title: MSCs+SCR_3

city: Miami

first: Lina

last: Shehadeh

state: FL

department: Medicine

institute: University of Miami

description: Gene Expression Data from MSCs expressing a Scrambled oligo.

hyb_protocol: cRNA probes were then purified, fragmented, and hybridized on Mouse Gene 1.0 ST expression arrays.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing:
The data was analyzed using GeneSpring software. Normalization: Quantile; Baseline Transformation: Median of all samples; Filtering: Percentile between 20 and 100.
Background noise, housekeeping gene expression and 3'/5' ratio values of all chips were within quality control limits set by Affymetrix. Expression ratios were calculated as the power-2 exponential of the log2 differences. The acceptance criteria for gene array expression changes was a minimum 2-fold change in log2 (equivalent to 4 fold) and a one-way Analysis of Variance (ANOVA) t-test p-value of <0.05.

source_name: bone marrow-derived MSCs, scrambled oligo

label_protocol: Total RNA was reverse transcribed using a T7-Oligo (dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated-DNA polymerase I-second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template for in vitro transcription in the presence of T7RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix, producing biotin-labeled complementary RNA (cRNA).

extract_protocol: SMCs and MSCs were lysed using Cell Disruption Buffer (Mirvana Paris Kit) and total RNA was extracted using Mirvana Paris Kit to yield a 260-280 nm absorbance ratio of 2.0. RNA concentration and integrity were determined by using an Agilent Bioanalyzer. A 1 µg aliquot of total RNA from each of three samples was processed using instructions and reagents supplied by the manufacturer (Affymetrix, Santa Clara, CA).

tag: strain/background

value: bone marrow-derived mesenchymal stem cells (MSCs)

value: scrambled oligo


title: backcross mouse ID  23506

status: Public on Jan 30 2015

type: RNA

city: San Francisco

first: William

middle: A.

last: Weiss

state: CA

address: 1450 3rd Street, HD-220

department: Neurology

country: USA

institute: University of California, San Francisco

description: pooled pair of SCG from single backcross mouse

hyb_protocol: 200 ul of hybridization cocktail were injected into microarrays and hybridized at 45°C for 16 hr at 60 rpm.  Arrays were washed with fluidics station protocol: FS450_0001

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing:
Expression was based on RMA values assessed using the Bioconductor XPS package in R on only core probes
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: (129xFVBN) F1 x129 backcross mouse

label_protocol: Labeling was performed according to the Affymetrix (Santa Clara, CA) GeneChip Whole Transcript (WT) Sense Target Labeling Assay manual using kit 900652.

growth_protocol: Superior Cervical Ganglia were dissected from backcrossed mice at time of tumor harvest or 1 year of age

extract_protocol: Total RNA was extracted and purified using the Rneasy mini kit

tag: Sex

tag: tumor

tag: age (days)


title: MSCs+AntimiR-30e_2

middle: A

description: Gene Expression Data from MSCs expressing Anti-miR-30e oligo.

source_name: bone marrow-derived MSCs, anti-miR-30e oligo

tag: cell type

tag: treatment

value: anti-miR-30e oligo


title: backcross mouse ID  23498


title: backcross mouse ID  23447


title: backcross mouse ID  23448


title: backcross mouse ID  23784


title: MSCs+AntimiR-30e_3


title: hTERT/E6/E7-MSCV Replicate 2

city: Braga

first: Bruno

middle: M.

last: Costa

address: Universidade do Minho, Campus de Gualtar

department: Life and Health Sciences Research Institute (ICVS)

country: Portugal

institute: University of Minho

description: Gene expression in hTERT/E6/E7-Control cells.

hyb_protocol: 1.65 µg cyanine 3-labeled and linearly amplified cRNA was fragmented for 30 minutes at 60ºC using the One-Color Microarray-Based Gene Expression Analysis Kit (Quick Amp Labeling; Agilent) according to manufacturer’s instructions for 44K microarrays. Fragmentation was stopped by addition of 2X Hybridization Buffer, and hybridized to an Agilent Microarray Hybridization Chamber Kit (G2534A) for 17 hours at 65ºC in a hybridization oven. Microarrays were then washed with Agilent wash buffers according to manufacturer’s instructions.

scan_protocol: Slides were scanned on the Agilent Technologies Scanner G2505B using one color settings for 44K slides. Dye channel was set to Green, and Green PMT at 100% for replicates 1, 3 and 4, and 40% for replicate 2.

data_processing: Data is processed using the limma package from Bioconductor: background correction (using the normexp method) is performed, normalisation between arrays is performed using quantile normalisation and the resulting data is transformed using log2. Probes representing control spots are filtered, keeping only the ones with status equal to “Gene”. Replicated probes (same ProbeName) are averaged.

organism: Homo sapiens

source_name: hTERT/E6/E7, immortalized human astrocytes; Control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1000ng of total RNA using the One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling; Agilent) according to the manufacturer’s protocol. cRNA quantification and dye incorporation were checked using a NanoDrop ND-1000 Spectrophotometer and calculated according to the manufacturer’s instructions.

growth_protocol: Cell lines were grown in DMEM supplemented with 10% FBS and 1% Penicillin-Streptomycin, and continuously selected with 500µg/mL G418.

extract_protocol: Total RNA extracted with RNeasy Total RNA Isolation kit (Qiagen) according to manufacturer's protocol. RNA was quantified by a NanoDrop-1000 spectrophotometer, followed by RNA quality control by RNA Bioanalyzer (Agilent) analyses.

value: hTERT/E6/E7 immortalized human astrocytes

tag: overexpression vector

value: MSCV-Control


title: MSCs+SCR_1


title: MSCs+miR-30e_1

description: Gene expression data from MSCs stably expressing miR-30e lentivirus.

source_name: bone marrow-derived MSCs, miR-30e

value: miR-30e lentivirus


title: backcross mouse ID  23445


title: MSCs+miR-30e_2


title: MSCs+ct-miR_3

description: Gene expression data from MSCs stably expressing control lentivirus.

source_name: bone marrow-derived MSCs, control

value: control lentivirus


title: MSCs+ct-miR_2


title: MSCs+ct-miR_1


title: backcross mouse ID  23442


title: MSCs+AntimiR-30e_1


title: MSCs+SCR_2


title: MSCs+miR-30e_3


title: backcross mouse ID  23287


title: SMCs+miR-30e_2

description: Gene expression data from SMCs stably expressing miR-30e lentivirus.

source_name: aortic SMCs, miR-30e

value: aortic smooth muscle cells (SMCs)


title: SMCs+miR-30e_1


title: SMCs+miR-30e_3


title: backcross mouse ID  23274


title: backcross mouse ID  23056


title: backcross mouse ID  23054


title: backcross mouse ID  23062


title: backcross mouse ID  22956


title: backcross mouse ID  23283


title: SMCs+ct-miR_2

description: Gene expression data from SMCs stably expressing control lentivirus.

source_name: aortic SMCs, control


title: backcross mouse ID  22510


title: backcross mouse ID  22027


title: backcross mouse ID  22969


title: backcross mouse ID  22967


title: backcross mouse ID  21540


title: backcross mouse ID  21516


title: backcross mouse ID  21395


title: backcross mouse ID  21387


title: backcross mouse ID  21384


title: backcross mouse ID  21226


title: SMCs+ct-miR_1


title: Sorted M-BMM biological rep2

city: Seoul

first: Yi Rang

address: 101, daehak-ro Jongro-gu

department: Microbiology and Immunology

country: South Korea

institute: Seoul National University College of Medicine

description: Gene expression data from M-CSF grown bone marrow derived CD11b+F4/80+ macrophage

hyb_protocol: Fragmented end-labeled cDNA was  hybridized to the GeneChip® Mouse Gene 1.0 ST arrays for 16 hours at 45 “C and 60 rpm as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

scan_protocol: After hybridization, the chips were stained and washed in a Genechip Fluidics Station 450(Affymetrix) and scanned by using a Genechip Array scanner 3000 7G (Affymetrix).

data_processing: Expression data were generated by Affymetrix Expression Console software version1.1. For the normalization, RMA (Robust Multi-Average) algorithm implemented in Affymetrix Expression Console software was used.

source_name: Differentiated bone marrow cells

label_protocol: 300 ng of total RNA from each sample was converted to double-strand cDNA Using a random hexamer incorporating a T7 promoter, amplified RNA( cRNA) was generated from the double-stranded cDNA template though an IVT( in-vitro transcription) reaction and purified with the Affymetrix sample cleanup module. cDNA was regenerated through a random-primed reverse transcription using a dNTP mix containing dUTP. The cDNA was then fragmented by UDG and APE 1 restriction endonucleases and end-labeled by terminal transferase reaction incorporating a biotinylated dideoxynucleotide.

growth_protocol: Bone marrow cells were differentiated for 7 days in the 10% FBS, penicillin/streptomycin, L-glutamine supplemented RPMI media at 37℃, 5% CO2 maintined incubator.

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

treatment_protocol: For GM-BMDC and GM-BMM, 25 ng/ml of GM-CSF was supplemented for whole differentiation period. For M-BMM, 20% L cell conditioned medium was added as a M-CSF supplier.

tag: gender

value: male

tag: age

tag: strain

value: macrophage

value: M-CSF


title: SMCs+ct-miR_3


title: backcross mouse ID  21534


title: backcross mouse ID  20568


title: backcross mouse ID  20457


title: backcross mouse ID  22960


title: backcross mouse ID  20965


title: backcross mouse ID  20969


title: backcross mouse ID  20574


title: backcross mouse ID  20577


title: backcross mouse ID  22038


title: backcross mouse ID  20576


title: Sorted GM-BMM, biological rep2

description: Gene expression data from GM-CSF grown bone marrow derived MHCIIlowF4/80high macrophage

value: GM-CSF


title: Sorted GM-BMDC, biological rep2

description: Gene expression data from GM-CSF grown bone marrow derived MHCIIhighF4/80low dendritic cells

value: dendritic cell


title: backcross mouse ID  20572


title: Sorted GM-BMDC, biological rep1


title: backcross mouse ID  20578


title: Sorted M-BMM, biological rep1


title: backcross mouse ID  20570


title: Sorted GM-BMM, biological rep1


title: backcross mouse ID  20455


title: nyvaccdb8rb19r_6h Donor 5 [5826629001_K]

city: Cleveland

first: Peter

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

description: S134; 5826629001_K

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol.

