title: MCF7 -Val 24h-rep1

description: Sample name: MCF7 -Val-1

source_name: MCF7 cells deprived Valine for 24 hours, biological rep1


title: MCF7 -Leu 24h-rep2

status: Public on Apr 01 2015

type: RNA

city: Durham

first: Xiaohu

last: Tang

state: NC

address: CIEMAS Rm 2133, 101 Science Dr.

department: Department of Molecular Genetics and Microbiology

country: USA

institute: Duke University

description: Sample name: MCF7 -Leu-2

hyb_protocol: Hybridization was performed in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip® Fluidics Station 450 according to standard Affymetrix GeneChip® Hybridization and wash protocols. (Affymetrix, Santa Clara,CA).

scan_protocol: Fluorescent images were scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Stain protocols. (Affymetrix, Santa Clara,CA).

data_processing:
Expression data was extracted using the Affymetrix Expression Console version 1.1 (Affymetrix) and further generated by RMAExpress using Quantile/Median Polish normorlization/summarization methods. The results were shown in log2 scale.
All GeneChips were scaled to a median intensity setting of 500.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MCF7 cells deprived leucine for 24 hours, biological rep2

label_protocol: Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA)) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE). Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA.

growth_protocol: MCF7 or PC3 cells grew in the control full DMEM media supplement with 10% FBS and Penicillin/Streptomycin

extract_protocol: RNA was extracted by RNAeasy kits (Qiagen) according to the manufacturer's instructions.

treatment_protocol: MCF7 or PC3 cells were treated for 24 hours with the control or one (or all amino acids) deprived DMEM media supplemnent with 10% dialysed FBS and Penicillin/Streptomycin

