then magnetically separated using the EasySep® positive selection kit (STEMCELL Technologies, USA) according to the manufacturer's instructions.
cell separation protocol: Co-cultured cell populations were trypsinized and dispersed into a single suspension. The separation was based on the expression of the epithelial tissue specific antigen CD326 (EpCAM)(Litvinov et al. 1994). EasySep® positive selection cocktail, CD326-mouse specific antibody (clone number G8.8, BioLegend, USA) and magnetic nanoparticles were added during serial incubations on ice. The magnetic nanoparticles selectively bound to viable epithelial cells expressing the CD326 antigen, which were positively selected by placing the tube in a magnet (STEMCELL Technologies, USA). Retrieved cells were centrifuged and RNA was extracted from cultured cells using EZ RNA kit (Biological industries, Beth HaEmek, Israel). Mono-cultured MBA-15 or DA3 cells, simultaneously seeded and maintained with identical confluence of the co-culture, were referred to as control cells.

extract_protocol: according to the manufacturer's protocol (Trizol, Sigma-Aldrich)

tag: cell line

value: mammary adenocarcinoma

tag: culture type

value: mono-cultured (control)

tag: culture date


title: MBA-15_Co-culture rep1

description:
C185_Neg_Fract_coc1-24_Assay4_(MoGene-1_0-st-v1).CEL.pimg
gene expression data of co-cultured MBA-15 cells

scan_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

value: pre-osteoblastic stromal cells

value: co-cultured


title: DA3_Co-culture rep2

description:
C205_Pos_Fract_coc24_Assay5_(MoGene-1_0-st-v1).CEL.pimg
gene expression data of co-cultured DA3 cells

label_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)


title: DA3_alone rep1

description:
C187_Pos_Fract_24mix_Assay4_(MoGene-1_0-st-v1).CEL.pimg
gene expression data of DA3 cells alone


title: rapeseed - osmopriming -drying-replicat2

city: Poznań

first: Małgorzata

last: Garnczarska

state: wielkopolska

address: Umultowska 89

department: Plant Physiology

country: Poland

institute: Adam Mickiewicz University

description: biological replicate 2 of 2

hyb_protocol: Hybridization of the labeled cDNA (0.3 microg per sample) were added to hybridization buffer (Agilent In Situ Hybridization Kit Plus)  and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially according to Agilent instructions.

scan_protocol: Scanned on an Agilent Scanner G2565B Images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: Agilent Feature Extraction Software (v 9.1) was used for background subtraction and LOWESS normalization.

label: Alexa Fluor 555

organism: Brassica napus

source_name: rapeseed_osmopriming_drying [Pnd]

label_protocol:
First strand cDNA was synthetized from 10 micrograms RNA. Synthesized cDNA were purified and labeled with Alexa Fluor 555 and Alexa Fluor 647. Experiments were carried out according to instructions of the Superscript Plus Indirect cDNA Labeling system (Invitrogen).
The quality of the labeled cDNA and its concentration were respectively measured with the 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA) and ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE).

growth_protocol: Seeds were germinated for 7 hours at 25 °C in the darknesss. Germination were caried out on Petri dishes lined with 3 layers of filter paper wetted with 10 mL of water

extract_protocol: Total RNA was prepared from 1 g of seeds according to procedure described by Asif et al. 2000.

treatment_protocol: During osmopriming dry untreated seeds were exposed to PEG solution (-1.2 MPa osmotic potential) for 7 days at 25 °C in the darkness. Osmopriming was carried out on Petri dishes lined with 3 layers of filter paper wetted with 10 mL of PEG solution. After incubation seed were dried at room temperature until the initial moisture content.

tag: cultivar/variety

value: cv 'Libomir'

tag: developmental stage

value: seeds

tag: sample group

value: soaked in PEG (-1.2 MPa osmotic potential)

tag: treatment duration

value: 7 days

label: Alexa Fluor 647

source_name: rapeseed_dry treated [Pd]

value: dry treated


title: rapeseed - post-priming germination-replicat2

description: biological replicate 2 of 2

source_name: rapeseed_post-priming germination [P7h]

value: treated imbibed on water

value: 7 hours

source_name: rapeseed_untreated imbibed on water [UP7h]

value: untreated imbibed on water


title: MSCs from healthy donor cocultured with MM.1S cells_07mscCoD_0019

description:
Gene expression data from human clinical samples
07mscCoD_0019

value: bone marrow

tag: cell type

value: primary Mesenchymal Stromal Cells (MSC)


title: MSCs from healthy donor cocultured with MM.1S cells_02mscCoD_0014

description:
Gene expression data from human clinical samples
02mscCoD_0014

value: healthy donor


title: rapeseed - osmopriming -general-replicat2

description: biological replicate 2 of 2

source_name: rapeseed_osmopriming_general [Pd]

source_name: rapeseed_dry untreated [Upd]

value: dry untreated


title: MSCs from healthy donor cocultured with MM.1S cells_03mscCoD_0015

description:
Gene expression data from human clinical samples
03mscCoD_0015

value: cocultured with MM.1S cells


title: DA3_Co-culture rep1

description:
C191_Coc(+)24h_Assay3_(MoGene-1_0-st-v1).CEL.pimg
gene expression data of co-cultured DA3 cells

value: mammary adenocarcinoma


title: rapeseed - post-priming germination-replicat1

description: biological replicate 1 of 2


title: MBA-15_alone rep2

description:
C190_Mix(-)24h-1_Assay3_(MoGene-1_0-st-v1).CEL.pimg
gene expression data of MBA-15 cells alone

value: mono-cultured (control)


title: MSCs from healthy donor cocultured with MM.1S cells_06mscCoD_0018

description:
Gene expression data from human clinical samples
06mscCoD_0018


title: MBA-15_Co-culture rep2

description:
C189_Coc(-)24h-1_Assay3_(MoGene-1_0-st-v1).CEL.pimg
gene expression data of co-cultured MBA-15 cells

value: pre-osteoblastic stromal cells


title: rapeseed - osmopriming -soaking-replicat1

description: biological replicate 1 of 2

source_name: rapeseed_osmopriming_soaking [Pnd]


title: MSCs from healthy donor cocultured with MM.1S cells_01mscCoD_0013

description:
Gene expression data from human clinical samples
01mscCoD_0013


title: MBA-15_alone rep1

description:
C186_Neg_Fract_mix1-24_Assay4_(MoGene-1_0-st-v1).CEL.pimg
gene expression data of MBA-15 cells alone


title: rapeseed - osmopriming -soaking-replicat2

description: biological replicate 2 of 2


title: MSCs from healthy donor cocultured with MM.1S cells_04mscCoD_0016

description:
Gene expression data from human clinical samples
04mscCoD_0016


title: rapeseed - osmopriming -general-replicat1

description: biological replicate 1 of 2


title: T72 Control

status: Public on Nov 22 2014

city: Bangalore

first: Pradip

middle: K

last: Majumder

address: Suite 202, Narayana Nethralaya, Narayana Hrudayalaya Health City, Hosur Main Road, Bangalore 99, Karnataka State.

country: India

institute: Mitra Biotech Pvt Ltd.

description: Primary tumor cultured on uncoated plate

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8*60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Primary tumor

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using the Qiagen's Micro Kit following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The primary HNSCC tumor was cultured under different conditions to see which condition best mimics the baseline condition.

value: Tumor

value: M


title: Xenograft_322

description: Gene expression in CRC tumors passaged in mice for two generations

source_name: Xenograft Tumor

treatment_protocol: The primary CRC tumors were derived from patients and xenograft tumors were grown in mice for two generations without any additional treatment

tag: host

value: Mouse


title: T72 AS

description: Primary tumor cultured on plate coated with 2% autologous serum


title: T72 AS+TMP

description: Primary tumor cultured on plate coated with 2% autologous serum and tissue metalloproteinases


title: Primary_322

description: Gene expression in tumors derived from CRC patients

source_name: Primary Tumor


title: Xenograft_210


title: Primary_170

value: F


title: Xenograft_170


title: Baseline

description: Primary Tumor


title: Primary_210


title: Primary_117


title: Xenograft_117


title: OV90_PD0332991/SNS032-resistant_replicate 2

city: Los Angeles

first: Wolf

last: Wiedemeyer

state: California

address: 8700 Beverly Blvd.

department: BMS

institute: Cedars-Sinai

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw intensities were quantile-normalized with background subtraction, no imputation of data of missing beads.  All intensity values less than the median intensity value of the dataset (11) were increased to this value.