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the quantified output data was conducted using the limma from the R statistical language and various software packages from Bioconductor.  Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

label: Biotin

source_name: nyvaccdb8rb19r_6h_sorted cells

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

growth_protocol: Human primary monocytes were infected for 1h with the NYVAC-C, NYVAC-C- B19R, or NYVAC-C- B8RB19R vectors at a multiplicity of infection (MOI) of 1 or 5 PFU/cell. Cell culture medium was removed, and incubation was continued to the chosen time point 6h.

extract_protocol: Cells were washed twice with cold PBS and lysed with 100 µl of cold RLT buffer (QIAGEN, Germany) supplemented with 1% beta-mercaptoethanol (BM) (Sigma, St. Louis, MO USA), and transferred to 1.7 ml tubes with 250 µl of cold RLT/BM buffer and quickly stored at -80oC. The samples underwent nucleic acid isolation in a designated Pre-PCR room using Qiagen’s RNeasy Micro Kit and underwent DNase I treatment.  Total RNA concentrations were quantified using a NanoDrop 2000c spectrophotometer and quality was assessed using BioRad’s Experion automated electrophoresis system.  With each batch of samples a 500 ng HeLa RNA control and two water non-template negative controls were included.

treatment_protocol: Peripheral blood mononuclear cells from healthy donors (recruited by the Blood Center, Lausanne, Switzerland) were obtained by use of a Ficoll-Hypaque density gradient (GE Healthcare, Glattbrugg, Switzerland). Human primary monocytes (purity,  97%) were isolated using anti-CD14 beads (Miltenyi Biotech, Bergisch Gladbach, Germany)

tag: donor id

value: donor 5

value: primary human monocytes

tag: sample group

value: infected

tag: infected with

value: nyvaccd8rb19r for 1hr

tag: timepoint


title: nyvaccdb8rb19r_6h Donor 2 [5727946084_K]

description: S52; 5727946084_K

value: donor 2


title: nyvaccdb8rb19r_6h Donor 3 [5826629022_C]

description: S80; 5826629022_C

value: donor 3


title: nyvaccdb19r_6h Donor 3 [5727946083_L]

description: S77; 5727946083_L

source_name: nyvaccdb19r_6h_sorted cells

value: nyvaccdb19r for 1hr


title: nyvaccdb8rb19r_6h Donor 1 [5727946084_I]

description: S25; 5727946084_I

value: donor 1


title: backcross mouse ID  20447


title: nyvaccdb8rb19r_6h Donor 4 [5727946084_F]

description: S106; 5727946084_F

value: donor 4


title: backcross mouse ID  20445


title: backcross mouse ID  20446


title: nyvaccdb19r_6h Donor 5 [5826629025_D]

description: S131; 5826629025_D


title: backcross mouse ID  20442


title: backcross mouse ID  20375


title: nyvaccdb19r_6h Donor 4 [5826629001_C]

description: S105; 5826629001_C


title: nyvaccdb19r_6h Donor 2 [5727946083_I]

description: S51; 5727946083_I


title: backcross mouse ID  20317


title: nyvaccdb19r_6h Donor 1 [5727946084_B]

description: S23; 5727946084_B


title: backcross mouse ID  20448


title: nyvacc_6h Donor 5 [5826629029_C]

description: S129; 5826629029_C

source_name: nyvacc_6h_sorted cells

value: nyvacc for 1hr


title: backcross mouse ID  20260


title: nyvacc_6h Donor 4 [5826629022_H]

description: S100; 5826629022_H


title: nyvacc_6h Donor 2 [5826629022_I]

description: S48; 5826629022_I


title: nyvacc_6h Donor 1 [5727946083_E]

description: S21; 5727946083_E


title: backcross mouse ID  20257


title: MGH131-1

city: Boston

first: Kenneth

middle: N

last: Ross

state: MA

address: 450 Brookline Ave., Rm M640

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: Patient derived cell line (PDCL) from patient MGH131 from biopsy 1 of EGFR mutant NSCLC that had transformed to SCLC

hyb_protocol: Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133plus arrays at 45°C for 16 hours.

scan_protocol: Scans were performed on Affymetrix scanners.

data_processing: Raw expression values were normalized using Robust Multiarray Averaging (RMA) in R version 2.15.1 using Bioconductor's affy library version 1.36.1.

source_name: Patient derived cell line (PDCL) model of EGFR mutant non-small cell lung cancer (NSCLC)

label_protocol: First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.

growth_protocol: MGH119, MGH119-R, MGH121, MGH134, MGH141, and MGH157 cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS).  MGH125, MGH126, MGH131-1, MGH131-2 cells were cultured in ACL4 supplemented with 10% FBS.

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (QIAGEN, Valencia, CA) and cDNA was generated using QuantiTect Reverse Transcription Kit (QIAGEN) with 1ug total RNA according to manufacturer instructions.

tag: patient id

tag: egfr mutation

value: Exon 19 del

tag: tki status

value: Resistant

tag: resistance mechanism

value: NSCLC -> SCLC


title: control Donor 4 [5826629089_F]

description: S82; 5826629089_F

source_name: control_sorted cells

value: control

value: none (control)


title: nyvacc_6h Donor 3 [5727946083_C]

description: S75; 5727946083_C


title: MGH157

description: Patient derived cell line (PDCL) from patient MGH157 from biopsy of EGFR mutant NSCLC


title: control Donor 5 [5826629031_C]

description: S111; 5826629031_C


title: MGH131-2

description: Patient derived cell line (PDCL) from patient MGH131 from biopsy 2 of EGFR mutant NSCLC that had transformed to SCLC


title: MGH134

description: Patient derived cell line (PDCL) from patient MGH134 from biopsy of EGFR mutant NSCLC


title: backcross mouse ID  20256

tag: Sex


title: MGH141

description: Patient derived cell line (PDCL) from patient MGH141 from irradiated fibroblasts from normal patient tissue


title: control Donor 3 [5826629022_E]

description: S57; 5826629022_E


title: backcross mouse ID  20255

tag: tumor


title: MGH125

description: Patient derived cell line (PDCL) from patient MGH125 from biopsy of EGFR mutant NSCLC


title: control Donor 2 [5826629001_J]

description: S28; 5826629001_J


title: backcross mouse ID  20253

tag: age (days)


title: backcross mouse ID  19824


title: backcross mouse ID  20033


title: MGH126

description: Patient derived cell line (PDCL) from patient MGH126 from biopsy of EGFR mutant NSCLC

value: EMT


title: MGH121

description: Patient derived cell line (PDCL) from patient MGH121 from biopsy of EGFR mutant NSCLC


title: backcross mouse ID  19726

description: pooled pair of SCG from single backcross mouse


title: backcross mouse ID  19790


title: backcross mouse ID  19719


title: backcross mouse ID  19734


title: control Donor 1 [5727946083_B]

description: S02; 5727946083_B

tag: cell type


title: backcross mouse ID  19721


title: MGH119-R

description: Patient derived cell line (PDCL) from patient MGH119 from biopsy of EGFR mutant NSCLC (gefitinib resistant sample from invitro treatment)


title: backcross mouse ID  19716


title: hSKP-HPC control condition, biological rep3

city: Brussels

first: Robim

middle: M

last: Rodrigues

address: Laarbeeklaan 103

department: IVTD

country: Belgium

institute: Vrije Universiteit Brussel

description: hSKP-HPC CTL 3

hyb_protocol: 12.5 μg fragmented aRNA was hybridized to Affymetrix Human Genome U133 plus 2.0 arrays along with a hybridization cocktail solution and then placed in a Genechip Hybridization Oven-645 (Affymetrix) rotating at 60 rpm at 45 ºC for 16 h. After incubation, arrays were washed on a Genechip Fluidics Station-450 (Affymetrix) and stained with the Affymetrix HWS kit as indicated by the manufacturer’s protocols.

scan_protocol: The chips were scanned with an Affymetrix Gene-Chip Scanner-3000-7G and the quality control matrices were confirmed with the Affymetrix GCOS software following the manufacturer’s guidelines.

data_processing: Background correction, summarization (median polish) and normalization (quantile) were done with Robust Multi-array Analysis using RMAExpress v1.0.5

source_name: hSKP-HPC at 24h without exposure to Na-VPA

label_protocol: Total RNA (100 ng) was used for amplification and in vitro transcription using the Genechip 3’ IVT Express Kit following the manufacturer’s instructions (Affymetrix). The amplified RNA was purified with magnetic beads and 15 μg Biotin-aRNA was treated with fragmentation reagent.

growth_protocol: Approximately two weeks after isolation, hSKP spheroids were broken down to single cells using Liberase DH at 37 °C. They were subsequently cultivated in hSKP growth medium supplemented with 5 % (v/v) FBS to promote adherence of the cells to the plastic. The next day, the attached hSKP were washed and further cultivated in hSKP growth medium without FBS until further use.

extract_protocol: Total mRNA was extracted using the TriPure Isolation ReagentTM (Roche Applied Science) according to the manufacturer's instructions.

treatment_protocol: hSKP-HPC were exposed for 24 h to 27.7mM Na-VPA

value: male

tag: tissue

value: foreskin

tag: source cell type

value: Human skin-derived precursor cells (hSKP)

tag: exposed to

value: none (untreated)

value: hSKP-derived hepatic progenitor cells (hSKP-HPC)


title: backcross mouse ID  19508


title: hSKP-HPC + Na-VPA, biological rep3

description: hSKP-HPC + Na-VPA 3

source_name: hSKP-HPC at 24h exposed to Na-VPA

tag: gender

value: 27.7mM sodium valproate (Na-VPA) for 24hrs


title: MGH119

description: Patient derived cell line (PDCL) from patient MGH119 from biopsy of EGFR mutant NSCLC (gefitinib treatment naïve sample)

value: Sensitive


title: hSKP-HPC + Na-VPA, biological rep2

description: hSKP-HPC + Na-VPA 2


title: hSKP-HPC + Na-VPA, biological rep1

description: hSKP-HPC + Na-VPA 1


title: backcross mouse ID  19713


title: HEY cell_ Negative Control miRNA treated_analyzed_with_mirM14_rep3

city: Atlanta

first: Neda

last: Jabbari

state: GA

address: 315 Ferst Dr

department: Biology

institute: Georgia Institute of Technology

description: HEY human ovarian carcinoma cell line was derived from a human ovarian cancer xenograft (HX-62) in immunologically deprived CBA/CJ mice originally grown from a peritoneal deposit of a patient.

hyb_protocol: Labeled mRNA was hybridized to GeneChip Human Genome U133 Plus 2.0 Arrays in the GeneChip Hybridization oven 640, further processed with the GeneChip Fluidics Station 450 and scanned with the GeneChip Scanner 3000.

scan_protocol: as per manufacturer's protocol using GeneChip Scanner 3000.

data_processing: GCRMA at www.arrayanalysis.org for signals and FDR using SAM (http://www-stat.stanford.edu/~tibs/SAM/) and MAS5 from Affymetrix Expression Console for present/absent calls. Probe_sets lacking a gene symbol annotation and x_at probes are ignored.  Normalized using log2 of GCRMA signal

source_name: HEY ovarian cancer cell, Negative Control miRNA treated, rep 3

label_protocol: mRNAs were converted to double stranded (ds)-cDNA and amplified using Applause 3’-Amp System (NuGen, San Carlos, CA). This cDNA was then biotin labeled and fragmented by using Encore Biotin Module (NuGen)

growth_protocol: HEY ovarian cancer cell lines were cultured in RPMI 1640 (Mediatech, Manassas, VA) supplemented with 10% v/v Fetal Bovine Serum (Atlanta Biologicals, Lawrenceville, GA) and 1% v/v antibiotic-antimycotic solution (10,000 I.U. Penicillin (per mL), 10,000 µg/mL Streptomycin and 25 µg/mL Amphotericin, Mediatech-Cellgro, Manassas, VA).