tag: cell line

tag: treatment

value: deprived of leucine

tag: time

value: 24 hours


title: MCF7 -Ile 24h-rep3

description: Sample name: MCF7 -Ile-3

source_name: MCF7 cells deprived isoleucine for 24 hours, biological rep3

value: deprived of isoleucine


title: MCF7 -Ile 24h-rep4

description: Sample name: MCF7 -Ile-4

source_name: MCF7 cells deprived isoleucine for 24 hours, biological rep4


title: MCF7 -Val 24h-rep4

description: Sample name: MCF7 -Val-4

source_name: MCF7 cells deprived Valine for 24 hours, biological rep4

value: deprived of Valine


title: MCF7 -Leu 24h-rep1

description: Sample name: MCF7 -Leu-1

source_name: MCF7 cells deprived leucine for 24 hours, biological rep1


title: MCF7 -His 24h-rep2

description: Sample name: MCF7 -His-2

source_name: MCF7 cells deprived histidine for 24 hours, biological rep2

value: deprived of histidine


title: MCF7 -Ile 24h-rep1

description: Sample name: MCF7 -Ile-1

source_name: MCF7 cells deprived isoleucine for 24 hours, biological rep1


title: MCF7 -Leu 24h-rep4

description: Sample name: MCF7 -Leu-4

source_name: MCF7 cells deprived leucine for 24 hours, biological rep4


title: MCF7 -His 24h-rep3

description: Sample name: MCF7 -His-3

source_name: MCF7 cells deprived histidine for 24 hours, biological rep3


title: MCF7 -AA 24h-rep4

description: Sample name: MCF7 -AA-4

source_name: MCF7 cells deprived all amino acids for 24 hours, biological rep4

value: deprived of all amino acids


title: MCF7 -Gln 24h-rep4

description: Sample name: MCF7 -Gln-4

source_name: MCF7 cells deprived glutamine for 24 hours, biological rep4

value: deprived of glutamine


title: MCF7 -AA 24h-rep1

description: Sample name: MCF7 -AA-1

source_name: MCF7 cells deprived all amino acids for 24 hours, biological rep1


title: MCF7 -AA 24h-rep3

description: Sample name: MCF7 -AA-3

source_name: MCF7 cells deprived all amino acids for 24 hours, biological rep3


title: MCF7 -Gln 24h-rep1

description: Sample name: MCF7 -Gln-1

source_name: MCF7 cells deprived glutamine for 24 hours, biological rep1


title: MCF7 -His 24h-rep4

description: Sample name: MCF7 -His-4

source_name: MCF7 cells deprived histidine for 24 hours, biological rep4


title: MCF7 Con 24h-rep3

description: Sample name: MCF7 Con-3

source_name: MCF7 cells in the control media for 24 hours, biological rep3

value: control media


title: MCF7 -Gln 24h-rep2

description: Sample name: MCF7 -Gln-2

source_name: MCF7 cells deprived glutamine for 24 hours, biological rep2


title: MCF7 -Phe 24h-rep4

description: Sample name: MCF7 -Phe-4

source_name: MCF7 cells deprived Phenylalanine for 24 hours, biological rep4

value: deprived of Phenylalanine


title: MCF7 -Trp 24h-rep2

description: Sample name: MCF7 -Trp-2

source_name: MCF7 cells deprived Tryptophan for 24 hours, biological rep2

value: deprived of Tryptophan


title: MCF7 -Gln 24h-rep3

description: Sample name: MCF7 -Gln-3

source_name: MCF7 cells deprived glutamine for 24 hours, biological rep3


title: MCF7 Con 24h-rep4

description: Sample name: MCF7 Con-4

source_name: MCF7 cells in the control media for 24 hours, biological rep4


title: MCF7 -Ile 24h-rep2

description: Sample name: MCF7 -Ile-2

source_name: MCF7 cells deprived isoleucine for 24 hours, biological rep2


title: MCF7 -His 24h-rep1

description: Sample name: MCF7 -His-1

source_name: MCF7 cells deprived histidine for 24 hours, biological rep1


title: MCF7 -AA 24h-rep2

description: Sample name: MCF7 -AA-2

source_name: MCF7 cells deprived all amino acids for 24 hours, biological rep2


title: MCF7 Con 24h-rep2

description: Sample name: MCF7 Con-2

source_name: MCF7 cells in the control media for 24 hours, biological rep2


title: Human NK cell, medium control, donor 7

city: Columbus

first: Kelly

last: Regan

state: Ohio

address: 1800 Cannon Drive

department: Biomedical Informatics

institute: The Ohio State Univ

description:
Gene expression data of human NK cells (medium)
nkco_m7_hu133a_081103_ab

hyb_protocol: Affymetrix GeneChip expression array U133A was hybridized with each prepared cRNA target in duplicate, according to manufacturer's instructions.

scan_protocol: GeneChip Scanner 3000

data_processing: The DNA-Chip Analyzer (dChip) software package implementing model-based expression analysis of oligonucleotide arrays was used to obtain gene expression estimates for the samples in the study. The scanned microarray images were normalized using the invariant set scaling method at the probe level, and then model-based gene expression estimates using the Perfect Match (PM) Only Model were obtained using dChip software.

source_name: NK cell_medium control

label_protocol: First and second strand cDNA was prepared from 8μg of total RNA, and the cDNA was subjected to in vitro transcription in the presence of biotinylated nucleoside triphosphates. The biotinylated cRNA was fragmented to uniform sizes and the integrity of the labeled cRNA was verified by gel electrophoresis.

growth_protocol: Human NK cells were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated pooled human AB serum (HAB) (C-six Diagnostics; Germantown, WI), 100 units/mL of penicillin, 100 μg/mL of streptomycin, and 0.25μg/mL of amphotericin B (10% HAB medium).

extract_protocol: Total cellular RNA from NK cells obtained from individual donors (n=8) was islated and subjected to a cleanup protocol with RNeasy mini kits (Qiagen, Valencia, CA), according to the manufacturer's specifications. The quality of total RNA was assessed using Agilent Bioanalyzer.

treatment_protocol: NK cells were isolated directly from fresh peripheral blood Leukopaks (American Red Cross, Columbus, OH) by 30-minute incubation with RossetteSep cocktail (Stem Cell Technologies, Vancouver, BC), followed by ficoll hypaque density gradient centrifugation. NK cells were > 95% CD65+ by FACS analysis. The CD56dimCD16+ human NK cell population was isolated via FACS sorting of cells stained with CD56-PE and CD16-FITC antibodies, yiellding a population that was >98% pure

tag: donor id

value: donor 7

tag: cell type

value: human natural killer (NK) cells

tag: stimulation condition

value: medium control


title: Human NK cell, medium control, donor 8

description:
Gene expression data of human NK cells (medium)
nkco_m8_hu133a_081103_ab

value: donor 8


title: MCF7 Con 24h-rep1

description: Sample name: MCF7 Con-1

source_name: MCF7 cells in the control media for 24 hours, biological rep1


title: Human NK cell, medium control, donor 5

description:
Gene expression data of human NK cells (medium)
nkco_m5_hu133a_081103_ab

value: donor 5


title: Human NK cell, medium control, donor 2

description:
Gene expression data of human NK cells (medium)
nkcell_M2_133a_060203_ab

value: donor 2


title: Human NK cell, medium control, donor 3

description:
Gene expression data of human NK cells (medium)
nkco_m3_hu133a_081103_ab

value: donor 3


title: Human NK cell, IL-12 stimulation, donor 8

description:
Gene expression data of human NK cells stimulated with IL-12
nkco_il8_hu133a_081103_ab

source_name: NK cell_IL-12 stimulation

value: IL-12 stimulation


title: Human NK cell, medium control, donor 6

description:
Gene expression data of human NK cells (medium)
nkco_m6_hu133a_081103_ab

value: donor 6


title: Human NK cell, IL-12 stimulation, donor 7

description:
Gene expression data of human NK cells stimulated with IL-12
nkco_il7_hu133a_081103_ab


title: Human NK cell, medium control, donor 1

description:
Gene expression data of human NK cells (medium)
nkcell_M1_133a_060203_ab

value: donor 1


title: Human NK cell, IL-12 stimulation, donor 2

description:
Gene expression data of human NK cells stimulated with IL-12
nkcell_IL2_133a_060203_ab


title: Human NK cell, IL-12 stimulation, donor 5

description:
Gene expression data of human NK cells stimulated with IL-12
nkco_il5_hu133a_081103_ab


title: Human NK cell, medium control, donor 4

description:
Gene expression data of human NK cells (medium)
nkco_m4_hu133a_081103_ab