label_protocol: Biotinylated cRNA were prepared with the Ambion® Illumina® TotalPrep™ RNA Amplification Kit  (Ambion®)  for Illumina arrays

growth_protocol: Asynchronously growing cells in DMEM with 10% FBS, medium changed every other day, cells split 1:5 once a week if confluent. Subconfluent populations were harvested after 48h in normal DMEM (including 10% FBS = 10%), or medium containing 0.2 micromolar SNS032 or 0.5 micromolar PD0332991. CDKi-resistant cells were kept in 0.2 micromolar SNS032 (SNS-R), 0.2 micromolar PD0332991 (PD-R) or both. RNA was harvested 48h after medium change

extract_protocol: Trizol extraction followed by Qiagen Rneasy including DNAse digestion

treatment_protocol: 48h with or without the specific CDKi

tag: cell line/subline

value: Ovarian cancer cell line

tag: cell subtype/phenotype


title: SKOV3_parental_replicate 2

value: parental


title: SKOV3_PD0332991/SNS032-resistant_late_CDKi release_replicate 2

description: SKOV3-PD/SNS-R-1 release-2


title: SKOV3_parental_replicate 1


title: SKOV3_SNS032-resistant_replicate 1


title: SKOV3_SNS032-resistant_replicate 2


title: SKOV3_PD0332991/SNS032-resistant_late_replicate 2

description: SKOV3-PD/SNS-R-1 OLD-2


title: OV90_SNS032-resistant_replicate 1


title: OV90_parental_replicate 1


title: SKOV3_PD0332991/SNS032-resistant_early_replicate 1


title: SKOV3_PD0332991/SNS032-resistant_late_CDKi release_replicate 1

description: SKOV3-PD/SNS-R-1 release-1


title: OAW28_SNS032-resistant_replicate 1


title: OAW28_SNS032-resistant_replicate 2


title: OAW28_PD0332991/SNS032-resistant_replicate 2


title: HEY_PD0332991/SNS032-resistant_replicate 2


title: OAW28_PD0332991/SNS032-resistant_replicate 1


title: HEY_PD0332991-resistant_replicate 2


title: OV90_PD0332991/SNS032-resistant_replicate 1


title: HEY_SNS032-resistant_replicate 2


title: SKOV3_PD0332991/SNS032-resistant_early_replicate 2


title: SKOV3_PD0332991/SNS032-resistant_late_replicate 1

description: SKOV3-PD/SNS-R-1 OLD-1


title: OAW28_parental_replicate 2


title: HEY_PD0332991-resistant_replicate 1


title: HEY_PD0332991/SNS032-resistant_replicate 1


title: OAW28_parental_replicate 1


title: OV90_SNS032-resistant_replicate 2


title: OV90_parental_replicate 2


title: Cited4-siRNA-transduced cells at day 6.5 and nontransduced cells at day 6.5

city: Yonago

first: Junichiro

last: Miake

address: 36-1 Nishi-cho

department: Multidisciplinary Internal Medicine

country: Japan

institute: Tottori University Faculty of Medicine

description: embryoid body formed with Cited4-siRNA-transduced mouse ES cells and embryoid body formed with nontransduced mouse ES cells

hyb_protocol: Hybridization for 20h at 50℃. Hybridization buffer and washing protocol was followed by the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc./AceGene)

scan_protocol: The arrays were scanned by FLA-8000 (Fuji Photo Film). Images were quantified using Array Gauge Ver2.0 (Fuji Photo Film).

data_processing: These data were analyzed by DNASIS array software (Hitachi Software Engineering Co., Ltd), which converted the signal intensity of each spot into text format. Data from microarray were normalized by Global normalization.

source_name: embryoid body

label_protocol: Amino Allyl aRNA was synthesed by Amino Allyl MessageAmp™ aRNA Amplification Kit (Amibion). CyeDye Coupling and fragmentation were performed as the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc./AceGene)

extract_protocol: Total RNA was extracted using RNeasy Mini Kit following manufacturer's instructions

tag: sample type

tag: treatment

value: Cited4 siRNA

value: control


title: HEY_SNS032-resistant_replicate 1


title: HEY_PD0332991-treated_replicate 2

value: HEY

tag: treated with


title: A8_C8_nasal_stem_cell_rep1

city: MARSEILLE CEDEX 09

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

country: France

institute: TAGC INSERM U1090

description: comparaison of nasal olfactory stem cells from autistic and control individus

hyb_protocol: Sample hybridization was performed with the Agilent two-color microarray-base analysis (low input quick amp labeling) protocol (Agilent Technologies). Labeled cRNA was purified and fragmented before hybridization on Agilent whole human genome Expression Arrays, containing 45 220 oligonucleotide probes, at 65°C for 17 hours.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE2-v5_10_Apr08 and Grid: 014850_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities. All data were normalized by quantile normalization.

label_protocol: Sample amplification and labelling were performed with the Agilent two-color microarray-base analysis (low input quick amp labeling) protocol (Agilent Technologies). Total RNA was reverse transcribed into cDNA using the T7 promoter primer. The reaction intending to synthesize cyanine-3 or cyanine-5 labeled cRNA from cDNA was performed in a solution containing dNTP mix, T7 RNA polymerase and cyanine 3-dCTP and then incubated at 40°C for 2 hours.

growth_protocol: Nasal biopsies were collected and immediately placed in growth medium containing DMEM/Ham F12 supplemented with 10% Fetal Bovine Serum (FBS) and 100 units/mL of penicillin and 100 µg/mL of streptomycin (Invitrogen/Life Technologies). Olfactory ecto-mesenchymal stem cells (OE-MSC) were purified from the lamina propria and cultivated as described before (Delorme et al, 2010; Girard et al, 2011; Nivet et al, 2011). All experiments were performed using OE-MSCs with a low passage number (P1 to P5). When the two cohorts were compared, the same passage number was used. In order to limit biases, stem cells from the 22 individuals were harvested by the same operator, under the same conditions: identical culture medium and level of confluency (100%), equal passaging (P3).

extract_protocol: In order to avoid any circadian rhythm-related variations in gene expression, cells were collected at the same time of the day. Total RNA was then isolated using RNeasy Mini kit (Qiagen), according to the manufacturer’s instructions. RNA concentration was determined using a nanodrop 2000 spectrophotometer (Thermo Scientific) and RNA integrity assessed on an Agilent 2100 Bioanalyzer.

tag: status

value: autism


title: HEY_PD0332991-treated_replicate 1


title: HEY_control_replicate 2

value: none (control)


title: A10_C10_nasal_stem_cell_rep1


title: A7_C7_nasal_stem_cell_rep1


title: HEY_SNS032-treated_replicate 2


title: A9_C9_nasal_stem_cell_rep1


title: HEY_SNS032-treated_replicate1


title: A6_C6_nasal_stem_cell_rep1


title: A11_C11_nasal_stem_cell_rep1


title: A5_C5_nasal_stem_cell_rep1


title: A3_C3_nasal_stem_cell_rep1


title: HEY_control_replicate1


title: A1_C1_nasal_stem_cell_rep1


title: A2_C2_nasal_stem_cell_rep1


title: A4_C4_nasal_stem_cell_rep1


title: control newborn mouse heart, biological rep 1

city: Rostock

first: Leila

last: Taher

address: Ernst-Heydemann-Str. 8

country: Germany

institute: University of Rostock

description: SAMPLE 10

hyb_protocol: Hybridization of biotin-labeled cRNA fragment to Mouse Genome 430 2.0 array, washing, staining, and signal amplification were performed according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000.

data_processing: Gene expression data was processed using Robust Multi-array Average (RMA), as implemented in the affy R/Bioconductor package. RMA performs normalization, background correction and data summarization. Differential expression analysis was conducted using the 'limma' R/Bioconductor package.

source_name: control newborn mouse heart

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

growth_protocol: All mice were housed normally.

extract_protocol: RNA was isolated and purified using the Qiagen RNeasy kit with on-column DNaseI treatment.

treatment_protocol: Heart-specific LacZ excision was performed by breeding floxed HMGN5-TG mice with alphaMHC-cre mice.

tag: strain background

tag: genotype/variation

value: wild-type

tag: age

value: newborn

tag: tissue

value: heart


title: control newborn mouse heart, biological rep 2

description: SAMPLE 11


title: HMGN5 transgenic newborn mouse heart, biological rep 2

description: SAMPLE 8

source_name: HMGN5 transgenic newborn mouse heart

value: HMGN5 transgenic


title: HMGN5 transgenic newborn mouse heart, biological rep 3

description: SAMPLE 9


title: rapeseed - osmopriming -drying-replicat1

description: biological replicate 1 of 2

value: cv 'Libomir'

value: seeds

value: soaked in PEG (-1.2 MPa osmotic potential)

value: 7 days

value: dry treated


title: patient 46_malignant mesothelioma_250Ksty

city: Nishinomiya

first: Yoshie

last: Yoshikawa

state: Hyogo

address: 1-1 Mukogawa-cho

department: Genetics

institute: Hyogo College of Medicine

description: Hybridized to 250K_Sty

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The probe intensities at each locus were determined in the Affymetrix GeneChip Operating System GCOS software, and genotype calls were generated using the Affymetrix Genotyping Console GTC Software (Version 3.0.2). Primary data analysis was performed using GTC software, and further statistical studies were analyzed using the CNAG (Copy Number Analyzer for Affymetrix GeneChip Mapping arrays) software, version 2.0 (Genome Laboratory, The University of Tokyo, http://www.genome.umin.jp) for Mapping 500K set. For SNP6.0 array, genotype calls were generated using the Affymetrix Genotyping Console GTC Software (Version 3.0.2) using birdseed version 2 algorithm with other 100 files.
Call (SNP call): AA, AB, BB, and NoCall; Log2Ratio: copy number log2 ratio between the test and reference samples of zero; LOH: posibility of loss of heterozygosity (bigger number means higher posibility of LOH for CNAG, but Genotyping Console gave 1 with posibility of LOH)

source_name: primary cultured cell line MM46 derived from patient 46

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: After centrifugation, primary cells in pleural effusions or ascites were cultured in -MEM (Invitrogen, Carlsbad, CA, USA) supplemented with 10% FBS (Equitech-Bio, Ingram, TX, USA). Surgically resected tumors were cut into small pieces. These pieces were plated on culture dishes and gently overlaid with culture medium. Primary outgrowth cells were cultured in -MEM–10% FBS. Adherent cells were expanded by several passages for several weeks or months.