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

treatment_protocol: 60,000 cells were seeded per well on 24-well plates in growth medium and allowed to adhere overnight at 37  ͦC in a 5% CO2 atmosphere. Cells were then transfected with 30 nM M14 miRNA purchased as Pre-miR miRNA Precursor (Ambion, Austin, TX) using Lipofectamine 2000 (Invitrogen, Carlsbad, CA) and according to the manufacturer’s instructions. For negative control, cells were transfected with negative control miRNA (nc-miR) purchased as Pre-miR miRNA Precursor Negative Control #1(Ambion, Austin, TX). Cells were allowed to grow for 48 hours before RNA isolation.

tag: originial tumor type of initial cell

value: Papillary Cystadenocarcinoma of the ovary

tag: cell line

value: HEY


title: backcross mouse ID  19408


title: backcross mouse ID  19305


title: hSKP-HPC control condition, biological rep1

description: hSKP-HPC CTL 1


title: backcross mouse ID  19306


title: HEY cell_ Negative Control miRNA treated_analyzed_with_mirM14_rep2

source_name: HEY ovarian cancer cell, Negative Control miRNA treated, rep 2


title: HEY cell_ Negative Control miRNA treated _analyzed_with_M5_rep3

data_processing: GCRMA at www.arrayanalysis.org for signals and FDR using SAM (http://www-stat.stanford.edu/~tibs/SAM/) and MAS5 from Affymetrix Expression Console for present/absent calls. Probe_sets lacking a gene symbol annotation and x_at probes are ignored. Normalized using log2 of GCRMA signal

treatment_protocol: 60,000 cells were seeded per well on 24-well plates in growth medium and allowed to adhere overnight at 37  ͦC in a 5% CO2 atmosphere. Cells were then transfected with 30 nM M5 miRNA purchased as Pre-miR miRNA Precursor (Ambion, Austin, TX) using Lipofectamine 2000 (Invitrogen, Carlsbad, CA) and according to the manufacturer’s instructions. For negative control, cells were transfected with negative control miRNA (nc-miR) purchased as Pre-miR miRNA Precursor Negative Control #1(Ambion, Austin, TX). Cells were allowed to grow for 48 hours before RNA isolation.


title: backcross mouse ID  19300

source_name: (129xFVBN) F1 x129 backcross mouse


title: backcross mouse ID  19296


title: backcross mouse ID  19506


title: HEY cell_M14 treated_rep3

source_name: HEY ovarian cancer cell, M14 treated, rep 3


title: HEY cell_M14 treated_rep2

source_name: HEY ovarian cancer cell, M14 treated, rep 2


title: backcross mouse ID  19150


title: backcross mouse ID  19299


title: HEY cell_ Negative Control miRNA treated_analyzed_with_mirM14_rep1

source_name: HEY ovarian cancer cell, Negative Control miRNA treated, rep 1


title: backcross mouse ID  19127


title: HEY cell_ Negative Control miRNA treated_analyzed_with_M5_rep2


title: backcross mouse ID  19298


title: hSKP-HPC control condition, biological rep2

description: hSKP-HPC CTL 2


title: HEY cell_M5 treated_rep2

source_name: HEY ovarian cancer cell, M5 treated, rep 2


title: backcross mouse ID  19126


title: HEY cell_M5 treated_rep1

source_name: HEY ovarian cancer cell, M5 treated, rep 1


title: backcross mouse ID  19123


title: backcross mouse ID  19124


title: HEY cell_M14 treated_rep1

source_name: HEY ovarian cancer cell, M14 treated, rep 1


title: HEY cell_M5 treated_rep3

source_name: HEY ovarian cancer cell, M5 treated, rep 3


title: backcross mouse ID  18922


title: backcross mouse ID  19005


title: HEY cell_ Negative Control miRNA treated_analyzed_with_M5_rep1


title: backcross mouse ID  18891


title: HEY cell_Negative Control miRNA treated_2-3_rep3

description:
HEY human ovarian carcinoma cell line was derived from a human ovarian cancer xenograft (HX-62) in immunologically deprived CBA/CJ mice originally grown from a peritoneal deposit of a patient.
nc-miR-2-3.CEL was analyzed together only with miR-12 samples

data_processing:
GCRMA at www.arrayanalysis.org for signals and FDR using SAM (http://www-stat.stanford.edu/~tibs/SAM/) and MAS5 from Affymetrix Expression Console for present/absent calls. Probe_sets lacking a gene symbol annotation and x_at probes are ignored.
normalized using log2 of GCRMA signal

treatment_protocol: 60,000 cells were seeded per well on 24-well plates in growth medium and allowed to adhere overnight at 37  ͦC in a 5% CO2 atmosphere. Cells were then transfected with 30 nM M12 miRNA purchased as Pre-miR miRNA Precursor (Ambion, Austin, TX) using Lipofectamine 2000 (Invitrogen, Carlsbad, CA) and according to the manufacturer’s instructions. For negative control, cells were transfected with negative control miRNA (nc-miR) purchased as Pre-miR miRNA Precursor Negative Control #1(Ambion, Austin, TX). Cells were allowed to grow for 48 hours before RNA isolation.

tag: original tumor type of initial cell


title: backcross mouse ID  18805


title: HEY cell_Negative Control miRNA treated_2-1_rep1

description:
HEY human ovarian carcinoma cell line was derived from a human ovarian cancer xenograft (HX-62) in immunologically deprived CBA/CJ mice originally grown from a peritoneal deposit of a patient.
nc-miR-2-1.CEL was analyzed together only with miR-12 samples


title: backcross mouse ID  18607


title: backcross mouse ID  18423


title: backcross mouse ID  18424


title: HEY cell_M12 treated_rep3

source_name: HEY ovarian cancer cell, M12 treated, rep 3


title: HEY cell_Negative Control miRNA treated_2-2_rep2

description:
HEY human ovarian carcinoma cell line was derived from a human ovarian cancer xenograft (HX-62) in immunologically deprived CBA/CJ mice originally grown from a peritoneal deposit of a patient.
nc-miR-2-2.CEL was analyzed together only with miR-12 samples


title: backcross mouse ID  18529


title: backcross mouse ID  18412


title: HEY cell_Negative Control miRNA treated_analyzed_with_miR429_rep2

description:
HEY human ovarian carcinoma cell line was derived from a human ovarian cancer xenograft (HX-62) in immunologically deprived CBA/CJ mice originally grown from a peritoneal deposit of a patient.
nc-miR-1-2.cel was analyzed together only with miR-429 samples

treatment_protocol: 60,000 cells were seeded per well on 24-well plates in growth medium and allowed to adhere overnight at 37  ͦC in a 5% CO2 atmosphere. Cells were then transfected with 30 nM miR-429 miRNA purchased as Pre-miR miRNA Precursor (Ambion, Austin, TX) using Lipofectamine 2000 (Invitrogen, Carlsbad, CA) and according to the manufacturer’s instructions. For negative control, cells were transfected with negative control miRNA (nc-miR) purchased as Pre-miR miRNA Precursor Negative Control #1(Ambion, Austin, TX). Cells were allowed to grow for 48 hours before RNA isolation.


title: backcross mouse ID  18413


title: HEY cell_M12 treated_rep1

source_name: HEY ovarian cancer cell, M12 treated, rep 1


title: HEY cell_Negative Control miRNA treated_analyzed_with_miR429_rep1

description:
HEY human ovarian carcinoma cell line was derived from a human ovarian cancer xenograft (HX-62) in immunologically deprived CBA/CJ mice originally grown from a peritoneal deposit of a patient.
nc-miR-1-1.cel was analyzed together only with miR-429 samples


title: HEY cell_miR-429 treated_rep3

source_name: HEY ovarian cancer cell, miR-429 treated, rep 3


title: HEY cell_Negative Control miRNA treated_analyzed_with_miR429_rep3

description:
HEY human ovarian carcinoma cell line was derived from a human ovarian cancer xenograft (HX-62) in immunologically deprived CBA/CJ mice originally grown from a peritoneal deposit of a patient.
nc-miR-1-3.cel was analyzed together only with miR-429 samples


title: backcross mouse ID  18009


title: HEY cell_miR-429 treated_rep2

source_name: HEY ovarian cancer cell, miR-429 treated, rep 2


title: HEY cell_M12 treated_rep2

source_name: HEY ovarian cancer cell, M12 treated, rep 2


title: backcross mouse ID  17962


title: HEY cell_miR-429 treated_rep1

source_name: HEY ovarian cancer cell, miR-429 treated, rep 1


title: backcross mouse ID  17739


title: backcross mouse ID  18303


title: backcross mouse ID  17654


title: backcross mouse ID  17656


title: backcross mouse ID  17564


title: backcross mouse ID  17561


title: backcross mouse ID  17338


title: backcross mouse ID  17651


title: Nobeokabouzu-komugi 7 DAI treated_rep3

city: Yokohama

first: Alagu

last: Manickavelu

state: Kanagawa

address: Maioka 641-12

country: Japan

institute: Yokohama City University

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ml containing 25x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55μl of 2x GE Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent-015520 Custom wheat 38k array  for 17 hours at 65°C in a 10rpm rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k 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 9.5.1.1 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 015520_D_F_20061122) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Triticum aestivum

source_name: Nobeokabouzu-komugi florets_treated_7 days after inoculation

label_protocol: Total RNA was converted to cRNA labeled using Low Input Quick Amp Labeling kit (Agilent technologies) and fluorophore cy3-CTP. The samples were cleaned using RNeasy MinElute Clean up kit (Qiagen).

growth_protocol: Plants were grown in glass without any stress, the temperature and moisture inside the glass house were maintained 25 °C and 50%respectively

extract_protocol: Total RNA was extracted from the florets by using Nucleo Spin RNA plant kit (Macherey-Nagel, Germany)

treatment_protocol: At the early anthesis time, single floret inoculation with F. graminearum strain H3 was carried out by pipetting 10μl of the fungal suspension (1x10^5 macroconidia ml-1) between lemma and palea of each floret. Same time control plants (mock) were inoculated with 10 μl of distilled water. The inoculated spikes were covered with a plastic bag for 72 hours.

tag: genotype

value: Nobeokabouzu-komugi

tag: infected with

value: F. graminearum suspension

value: floret

tag: time point

value: 7 day after inoculation


title: MGH131-1_PostSCLC_Cell_Line

type: genomic

hyb_protocol: Incubation at 95 degrees for 3 minutes then a 30 minute pre-hybridization step at 37 degrees, then hybridization for 35-40 hours at 65 degrees. Slides were then washed with Agilent Oligo ArrayCGH wash buffer 1 for 5 minutes at room temperature and wash buffer 2 for 1 minute at 37°C.

scan_protocol: Slides were scanned using the Agilent G2505C Microarray Scanner

data_processing: Agilent CytoGenomics software v 2.0.

molecule: genomic DNA

source_name: MGH131-1 Resistant SCLC Cell Line

label_protocol: Briefly, 1μg of tumor and control DNA (normal female gDNA, Corriell Institute) were heated to 95°C for 5 minutes.  Random priming was used to label DNA with CY3-dUTP (control) and CY5-dUTP (tumor) dyes from the Agilent SureTag DNA Labeling Kit. The labeled DNA was then purified over columns (Agilent) and mixed in equal proportion along with Cot-1 Human DNA (Agilent) for the hybridization steps.