value: donor 4


title: Human NK cell, combined stimulation with IgG and IL-12, donor 8

description:
Gene expression data of human NK cells stimulated with a combination of IgG and IL-12
nkco_gil8_hu133a_081103_ab

source_name: NK cell_combined stimulation with IgG and IL-12

value: Combined stimulation with IgG and IL-12


title: Human NK cell, IL-12 stimulation, donor 1

description:
Gene expression data of human NK cells stimulated with IL-12
nkcell_IL1_133a_060203_ab


title: Human NK cell, IL-12 stimulation, donor 3

description:
Gene expression data of human NK cells stimulated with IL-12
nkco_il3_hu133a_081103_ab


title: Human NK cell, IL-12 stimulation, donor 4

description:
Gene expression data of human NK cells stimulated with IL-12
nkco_il4_hu133a_081103_ab


title: Human NK cell, combined stimulation with IgG and IL-12, donor 6

description:
Gene expression data of human NK cells stimulated with a combination of IgG and IL-12
nkco_gil6_hu133a_081103_ab


title: Human NK cell, IL-12 stimulation, donor 6

description:
Gene expression data of human NK cells stimulated with IL-12
nkco_il6_hu133a_081103_ab


title: Human NK cell, combined stimulation with IgG and IL-12, donor 5

description:
Gene expression data of human NK cells stimulated with a combination of IgG and IL-12
nkco_gil5_hu133a_081103_ab


title: Human NK cell, combined stimulation with IgG and IL-12, donor 7

description:
Gene expression data of human NK cells stimulated with a combination of IgG and IL-12
nkco_gil7_hu133a_081103_ab


title: Human NK cell, combined stimulation with IgG and IL-12, donor 4

description:
Gene expression data of human NK cells stimulated with a combination of IgG and IL-12
nkco_gil4_hu133a_081103_ab


title: Human NK cell, FcR stimulation by immobilized IgG, donor 6

description:
Gene expression data of human NK cells with FcR stimulation by immobilized IgG
nkco_g6_hu133a_081103_ab

source_name: NK cell_FcR stimulation by immobilized IgG

value: FcR stimulation by immobilized IgG


title: Human NK cell, FcR stimulation by immobilized IgG, donor 7

description:
Gene expression data of human NK cells with FcR stimulation by immobilized IgG
nkco_g7_hu133a_081103_ab


title: Human NK cell, FcR stimulation by immobilized IgG, donor 8

description:
Gene expression data of human NK cells with FcR stimulation by immobilized IgG
nkco_g8_hu133a_081103_ab


title: Human NK cell, FcR stimulation by immobilized IgG, donor 3

description:
Gene expression data of human NK cells with FcR stimulation by immobilized IgG
nkco_g3_hu133a_081103_ab


title: Human NK cell, combined stimulation with IgG and IL-12, donor 1

description:
Gene expression data of human NK cells stimulated with a combination of IgG and IL-12
nkcell_GIL1_133a_060203_ab


title: Human NK cell, FcR stimulation by immobilized IgG, donor 4

description:
Gene expression data of human NK cells with FcR stimulation by immobilized IgG
nkco_g4_hu133a_081103_ab


title: Human NK cell, FcR stimulation by immobilized IgG, donor 2

description:
Gene expression data of human NK cells with FcR stimulation by immobilized IgG
nkcell_G2_133a_060203_ab


title: Human NK cell, combined stimulation with IgG and IL-12, donor 2

description:
Gene expression data of human NK cells stimulated with a combination of IgG and IL-12
nkcell_GIL2_133a_060203_ab


title: Human NK cell, combined stimulation with IgG and IL-12, donor 3

description:
Gene expression data of human NK cells stimulated with a combination of IgG and IL-12
nkco_gil3_hu133a_081103_ab


title: Human NK cell, FcR stimulation by immobilized IgG, donor 1

description:
Gene expression data of human NK cells with FcR stimulation by immobilized IgG
nkcell_G1_133a_060203_ab


title: Human NK cell, FcR stimulation by immobilized IgG, donor 5

description:
Gene expression data of human NK cells with FcR stimulation by immobilized IgG
nkco_g5_hu133a_081103_ab


title: Slide 36_hemA vs. WT t=0_biol rep 1_Cy3 hemA Cy5 WT

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

country: United Kingdom

institute: University of Sheffield

description: The labelling procedure uses equal quantities of RNA from adequate CORM-3/iCORM-3 samples and samples prior to addition of CORM-3/iCORM-3.

hyb_protocol: For hybridization to the microarray slides, 400 ng cDNA was added to 25 μl 2 x Hi-RMP Hybridization Buffer and 5 μl 10 x Gene Expression Blocking Agent (Agilent Technologies) to give 50 μl total volume. Custom Gene Expression Microarray slides each containing 8 x 15K arrays were purchased from Agilent Technologies. For hybridization one 8 x Gasket Slide was placed inside a Microarray Hybridization Chamber and samples loaded for 8 different conditions, followed by placement of the microarray slide over the gasket. After sealing the chamber the arrays were incubated at 65 °C, rotating at 10 rpm for ~17 h. Following incubation, the slides were washed in Gene Expression Wash Buffer 1 for 1 min, followed by washing in Gene Expression Wash Buffer 2 for 1 min. Slides were dried and scanned in a microarray scanner (Agilent).