extract_protocol: Genomic DNA from cultured cells were isolated with an AllPrep DNA/RNA mini kit (Qiagen, Hilden, Germany) following the manufacturer's protocol. Genomic DNA from peripheral blood was isolated with a QIAamp DNA Blood Mini Kit (Qiagen).

tag: cell

value: malignant mesothelioma


title: HMGN5 transgenic newborn mouse heart, biological rep 1

description: SAMPLE 7


title: control adult mouse heart, biological rep 3

description: SAMPLE 6

source_name: control adult mouse heart

value: adult


title: control adult mouse heart, biological rep 2

description: SAMPLE 5


title: HMGN5 transgenic adult mouse heart, biological rep 2

description: SAMPLE 2

source_name: HMGN5 transgenic adult mouse heart


title: patient 45_malignant mesothelioma_250Ksty

description: Hybridized to 250K_Sty

source_name: primary cultured cell line MM45 derived from patient 45


title: HMGN5 transgenic adult mouse heart, biological rep 3

description: SAMPLE 3


title: patient 39_malignant mesothelioma_250Ksty

description: Hybridized to 250K_Sty

source_name: primary cultured cell line MM39 derived from patient 39


title: patient 34_malignant mesothelioma_250Ksty

description: Hybridized to 250K_Sty

source_name: primary cultured cell line MM34 derived from patient 34


title: PE04

city: Philadelphia

first: Hongzhe

last: Li

state: Pennsylvania

address: 415  Curie Blvd

department: Biostatistics and Epidemiology

institute: University of Pennsylvania

hyb_protocol: RNA were reverse transcribed into cDNAs followed by fragmentation

scan_protocol: After hybridization to the GeneChip Human Gene 1.0 ST Arrays, the chips were labeled with a WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA) and scanned on a GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA).

data_processing: Data were normalized using the Robust Multi-Chip Average (RMA) method and Log2 transformed using Partek Genomics Suite 6.4 (Partek Inc., St. Louis, MO).

source_name: ovary

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

extract_protocol: Qiagen miRNeasy Mini kit

value: ovary

value: ovarian cancer

tag: Stage

value: tumor


title: HMGN5 transgenic adult mouse heart, biological rep 1

description: SAMPLE 1


title: SKOV3


title: patient 46_peripheral blood_250Ksty

description: Hybridized to 250K_Sty

source_name: patient 46_peripheral blood

value: peripheral blood


title: patient 45_peripheral blood_250Ksty

description: Hybridized to 250K_Sty

source_name: patient 45_peripheral blood


title: patient 30_malignant mesothelioma_250Ksty

description: Hybridized to 250K_Sty

source_name: primary cultured cell line MM30 derived from patient 30


title: patient 34_peripheral blood_250Ksty

description: Hybridized to 250K_Sty

source_name: patient 34_peripheral blood


title: OAW42


title: control adult mouse heart, biological rep 1

description: SAMPLE 4


title: PE01


title: patient 26_malignant mesothelioma_250Ksty

description: Hybridized to 250K_Sty

source_name: primary cultured cell line MM26 derived from patient 26


title: skin fibroblasts_AKR_37

city: Leipzig

first: Marianne

last: Schauer

address: Johannissallee 30

department: Department of Dermatology

institute: University Leipzig

description: control

hyb_protocol: not provided

scan_protocol: scanned on the Illumina HiScan instrument according to manufacturer’s specifications

data_processing: Raw data of 25.600 probes was extracted and quantile normalized by Illumina GenomeStudio®. Expression values were background subtracted if necessary. We considered probes as present for a detection p-value < 0.01. Thereafter, we used Student’s t-tests to identify differentially expressed genes. The results were corrected for multiple testing using the Benjamini-Hochberg method. Genes were considered significantly differently expressed if p < 0.05.

source_name: skin fibroblasts_AKR_37_control

label_protocol: not provided

growth_protocol: Fibroblasts were cultivated in DMEM; 10 % FCS; Pen/Strep

extract_protocol: Fibroblasts from skin were extracted by standard dissociation protocol adapted to the Liberase DL Research Grade (low dispase) protocol of Roche Diagnostics (Mannheim, Germany). Total RNA from cells was extracted using the RNeasy MiniKit (Qiagen, Hilden, Germany )

tag: gender

value: female

tag: strain

value: fibroblasts

value: skin

value: 12 month old mice


title: patient 21_malignant mesothelioma_250Ksty

description: Hybridized to 250K_Sty

source_name: primary cultured cell line MM21 derived from patient 21


title: skin fibroblasts_AKR_17

description: control

source_name: skin fibroblasts_AKR_17_control

value: male


title: OV7M


title: patient 26_peripheral blood_250Ksty

description: Hybridized to 250K_Sty

source_name: patient 26_peripheral blood


title: patient 19_peripheral blood_250Ksty

description: Hybridized to 250K_Sty

source_name: patient 19_peripheral blood


title: patient 21_peripheral blood_250Ksty

description: Hybridized to 250K_Sty

source_name: patient 21_peripheral blood


title: patient 19_malignant mesothelioma_250Ksty

description: Hybridized to 250K_Sty

source_name: primary cultured cell line MM19 derived from patient 19


title: OV95


title: OVCAR8


title: skin fibroblasts_ALR_35

description: Nd2 mutant

source_name: skin fibroblasts_ALR_35_Nd2mutant


title: patient 45_malignant mesothelioma_250Knsp

description: Hybridized to 250K_Nsp

source_name: primary cultured cell line MM45 derived from patient 45


title: patient 46_peripheral blood_250Knsp

description: Hybridized to 250K_Nsp


title: skin fibroblasts_AKR_15

description: control

source_name: skin fibroblasts_AKR_15_control


title: skin fibroblasts_AKR_16

description: control

source_name: skin fibroblasts_AKR_16_control


title: patient 46_malignant mesothelioma_250Knsp

description: Hybridized to 250K_Nsp

source_name: primary cultured cell line MM46 derived from patient 46


title: patient 19_reactive mesothelial cells_250Ksty

description: Hybridized to 250K_Sty

source_name: primary cultured reactive mesothelial cells derived from patient 19

value: reactive mesothelial cells


title: patient 45_peripheral blood_250Knsp

description: Hybridized to 250K_Nsp

source_name: patient 45_peripheral blood


title: OVCAR5

source_name: ovary


title: OVCAR4


title: OVCAR10


title: patient 34_malignant mesothelioma_250Knsp

description: Hybridized to 250K_Nsp

source_name: primary cultured cell line MM34 derived from patient 34


title: skin fibroblasts_ALR_32

description: Nd2 mutant

source_name: skin fibroblasts_ALR_32_Nd2mutant


title: patient 34_peripheral blood_250Knsp

description: Hybridized to 250K_Nsp

source_name: patient 34_peripheral blood


title: patient 16_malignant mesothelioma_250Ksty

description: Hybridized to 250K_Sty

source_name: primary cultured cell line MM16 derived from patient 16


title: patient 39_malignant mesothelioma_250Knsp

description: Hybridized to 250K_Nsp

source_name: primary cultured cell line MM39 derived from patient 39


title: patient 26_malignant mesothelioma_250Knsp

description: Hybridized to 250K_Nsp

source_name: primary cultured cell line MM26 derived from patient 26


title: OVCAR3


title: patient 21_peripheral blood_250Knsp

description: Hybridized to 250K_Nsp


title: Aspirin treated rep 2 on chip2

city: Waurnponds

first: sivapriya

last: pavuluri

state: VIC

address: 75, Pigdons Road

department: School of Medicine

country: Australia

institute: Deakin University

hyb_protocol: Using standard Illumina hybridization protocol

scan_protocol: Using standard Illumina scanning protocol

data_processing: Data was further processed by gene expression module of genome studio version 1.9.0 & using quantile normalization

source_name: SCC25 oral squamous cell carcinoma cell line, aspirin

label_protocol: Biotinylated cRNA samples were prepared using Ambion kit following manufacturer's instructions

growth_protocol: SCC25 cells treated with and without aspirin were grown at 37°C for 72h

extract_protocol: Total RNA from treated and untreated cells was isolated using Qiagen Rneasy mini kit according to manufacturer's instructions.

treatment_protocol: SCC25 cells were subjected to aspirin treatment of 2.0 mM concentration and cells without treatment was considered as control

tag: cell line

value: Treated with 2.0 mM Aspirin


title: Aspirin treated rep 3 on chip1

value: SCC25 oral squamous cell carcinoma cell line


title: patient 21_malignant mesothelioma_250Knsp

description: Hybridized to 250K_Nsp

source_name: primary cultured cell line MM21 derived from patient 21


title: patient 19_reactive mesothelial cells_250Knsp

description: Hybridized to 250K_Nsp


title: patient 30_malignant mesothelioma_250Knsp

description: Hybridized to 250K_Nsp

source_name: primary cultured cell line MM30 derived from patient 30


title: OVCAR2

tag: cell type


title: patient 26_peripheral blood_250Knsp

description: Hybridized to 250K_Nsp

source_name: patient 26_peripheral blood


title: Control rep 3 on chip1

source_name: SCC25 oral squamous cell carcinoma cell line, control

value: Untreated with Aspirin


title: Control rep 2 on chip2


title: Control rep 1 on chip1


title: patient 19_malignant mesothelioma_250Knsp

description: Hybridized to 250K_Nsp

source_name: primary cultured cell line MM19 derived from patient 19


title: patient 16_malignant mesothelioma_250Knsp

description: Hybridized to 250K_Nsp


title: A2008


title: skin fibroblasts_ALR_28

description: Nd2 mutant

source_name: skin fibroblasts_ALR_28_Nd2mutant


title: prostate_cancer_primary_179

status: Public on Nov 21 2014

city: Vancouver

first: Elai

last: Davicioni

state: British Columbia

address: 1038 Homer st

country: Canada

institute: GenomeDx Biosciences Inc

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using SCAN software package (Bioconductor)
HuEx-1_0-st-v1.r2.pgf

source_name: primary prostate cancer FFPE tissue sample

label_protocol: RNA was amplified, fragmented and biotinylated using the Ovation FFPE system v 3.0 (NuGEN)

extract_protocol: RNA was extracted using the Formapure nucleic acid extraction kit (Agencourt Biosciences).