extract_protocol: Tumor samples - DNA was extracted from FFPE using the FormaPure kit from Agencourt, Cell lines - DNA was extracted the Dneasy kit from Qiagen

tag: patient id

value: Male

tag: diagnosis

value: SCLC

value: Patient-derived Cell Line

value: Female

value: Normal Tissue


title: Patient1_PostSCLC_Adrenal2

source_name: Patient1 Resistant SCLC Adrenal Tumor Sample 2

value: Adrenal Tumor


title: backcross mouse ID  17658

source_name: (129xFVBN) F1 x129 backcross mouse


title: Nobeokabouzu-komugi 7 DAI control_rep1

source_name: Nobeokabouzu-komugi florets_control_7 days after inoculation

value: distilled water (control)


title: Patient7_PostNSCLC_Diaphragm

source_name: Patient7 Resistant NSCLC Diaphragmatic Tumor

value: NSCLC

value: Diaphragmatic Tumor


title: Patient7_PostSCLC_Liver

source_name: Patient7 Resistant SCLC Liver Tumor

value: Liver Tumor


title: MGH125_PostNSCLC_Cell_Line

source_name: MGH125 Resistant NSCLC Cell Line


title: Nobeokabouzu-komugi 7 DAI treated_rep1


title: backcross mouse ID  17337


title: Nobeokabouzu-komugi 7 DAI control_rep3


title: Patient1_PostSCLC_Adrenal1

source_name: Patient1 Resistant SCLC Adrenal Tumor Sample1


title: Nobeokabouzu-komugi 3 DAI treated_rep3

source_name: Nobeokabouzu-komugi florets_treated_3 days after inoculation

value: 3 day after inoculation


title: Nobeokabouzu-komugi 7 DAI treated_rep2


title: Nobeokabouzu-komugi 7 DAI control_rep2


title: backcross mouse ID  17335


title: backcross mouse ID  17016


title: backcross mouse ID  17015


title: Nobeokabouzu-komugi 3 DAI control_rep2

source_name: Nobeokabouzu-komugi florets_control_3 days after inoculation


title: Nobeokabouzu-komugi 3 DAI treated_rep1


title: backcross mouse ID  16860


title: backcross mouse ID  16825


title: Nobeokabouzu-komugi 3 DAI treated_rep2


title: backcross mouse ID  16856


title: Nobeokabouzu-komugi 3 DAI control_rep3


title: Nobeokabouzu-komugi 3 DAI control_rep1


title: backcross mouse ID  16810


title: Sumai 3 7 DAI treated_rep3

source_name: Sumai 3 florets_treated_7 days after inoculation

value: Sumai 3


title: Sumai 3 7 DAI control_rep3

source_name: Sumai 3 florets_control_7 days after inoculation


title: Sumai 3 7 DAI treated_rep1


title: backcross mouse ID  16957


title: backcross mouse ID  16714


title: Sumai 3 7 DAI control_rep2


title: backcross mouse ID  16692


title: backcross mouse ID  17284


title: Sumai 3 7 DAI treated_rep2


title: Sumai 3 7 DAI control_rep1


title: backcross mouse ID  15750


title: backcross mouse ID  15444


title: Sumai 3 3 DAI treated_rep3

source_name: Sumai 3 florets_treated_3 days after inoculation


title: Sumai 3 3 DAI treated_rep1


title: backcross mouse ID  16293


title: Sumai 3 3 DAI treated_rep2


title: backcross mouse ID  16391


title: backcross mouse ID  14978


title: backcross mouse ID  14939


title: backcross mouse ID  14446


title: Sumai 3 3 DAI control_rep2

source_name: Sumai 3 florets_control_3 days after inoculation


title: Sumai 3 3 DAI control_rep3


title: backcross mouse ID  15019


title: Gamenya 7 DAI treated_rep3

source_name: Gamenya florets_treated_7 days after inoculation

value: Gamenya


title: backcross mouse ID  15929


title: Sumai 3 3 DAI control_rep1


title: Gamenya 7 DAI treated_rep1


title: Gamenya 7 DAI control_rep3

source_name: Gamenya florets_control_7 days after inoculation


title: Gamenya 7 DAI control_rep1


title: Gamenya 3 DAI treated_rep3

source_name: Gamenya florets_treated_3 days after inoculation


title: Gamenya 7 DAI control_rep2


title: Gamenya 3 DAI treated_rep2


title: Gamenya 3 DAI treated_rep1


title: Gamenya 7 DAI treated_rep2


title: Gamenya 3 DAI control_rep2

source_name: Gamenya florets_control_3 days after inoculation


title: trans3

city: Warsaw

first: Magdalena

last: Łój

address: Nowoursynowska 166

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

description: Biological replicate 3 of 3. Cells treated with trans10,cis12-CLA isomer.

hyb_protocol: According to the manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

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

source_name: MCF-7 cells treated with trans10,cis12-CLA isomer, Replicate 3

growth_protocol: Cells were cultured in medium (Sigma) with an addition of 10% FBS and other supplements , according to procedure of ATCC, under control condition in incubator (temp. 37°C, 95% air , 5% CO2).

extract_protocol: Total lipids of each sample (1g) were extracted by overnight agitation on the laboratory shaker with chloroform/methanol (2:1), containing 1 g/L of butylated hydroxytoluen (BHT). Extracted lipids were filtrated through Whatman #1 filter paper and mixed with 4 mL of 0.88% sodium chloride solution. After phase separation, the top layer was completely removed and chloroform layer was then carefully dried under N2. 10 mg of each sample when then subjected to saponification (20 min, 60OC) with 0.5 M KOH in methanol. Free fatty acids were then methylated with 14% (v/v) BF3 in methanol (15 min, 60OC). Finally, fatty acid methyl esters (FAME) were extracted with hexane. The FAME mixtures were then analyzed on a Simadzu (QP 5050A) gas chromatograph

treatment_protocol: Cells were seeded in culture plates for 24 h. After that growing medium was replaced by medium containing a) fatty acids extract from CLA-enriched egg yolks (CLA) and b) fatty acids extract from non-enriched egg yolks (KT), both at the concentration of 0.5 mg/ml and Et-OH as a solvent at final concentration 0.05%. As a negative control we used c) cell cultures only in growth medium (K) and d) cell cultures treated with only a solvent of fatty acids (Et-ethanol) at final concentration 0.05%. In all studies, at least 3 wells were examined per treatment. Experiments were repeated 3 times.

value: MCF-7 (HTB-22, ATCC)

value: mammary gland

source_name: breast; derived from metastatic site: pleural effusion

value: epithelial

value: female

tag: age

value: 69 years adult

tag: sample type

value: common reference sample compsed of a pool of equal amounts of total RNA from control cells


title: Gamenya 3 DAI control_rep3

value: floret


title: cis3

description: Biological replicate 3 of 3. Cells treated with cis9,trans11-CLA isomer.

source_name: MCF-7 cells treated with cis9,trans11-CLA isomer, Replicate 3

label_protocol: According to the manufacturer's protocol


title: trans2

description: Biological replicate 2 of 3. Cells treated with trans10,cis12-CLA isomer.

source_name: MCF-7 cells treated with trans10,cis12-CLA isomer, Replicate 2


title: trans1

description: Biological replicate 1 of 3. Cells treated with trans10,cis12-CLA isomer.

source_name: MCF-7 cells treated with trans10,cis12-CLA isomer, Replicate 1


title: KT + trans3

description: Biological replicate 3 of 3. Cells treated with fatty acids from CLA-unenriched egg yolks and trans10,cis12-CLA isomer.

source_name: MCF-7 cells treated with fatty acids from CLA-unenriched egg yolks and trans10,cis12-CLA isomer, Replicate 3


title: Helveticoside_15nM

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

institute: Korea Institute of Oriental Medicine

description: Helveticoside treatment at 15nM

hyb_protocol: The labelled RNA were hybridized to a microarray (Agilent Human whole genome 44K, Agilent Technologies) containing approximately 44,000 probes (~26,600 unique genes) in accordance with the manufacturer's instructions.

scan_protocol: Arrays were scanned with an Agilent DNA Microarray Scanner.

data_processing: Signal intensities of genes were normalized by the quantile method.

source_name: Cell Line

label_protocol: The pooled RNA was amplified and labeled using Agilent’s Low RNA Input Linear Amplification kit PLUS (Agilent Technologies, USA).

growth_protocol: A549 human lung cancer cells were grown in RPMI1640 supplemented with 10% (v/v) fetal bovine serum, 100 U/mL of penicillin, and 100 ug/mL of streptomycin in 5% CO2 humidified air at 37°C. Cell viability was determined with the EZ-Cytox cell proliferation assay kit (Daeillab Service, Seoul, Republic of Korea).

extract_protocol: Total RNA was prepared from A549 cells using the Easy-SpinTM total RNA extraction kit (iNtRON Biotechnology, Seoul, Republic of Korea) following the manufacturer’s instructions. RNA quality was determined using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Only samples with an RNA integrity number (RIN) greater than 7.0 were included in the microarray analysis. RNAs from triplicate experiments were pooled to exclude experimental bias.

treatment_protocol: After 24h, cells were treated with drugs and further incubated for 48 h. The cultured medium was removed and the cells were washed once with phosphate-buffered cell line. Color development was initiated by adding the diluted Ez-Cytox working solution into each well and monitored using a microplate reader equipped with 450 nm filter.

value: lung cancer cells


title: Helveticoside_60nM

description: Helveticoside treatment at 60nM


title: KT + trans2

description: Biological replicate 2 of 3. Cells treated with fatty acids from CLA-unenriched egg yolks and trans10,cis12-CLA isomer.

source_name: MCF-7 cells treated with fatty acids from CLA-unenriched egg yolks and trans10,cis12-CLA isomer, Replicate 2


title: KT + cis2

description: Biological replicate 2 of 3. Cells treated with fatty acids from CLA-uenriched egg yolks and cis9,trans11-CLA isomer.

source_name: MCF-7 cells treated with fatty acids from CLA-unenriched egg yolks and cis9,trans11-CLA isomer, Replicate 2


title: KT + trans1

description: Biological replicate 1 of 3. Cells treated with fatty acids from CLA-uenriched egg yolks and trans10,cis12-CLA isomer.

source_name: MCF-7 cells treated with fatty acids from CLA-unenriched egg yolks and trans10,cis12-CLA isomer, Replicate 1


title: cis1

description: Biological replicate 1 of 3. Cells treated with cis9,trans11-CLA isomer.

source_name: MCF-7 cells treated with cis9,trans11-CLA isomer, Replicate 1


title: KT + cis3

description: Biological replicate 3 of 3. Cells treated with fatty acids from CLA-unenriched egg yolks and cis9,trans11-CLA isomer.

source_name: MCF-7 cells treated with fatty acids from CLA-unenriched egg yolks and cis9,trans11-CLA isomer, Replicate 3


title: Helveticoside_3.75nM

description: Helveticoside treatment at 3.75nM


title: pap1 deletion mutant treated, biological rep2

city: Kolkata

first: Sanjay

last: Ghosh

state: West Bengal

address: Dept. of Biochemistry, 35, Ballygunge Circular Road, Kolkata-700019

department: Biochemistry

country: India

institute: University of Calcutta

description:
AV25 T2
AV25 T2_(Yeast_2).CEL

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C at 60 rpm on Yeast 2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The raw Affymetrix data files (.cel) were pre-processed using the software RMA Express (v1.0.4), In RMA express the output data file is a .txt file (tab delimited text file) which is read for analysis in Multi Experiment Viewer (MEV). In MEV, we loaded data as RMA file under Affymetrix file section; we downloaded the annotation file for yeast 2 array from Affymetrix website. The annotation file was loaded after loading the expression data file. We set the percentage cut off filter at 100 i.e. all genes having significant expression in all the samples would only be included in analysis. Next we normalized Genes/Rows i.e. this would transform values using the mean and the standard deviation of the row of the matrix to which the value belongs, using the following formula: Value = [(Value) – Mean (Row)]/[Standard deviation (Row)]. We found out the differentially expressed genes between the control and treated sets using one way ANOVA using the threshold p-value 0.01. The genes that were differentially expressed between the 972h- Treated and 972h- Control by a minimum of 2 folds were considered significant.  Hierarchical Clustering of the significantly induced and repressed genes were performed using the metric Pearson correlation co-efficient with the linkage method being Average Linkage.