scan_protocol: Scanned on an Agilent DNA microarray scanner with SureScan high-resolution technology.

data_processing: Agilent Feature Extraction Software (v 10.10.1.1) was used for background subtraction and LOWESS normalization.

organism: Escherichia coli

source_name: Batch anaerobically grown cultures in hemA defined medium, prior to CORM-3 addition (t=0)

label_protocol: cDNA synthesis was carried out using 16 μg of RNA, primed with 5 μg Random Primers (Invitrogen). Reaction mixes (30 μl) containing 0.5 mM dATP, dTTP, and dGTP, 0.2 mM dCTP, and 67 μM Cy-3 or Cy-5-dCTP were incubated at 25 °C for 5 min, then at 50 °C overnight with 300 U of Superscript III Reverse Transcriptase (Invitrogen). Following synthesis, cDNA was purified using a PCR purification kit (Qiagen).

extract_protocol: Cells were harvested directly into phenol:ethanol to stabilize RNA and total RNA was purified using Qiagen’s RNeasy Mini Kit, according to the manufacturer's instructions.

tag: strain

value: Wild type strain MG1655

value: prior to CORM-3 addition (t=0)

value: hemA strain MG1655


title: Slide 36_hemA_iCORM-3_biol rep 2_Cy3 120 Cy5 0

source_name: Batch anaerobically grown cultures in hemA defined medium, prior to iCORM-3 addition

value: prior to iCORM-3 addition (t=0)

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM iCORM-3 for 120min

value: exposed to 100uM iCORM-3 for 120min


title: Slide 36_hemA vs. WT t=0_biol rep 2_Cy3 hemA Cy5 WT


title: SSc P42 vs PDGF 12hr

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

description:
PDGF Treatment Time Course 2 12hr
EXPT_ID: 78127
PRINT_ID: 1164

hyb_protocol: Hybridized using Agilent Hyb Kit.

scan_protocol: Data for this experiment was produced with the Agilent Feature Extractor Software.

data_processing: Data for both channels were Lowess-normalized and then the log(2) ratio was taken. Data were filtered for genes with >80% good data.

source_name: SSc P42 vs PDGF 12hr

label_protocol: Labeled using Agilent Quick Amp Labeling Kit.

extract_protocol: Total RNA isolated using Qiagen RNeasy Mini Kit.

treatment_protocol: Storage of human tissue in RNAlater.

value: cultured normal human dermal fibroblasts

source_name: Stratagene Universal Human Reference

extract_protocol: Total RNA isolated by Stratagene.

tag: sample type

value: reference


title: Slide 36_hemA_iCORM-3_biol rep 2_Cy3 60 Cy5 0

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM iCORM-3 for 60min

value: exposed to 100uM iCORM-3 for 60min


title: Slide 36_WT vs. hemA t=0_biol rep 1_Cy3 WT Cy5 hemA


title: SSc P42 vs PDGF 24hr

description:
PDGF Treatment Time Course 2 24hr
EXPT_ID: 78126
PRINT_ID: 1164

source_name: SSc P42 vs PDGF 24hr


title: Slide 35_hemA_iCORM-3_biol rep 2_Cy3 10 Cy5 0

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM iCORM-3 for 10min

value: exposed to 100uM iCORM-3 for 10min


title: Slide 36_WT vs. hemA t=0_biol rep 2_Cy3 WT Cy5 hemA


title: SSc C18 (#2) vs PDGF 24hr

description:
PDGF Treatment Time Course 4 24hr
EXPT_ID: 78118
PRINT_ID: 1164

source_name: SSc C18 (#2) vs PDGF 24hr


title: Slide 36_hemA_iCORM-3_biol rep 2_Cy3 40 Cy5 0

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM iCORM-3 for 40min

value: exposed to 100uM iCORM-3 for 40min


title: Slide 35_hemA_iCORM-3_biol rep 2_Cy3 0 Cy5 120


title: SSc C18 (#2) vs PDGF 8hr

description:
PDGF Treatment Time Course 4 8hr
EXPT_ID: 78112
PRINT_ID: 1164

source_name: SSc C18 (#2) vs PDGF 8hr


title: SSc P42 vs PDGF 0hr (B)

description:
PDGF Treatment Time Course 2 0hr (B)
EXPT_ID: 78124
PRINT_ID: 1164

source_name: SSc P42 vs PDGF 0hr (B)


title: SSc C18 (#2) vs PDGF 4hr

description:
PDGF Treatment Time Course 4 4hr
EXPT_ID: 78113
PRINT_ID: 1164

source_name: SSc C18 (#2) vs PDGF 4hr


title: SSc P42 vs PDGF 0hr (C)

description:
PDGF Treatment Time Course 2 0hr (C)
EXPT_ID: 78123
PRINT_ID: 1164

source_name: SSc P42 vs PDGF 0hr (C)


title: Slide 35_hemA_iCORM-3_biol rep 2_Cy3 0 Cy5 60


title: SSc P42 vs PDGF 8hr

description:
PDGF Treatment Time Course 2 8hr
EXPT_ID: 78120
PRINT_ID: 1164

source_name: SSc P42 vs PDGF 8hr


title: SSc P42 vs PDGF 0hr (A)