tag: pathgs

tag: cstage


title: patient 19_peripheral blood_250Knsp

description: Hybridized to 250K_Nsp

source_name: patient 19_peripheral blood


title: prostate_cancer_primary_178


title: prostate_cancer_primary_182


title: prostate_cancer_primary_180


title: Aspirin treated rep 1 on chip1


title: prostate_cancer_primary_176


title: prostate_cancer_primary_177


title: prostate_cancer_primary_175


title: prostate_cancer_primary_173


title: prostate_cancer_primary_174


title: prostate_cancer_primary_167


title: prostate_cancer_primary_171


title: prostate_cancer_primary_168


title: prostate_cancer_primary_166


title: prostate_cancer_primary_172


title: prostate_cancer_primary_170


title: prostate_cancer_primary_169


title: prostate_cancer_primary_165


title: prostate_cancer_primary_164


title: prostate_cancer_primary_158


title: prostate_cancer_primary_155


title: prostate_cancer_primary_157


title: prostate_cancer_primary_154


title: prostate_cancer_primary_162


title: prostate_cancer_primary_163


title: prostate_cancer_primary_181


title: prostate_cancer_primary_156


title: prostate_cancer_primary_152


title: prostate_cancer_primary_159


title: prostate_cancer_primary_161


title: prostate_cancer_primary_150


title: prostate_cancer_primary_149


title: prostate_cancer_primary_153


title: prostate_cancer_primary_151


title: prostate_cancer_primary_147


title: prostate_cancer_primary_146


title: prostate_cancer_primary_148


title: prostate_cancer_primary_143


title: skin fibroblasts_ALR_34

description: Nd2 mutant

source_name: skin fibroblasts_ALR_34_Nd2mutant


title: prostate_cancer_primary_144


title: prostate_cancer_primary_142


title: prostate_cancer_primary_145


title: prostate_cancer_primary_140


title: prostate_cancer_primary_141


title: prostate_cancer_primary_137


title: prostate_cancer_primary_134


title: prostate_cancer_primary_139


title: prostate_cancer_primary_138


title: prostate_cancer_primary_136


title: prostate_cancer_primary_130


title: prostate_cancer_primary_128


title: prostate_cancer_primary_133


title: prostate_cancer_primary_131


title: prostate_cancer_primary_125


title: prostate_cancer_primary_124


title: prostate_cancer_primary_127


title: prostate_cancer_primary_132


title: prostate_cancer_primary_122


title: prostate_cancer_primary_123


title: prostate_cancer_primary_121


title: postMBT_inh_H3K27me3 Repl2

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

hyb_protocol: Hybridization done by Nimblegen as per normal service protocol

scan_protocol: Scanning done by Nimblegen as per normal service protocol

data_processing: log2 (ChIP/Input) with biweight mean of values subtracted

organism: Danio rerio

source_name: postMBT DZNeP treated H3K27me3 ChIP DNA

label_protocol: Labeling done by Nimblegen as per normal service protocol

growth_protocol: Fish and embryos grown as per AAALAC certification with 10 uM DZNeP/DMSO

extract_protocol: Histone ChIPs were done as described (Dahl, Collas, 2007) using 0.5 A260 units chromatin per ChIP. In short, dechorionated embryos were cross-linked with 1% formaldehyde for 8 min and quenched with glycine. Lysis buffer was added and samples incubated for 5 min on ice. Cells were sonicated on ice using a Bioruptor (Diagenode) to produce fragments of 400 bp or less. The lysate was centrifuged, the supernatant collected, and chromatin was incubated with 2.4 μg antibody coupled to Dynabeads Protein A (Invitrogen) for 2 h ro overnight at 4oC. ChIP material was washed, elution buffer containing 1 % SDS and 50 µg/ ml Proteinase K was added and samples incubated for 2 h at 68oC on a Thermomixer (Eppendorf); after a second extraction both supernatants were pooled. ChIP DNA was purified by phenol-chloroform isoamylalcohol extraction, ethanol-precipitated. 5 µg (10 µl) RNase A (Roche) was added before ChIP DNA elution. ChIP DNA samples were dissolved in 11 μl MilliQ water. Input DNA (channel 2) was purified by phenol-chloroform isoamylalcohol extraction and RNAse-treated as above.