organism: Schizosaccharomyces pombe

source_name: pap1 deletion mutan_treated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Affymetrix 3’ IVT Express manual).

growth_protocol: The two strains were cultured in yeast extract (YE) medium at 30°C, shaken in flasks at 140 rpm until reaching O.D.600 = 0.5 (1 x 10^7 cells/ml). Cells were harvested from the medium, re-suspended in 1x PBS to the same density and distributed from the same flask as sets of controls and treatment for both the strains.

extract_protocol: Total RNA was isolated according to the protocol provided in RNeasy Mini Handbook 04/2006 from Qiagen page 45 using RNeasy Mini Kit. The lysis was done according to mechanical lysis method provided in the handbook.

treatment_protocol: Stress treatments were done for exactly 15 minutes at 30°C in flasks shaking at 140 rpm. Stress conditions are described as follows: Nitrosative stress: Pure Nitric oxide donor compound detaNONOate (Enzo Life Sciences) was dissolved in 0.01N NaOH solution to a stock solution of 100 mM and added to the cells at a final concentration of 3 mM. A decomposed detaNONOate solution was added to the cells at the same concentration as control. The control and the treated cells were harvested by gentle centrifugation of 3000 rpm for 3 minutes and cell pellets were immediately resuspended in RNAlater solution (Ambion; Life Technologies) and frozen in -80°C freezer.

tag: strain

tag: genotype/variation

value: pap1 deletant; h- pap1::kanMX6

tag: treated with

value: detaNONOate for 15m


title: cis2

description: Biological replicate 2 of 3. Cells treated with cis9,trans11-CLA isomer.

source_name: MCF-7 cells treated with cis9,trans11-CLA isomer, Replicate 2

tag: tissue

tag: cell type


title: Gamenya 3 DAI control_rep1

value: distilled water (control)


title: Control_helveticoside

description: Control for helveticoside


title: KT3

description: Biological replicate 3 of 3. Cells treated with extract from fatty acids of CLA unenriched egg yolks

source_name: MCF-7 cells treated with fatty acids from CLA-unenriched egg yolks, Replicate 3


title: EEDS_20ug/ml

description: EEDS treatment at 20ug/ml


title: EEDS_1.25ug/ml

description: EEDS treatment at 1.25ug/ml


title: CLA2

description: Biological replicate 2 of 3. Cells treated with extract from fatty acids of CLA enriched egg yolks

source_name: MCF-7 cells treated with fatty acids from CLA-enriched egg yolks, Replicate 2


title: KT + cis1

description: Biological replicate 1 of 3. Cells treated with fatty acids from CLA- unenriched egg yolks and cis9,trans11-CLA isomer.

source_name: MCF-7 cells treated with fatty acids from CLA-unenriched egg yolks and cis9,trans11-CLA isomer, Replicate 1


title: EEDS_5ug/ml

description: EEDS treatment at 5ug/ml


title: CLA1

description: Biological replicate 1 of 3. Cells treated with extract from fatty acids of CLA enriched egg yolks

source_name: MCF-7 cells treated with fatty acids from CLA-enriched egg yolks, Replicate 1


title: KT2

description: Biological replicate 2 of 3. Cells treated with extract from fatty acids of CLA unenriched egg yolks

source_name: MCF-7 cells treated with fatty acids from CLA-unenriched egg yolks, Replicate 2

source_name: breast; derived from metastatic site: pleural effusion


title: CLA3

description: Biological replicate 3 of 3. Cells treated with extract from fatty acids of CLA enriched egg yolks

source_name: MCF-7 cells treated with fatty acids from CLA-enriched egg yolks, Replicate 3


title: pap1 deletion mutant control, biological rep2

description:
AV25 C2
AV25 C2_(Yeast_2).CEL

source_name: pap1 deletion mutant_control

value: decomposed detaNONOate solution (control)


title: KT1

description: Biological replicate 1 of 3. Cells treated with extract from fatty acids of CLA unenriched egg yolks

source_name: MCF-7 cells treated with fatty acids from CLA-unenriched egg yolks, Replicate 1


title: Breast cancer_cell line_untreated_DNA_AU565

city: Oslo

first: Sandra

last: Jernström

address: Ullernchausséen 70

department: Genetics

country: Norway

institute: OUS The Norwegian Radium hospital

hyb_protocol: Labeled tumor and reference samples were pooled and hybridized onto the arrays according to the protocol provided by Agilent Technologies.

scan_protocol: The arrays were scanned with a laser scanner (G2565 Scanner, Agilent Technologies).

data_processing: Feature Extraction software version 7.5.1 (Agilent Technologies) was used for the pre-processing of the signal intensities to obtain normalized intensity ratios.

source_name: HER2 positive breast cancer cell line, untreated

label_protocol: One μg of digested and purified tumor and reference DNA was labeled with Cy5-dUTP and Cy3-dUTP (Perkin–Elmer, Wellesley, MA), respectively, in a random priming reaction using BioPrime DNA Labeling System (Invitrogen, Carlsbad, CA).

growth_protocol: All cells were grown according to protocol provided by manufacturer.

extract_protocol: TriZOL

treatment_protocol: No treatment

tag: her2 status

value: positive

source_name: Normal female DNA_reference


title: pap1 deletion mutant treated, biological rep1

description:
AV25 T1
AV25 T1_(Yeast_2).CEL


title: Breast cancer_cell line_untreated_DNA_HCC1419

tag: gender


title: pap1 deletion mutant control, biological rep1

description:
AV25 C1
AV25 C1_(Yeast_2).CEL


title: Control_EEDS

description: Control for EEDS

source_name: Cell Line


title: Breast cancer_cell line_untreated_DNA_EFM192A


title: B3

type: mixed

city: Princeton

first: Bess

middle: B

last: Ward

state: NJ

address: Washington Road

department: Geosciences

institute: Princeton University

description: The same sample was hybridized to two arrays for use as replicates.

hyb_protocol: Samples were hybridized to single or duplicate arrays by overnight incubation at 64°C and washed.

scan_protocol: The arrays were scanned with a laser scanner (Molecular Devices 4300) Images were analyzed with Gene Pix Pro 6.0 software (Molecular Devices)

data_processing:
Quality control was employed to remove noise. For each channel, i.e. 532 nm (Cy3) and 635 nm (Cy5), the average background fluorescence was recalculated after excluding background fluorescence values greater than the upper whisker of all of the background fluorescences. This limit was defined as the 75th percentile plus 1.5 times the interquartile range.
Cy3/Cy5 fluorescence intensities were standardized to the highest Cy3/Cy5 fluorescence across the AOA probe set (normalized fluorescence ratio; FRN). The data for each sample were then averaged among replicates except when one replicate was zero, in which case the zero value was ignored.

molecule: other

organism: synthetic construct

source_name: Universal Internal Standard + 70-mer

label_protocol: PCR amplification using the nirS1F and nirS6R primers of Braker et al (1998).  The PCR fragments were labeled with amino-allyl-dUTP (Ambion) during linear amplification using random octamers and a Klenow polymerase (Applied Biosystems). The reaction contained 3.96 mM d(AGC)TP, 0.44 mM dTTP, and 4.84 mM dUaa and was amplified for 3 h at 37°C. The Klenow product was purified and conjugated with Cy3. The Cy3-labelled target (200 ng) was combined with 2x hybridization buffer (1x final concentration; Agilent) and 0.25 pmol of a Cy5-labelled complementary 20-mer standard oligonucleotide and incubated at 95°C for 5 min before being cooled to room temperature.

extract_protocol: DNA was extracted from the filters using the PureGene DNA kit (Gentra, Minneapolis, MN) or the AllPrep DNA/RNA Mini Kit (Qiagen Sciences, Maryland, USA) with slight modifications (as in Ward 2008).

tag: molecule type

value: 70-mer probe conjugated to the 20-mer standard DNA oligo

organism: aquatic metagenome

source_name: marine sediment

tag: location

value: Mesocoxm H1 day 3

tag: location coordinates

value: station CT2 in Chesapeake Bay, 38°37.191′ N 76°08.061′ W

value: PCR fragment,  nirS gene from denitrifying bacteria amplified from DNA extracted from marine sediments


title: A3

description: The same sample was hybridized to three arrays for use as replicates.

value: Mesocosm L1 day 3


title: A38

value: Mesocosm L1 day 38


title: Et1

description: Biological replicate 1 of 3. Control  cells, treated with ethanol as the solvent of fatty acids

source_name: MCF-7 cells treated with solvent of fatty acids (ethanol), Replicate 1

tag: cell line

value: MCF-7 (HTB-22, ATCC)

value: mammary gland

value: epithelial


title: mRNA-Seq data from pregnant dog endometrium

type: SRA

city: Chicago

first: Vincent

middle: J.

last: Lynch

address: 920 E. 58th Street

department: Human Genetics

institute: The University of Chicago

description: mRNA

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software was used for basecalling.
Sequenced reads were mapped to appropriate ENSEMBL Gene builds using bowtie with parameters allowing two mismatches and discarding reads that mapped to more than one gene. Uniquely mapped reads for each gene were counted.
Genome_build: BROADD2 (Dog)
Supplementary_files_format_and_content: Dog.txt contains mapped mRNA-Seq data as the number of unique reads (reads) and bases covered by reads (Mapped bases), the RPKM values (rel) that map to ENSEMBL genes (Ensembl_Gene_ID) and the associated gene name for each ENSEMBL gene (Associated_Gene_Name).

organism: Canis lupus familiaris

source_name: Pregnant dog endometrium

extract_protocol:
Qiagen RNeasy followed by on-column DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: pregnant endometrium


title: wild type strain treated, biological rep2

description:
972 T2
972 T2_(Yeast_2).CEL

source_name: wild type_treated

value: wild type; h-


title: wild type strain treated, biological rep1

description:
972 T1
972 T1_(Yeast_2).CEL


title: Breast cancer_cell line_untreated_DNA_MDAMB453

value: female


title: Et3

description: Biological replicate 3 of 3. Control  cells, treated with ethanol as the solvent of fatty acids

source_name: MCF-7 cells treated with solvent of fatty acids (ethanol), Replicate 3

value: 69 years adult

value: common reference sample compsed of a pool of equal amounts of total RNA from control cells


title: B38

value: Mesocoxm H1 day 38


title: Et2

description: Biological replicate 2 of 3. Control  cells, treated with ethanol as the solvent of fatty acids

source_name: MCF-7 cells treated with solvent of fatty acids (ethanol), Replicate 2


title: K1

description: Biological replicate 1 of 3. Control  cells, untreated.

source_name: MCF-7 adenocarcinoma cells, control, Replicate 1


title: K3

description: Biological replicate 3 of 3. Control  cells, untreated.

source_name: MCF-7 adenocarcinoma cells, control, Replicate 3


title: K2

description: Biological replicate 2 of 3. Control  cells, untreated.

source_name: MCF-7 adenocarcinoma cells, control, Replicate 2


title: Esrrb-overexpressing NS Tet-off ESC Dox untreated

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Research Center for Genomic Medicine

institute: Saitama Medical University

description: gene expression data

hyb_protocol: Labelled samples were hybridized to the microarrays according to the manufacturer’s protocol with Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneArray Scanner 3000. Scanning was preformed as described elsewhere. (Irizarry et al, Nucleic Acids Res 31, e15, 2003)

data_processing: The intensity  data was background-subtracted and normalized with the robust multi-array analysis (RMA; Irizarry et al.  Nucleic Acids Res  31(4): e15, 2003) via R/Bioconductor 2.7 affy package using default analysis settings.