description:
PDGF Treatment Time Course 2 0hr (A)
EXPT_ID: 78125
PRINT_ID: 1164

source_name: SSc P42 vs PDGF 0hr (A)


title: Slide 36_hemA_iCORM-3_biol rep 2_Cy3 20 Cy5 0

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM iCORM-3 for 20min

value: exposed to 100uM iCORM-3 for 20min


title: SSc C18 (#2) vs PDGF 2hr

description:
PDGF Treatment Time Course 4 2hr
EXPT_ID: 78114
PRINT_ID: 1164

source_name: SSc C18 (#2) vs PDGF 2hr


title: SSc P42 vs PDGF 4hr

description:
PDGF Treatment Time Course 2 4hr
EXPT_ID: 78121
PRINT_ID: 1164

source_name: SSc P42 vs PDGF 4hr


title: Slide 35_hemA_iCORM-3_biol rep 2_Cy3 0 Cy5 40

source_name: Batch anaerobically grown cultures in hemA defined medium, prior to iCORM-3 addition


title: Slide 35_hemA_iCORM-3_biol rep 2_Cy3 0 Cy5 10


title: Slide 35_hemA_iCORM-3_biol rep 2_Cy3 0 Cy5 20


title: Slide 35_hemA_iCORM-3_biol rep 1_Cy3 120 Cy5 0

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM iCORM-3 for 120min


title: Slide 34_hemA_iCORM-3_biol rep 1_Cy3 40 Cy5 0


title: Slide 35_hemA_iCORM-3_biol rep 1_Cy3 60 Cy5 0


title: SSc C18 (#2) vs PDGF 0hr (C)

description:
PDGF Treatment Time Course 4 0hr (C)
EXPT_ID: 78115
PRINT_ID: 1164

source_name: SSc C18 (#2) vs PDGF 0hr (C)

source_name: Stratagene Universal Human Reference


title: SSc C18 (#2) vs PDGF 12hr

description:
PDGF Treatment Time Course 4 12hr
EXPT_ID: 78128
PRINT_ID: 1164

source_name: SSc C18 (#2) vs PDGF 12hr


title: SSc P42 vs PDGF 2hr

description:
PDGF Treatment Time Course 2 2hr
EXPT_ID: 78122
PRINT_ID: 1164

source_name: SSc P42 vs PDGF 2hr


title: Slide 34_hemA_iCORM-3_biol rep 1_Cy3 20 Cy5 0


title: Slide 34_hemA_iCORM-3_biol rep 1_Cy3 10 Cy5 0

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM iCORM-3 for 10min


title: SSc C18 (#2) vs PDGF 0hr (B)

description:
PDGF Treatment Time Course 4 0hr (B)
EXPT_ID: 78116
PRINT_ID: 1164

source_name: SSc C18 (#2) vs PDGF 0hr (B)


title: Slide 34_hemA_iCORM-3_biol rep 1_Cy3 0 Cy5 120


title: SSc C18 (#1) vs PDGF 12hr

description:
PDGF Treatment Time Course 3 12hr
EXPT_ID: 78184
PRINT_ID: 1164

source_name: SSc C18 (#1) vs PDGF 12hr


title: SSc C18 (#1) vs PDGF 0hr (B)

description:
PDGF Treatment Time Course 3 0hr (B)
EXPT_ID: 78183
PRINT_ID: 1164

source_name: SSc C18 (#1) vs PDGF 0hr (B)


title: Slide 34_hemA_iCORM-3_biol rep 1_Cy3 0 Cy5 60

description: The labelling procedure uses equal quantities of RNA from adequate CORM-3/iCORM-3 samples and samples prior to addition of CORM-3/iCORM-3.

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM iCORM-3 for 60min


title: SSc C18 (#1) vs PDGF 8hr

description:
PDGF Treatment Time Course 3 8hr
EXPT_ID: 78182
PRINT_ID: 1164

source_name: SSc C18 (#1) vs PDGF 8hr


title: SSc C18 (#2) vs PDGF 0hr (A)

description:
PDGF Treatment Time Course 4 0hr (A)
EXPT_ID: 78117
PRINT_ID: 1164

source_name: SSc C18 (#2) vs PDGF 0hr (A)


title: SSc C18 (#1) vs PDGF 2hr

description:
PDGF Treatment Time Course 3 2hr
EXPT_ID: 78189
PRINT_ID: 1164

source_name: SSc C18 (#1) vs PDGF 2hr


title: SSc C18 (#1) vs PDGF 4hr

description:
PDGF Treatment Time Course 3 4hr
EXPT_ID: 78187
PRINT_ID: 1164

source_name: SSc C18 (#1) vs PDGF 4hr


title: Slide 34_hemA_iCORM-3_biol rep 1_Cy3 0 Cy5 20

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM iCORM-3 for 20min


title: Slide 14_Wild type_CORM-3_biol rep 2_Cy3 120 Cy5 0

source_name: Batch anaerobically grown cultures in hemA defined medium, prior to CORM-3 addition