value: Embryonic cells

value: AB

tag: developmental stage

value: postMBT, 5.3 hpf, 50% epiboly

tag: chip antibody

value: H3K27me3, Millipore 07-449

source_name: postMBT DZNeP treated H3K27me3 Input DNA

tag: fraction

value: input


title: prostate_cancer_primary_120


title: prostate_cancer_primary_117


title: prostate_cancer_primary_115


title: prostate_cancer_primary_118


title: patient 67_peripheral blood_snp6

description: Hybridized to SNP6.0

source_name: patient 67_peripheral blood


title: prostate_cancer_primary_114


title: prostate_cancer_primary_119


title: prostate_cancer_primary_112


title: prostate_cancer_primary_113


title: prostate_cancer_primary_109


title: prostate_cancer_primary_106


title: prostate_cancer_primary_111


title: prostate_cancer_primary_110


title: prostate_cancer_primary_107


title: prostate_cancer_primary_126


title: postMBT_inh_H3K27me3 Repl1


title: postMBT_inh_H3K4me3 Repl1

source_name: postMBT DZNeP treated H3K4me3 ChIP DNA

value: H3K4me3, Diagenode pAb-003-050

source_name: postMBT DZNeP treated H3K4me3 Input DNA


title: prostate_cancer_primary_108


title: prostate_cancer_primary_116


title: prostate_cancer_primary_103


title: prostate_cancer_primary_101


title: prostate_cancer_primary_105


title: patient 67_malignant mesothelioma_snp6

description: Hybridized to SNP6.0

source_name: primary cultured cell line MM67 derived from patient 67

value: malignant mesothelioma


title: postMBT_inh_H3K9me3 Repl2

source_name: postMBT DZNeP treated H3K9me3 ChIP DNA

value: H3K9me3, Diagenode pAb-056-50

source_name: postMBT DZNeP treated H3K9me3 Input DNA


title: prostate_cancer_primary_100


title: postMBT_inh_H3K9me3 Repl1


title: prostate_cancer_primary_96


title: prostate_cancer_primary_97


title: prostate_cancer_primary_98


title: prostate_cancer_primary_99


title: prostate_cancer_primary_92


title: prostate_cancer_primary_95


title: prostate_cancer_primary_89


title: prostate_cancer_primary_102


title: prostate_cancer_primary_135


title: prostate_cancer_primary_94


title: prostate_cancer_primary_129


title: prostate_cancer_primary_84


title: prostate_cancer_primary_90


title: prostate_cancer_primary_86


title: prostate_cancer_primary_93


title: prostate_cancer_primary_88


title: prostate_cancer_primary_87


title: prostate_cancer_primary_83


title: prostate_cancer_primary_82


title: prostate_cancer_primary_81


title: prostate_cancer_primary_79


title: prostate_cancer_primary_85


title: prostate_cancer_primary_77


title: prostate_cancer_primary_80


title: prostate_cancer_primary_75


title: prostate_cancer_primary_72


title: prostate_cancer_primary_76


title: prostate_cancer_primary_70


title: prostate_cancer_primary_73


title: prostate_cancer_primary_71


title: prostate_cancer_primary_68


title: prostate_cancer_primary_74


title: prostate_cancer_primary_78


title: prostate_cancer_primary_66


title: prostate_cancer_primary_58


title: prostate_cancer_primary_63


title: prostate_cancer_primary_60


title: prostate_cancer_primary_65


title: prostate_cancer_primary_67


title: prostate_cancer_primary_59


title: prostate_cancer_primary_57


title: prostate_cancer_primary_69


title: prostate_cancer_primary_160


title: prostate_cancer_primary_56


title: prostate_cancer_primary_62


title: prostate_cancer_primary_54


title: postMBT_inh_H3K4me3 Repl2


title: prostate_cancer_primary_51


title: prostate_cancer_primary_53


title: prostate_cancer_primary_55


title: prostate_cancer_primary_52


title: prostate_cancer_primary_50


title: prostate_cancer_primary_45


title: prostate_cancer_primary_44


title: prostate_cancer_primary_48


title: prostate_cancer_primary_42


title: prostate_cancer_primary_47


title: prostate_cancer_primary_43


title: prostate_cancer_primary_38


title: prostate_cancer_primary_46


title: prostate_cancer_primary_40


title: prostate_cancer_primary_36


title: prostate_cancer_primary_39


title: prostate_cancer_primary_34


title: prostate_cancer_primary_35


title: prostate_cancer_primary_41


title: prostate_cancer_primary_49


title: prostate_cancer_primary_33


title: prostate_cancer_primary_30


title: prostate_cancer_primary_32


title: prostate_cancer_primary_104


title: prostate_cancer_primary_37


title: prostate_cancer_primary_28


title: prostate_cancer_primary_26


title: prostate_cancer_primary_27


title: prostate_cancer_primary_24


title: prostate_cancer_primary_23


title: prostate_cancer_primary_22


title: prostate_cancer_primary_20


title: prostate_cancer_primary_19


title: prostate_cancer_primary_18


title: prostate_cancer_primary_29


title: prostate_cancer_primary_16


title: prostate_cancer_primary_8


title: prostate_cancer_primary_14


title: prostate_cancer_primary_15


title: prostate_cancer_primary_7


title: prostate_cancer_primary_17


title: prostate_cancer_primary_11


title: prostate_cancer_primary_10


title: prostate_cancer_primary_6


title: prostate_cancer_primary_25


title: prostate_cancer_primary_9


title: prostate_cancer_primary_91


title: prostate_cancer_primary_13


title: prostate_cancer_primary_12


title: prostate_cancer_primary_4


title: prostate_cancer_primary_2


title: prostate_cancer_primary_5


title: prostate_cancer_primary_1


title: prostate_cancer_primary_3


title: Liver from SMRT and NCoR double floxed mice (control group), replicate 3

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

description: DKO-C 169

hyb_protocol: Affymetrix GeneChip® Mouse Gene 2.0 ST arrays were washed, stained and scanned according to the protocol described in GeneChip® WT Terminal Labeling and Hybridization User Manual (Fluidics Protocol FS450_0002)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA Signal extraction, normalization and filtering was performed as described using the comprehensive R- and bioconductor-based web service for  microarray data analysis – ‘CARMAWeb’

source_name: Liver_SMRT and NCoR double floxed (control group)

label_protocol: 200ng of total RNA were amplified and labeled using the Ambion Whole Transcript Expression Kit (Catalog Number 4425209, Ambion, Austin, TX) and Affymetix Genechip Whole Transcript Terminal Labeling Kit (Catalog Number 900671, Affymetrix, Santa Clara, CA)

growth_protocol: Mice were housed  with a 12 hour light/dark cycle and supplied with food and water ad libitum.

extract_protocol: Perfect Pure RNA tissue kit (5 Prime)

treatment_protocol: At 7-9 weeks of age on standard chow (Harlan Teklad F6 Rodent Diet 8664) mice were sacrificed and RNA isolated.

value: 129SV/B6 mixed

value: SMRT and NCoR fl/fl

value: female

value: 7-9 weeks

value: liver


title: prostate_cancer_primary_21


title: Liver from SMRT and NCoR double knock out mice, replicate 1

description: DKO 40

source_name: Liver_SMRT and NCoR double knock out

value: SMRT and NCoR KO


title: Liver from SMRT knock out mice, replicate 2

description: SKO 367

source_name: Liver_SMRT knock out

value: SMRT KO


title: Liver from SMRT and NCoR double floxed mice (control group), replicate 2

description: DKO-C 57


title: Liver from SMRT and NCoR double knock out mice, replicate 2

description: DKO 42


title: pfc_pairfed_adjuvant_day16_62_rep9

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

description: Sample name: 5398636044_H

hyb_protocol: Gene expression was analyzed for both the PFC and HPC using the Illumina RatRef-12 Expression BeadChip microarray, which has 12 arrays per chip. PFC and HPC samples were run separately on different dates, due a limit of processing 8 chips (96 arrays) per batch. 750 ng of cRNA was applied to each array, with one sample per array. Experimental groups were counter-balanced across the arrays, such that chip batch was not confounded with any experimental treatment group, amplification batch, or dissection batch. Additional arrays included an amplification replicate and several hybridization replicates, yielding a total of 96 arrays run per tissue. Microarrays were scanned on the Illumina iScan, and bead-level expression data was collected.

data_processing: Detection p-values were identified using calculateDetection in the R package beadArray. Data were then filtered to remove non-gene probes and processed by quantile normalization using the normalizeIllumina function of the beadArray package in R.

organism: Rattus norvegicus

source_name: prefrontal cortex, pairfed diet, adjuvant injected, day 16 post injection

label_protocol: To generate cRNA for microarray analysis, 250 ng of total RNA from each sample was amplified using the Ambion Illumina TotalPrep RNA Amplification kit, in batches of ~24 samples at a time. Samples were distributed across amplification batches such that batch was not confounded with experimental treatment group.

extract_protocol: Brains were gradually thawed to 4 °C, and the prefrontal cortex (PFC) and hippocampus (HPC) were dissected using RNase-free technique. Dissected tissues were placed in RNAlater and stored at -20 °C. Total RNA and DNA were simultaneously extracted from the dissected tissues using the Qiagen AllPrep DNA/RNA Mini kit, and a DNase digestion step was included in the RNA extraction process. RNA integrity was determined using the Agilent BioAnalyzer mRNA Nano assay, and no samples were excluded due to low RNA integrity. Only one sample was excluded at this stage (PF hippocampus from the Day 39 Adjuvant group), due to suspected contamination.

treatment_protocol: Breeding and prenatal alcohol exposure: Rats were obtained from the Animal Care Center at the University of British Columbia, and were group- housed 1-2 weeks before breeding, with ad libitum access to standard lab chow (Jamieson’s Pet Food Distributors, Ltd., Delta, BC, Canada). Details of the procedures for breeding and handling have been published previously (Glavas et al. 2007). Briefly, females and males were co-housed in stainless steel cages with mesh front and floors, and wax paper under the cages was checked daily for the presence of vaginal plugs, which indicated day 1 of gestation. Thereafter pregnant dams were singly housed, and were assigned to one of three groups – a control group (C; fed laboratory chow ad libitum), pair-fed group (PF; liquid-control diet, with maltose-dextrin isocalorically substituted for ethanol, in the amount consumed by an ethanol- consuming partner, matched for g/kg body weight/day of gestation), or an ethanol-fed group (E; ad libitum access to liquid ethanol diet, with 36% calories derived from ethanol). All animals had ad libitum access to water, and diets were fed from gestation days 1-21 (Weinberg/Kiever Ethanol Diet #710324, Weinberg/Kiever Control Diet #710109, Dyets Inc., Bethlehem, PA). After gestational day 21, all animals were given laboratory chow and water ad libitum. Litters were weighed and culled at birth to 5 males and 5 females, when possible. Following weaning (on postnatal day 22) female offspring were group-housed by litter (2-3 rats per cage) until the start of testing.  Induction of adjuvant-induced arthritis: Details of the postnatal induction of adjuvant-induced arthritis in these animals have been previously published (Zhang et al. 2012). Briefly, female offspring (50-65 days of age) from the C, PF, and E groups were divided into two postnatal treatment groups, in which animals received an intradermal injection at the base of the tail of either 0.1 ml of 12 mg/ml suspension of complete Freund’s adjuvant (CFA) (Adjuvant group), or 0.1ml saline (Saline group). All animals were single-housed after injection, and monitored for clinical signs of arthritis, from the onset of AA through to resolution. To evaluate clinical signs of arthritis, animals were lightly anesthetized with isofluorane, and paws were scored for severity of redness and swelling, on days 7, 10, and every other day afterwards, following injection (results published previously in Zhang et al., 2012).  Termination of animals: Animals were terminated in two cohorts for analysis of gene expression. One cohort was terminated on day 16 post-injection (at the peak of adjuvant-induced arthritis), and another on day 39 post-injection (during resolution phase of arthritis). Each cohort contained 27 adjuvant-injected animals (9 each of C, PF, and E) and 15-18 saline-injected animals (5-6 each of C, PF, and E). For termination, animals were singly removed from their colony room, exposed to CO2 for 30 seconds, and then quickly decapitated. Brains were rapidly removed, immediately frozen on dry ice, wrapped in foil, and stored at -70 °C.