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

growth_protocol: NS tet off ESCs were cultured under conventional ESC culture condition with LIF and serum or that with MEK and GSK3b inhibitors (2i condition).

extract_protocol: Total RNAs were prepared by using TRIzol reagent from invitrogen (15596-026).

treatment_protocol: NS tet off ESCs were untreated (NS-expressing) or treated (NS-non-expressing) with Doxycycline.

value: male

tag: strain background

value: ES cells

value: Esrrb-overexpressing NS Tet-off ESC

value: none (untreated)


title: Esrrb-overexpressing NS Tet-off ESC Dox-treated (6days)

description: gene expression data

source_name: Esrrb-overexpressing NS Tet-off ESC Dox treated for 6 days

value: Dox for 6days


title: Nanog-overexpressing NS Tet-off ESC Dox-treated (6days)

description: gene expression data

source_name: Nanog-overexpressing NS Tet-off ESC Dox treated for 6 days

value: Nanog-overexpressing NS Tet-off ESC


title: wild type strain control, biological rep1

description:
972 C1
972C1_(Yeast_2).CEL

source_name: wild type_control

value: decomposed detaNONOate solution (control)


title: Nanog-overexpressing NS Tet-off ESC Dox untreated

description: gene expression data


title: Stat3mut-overexpressing NS Tet-off ESC Dox-treated (6days)

description: gene expression data

source_name: Stat3mut-overexpressing NS Tet-off ESC Dox treated for 6 days

value: Stat3mut-overexpressing NS Tet-off ESC


title: HFD 30d E

city: London

first: Katrin

last: Kierdorf

address: New Maze Pond

country: United Kingdom

institute: King's College London

hyb_protocol: Cy3 labeled cDNAs were hybridized overnight (17 hours, 65°C) to Agilent Whole Drosophila Genome Oligo Custom 8x60K  Microarrays (Design ID 068787) using Agilent’s recommended hybridization chamber and oven. Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C.

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

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

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: hemocytes, lipid enriched diet, 30 days

label_protocol: 250 ng of each of the amplified cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

growth_protocol: Adult male flies were put on normal diet or 15% lipid enriched diet 2-3 days after eclosion. Flies were tipped over to fresh food every other day and maintained at 25C in a constant 12h dark/light cycle. After 30 days hemocytes were isolated from the flies via mechanical dissociation and FACS-sorted with an BD FACS Aria II (5.000-10.000 cells/sample).

extract_protocol: Cell samples were lysed using SuperAmp Lysis Buffer following manufacturer’s instructions. SuperAmplification was performed according to Miltenyi Biotec’s undisclosed protocol. Briefly, the amplification is based on a global PCR protocol of mRNA-derived cDNA. mRNA was isolated via magnetic bead technology.

treatment_protocol: Adult male flies were kept for 30days either on a 15% lipid enriched diet or on a control diet.

tag: genotype

value: w; Hml-Gal4, UAS-2xeGFP

tag: developmental stage

value: adult

value: hemocyte

tag: treatment

value: lipid enriched diet


title: HFD 30d C


title: Stat3mut-overexpressing NS Tet-off ESC Dox untreated

description: gene expression data


title: Breast cancer cell line untreated gene expression SUM225

hyb_protocol: 15 µg of fragmented cRNA was used for hybridization. The arrays were stained with phycoerythrin-streptavidin and the signal intensity was amplified by treatment with a biotin-conjugated anti-streptavidin antibody, followed by a second staining using phycoerythrin-streptavidin.

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: Data were pre-processed using the R language and the RMA method implementation in Bioconductor package ‘affy’. ‘Alternative CDF files’ (version 14) mapping Affymetrix probes directly to Ensembl gene ids were used in pre-processing, resulting in one expression value per Ensembl gene id. Ensembl gene positions are based on Ensembl database version 63 (hg19).

source_name: HER2 positive breast cancer cell line, untreated

label_protocol: 3μg of total RNA per sample was prepared according to the manufacturer's protocols (Affymetrix).

extract_protocol: Total RNA was isolated from all cell lines using the Rneasy kit by Qiagen, and isolated according to the protocol provided by Qiagen.


title: 2i-treated NS Tet-off ESC empty Dox-treated (6day)

description: gene expression data

source_name: 2i-treated empty vector-bearing NS Tet-off ESC Dox treated for 6 days


title: HFD 30d D


title: HFD 30d B


title: 2i-treated NS Tet-off ESC Dox untreated

description: gene expression data

source_name: 2i-treated empty vector-bearing NS Tet-off ESC Dox untreated


title: Breast cancer cell line untreated gene expression SKBR3


title: Breast cancer cell line untreated gene expression SUM190PT


title: ND 30d E

source_name: hemocytes, normal diet, 30 days

value: normal diet


title: control NS Tet-off ESC Dox untreated

description: gene expression data

source_name: empty vector-bearing NS Tet-off ESC Dox untreated

value: empty vector-bearing NS Tet-off ESC


title: Breast cancer cell line untreated gene expression MDA-MB-453

value: female


title: Breast cancer cell line untreated gene expression JIMT1


title: HFD 30d A


title: Primary human corneal epithelial cells Collagen type IV rep1

city: Québec

first: Karine

last: Zaniolo

state: Québec

address: 1050 Chemin Sainte-Foy

department: CUO-Recherche

country: Canada

institute: Centre de recherche du CHU de Québec

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScanner (G4900DA) using one color scan setting for 1x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10,7 (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 human corneal epithelial cells cultivated on Collagen type IV

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Toronto, ON).  Dye incorporation and cRNA yield were checked with the Nanophotometer pearl (Montréal Biotech).

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Toronto, ON)  from HCEC isolated from normal eyes supplied by the National Eyes Bank from the CHU de Québec (QC, Canada), and cultivated on BSA, Collagen type I and Collagen tye IV matrix.

value: Primary human corneal epithelial cells

value: Sex unknown

tag: age

value: 45 years

value: cultivated on Collagen type IV


title: ND 30d D

value: male


title: Primary human corneal epithelial cells Collagen type IV rep2

value: 52 years


title: Breast cancer cell line untreated gene expression HCC202


title: Breast cancer cell line untreated gene expression KPL4


title: ND 30d C


title: Primary human corneal epithelial cells Collagen type I rep2

source_name: Primary human corneal epithelial cells cultivated on Collagen type I

value: cultivated on Collagen type I


title: ND 30d A


title: Primary human corneal epithelial cells Collagen type I rep1

value: 44 years


title: Breast cancer cell line untreated gene expression HCC1954


title: Breast cancer cell line untreated gene expression HCC1569


title: Ratios of RNA levels of BYAT526 compared to BYAT581-0

city: Paris

first: Varun

last: Khanna

address: 25 28 Rue du Docteur Roux

department: Genomes and Genetics

country: France

institute: institut Pasteur

description:
BYAT526_vs_BYAT581-0
Comparison of hybridization of RNA from two strains.

hyb_protocol: Total RNAs were hybridized against custom-designed Agilent microarrays of 50-mer synthetic oligonucleotides (AMADID 050530).

scan_protocol: Comparative hybridizations (with dye swap) were scanned on AXON GENEPIX 4200AL scanner

data_processing: Data were analyzed using GenePix Pro 7 (Molecular Devices). The values from the obtained gpr files were filtered to keep only values for spots with an SNR > 3.

organism: Saccharomyces cerevisiae

label_protocol: Total RNAs were reversed transcribed with Cy3 or Cy5 labels with InVitroGen Superscript indirect cDNA Labeling System

growth_protocol: Cells in exponential growth were recovered by centrifugation, washed once in cold water and stored at -80C until RNA or DNA extraction

extract_protocol: RNA was extracted using Guanidium Thiocyanate procedure.

value: diploid strains derived from S288c


title: Primary human corneal epithelial cells BSA rep1

source_name: Primary human corneal epithelial cells cultivated on BSA

value: cultivated on BSA


title: Primary human corneal epithelial cells BSA rep2


title: ND 30d B

value: w; Hml-Gal4, UAS-2xeGFP


title: Breast cancer cell line untreated gene expression EFM-192A


title: Breast cancer cell line untreated gene expression HCC1419


title: control NS Tet-off ESC Dox-treated (6day)

description: gene expression data

source_name: empty vector-bearing NS Tet-off ESC Dox treated for 6 days

value: ES cells

value: Dox for 6days


title: Ratios of RNA levels of BYAT580-0 compared to BYAT521

description:
BYAT580-0_vs_BYAT521
Comparison of hybridization of RNA from two strains.


title: Ratios of RNA levels of BYAT580-345 compared to BYAT521

description:
BYAT580-345_vs_BYAT521
Comparison of hybridization of RNA from two strains.


title: Breast cancer cell line untreated gene expression BT474


title: Breast cancer cell line untreated gene expression AU565


title: Ratios of RNA levels of BYAT583-345 compared to BYAT581-0

description:
BYAT583-345_vs_BYAT581-0
Comparison of hybridization of RNA from two strains.


title: wild type strain control, biological rep2

description:
972 C2
972C2_(Yeast_2).CEL

value: wild type; h-

value: decomposed detaNONOate solution (control)


title: GerminalDiscRegion_hen102_FB

status: Public on Jan 29 2015

city: Wageningen

first: Dirkjan

last: Schokker

address: Droevendaalsesteeg 1

department: Wageningen Livestock Research

country: Netherlands

institute: Wageningen UR

hyb_protocol: Hybridization was performed as described in the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling protocol from Agilent in the hybridization oven (G2545A hybridization Oven Agilent Technologies). The hybridization temperature was 65°C with rotation speed 10 rpm for 17 hours. After 17 hours the arrays were washed as described in the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling protocol from Agilent.

scan_protocol: The arrays were scanned using the DNA microarray scanner with Surescan high resolution Technology from Agilent Technologies. Agilent Scan Control with resolution of 2µ, 16 bits and PMT of 100%.

data_processing: Feature extraction was performed using protocol 10.7.3.1 (v10.7) for 1 colour gene expression.

organism: Gallus gallus

label_protocol: Labelling was done as recommended by Agilent Technologies using the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling. The input was 10 ng of total RNA and 600 ng of labelled cRNA was used on the 8 pack array.

extract_protocol: RNA from the blastodiscs of F1 follicles from the selected hens was purified using master pure RNA purification kit from the Epicentre (Cat. No. MCR85102) and following protocol as described by the manufacturer. All the 16 purified RNA samples were checked for integrity on the Agilent bioanalyzer according to Agilent Technologies Protocol. The amount of RNA isolated from the germinal disc region per hen ranged from 1.5-5 µg.

value: germinal disc region

value: Female

tag: follicle stage


title: GerminalDiscRegion_hen78_MB


title: GerminalDiscRegion_hen96_FB


title: GerminalDiscRegion_hen99_MB


title: GerminalDiscRegion_hen104_FB


title: GerminalDiscRegion_hen67_MB


title: GerminalDiscRegion_hen69_MB


title: GerminalDiscRegion_hen54_FB


title: GerminalDiscRegion_hen98_FB


title: GerminalDiscRegion_hen41_MB


title: GerminalDiscRegion_hen35_MB


title: Nax knockdown HaCaT high sodium concentration 16 hour stimulation_2

first: Wei

last: Xu

state: IL

address: 303 E Chicago Ave, Tarry 4-714

department: Surgery

institute: Northwestern University, Feinberg School of Medicine

description: Sample name: HT_Nx_16h_2

hyb_protocol: Hybridization performed at the Interdisciplinary Center for Biotechnology Research Microarray Core, University of Florida. The microarray chips were Affymetrix GeneChip® Human Transcriptome Array 2.0