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM CORM-3 for 120min

value: exposed to 100uM CORM-3 for 120min


title: Slide 14_Wild type_CORM-3_biol rep 2_Cy3 60 Cy5 0

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM CORM-3 for 60min

value: exposed to 100uM CORM-3 for 60min


title: NHDF vs PDGF 12hr

description:
PDGF Treatment Time Course 1 12h
EXPT_ID: 78102
PRINT_ID: 1164

source_name: NHDF vs PDGF 12hr


title: SSc C18 (#1) vs PDGF 0hr (C)

description:
PDGF Treatment Time Course 3 0hr (C)
EXPT_ID: 78185
PRINT_ID: 1164

source_name: SSc C18 (#1) vs PDGF 0hr (C)

source_name: Stratagene Universal Human Reference


title: SSc C18 (#1) vs PDGF 24hr

description:
PDGF Treatment Time Course 3 24hr
EXPT_ID: 78188
PRINT_ID: 1164

source_name: SSc C18 (#1) vs PDGF 24hr


title: Slide 14_Wild type_CORM-3_biol rep 2_Cy3 40 Cy5 0

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM CORM-3 for 40min

value: exposed to 100uM CORM-3 for 40min


title: Slide 34_hemA_iCORM-3_biol rep 1_Cy3 0 Cy5 10

source_name: Batch anaerobically grown cultures in hemA defined medium, prior to iCORM-3 addition

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM iCORM-3 for 10min


title: Slide 14_Wild type_CORM-3_biol rep 2_Cy3 20 Cy5 0

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM CORM-3 for 20min

value: exposed to 100uM CORM-3 for 20min


title: Slide 34_hemA_iCORM-3_biol rep 1_Cy3 0 Cy5 40

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM iCORM-3 for 40min


title: NHDF vs PDGF 24hr

description:
PDGF Treatment Time Course 1 24h
EXPT_ID: 78093
PRINT_ID: 1164

source_name: NHDF vs PDGF 24hr


title: SSc C18 (#1) vs PDGF 0hr (A)

description:
PDGF Treatment Time Course 3 0hr (A)
EXPT_ID: 78186
PRINT_ID: 1164

source_name: SSc C18 (#1) vs PDGF 0hr (A)


title: NHDF vs PDGF 8hr

description:
PDGF Treatment Time Course 1 8h
EXPT_ID: 78087
PRINT_ID: 1164

source_name: NHDF vs PDGF 8hr


title: NHDF vs PDGF 4hr

description:
PDGF Treatment Time Course 1 4h
EXPT_ID: 78091
PRINT_ID: 1164

source_name: NHDF vs PDGF 4hr


title: NHDF vs PDGF 0hr (B)

description:
PDGF Treatment Time Course 1 0h #2
EXPT_ID: 78088
PRINT_ID: 1164

source_name: NHDF vs PDGF 0hr (B)


title: Slide 14_Wild type_CORM-3_biol rep 2_Cy3 0 Cy5 120

source_name: Batch anaerobically grown cultures in hemA defined medium, prior to CORM-3 addition


title: Slide 14_Wild type_CORM-3_biol rep 2_Cy3 0 Cy5 60


title: Slide 13_Wild type_CORM-3_biol rep 2_Cy3 0 Cy5 10

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM CORM-3 for 10min

value: exposed to 100uM CORM-3 for 10min


title: Slide 13_Wild type_CORM-3_biol rep 2_Cy3 0 Cy5 20


title: MCF7-E2+EGCG-2

city: Guwahati

first: Anil

middle: Mukund

last: Limaye

state: Assam

address: IIT Guwahati

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Guwahati

hyb_protocol: Agilent’s In situ Hybridization kit

scan_protocol: Agilent's Scanner with SureScan technology. 5 micron resolution

data_processing: Data processing was done in R software environment using LIMMA package. Raw median signal intensities were background subtracted by normexp method and between arrays normalization was done by quantile method. Probe ID replicates were averaged. Lmfit and eBayes (Empirical Bayes) methods were used to identify differentially regulated genes.

source_name: breast cancer cell line (MCF7)

label_protocol: T7 promoter based-linear amplification to generate labeled complementary RNA (One-Color Microarray-Based Gene Expression Analysis). Kit: Agilent’s Low input RNA linear amplification Kit one color

growth_protocol: MCF7 cells were maintained in phenol red containing DMEM-F12 supplemented with 10%FBS. For experiments cells were seeded in 6 well plates at a density of 2*10^5 cells/well in phenol red containing medium. After 48hr spent medium was removed, cells were washed with DPBS and phenol red free DMEM-F12, supplemented with 10% charcoal stripped dextran treated FCS, was added.

extract_protocol: After the After 24hr of treatment the spent medium was removed and cells were lysed in RLT lysis buffer and total RNA was isolated by Qiagen’s RNeasy minikit.

treatment_protocol: Cells were incubated in phenol red free medium for 4hr (to ensure complete removal of phenol red) and treatment was started, after a DPBS wash, by adding fresh phenol red free medium along with appropriate drug or vehicle.