value: Sprague Dawley

value: adult

value: prefrontal cortex

tag: prenatal diet

value: pairfed

tag: adult treatment

value: adjuvant injection

tag: termination time point (post injection)

value: day 16

tag: animal id

tag: sample type

value: sample


title: pfc_ethanol_adjuvant_day16_61_rep9

description: Sample name: 5398636044_L

source_name: prefrontal cortex, ethanol diet, adjuvant injected, day 16 post injection

tag: tissue

value: ethanol


title: pfc_control_saline_day39_105_rep6

description: Sample name: 5398636044_D

source_name: prefrontal cortex, control diet, saline injected, day 39 post injection

value: control

value: saline injection

value: day 39


title: pfc_pairfed_adjuvant_day39_113_rep9

description: Sample name: 5398636044_J

source_name: prefrontal cortex, pairfed diet, adjuvant injected, day 39 post injection


title: pfc_pairfed_saline_day16_65_rep5

description: Sample name: 5398636044_F

source_name: prefrontal cortex, pairfed diet, saline injected, day 16 post injection


title: pfc_pairfed_saline_day16_77_rep4

description: Sample name: 5398636039_L


title: pfc_ethanol_saline_day39_88_rep6

description: Sample name: 5398636044_B

source_name: prefrontal cortex, ethanol diet, saline injected, day 39 post injection


title: prostate_cancer_primary_61

source_name: primary prostate cancer FFPE tissue sample

tag: age


title: Liver from SMRT knock out mice, replicate 3

description: SKO 119

tag: strain background

value: 129SV/B6 mixed

tag: genotype/variation


title: Liver from SMRT knock out mice, replicate 1

description: SKO 13

tag: gender

value: female


title: pfc_control_saline_day39_105_amplificationrep1

description: Sample name: 5398636044_I

source_name: prefrontal cortex, control diet, saline injected, day 39 post injection, RNA amplification replicate

tag: strain

value: amplification replicate


title: Liver from SMRT and NCoR double floxed mice (control group), replicate 1

description: DKO-C 43

value: SMRT and NCoR fl/fl

value: 7-9 weeks

value: liver


title: pfc_ethanol_adjuvant_day39_115_rep9

description: Sample name: 5398636044_E

source_name: prefrontal cortex, ethanol diet, adjuvant injected, day 39 post injection

value: Sprague Dawley


title: pfc_control_adjuvant_day16_45_rep9

description: Sample name: 5398636044_A

source_name: prefrontal cortex, control diet, adjuvant injected, day 16 post injection

value: adult


title: prostate_cancer_primary_31


title: Liver from SMRT and NCoR double knock out mice, replicate 3

description: DKO 184

value: SMRT and NCoR KO


title: pfc_ethanol_saline_day16_64_rep5

description: Sample name: 5398636044_K

source_name: prefrontal cortex, ethanol diet, saline injected, day 16 post injection

value: prefrontal cortex


title: pfc_control_adjuvant_day16_51_hybridizationrep8

description: Sample name: 5398636044_C

source_name: prefrontal cortex, control diet, adjuvant injected, day 16 post injection, array hybrization replicate

value: adjuvant injection

value: hybridization replicate


title: pfc_control_adjuvant_day39_102_rep9

description: Sample name: 5398636044_G

source_name: prefrontal cortex, control diet, adjuvant injected, day 39 post injection

value: sample


title: pfc_control_adjuvant_day16_75_rep8

description: Sample name: 5398636039_K

value: day 16


title: prostate_cancer_primary_64


title: pfc_control_adjuvant_day16_63_rep6

description: Sample name: 5398636036_J

value: control


title: pfc_ethanol_adjuvant_day39_91_rep8

description: Sample name: 5398636039_H

value: ethanol


title: B1920_50_mM.4

city: Utrecht

first: Aldert

last: Zomer

address: Yalelaan 1

department: Department of Infectious Diseases and Immunology,Faculty of Veterinary Medicine

country: Netherlands

institute: Utrecht University

description: ptxP3 strain, 50 mM sulfate

hyb_protocol: 2 µg of labeled cDNA was applied to 4x72K custom design NimbleGen arrays. Overnight hybridization at 42°C and subsequent washing of arrays was performed according to the manufacturer’s instructions (available from www.nimblegen.com).

scan_protocol: Array images were acquired with a NimbleGen MS200 scanner following their standard operation protocol, using the autogain function per subarray.

data_processing: Normalized expression data was analyzed by ArrayStar (DNASTAR, Madison, WI, USA) using the Robust Multiarray Analysis (RMA) algorithm for background correction and quantile normalization. For the identification of sulfate-modulated genes the raw expression data under low, medium, and high sulfate was normalized individually for each strain. To identify absolute differences in gene expression between the ptxP1 and ptxP3 strain, normalization was performed using the raw expression data of both strains under all sulfate conditions. Log2 transformed signals were used to generate kernel density plots using a Gaussian model with stepwise increasing bandwidth until a single local minimum was found between the distributions of background signal and gene expression. Positions where the first derivative of the density traverses from values below to values above zero were considered local minima. The corresponding expression value is the value closest to the minimum between the peaks of expressed and non-expressed genes and was therefore considered as a cutoff value to determine whether a gene was expressed or not.

organism: Bordetella pertussis B1920

source_name: ptxP3 strain, 50 mM sulfate

label_protocol: Total RNA (5 µg) was labeled according to standard Nimblegen gene expression array protocols.

growth_protocol: Cultures were grown at 37°C in chemically defined THIJS medium supplemented with 0.2 mg/ml Heptakis-cyclodextrin with different sulfate concentrations until a mid-log OD620 of 0.5 to 0.6 at which point the bacteria were harvested for RNA isolation .

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen) and DNA was removed by DNase digestion with the DNA-free kit (Ambion).

treatment_protocol: Bacteria were treated with 2 volumes of RNAprotect bacteria reagent (Qiagen).

tag: treatment

value: 50 mM sulfate


title: pfc_control_adjuvant_day39_87_rep7

description: Sample name: 5398636038_I

value: day 39


title: pfc_pairfed_saline_day16_53_rep3

description: Sample name: 5398636038_A

value: female

value: pairfed

value: saline injection


title: pfc_ethanol_adjuvant_day16_67_rep7

description: Sample name: 5398636038_C


title: pfc_pairfed_saline_day39_95_rep5

description: Sample name: 5398636038_J

source_name: prefrontal cortex, pairfed diet, saline injected, day 39 post injection


title: pfc_pairfed_adjuvant_day16_59_rep8

description: Sample name: 5398636039_J


title: pfc_control_saline_day16_54_rep3

description: Sample name: 5398636036_K

source_name: prefrontal cortex, control diet, saline injected, day 16 post injection


title: pfc_ethanol_saline_day39_118_rep5

description: Sample name: 5398636039_F


title: pfc_control_saline_day16_48_rep4

description: Sample name: 5398636038_F


title: pfc_control_adjuvant_day16_51_hybridizationrep7

description: Sample name: 5398636039_C


title: pfc_pairfed_saline_day39_104_rep6

description: Sample name: 5398636039_D


title: pfc_ethanol_adjuvant_day39_85_rep6

description: Sample name: 5398636038_L


title: pfc_pairfed_adjuvant_day16_56_rep7

description: Sample name: 5398636038_H


title: pfc_ethanol_adjuvant_day39_100_rep7

description: Sample name: 5398636039_B


title: pfc_pairfed_adjuvant_day39_122_rep8

description: Sample name: 5398636039_G


title: pfc_ethanol_saline_day39_109_rep4

description: Sample name: 5398636038_D


title: pfc_control_adjuvant_day16_51_hybridizationrep6

description: Sample name: 5398636038_G


title: pfc_control_adjuvant_day16_51_hybridizationrep5

description: Sample name: 5398636036_L


title: pfc_ethanol_adjuvant_day16_43_rep6

description: Sample name: 5398636038_B


title: B1920_50_mM.3

description: ptxP3 strain, 50 mM sulfate


title: pfc_control_adjuvant_day39_99_rep8

description: Sample name: 5398636039_E


title: pfc_ethanol_adjuvant_day16_58_rep8

description: Sample name: 5398636039_I


title: pfc_pairfed_adjuvant_day39_101_rep7

description: Sample name: 5398636038_K


title: pfc_control_saline_day16_78_rep5

description: Sample name: 5398636039_A


title: pfc_control_adjuvant_day16_69_rep7

description: Sample name: 5398636038_E


title: B1920_50_mM.2

description: ptxP3 strain, 50 mM sulfate


title: B1920_50_mM.1

description: ptxP3 strain, 50 mM sulfate


title: pfc_control_adjuvant_day39_117_rep6

description: Sample name: 5398636036_I


title: B1920_5_mM.4

description: ptxP3 strain, 5 mM sulfate

source_name: ptxP3 strain, 5 mM sulfate

value: 5 mM sulfate


title: pfc_pairfed_adjuvant_day39_98_rep6

description: Sample name: 5398636036_F


title: pfc_pairfed_adjuvant_day16_83_rep6

description: Sample name: 5398636036_E

source_name: prefrontal cortex, pairfed diet, adjuvant injected, day 16 post injection


title: pfc_control_saline_day39_126_rep5

description: Sample name: 5398636036_H


title: B1920_5_mM.3

description: ptxP3 strain, 5 mM sulfate


title: pfc_ethanol_saline_day39_103_rep3

description: Sample name: 5398636036_D


title: B1920_5_mM.1

description: ptxP3 strain, 5 mM sulfate


title: pfc_pairfed_adjuvant_day39_107_rep5

description: Sample name: 5398636035_L


title: pfc_control_saline_day16_72_rep2

description: Sample name: 5398636035_F


title: pfc_control_adjuvant_day39_129_rep5

description: Sample name: 5398636035_G


title: pfc_control_adjuvant_day16_51_hybridizationrep4

description: Sample name: 5398636035_H


title: pfc_ethanol_adjuvant_day39_127_rep5

description: Sample name: 5398636036_B


title: pfc_ethanol_adjuvant_day16_55_rep5

description: Sample name: 5398636036_A

source_name: prefrontal cortex, ethanol diet, adjuvant injected, day 16 post injection