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
The microarray data was processed with Affymetrix Expression Console and Transcriptome Analysis Console (Affymetrix).
RMA expression value derived from Expression Console software; core-exon analysis

source_name: keratinocyte cell line

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).

growth_protocol: Both wild type and Nax knockdown HaCaT cells were seeded in 12-well plates. 70-80% confluent cells were starved with fetal bovine serum (FBS) free Dulbecco's modiﬁed Eagle's medium (DMEM) overnight

extract_protocol: The total RNA from wild type and Nax knockdown HaCaT cells

treatment_protocol: A treatment with control medium (final150 mM sodium) or medium plus 10% more sodium (final 165 mM sodium) was applied to each well. Cells were harvested at time point 0, 4, and 16 hours post treatment.

value: female

value: skin epithelium

value: HaCaT

value: Nax knockdown

value: high sodium concentration

tag: time

value: 16 hour


title: Nax knockdown HaCaT high sodium concentration 4 hour stimulation_2

description: Sample name: HT_Nx_4h_2

tag: genotype/variation

value: 4 hour


title: GerminalDiscRegion_hen34_FB


title: GerminalDiscRegion_hen23_MB


title: GerminalDiscRegion_hen24_MB


title: Nax knockdown HaCaT high sodium concentration 4 hour stimulation_7

description: Sample name: HT_Nx_4h_7


title: HaCaT wild type high sodium concentration 16 hour stimulation_8

description: Sample name: HT_WT_16h_8

value: wild type


title: Nax knockdown HaCaT high sodium concentration 16 hour stimulation_6

description: Sample name: HT_Nx_16h_6


title: Nax knockdown HaCaT high sodium concentration 16 hour stimulation_3

description: Sample name: HT_Nx_16h_3


title: Nax knockdown HaCaT high sodium concentration 4 hour stimulation_1

description: Sample name: HT_Nx_4h_1


title: Nax knockdown HaCaT control sodium concentration_4

description: Sample name: HT_Nx_0_4

value: control


title: Nax knockdown HaCaT control sodium concentration_6

description: Sample name: HT_Nx_0_6


title: GerminalDiscRegion_hen70_FB


title: Nax knockdown HaCaT control sodium concentration_3

description: Sample name: HT_Nx_0_3


title: Nax knockdown HaCaT high sodium concentration 4 hour stimulation_5

description: Sample name: HT_Nx_4h_5


title: Nax knockdown HaCaT high sodium concentration 4 hour stimulation_6

description: Sample name: HT_Nx_4h_6


title: Nax knockdown HaCaT high sodium concentration 16 hour stimulation_1

description: Sample name: HT_Nx_16h_1


title: Nax knockdown HaCaT high sodium concentration 16 hour stimulation_5

description: Sample name: HT_Nx_16h_5


title: Nax knockdown HaCaT control sodium concentration_8

description: Sample name: HT_Nx_0_8


title: Nax knockdown HaCaT control sodium concentration_2

description: Sample name: HT_Nx_0_2


title: HaCaT wild type high sodium concentration 16 hour stimulation_5

description: Sample name: HT_WT_16h_5


title: HaCaT wild type high sodium concentration 16 hour stimulation_4

description: Sample name: HT_WT_16h_4


title: HaCaT wild type high sodium concentration 16 hour stimulation_1

description: Sample name: HT_WT_16h_1


title: HaCaT wild type control sodium concentration_3

description: Sample name: HT_WT_0_3


title: HaCaT wild type high sodium concentration 4 hour stimulation_3

description: Sample name: HT_WT_4h_3


title: HaCaT wild type high sodium concentration 4 hour stimulation_7

description: Sample name: HT_WT_4h_7


title: HaCaT wild type control sodium concentration_5

description: Sample name: HT_WT_0_5


title: HaCaT wild type control sodium concentration_2

description: Sample name: HT_WT_0_2


title: CD45-Ter119-Tie2-AlphaV+Thy-6C3+CD105- rep1

city: Stanford

first: Charles

middle: Chan

last: KF

address: 265 Campus Drive

institute: Stanford

description: fore and hind limbs pooled litter

hyb_protocol: standard Affymetrix protocol

data_processing: Normalized Intenstity values were computed based on Gene Expression Commons Algorithum [ https://gexc.stanford.edu/]

source_name: wild-type, anterior posterior limb

label_protocol: Amplified cRNA was streptavidin-labeled, fragmented, and hybridized to Affymetrix 430-2.0 arrays as recommended by the manufacturer (Affymetrix, Santa Clara). Arrays were scanned with a Gene Chip Scanner 3000 (Affymetrix) running GCOS 1.1.1. software.

growth_protocol: Skeletal tissues were dissected from P3 GFP-labeled mice and dissociated by mechanical and enzymatic dissociation. Specifically, the tissue was placed in collagenase digestion buffer supplemented with DNase and incubated at 37oC for 40 minutes under constant agitation. After collagenase digestion and neutralization, undigested materials were gently triturated by repeated pipetting. Total dissociated cells were filtered through 40 m nylon mesh, pelleted at 200g at 4oC, resuspended in staining media (2% fetal calf serum in PBS), blocked with rat IgG and stained with fluorochrome-conjugated antibodies against CD45, Tie2, AlphaV integrin, CD105, Thy1.1, Thy 1.2, 6C3 and CD200 for fractionation by fluorescence activated-cell sorting.

extract_protocol: RNA was isolated with RNeasy Micro Kit (Qiagen, Germantown, MD) as per manufacturer’s instructions. RNA was twice amplified with a RiboAmp RNA amplification kit (Arcturus Engineering, Mountain View, CA).

value: postnatal day 3

value: fore and hind limbs

value: wild-type

tag: cell population


title: HaCaT wild type control sodium concentration_6

description: Sample name: HT_WT_0_6

tag: tissue


title: CD45-Ter119-Tie2-AlphaV+Thy+6C3+CD105- rep2

description: fore and hind limbs pooled litter

scan_protocol: Arrays were scanned with a Gene Chip Scanner 3000 (Affymetrix) running GCOS 1.1.1. software.


title: HaCaT wild type high sodium concentration 4 hour stimulation_1

description: Sample name: HT_WT_4h_1


title: HaCaT wild type high sodium concentration 16 hour stimulation_3

description: Sample name: HT_WT_16h_3


title: CD45-Ter119-Tie2-AlphaV+Thy+6C3+CD105- rep3

description: fore and hind limbs pooled litter


title: CD45-Ter119-Tie2-AlphaV+Thy+6C3+CD105+

description: fore and hind limbs pooled litter

source_name: sternum, ear

value: adult


title: CD45-Ter119-Tie2-AlphaV+Thy-6C3+CD105+ rep2

description: fore and hind limbs pooled litter


title: CD45-Ter119-Tie2-AlphaV+Thy-6C3+CD105+ rep3

description: fore and hind limbs pooled litter


title: HaCaT wild type control sodium concentration_1

description: Sample name: HT_WT_0_1


title: CD45-Ter119-Tie2-AlphaV+Thy-6C3+CD105+ rep1

description: fore and hind limbs pooled litter


title: HaCaT wild type high sodium concentration 4 hour stimulation_8

description: Sample name: HT_WT_4h_8


title: CD45-Ter119-Tie2-AlphaV+Thy+6C3-CD105- rep3

description: fore and hind limbs pooled litter


title: CD45-Ter119-Tie2-AlphaV+Thy+6C3-CD105- rep1

description: fore and hind limbs pooled litter


title: CD45-Ter119-Tie2-AlphaV+Thy+6C3-CD105- rep2

description: fore and hind limbs pooled litter


title: HaCaT wild type high sodium concentration 4 hour stimulation_4

description: Sample name: HT_WT_4h_4


title: CD45-Ter119-Tie2-AlphaV+Thy+6C3-CD105+ rep3

description: fore and hind limbs pooled litter


title: Mouse 14.5 days fetal brain P300, rep1

first: Chandr

middle: Sekhar Reddy

last: Chilamakuri

address: Fådveien 15

department: Tumor Biology

institute: The Norwegian Radium Hospital

hyb_protocol: Hybridization was performed according to the manufacturer's protocol to a HX1 (2.1 million  probes) custom microarray containing specific tiled regions encompassing 93.84 Mb of the mouse X chromosome (NimbleGen).

scan_protocol: Arrays were scanned on a NimbleGen MS 200 Microarray scanner (NimbleGen) using a laser power of 100% and 2 µm resolution. TIFF images were analysed using MS 200 Data Collection software to quantitate raw signal intensities.

data_processing: Arrays were processed using Ringo bioconductor package.

source_name: P300 ChIP DNA from fetal brain

label_protocol: ChIP DNA and input DNA were labeled with Cy5 and Cy3 dye-labelled random hexamers, respectively, using random priming according to the manufacturer's protocol (NimbleGen).

extract_protocol: Embryonic brain was isolated from mouse E14.5 embryos. Pools of whole brain were treated with 1.5% formaldehyde for 10 min. at room temperature. Crosslinking was stopped by the addition of glycine to a final concentration of 0.125 M. The brain tissue was chopped into small pieces (∼1 mm3) with a razor blade in cold 1× PBS and single cell suspension was made using dounce homogenizer. The cells were swelled on ice for 10 min. in 25 mM Hepes, pH 7.8, 1.5 mM MgCl2, 10 mM KCl, 0.1% NP-40, 1 mM DTT and protease inhibitor cocktail (Roche) and the nuclei were collected by centrifugation at 2500 rpm. Nuclei were resuspended in sonication buffer containing 50 mM Hepes pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS and protease inhibitors, and sonicated on ice to an average length of 200-500 bp. The samples were centrifuged at 14000 rpm and chromatin was precleared with protein-A-Dynabeads. Precleared chromatin were immunoprecipitated with 5µg of H3K4me1 (Abcam ab8895, lot# 899421) and 10µg of p300 (C-20; Santa Cruz sc-585X, lot# E2610) antibodies and the immune complexes were collected by incubating with protein-A-Dynabeads. The beads were washed twice with sonication buffer, twice with sonication buffer containing 500 mM NaCl, twice with 20 mM Tris, pH 8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate and twice with TE buffer. The immunocomplexes were eluted with 50 mM Tris, pH 8.0, 1 mM EDTA and 1% SDS at 65°C for 10 min., adjusted to 200 mM NaCl and incubated at 65°C overnight to reverse the cross-links. After successive treatments with 10 µg/ml RNase A and 20 µg/ml proteinase-K, the samples were eluted into 50µl H2O using the QIAquick Spin Gel Purification Kit (Qiagen).

tag: strain/background

value: fetal brain

tag: chip antibody

source_name: Input DNA from fetal brain


title: Human fetal brain H3K4Me1, rep2

hyb_protocol: Hybridization was performed according to the manufacturer's protocol to a HX1 (2.1 million  probes) custom microarray containing specific tiled regions encompassing 99.2 Mb of the human X chromosome (NimbleGen).