tag: tissue

value: mammary gland/breast

value: epithelial

tag: treated with

value: EGCG + estrogen for 24hrs


title: Slide 14_Wild type_CORM-3_biol rep 2_Cy3 0 Cy5 40

value: Wild type strain MG1655

value: prior to CORM-3 addition (t=0)


title: Slide 13_Wild type_CORM-3_biol rep 1_Cy3 60 Cy5 0

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM CORM-3 for 60min


title: Slide 13_Wild type_CORM-3_biol rep 1_Cy3 40 Cy5 0


title: MCF7-EGCG-2

value: EGCG for 24hrs


title: SSc P42 vs RZN 24 hr

description:
Rosigalitizone Treatment Time Course 2 24h
EXPT_ID: 78100
PRINT_ID: 1164

source_name: SSc P42 vs RZN 24 hr

value: cultured normal human dermal fibroblasts


title: Slide 13_Wild type_CORM-3_biol rep 1_Cy3 10 Cy5 0


title: SSc P42 vs RZN 8 hr

description:
Rosigalitizone Treatment Time Course 2 8h
EXPT_ID: 78094
PRINT_ID: 1164

source_name: SSc P42 vs RZN 8 hr

source_name: Stratagene Universal Human Reference

value: reference


title: NHDF vs PDGF 0hr (A)

description:
PDGF Treatment Time Course 1 0h #1
EXPT_ID: 78090
PRINT_ID: 1164

source_name: NHDF vs PDGF 0hr (A)


title: MCF7-E2+EGCG-1


title: NHDF vs PDGF 2hr

description:
PDGF Treatment Time Course 1 2h
EXPT_ID: 78092
PRINT_ID: 1164

source_name: NHDF vs PDGF 2hr


title: MCF7-E2-1

value: vehicle (EtOH) + estrogen for 24hrs


title: Slide 13_Wild type_CORM-3_biol rep 1_Cy3 0 Cy5 120

description: The labelling procedure uses equal quantities of RNA from adequate CORM-3/iCORM-3 samples and samples prior to addition of CORM-3/iCORM-3.

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM CORM-3 for 120min


title: SSc P42 vs RZN 12 hr

description:
Rosigalitizone Treatment Time Course 2 12h
EXPT_ID: 78101
PRINT_ID: 1164

source_name: SSc P42 vs RZN 12 hr


title: MCF7-EGCG-1


title: NHDF vs PDGF 0hr (C)

description:
PDGF Treatment Time Course 1 0h #3
EXPT_ID: 78089
PRINT_ID: 1164

source_name: NHDF vs PDGF 0hr (C)


title: Slide 15_Wild type_CORM-3_biol rep 1_Cy3 0 Cy5 60


title: Slide 13_Wild type_CORM-3_biol rep 1_Cy3 120 Cy5 0


title: MCF7-E2-2


title: MCF7-EtOH-2

value: vehicle (EtOH) for 24hrs


title: Slide 15_Wild type_CORM-3_biol rep 1_Cy3 0 Cy5 40

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM CORM-3 for 40min


title: Slide 14_Wild type_CORM-3_biol rep 2_Cy3 10 Cy5 0


title: SSc P42 vs RZN 4 hr

description:
Rosigalitizone Treatment Time Course 2 4h
EXPT_ID: 78095
PRINT_ID: 1164

source_name: SSc P42 vs RZN 4 hr


title: Slide 13_Wild type_CORM-3_biol rep 1_Cy3 20 Cy5 0

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM CORM-3 for 20min


title: Slide 15_Wild type_CORM-3_biol rep 1_Cy3 0 Cy5 20


title: Slide 15_hemA_CORM-3_biol rep 2_Cy3 60 Cy5 0

value: hemA strain MG1655


title: SSc P42 vs RZN 2 hr

description:
Rosigalitizone Treatment Time Course 2 2h
EXPT_ID: 78096
PRINT_ID: 1164

source_name: SSc P42 vs RZN 2 hr


title: Slide 15_hemA_CORM-3_biol rep 2_Cy3 120 Cy5 0


title: SSc P42 vs RZN 0 hr (C)

description:
Rosigalitizone Treatment Time Course 2 0h #3
EXPT_ID: 78097
PRINT_ID: 1164

source_name: SSc P42 vs RZN 0 hr (C)


title: Slide 15_Wild type_CORM-3_biol rep 1_Cy3 0 Cy5 10

source_name: Batch anaerobically grown cultures in hemA defined medium, prior to CORM-3 addition


title: Slide 15_hemA_CORM-3_biol rep 2_Cy3 20 Cy5 0


title: Slide 15_hemA_CORM-3_biol rep 2_Cy3 40 Cy5 0


title: SSc P42 vs RZN 0 hr (B)

description:
Rosigalitizone Treatment Time Course 2 0h #2
EXPT_ID: 78098
PRINT_ID: 1164

source_name: SSc P42 vs RZN 0 hr (B)


title: Slide 16_hemA_CORM-3_biol rep 2_Cy3 10 Cy5 0

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM CORM-3 for 10min


title: SSc P42 vs RZN 0 hr (A)

description:
Rosigalitizone Treatment Time Course 2 0h #1
EXPT_ID: 78099
PRINT_ID: 1164

source_name: SSc P42 vs RZN 0 hr (A)


title: NHDF vs RZN 12hr

description:
Rosigalitizone Treatment Time Course 1 12h
EXPT_ID: 78192
PRINT_ID: 1164