title: pfc_pairfed_saline_day16_47_rep2

description: Sample name: 5398636036_G


title: pfc_ethanol_saline_day16_70_rep4

description: Sample name: 5398636035_K


title: pfc_pairfed_saline_day39_125_rep3

description: Sample name: 5398636035_E


title: pfc_pairfed_adjuvant_day16_50_rep5

description: Sample name: 5398636035_I


title: B1920_0_mM.2

description: ptxP3 strain, 0 mM sulfate

source_name: ptxP3 strain, 0 mM sulfate

value: 0 mM sulfate


title: B1920_5_mM.2

description: ptxP3 strain, 5 mM sulfate


title: B1920_0_mM.4

description: ptxP3 strain, 0 mM sulfate


title: B1920_0_mM.1

description: ptxP3 strain, 0 mM sulfate


title: pfc_ethanol_adjuvant_day16_82_rep4

description: Sample name: 5398636035_D

value: Sprague Dawley


title: pfc_pairfed_adjuvant_day39_86_rep4

description: Sample name: 5398636035_B

source_name: prefrontal cortex, pairfed diet, adjuvant injected, day 39 post injection

value: adult


title: B1920_0_mM.3

description: ptxP3 strain, 0 mM sulfate


title: pfc_ethanol_adjuvant_day39_112_rep4

description: Sample name: 5398636035_J


title: B1917_50_mM.4

description: ptxP1 strain, 50 mM sulfate

organism: Bordetella pertussis B1917

source_name: ptxP1 strain, 50 mM sulfate


title: pfc_pairfed_saline_day39_89_rep4

description: Sample name: 5398636036_C


title: pfc_control_adjuvant_day16_60_rep5

description: Sample name: 5398636035_A


title: pfc_control_saline_day39_96_rep4

description: Sample name: 5398636035_C

source_name: prefrontal cortex, control diet, saline injected, day 39 post injection


title: pfc_ethanol_adjuvant_day16_79_rep3

description: Sample name: 5398636034_K


title: B1917_50_mM.3

description: ptxP1 strain, 50 mM sulfate


title: pfc_pairfed_adjuvant_day16_44_rep4

description: Sample name: 5398636034_J


title: B1917_50_mM.2

description: ptxP1 strain, 50 mM sulfate


title: pfc_control_adjuvant_day16_81_rep4

description: Sample name: 5398636034_H


title: B1917_5_mM.4

description: ptxP1 strain, 5 mM sulfate

source_name: ptxP1 strain, 5 mM sulfate


title: B1917_50_mM.1

description: ptxP1 strain, 50 mM sulfate


title: pfc_pairfed_saline_day39_119_rep2

description: Sample name: 5398636034_I


title: pfc_control_saline_day39_90_rep3

description: Sample name: 5398636034_G


title: pfc_pairfed_adjuvant_day16_80_rep3

description: Sample name: 5398636034_C


title: pfc_control_saline_day16_66_rep1

description: Sample name: 5398636034_B


title: pfc_ethanol_adjuvant_day39_106_rep3

description: Sample name: 5398636034_F


title: pfc_control_adjuvant_day39_93_rep3

description: Sample name: 5398636033_L


title: pfc_control_adjuvant_day39_114_rep2

description: Sample name: 5398636033_J


title: pfc_pairfed_saline_day39_110_rep1

description: Sample name: 5398636033_F


title: B1917_0_mM.4

description: ptxP1 strain, 0 mM sulfate

source_name: ptxP1 strain, 0 mM sulfate


title: B1917_5_mM.2

description: ptxP1 strain, 5 mM sulfate


title: B1917_5_mM.3

description: ptxP1 strain, 5 mM sulfate


title: pfc_ethanol_saline_day16_52_rep3

description: Sample name: 5398636034_E


title: pfc_ethanol_saline_day16_46_rep2

description: Sample name: 5398636033_B


title: B1917_5_mM.1

description: ptxP1 strain, 5 mM sulfate


title: B1917_0_mM.3

description: ptxP1 strain, 0 mM sulfate


title: B1917_0_mM.2

description: ptxP1 strain, 0 mM sulfate


title: pfc_pairfed_adjuvant_day39_128_rep2

description: Sample name: 5398636033_G


title: pfc_control_adjuvant_day39_123_rep4

description: Sample name: 5398636034_D


title: pfc_ethanol_adjuvant_day16_73_rep2

description: Sample name: 5398636033_I


title: pfc_pairfed_adjuvant_day39_92_rep3

description: Sample name: 5398636034_A


title: B1917_0_mM.1

description: ptxP1 strain, 0 mM sulfate


title: pfc_ethanol_saline_day39_124_rep2

description: Sample name: 5398636033_K

source_name: prefrontal cortex, ethanol diet, saline injected, day 39 post injection


title: pfc_control_saline_day39_120_rep2

description: Sample name: 5398636033_H


title: pfc_control_adjuvant_day16_51_hybridizationrep2

description: Sample name: 5398636033_D


title: pfc_control_adjuvant_day16_57_rep3

description: Sample name: 5398636033_C

source_name: prefrontal cortex, control diet, adjuvant injected, day 16 post injection


title: pfc_ethanol_adjuvant_day39_97_rep2

description: Sample name: 5398636033_A

source_name: prefrontal cortex, ethanol diet, adjuvant injected, day 39 post injection


title: pfc_control_adjuvant_day39_108_rep1

description: Sample name: 5398636011_H


title: pfc_control_adjuvant_day16_84_rep2

description: Sample name: 5398636011_L


title: pfc_pairfed_saline_day16_71_rep1

description: Sample name: 5398636011_I

source_name: prefrontal cortex, pairfed diet, saline injected, day 16 post injection


title: pfc_ethanol_saline_day39_94_rep1

description: Sample name: 5398636011_D


title: hipp_ethanol_saline_day39_94_rep5

description: Sample name: 5430261014_L

source_name: hippocampus, ethanol diet, saline injected, day 39 post injection

value: hippocampus


title: pfc_control_adjuvant_day16_51_hybridizationrep1

description: Sample name: 5398636011_E

source_name: prefrontal cortex, control diet, adjuvant injected, day 16 post injection, array hybrization replicate

value: prefrontal cortex


title: pfc_ethanol_adjuvant_day16_49_rep1

description: Sample name: 5398636011_J

value: adjuvant injection


title: pfc_control_saline_day39_111_rep1

description: Sample name: 5398636011_G


title: pfc_ethanol_saline_day16_76_rep1

description: Sample name: 5398636011_F

source_name: prefrontal cortex, ethanol diet, saline injected, day 16 post injection


title: hipp_control_saline_day39_126_rep6

description: Sample name: 5430261014_I

source_name: hippocampus, control diet, saline injected, day 39 post injection


title: pfc_control_adjuvant_day16_51_rep1

description: Sample name: 5398636011_C


title: hipp_control_saline_day16_54_rep3

description: Sample name: 5430261014_F

source_name: hippocampus, control diet, saline injected, day 16 post injection


title: hipp_control_adjuvant_day39_87_hybridizationrep3

description: Sample name: 5430261014_D

source_name: hippocampus, control diet, adjuvant injected, day 39 post injection, array hybrization replicate

value: hybridization replicate


title: hipp_control_adjuvant_day16_45_rep8

description: Sample name: 5430261014_J

source_name: hippocampus, control diet, adjuvant injected, day 16 post injection

value: sample


title: hipp_ethanol_adjuvant_day16_61_rep3

description: Sample name: 5430261013_L

source_name: hippocampus, ethanol diet, adjuvant injected, day 16 post injection

value: day 16


title: pfc_pairfed_adjuvant_day39_116_rep1

description: Sample name: 5398636011_A

source_name: prefrontal cortex, pairfed diet, adjuvant injected, day 39 post injection


title: hipp_ethanol_saline_day16_76_rep2

description: Sample name: 5430261014_K

source_name: hippocampus, ethanol diet, saline injected, day 16 post injection


title: hipp_pairfed_adjuvant_day39_92_rep6

description: Sample name: 5430261014_H

source_name: hippocampus, pairfed diet, adjuvant injected, day 39 post injection


title: hipp_ethanol_adjuvant_day16_49_rep4

description: Sample name: 5430261014_B


title: hipp_ethanol_adjuvant_day39_121_rep3

description: Sample name: 5430261014_C

source_name: hippocampus, ethanol diet, adjuvant injected, day 39 post injection


title: pfc_ethanol_adjuvant_day39_121_rep1

description: Sample name: 5398636011_B


title: hipp_pairfed_adjuvant_day39_128_rep5

description: Sample name: 5430261013_J


title: hipp_pairfed_saline_day16_77_rep3

description: Sample name: 5430261014_G

source_name: hippocampus, pairfed diet, saline injected, day 16 post injection


title: hipp_pairfed_adjuvant_day16_68_rep7

description: Sample name: 5430261014_E

source_name: hippocampus, pairfed diet, adjuvant injected, day 16 post injection


title: hipp_ethanol_saline_day16_64_rep1

description: Sample name: 5430261013_I


title: hipp_pairfed_saline_day16_53_rep2

description: Sample name: 5430261013_K


title: hipp_pairfed_saline_day39_104_rep6

description: Sample name: 5430261014_A

source_name: hippocampus, pairfed diet, saline injected, day 39 post injection


title: hipp_control_saline_day39_96_rep5

description: Sample name: 5430261013_H

value: control


title: pfc_pairfed_adjuvant_day16_74_rep2

description: Sample name: 5398636033_E

source_name: prefrontal cortex, pairfed diet, adjuvant injected, day 16 post injection


title: hipp_pairfed_saline_day39_95_rep5

description: Sample name: 5430261013_A


title: hipp_pairfed_adjuvant_day16_62_rep6

description: Sample name: 5430261013_E


title: hipp_ethanol_adjuvant_day39_100_hybridizationrep6

description: Sample name: 5430261013_D

source_name: hippocampus, ethanol diet, adjuvant injected, day 39 post injection, array hybrization replicate

value: ethanol


title: hipp_ethanol_adjuvant_day39_100_hybridizationrep5

description: Sample name: 5398636055_I


title: hipp_control_adjuvant_day39_123_rep2

description: Sample name: 5430261013_C

source_name: hippocampus, control diet, adjuvant injected, day 39 post injection


title: hipp_control_saline_day16_72_rep2

description: Sample name: 5430261013_B


title: hipp_pairfed_saline_day16_47_hybridizationrep12

description: Sample name: 5398636055_L

source_name: hippocampus, pairfed diet, adjuvant injected, day 16 post injection, array hybrization replicate


title: hipp_control_adjuvant_day16_75_rep7

description: Sample name: 5430261013_F


title: hipp_control_adjuvant_day16_69_rep6

description: Sample name: 5398636055_J


title: hipp_control_adjuvant_day39_93_rep1

description: Sample name: 5398636055_F


title: CTC006

city: Milan

first: Maurizio

last: Callari

address: Via Amadeo, 42

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

description: CTCs  isolated from patient with advanced breast cancer

hyb_protocol: cRNA were hybridazed onto Illumina HumanHT-12 WG-DASL V4.0 R2 expression beadchip according to the standard Illumina protocol.