source_name: H3K4Me1 ChIP DNA from fetal brain

extract_protocol: Embryonic brain was isolated from human (3 samples at 50 days of gestation). Pools of whole brain were treated with 1.5% formaldehyde for 10 min. at room temperature. Crosslinking was stopped by the addition of glycine to a final concentration of 0.125 M. The brain tissue was chopped into small pieces (∼1 mm3) with a razor blade in cold 1× PBS and single cell suspension was made using dounce homogenizer. The cells were swelled on ice for 10 min. in 25 mM Hepes, pH 7.8, 1.5 mM MgCl2, 10 mM KCl, 0.1% NP-40, 1 mM DTT and protease inhibitor cocktail (Roche) and the nuclei were collected by centrifugation at 2500 rpm. Nuclei were resuspended in sonication buffer containing 50 mM Hepes pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS and protease inhibitors, and sonicated on ice to an average length of 200-500 bp. The samples were centrifuged at 14000 rpm and chromatin was precleared with protein-A-Dynabeads. Precleared chromatin were immunoprecipitated with 5µg of H3K4me1 (Abcam ab8895, lot# 899421) and 5ug of H3K27Ac (Abcam ab4729) antibodies and the immune complexes were collected by incubating with protein-A-Dynabeads. The beads were washed twice with sonication buffer, twice with sonication buffer containing 500 mM NaCl, twice with 20 mM Tris, pH 8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate and twice with TE buffer. The immunocomplexes were eluted with 50 mM Tris, pH 8.0, 1 mM EDTA and 1% SDS at 65°C for 10 min., adjusted to 200 mM NaCl and incubated at 65°C overnight to reverse the cross-links. After successive treatments with 10 µg/ml RNase A and 20 µg/ml proteinase-K, the samples were eluted into 50µl H2O using the QIAquick Spin Gel Purification Kit (Qiagen).

value: 50 days gestation


title: CD45-Ter119-Tie2-AlphaV+Thy-6C3-CD105+ rep1

description: fore and hind limbs pooled litter


title: CD45-Ter119-Tie2-AlphaV+Thy+6C3-CD105+ rep2

description: fore and hind limbs pooled litter


title: CD45-Ter119-Tie2-AlphaV+Thy-6C3-CD105+ rep3

description: fore and hind limbs pooled litter


title: fibro_uninvestigated_a5

city: Bologna

first: Sabina

last: Capellari

address: via Altura, 3

department: Dibinem and UOC clinica Neurologica

country: Italy

institute: University of Bologna And IRCCS ISNB

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Image signal intensity was extracted; the background subtracted and normalized using Illumina Inc. BeadStudio software version 3.4.0. All statistical analyzes were performed in the R environment using specific packages of Bioconductor. The raw signal intensities (AVG_Signal) were processed with Lumi package applying variance-stabilizing transformation (VST) and quantile normalization.

source_name: uninvestigated fibroblasts cell line

label_protocol: standard labeling protocol with biotin wirh Cy3-streptavidin

extract_protocol: RNA from fibroblasts and whole blood was extracted using the RNeasy Plus Kit and PAXgeneTM Blood RNA System Kit (Qiagen). RNA quality was tested by Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, USA) and used when the integrity quality number (RIN) scored above 8.

tag: cell line/tissue source

value: uninvestigated sample

tag: cell line/tissue

value: fibroblasts cell line


title: Human fetal brain H3K27Ac, rep1

source_name: H3K27Ac ChIP DNA from fetal brain


title: CD45-Ter119-Tie2-AlphaV+Thy-6C3-CD105+ rep2

description: fore and hind limbs pooled litter


title: Mouse 14.5 days fetal brain H3K4Me1, rep1


title: fibro_ADLD_a3

source_name: ADLD fibroblast cell line

value: Adult-onset autosomal dominant leukodystrophy (ADLD)


title: fibro_Control_sib_a7

source_name: control fibroblast cell line

value: controls siblings


title: CD45-Ter119-Tie2-AlphaV+Thy-6C3-CD105- rep2

description: fore and hind limbs pooled litter


title: fibro_uninvestigated_av1


title: CD45-Ter119-Tie2-AlphaV+Thy-6C3-CD105- rep1

description: fore and hind limbs pooled litter


title: blood_ADLD_ms

description: MS

source_name: ADLD blood

value: whole blood


title: fibro_Control_sib_a10


title: fibro_ADLD_a9


title: CD45-Ter119-Tie2-AlphaV+Thy-6C3-CD105- rep3

description: fore and hind limbs pooled litter


title: Mouse 14.5 days fetal brain H3K4Me1, rep2


title: fibro_Control_C4

value: age-matched control


title: fibro_ADLD_a1


title: fibro_Control_sib_a4


title: blood_Control_sib_11-299

source_name: control blood


title: fibro_ADLD_a2


title: CD45-Ter119-Tie2-AlphaV+Thy+6C3-CD105+ rep1

description: fore and hind limbs pooled litter


title: fibro_Control_C3


title: Mouse 14.5 days fetal brain P300, rep2


title: blood_Control_sib_11-288


title: blood_Control_sib_11-298


title: blood_Control_sib_11-225


title: Human fetal brain H3K4Me1, rep1


title: blood_Control_sib_11-224


title: blood_ADLD_11-223


title: blood_Control_sib_11-220


title: blood_Control_sib_11-222


title: blood_ADLD_11-221


title: blood_Control_sib_11-213


title: IPMN High Risk sample4

city: Tampa

first: Jennifer

middle: Permuth

last: Wey

address: 12902 Magnolia Dr

institute: Moffitt Cancer Center

description: Gene expression data from High-risk IPMN tissue.

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Raw CEL files were normalized by RMA algorithm as implemented in the justRMA function in Bioconductor/R with default parameters.

source_name: human IPMN tissue

label_protocol: Samples were amplified and labeled using a custom automated version of the NuGEN Ovation v2 with WB (whole blood) reagents protocol (using Ribo-SPIA amplification). The labeled molecules are biotinylated-cRNA. Sample amplification and labeling were performed by LabCorp Clinical Trials-Genomic Services in Seattle, Washington.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification. Isolated total RNA samples were assayed for quality (Agilent Bioanalyzer) and yield (Ribogreen) metrics prior to amplification.

tag: risk

value: High-risk IPMN tissue

value: IPMN tissue


title: blood_uninvestigated_11-214

source_name: uninvestigated blood sample


title: IPMN High Risk sample15


title: IPMN High Risk sample6


title: IPMN High Risk sample3


title: IPMN High Risk sample9


title: blood_ADLD_11-219


title: IPMN High Risk sample16


title: IPMN High Risk sample13


title: IPMN High Risk sample17


title: IPMN High Risk sample11


title: IPMN Low Risk sample4

description: Gene expression data from Low-risk IPMN tissue.

value: Low-risk IPMN tissue


title: IPMN Low Risk sample6


title: IPMN High Risk sample7


title: IPMN High Risk sample8


title: IPMN Low Risk sample5


title: IPMN High Risk sample2


title: IPMN High Risk sample1


title: IPMN High Risk sample14


title: IPMN High Risk sample12


title: IPMN High Risk sample10


title: IPMN Low Risk sample1


title: IPMN High Risk sample5


title: MCF7 IRA exposed for 6 h to vehicle solution replicate 3

city: Leiden

first: Steven

last: Wink

state: Zuid Holland

address: Einsteinweg 55

department: Division of Toxicology

institute: LACDR

hyb_protocol: cRNA was denaturized to prepare for the hybridization on the array. The fragmented cRNA with a concentration of 0.0375 μg/μl was finally utilized for the hybridization on the Affymetrix HT HG U133 plus PM.  The Affymetrix HWS Kit (#901530) was used for the hybridization, washing and staining of the chips.

scan_protocol: Scanning of the Array Plates was performed using the Affymetrix GeneTitan scanner

data_processing: BRB Array Tools software was used to normalize the CEL data using the Robust Multichip Average (RMA) method. Significantly differentially expressed genes (p-value < 0.001) between the various experimental conditions were identified with an ANOVA test followed by calculation according to Benjamini and Hochberg (Benjamini and Hochberg, 1995).

source_name: MCF7 IRA

label_protocol: The Affymetrix 3' IVT-Express Labeling Kit (#901229) was used to synthesize Biotin-labeled cRNA. From each RNA sample 100 ng was used as input for the labeling reactions.

growth_protocol: MCF7 IRA, MCF7 IRB or MCF7 IGF1R cells (as described in Arch Toxicol. 2014 Apr;88(4):953-66. doi: 10.1007/s00204-014-1201-2. Epub 2014 Jan 25.) were cultured in RPMI supplemented with 5% (v/v) CDFBS (Hyclone) and used for experiments. Cells have been exposed for 1 or 6 hours to 10 nM of the indicated insulin-like molecule. As a control sample a vehicle stimulation was performed that contained everything except the active compound.

extract_protocol: RNA was isolated using the RNeasy® Plus Mini Kit (Qiagen, Venlo, the Netherlands) and RNA integrity and quality was assessed using the Agilent bioanalyser (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Prior to compound stimulation the cells were starved in 5% charcoal/dextran-stripped fetal bovine serum (CDFBS) containing medium. Stimulations included: insulin NPH (Insuman Basal, Sanofi Aventis), insulin glargine (Lantus, Sanofi Aventis), M1 (metabolite of glargine, Sanofi Aventis), M2 (metabolite of glargine, Sanofi Aventis), glulisine (Apidra, Sanofi Aventis), lispro (Humalog, Elly Lilly), Insulin X10 (not marketed, Novo Nordisk), aspart (B28Asp, Novo Nordisk), detemir (Levemir, Novo Nordisk) and IGF1 (Increlex, Ipsen). All insulin analogues were dissolved in their original vehicle solutions [18]. For the in vitro experiments 1000x stock concentrations were prepared. Except for the first exposure experiment (Figure 1C) in which a dose response of 10, 33 and 100 nM was used, all exposures have been performed with a concentration of 10 nM

tag: receptor

value: IRA

value: vehicle solution

tag: time point

value: 6 hrs


title: MCF7 IGF1R exposed for 6 h to vehicle solution replicate 3

source_name: MCF7 IGF1R

tag: cell line


title: MCF7 IRB exposed for 6 h to vehicle solution replicate 2

source_name: MCF7 IRB

value: IRB


title: IPMN Low Risk sample3


title: MCF7 IGF1R exposed for 6 h to vehicle solution replicate 1


title: MCF7 IRB exposed for 6 h to vehicle solution replicate 4


title: MCF7 IGF1R exposed for 6 h to vehicle solution replicate 4


title: MCF7 IRA exposed for 6 h to vehicle solution replicate 4


title: MCF7 IRB exposed for 6 h to vehicle solution replicate 3


title: MCF7 IRA exposed for 6 h to vehicle solution replicate 1


title: MCF7 IRB exposed for 1 h to vehicle solution replicate 3

value: 1 hr


title: MCF7 IGF1R exposed for 1 h to vehicle solution replicate 4


title: MCF7 IRB exposed for 1 h to vehicle solution replicate 4


title: Human fetal brain H3K27Ac, rep2


title: IPMN Low Risk sample2


title: MCF7 IGF1R exposed for 6 h to vehicle solution replicate 2


title: MCF7 IRB exposed for 6 h to vehicle solution replicate 1


title: MCF7 IRA exposed for 1 h to vehicle solution replicate 4


title: MCF7 IGF1R exposed for 1 h to vehicle solution replicate 3


title: MCF7 IRA exposed for 1 h to vehicle solution replicate 3


title: MCF7 IGF1R exposed for 6 h to IGF1 replicate 3


title: MCF7 IRA exposed for 1 h to vehicle solution replicate 2


title: MCF7 IRB exposed for 1 h to vehicle solution replicate 2