scan_protocol: Illumina BeadArray Reader was used for scanning the arrays and Illumina BeadScan was used for image acquisition and recovery of primary data.

data_processing:
Raw data were generated using the Illumina BeadStudio 3.8 software and analyzed with R/Bioconductor. For each gene, only the probe with higher interquartile range was selected.
According with the characteristics of the study, data normalization was not applicable

source_name: breast cancer

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

extract_protocol: Total RNA extraction was performed according to the manufacturer’s instructions and RNA was eluted in 5 or 10 ul of RNase-free water (Ambion), depending on the experimental setting.

tag: experiment

value: clinical sample

tag: cell number 5ml

tag: er status

value: pos

tag: pr status

tag: her2 status

value: neg

value: circulating tumor cells


title: CTC007


title: CTC004


title: CTC005


title: hipp_pairfed_adjuvant_day39_116_rep4

description: Sample name: 5398636055_K

value: female

tag: developmental stage

tag: prenatal diet

value: pairfed

value: day 39


title: pfc_pairfed_adjuvant_day16_68_rep1

description: Sample name: 5398636011_K

value: Sprague Dawley

tag: adult treatment

tag: termination time point (post injection)


title: hipp_ethanol_adjuvant_day39_91_rep9

description: Sample name: 5398636055_G

value: adult

tag: animal id

tag: sample type


title: hipp_ethanol_adjuvant_day16_58_rep2

description: Sample name: 5398636055_C

tag: tissue

value: hippocampus


title: CTC003


title: CTC002


title: hipp_ethanol_saline_day39_118_rep3

description: Sample name: 5398636055_D

source_name: hippocampus, ethanol diet, saline injected, day 39 post injection

value: saline injection


title: CTC001


title: hipp_control_saline_day39_90_rep4

description: Sample name: 5398636055_H

source_name: hippocampus, control diet, saline injected, day 39 post injection


title: hipp_pairfed_saline_day39_89_rep4

description: Sample name: 5398636055_E


title: hipp_control_saline_day16_66_rep1

description: Sample name: 5398636055_A

source_name: hippocampus, control diet, saline injected, day 16 post injection


title: hipp_pairfed_adjuvant_day16_59_rep5

description: Sample name: 5398636055_B

value: adjuvant injection


title: pfc_control_adjuvant_day16_51_hybridizationrep3

description: Sample name: 5398636034_L

source_name: prefrontal cortex, control diet, adjuvant injected, day 16 post injection, array hybrization replicate

value: prefrontal cortex

value: hybridization replicate


title: 50_spiked_MCF7_d2_c

description: healthy donor2 blood spiked with 50 MCF7 cells

value: spiked cells

tag: cell line

tag: donor

tag: replicate

value: c

value: blood


title: hipp_control_saline_day39_120_rep3

description: Sample name: 5398636052_L

tag: gender

tag: strain

value: control

value: sample


title: hipp_control_adjuvant_day16_63_rep5

description: Sample name: 5398636052_H

source_name: hippocampus, control diet, adjuvant injected, day 16 post injection

value: day 16


title: 10_spiked_MDA-MB-468_d1_c

description: healthy donor1 blood spiked with 10 MDA-MB-468 cells

tag: experiment


title: Control_blood_d1_AW_Yes_b3

description: healthy donor1 blood treated with AdnaWash

tag: cell number 5ml


title: hipp_pairfed_adjuvant_day39_113_rep3

description: Sample name: 5398636052_K


title: 5_spiked_MDA-MB-468_d1_c

description: healthy donor1 blood spiked with 5 MDA-MB-468 cells


title: 25_spiked_MDA-MB-468_d1_c

description: healthy donor1 blood spiked with 25 MDA-MB-468 cells


title: hipp_ethanol_adjuvant_day16_43_rep1

description: Sample name: 5398636052_G

source_name: hippocampus, ethanol diet, adjuvant injected, day 16 post injection

value: ethanol


title: hipp_control_adjuvant_day39_87_hybridizationrep2

description: Sample name: 5398636052_E

source_name: hippocampus, control diet, adjuvant injected, day 39 post injection, array hybrization replicate

value: female


title: 100_RNA_MDA-MB-468_c

description: 100 ng of RNA deriving from MDA-MB-468 cells

value: RNA

tag: rna quantity (ng)


title: hipp_pairfed_adjuvant_day39_107_hybridizationrep9

description: Sample name: 5398636052_D

source_name: hippocampus, pairfed diet, adjuvant injected, day 39 post injection, array hybrization replicate

value: pairfed

value: day 39


title: hipp_control_saline_day39_111_rep2

description: Sample name: 5398636051_L

value: Sprague Dawley

value: adult


title: hipp_control_adjuvant_day39_87_hybridizationrep1

description: Sample name: 5398636051_K

value: hippocampus


title: hipp_pairfed_saline_day39_125_rep3

description: Sample name: 5398636052_A

value: saline injection


title: hipp_ethanol_saline_day39_103_rep1

description: Sample name: 5398636051_H


title: 50_spiked_MDA-MB-468_d1_c

description: healthy donor1 blood spiked with 50 MDA-MB-468 cells


title: hipp_pairfed_saline_day39_119_rep2

description: Sample name: 5398636051_I


title: hipp_ethanol_saline_day39_109_rep2

description: Sample name: 5398636052_J


title: hipp_control_adjuvant_day39_114_rep8

description: Sample name: 5398636052_I

value: adjuvant injection


title: 100_RNA_MCF7_c

description: 100 ng of RNA deriving from MCF7 cells


title: hipp_pairfed_adjuvant_day16_56_rep4

description: Sample name: 5398636052_F


title: hipp_ethanol_adjuvant_day16_67_rep9

description: Sample name: 5398636052_C


title: hipp_control_adjuvant_day16_60_rep4

description: Sample name: 5398636051_J


title: hipp_ethanol_adjuvant_day39_85_rep8

description: Sample name: 5398636052_B

source_name: hippocampus, ethanol diet, adjuvant injected, day 39 post injection


title: hipp_pairfed_adjuvant_day39_101_rep2

description: Sample name: 5398636051_G

source_name: hippocampus, pairfed diet, adjuvant injected, day 39 post injection


title: 5_spiked_MCF7_d1_c

description: healthy donor1 blood spiked with 5 MCF7 cells


title: 10_spiked_MCF7_d1_c

description: healthy donor1 blood spiked with 10 MCF7cells


title: 25_spiked_MCF7_d1_c

description: healthy donor1 blood spiked with 25 MCF7 cells


title: 50_spiked_MCF7_d2_b

value: b


title: hipp_ethanol_adjuvant_day39_100_hybridizationrep4

description: Sample name: 5398636051_E

value: hybridization replicate


title: 100_RNA_MDA-MB-468_b2


title: 50_spiked_MCF7_d1_c

description: healthy donor1 blood spiked with 50 MCF7 cells

value: spiked cells

value: c


title: hipp_control_saline_day39_105_rep1

description: Sample name: 5398636050_E

value: control


title: hipp_ethanol_adjuvant_day39_115_rep2

description: Sample name: 5398636050_K

value: sample


title: Control_blood_d1_AW_Yes_b2

value: blood with AdnaWash

value: blood


title: hipp_ethanol_adjuvant_day39_112_rep6

description: Sample name: 5398636050_D

value: female

value: ethanol


title: hipp_pairfed_saline_day16_47_rep1

description: Sample name: 5398636051_C

source_name: hippocampus, pairfed diet, saline injected, day 16 post injection

value: pairfed

value: day 16


title: hipp_pairfed_adjuvant_day39_86_rep1

description: Sample name: 5398636050_G

value: Sprague Dawley

value: day 39


title: hipp_control_adjuvant_day39_99_rep6

description: Sample name: 5398636050_I

value: adult

value: hippocampus


title: hipp_pairfed_saline_day39_110_rep1

description: Sample name: 5398636050_J

source_name: hippocampus, pairfed diet, saline injected, day 39 post injection

value: saline injection


title: 10_spiked_MDA-MB-468_d1_b

value: b