source_name: NHDF vs RZN 12hr


title: Slide 16_hemA_CORM-3_biol rep 2_Cy3 0 Cy5 120


title: Slide 16_hemA_CORM-3_biol rep 2_Cy3 0 Cy5 40


title: NHDF vs RZN 24hr

description:
Rosigalitizone Treatment Time Course 1 24h
EXPT_ID: 78196
PRINT_ID: 1164

source_name: NHDF vs RZN 24hr


title: Slide 16_hemA_CORM-3_biol rep 2_Cy3 0 Cy5 60

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM CORM-3 for 60min


title: Slide 17_hemA_CORM-3_biol rep 1_Cy3 40 Cy5 0


title: NHDF vs RZN 8hr

description:
Rosigalitizone Treatment Time Course 1 8h
EXPT_ID: 78190
PRINT_ID: 1164

source_name: NHDF vs RZN 8hr

source_name: Stratagene Universal Human Reference


title: mir-3 ectopic replicate 3 vs. w1118 replicate 3

city: Bethesda

first: Anandarao

last: Ravulapalli

state: maryland

address: 9000 Rockville Pike

department: LBMB

institute: NCI

description: First biological replicate is dye swaped to avoid dye bias

hyb_protocol: Quick Amp Labeling kit (Agilent) Total RNA samples were labeled with Cy3 and Cy5, respectively, and hybridized to Agilent Drosophila melanogaster 4-by-44000 60-mer-oligonucleotide array slides and enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed and scanned.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.7.5).  The data was then processed with Gene Spring data analysis program.

organism: Drosophila melanogaster

source_name: mir-3 ectopic expressed embryo

label_protocol: Total RNA was extracted with Trizol reagent (Invitrogen) according to the manufacturer's instructions and then passed through the RNeasy Mini Kit columns(Qiagen) after DNAse I digestion. RNA quality was monitored using Agilent RNA Bioanalyzer 2100 analysis and RNA quantification was carried out on a Nanodrop ND-1000. Array analysis was performed according to the manufacturers instructions using the Quick Amp Labeling kit (Agilent).

growth_protocol: Wild type (w1118) and mir-3 ectopic expressed mutant flies were maintained at 25oC and collected embryo for 2 hours. After egg laying the embryo were kept at 6 hours at 25oC.Then isolated total RNA.

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

treatment_protocol: wild type and mir-3 ectopic expressed embryos were treated same.mutant embryos are homozygous for mir-3 ectopic expression.

tag: Stage

value: 6-8hr after egg laying

tag: genetic background

tag: genotype

value: miR-3 ectopic expressing mutant

value: embryo

source_name: w1118 embryo

value: wild type


title: Slide 16_hemA_CORM-3_biol rep 1_Cy3 120 Cy5 0

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM CORM-3 for 120min

value: exposed to 100uM CORM-3 for 120min


title: mir-3 ectopic replicate 1 vs. w1118 replicate 1


title: Slide 16_hemA_CORM-3_biol rep 1_Cy3 60 Cy5 0

value: exposed to 100uM CORM-3 for 60min


title: MCF7-EtOH-1

source_name: breast cancer cell line (MCF7)

value: mammary gland/breast


title: 8-miR cltr null replicate 3 vs. w1118 replicate 3

description: First biological replicate is dye swaped to avoid any dye bias

source_name: 8-miR cluster null embryo

growth_protocol: Wild type (w1118) and 8-miR cluster null mutant flies were maintained at 25oC and collected embryo for 2 hours. After egg laying the embryo were kept at 6 hours at 25oC.Then isolated total RNA.

treatment_protocol: Wild type and mir-3 ectopic expressed embryos were treated same. mutant embryos are homozygous for mir-3 ectopic expression.

value: miR-8 cluster null


title: Slide 17_hemA_CORM-3_biol rep 1_Cy3 10 Cy5 0

value: exposed to 100uM CORM-3 for 10min


title: Slide 16_hemA_CORM-3_biol rep 2_Cy3 0 Cy5 10


title: w1118 replicate 1 vs 8-miR cltr null replicate 1


title: mir-3 ectopic replicate 2 vs. w1118 replicate 2


title: Slide 16_hemA_CORM-3_biol rep 2_Cy3 0 Cy5 20

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM CORM-3 for 20min

value: exposed to 100uM CORM-3 for 20min


title: NHDF vs RZN 4hr

description:
Rosigalitizone Treatment Time Course 1 4h
EXPT_ID: 78195
PRINT_ID: 1164

source_name: NHDF vs RZN 4hr


title: w1118 replicate 1 vs mir-3 ectopic replicate 1


title: NHDF vs RZN 2hr

description:
Rosigalitizone Treatment Time Course 1 2h
EXPT_ID: 78197
PRINT_ID: 1164

source_name: NHDF vs RZN 2hr


title: 8-miR cltr null replicate 2 vs. w1118 replicate 2


title: NHDF vs RZN 0hr (B)

description:
Rosigalitizone Treatment Time Course 1 0h #2
EXPT_ID: 78191
PRINT_ID: 1164

source_name: NHDF vs RZN 0hr (B)


title: Slide 17_hemA_CORM-3_biol rep 1_Cy3 0 Cy5 60

source_name: Batch anaerobically grown cultures in hemA defined medium, prior to CORM-3 addition

value: prior to CORM-3 addition (t=0)


title: NHDF vs RZN 0hr (A)

description:
Rosigalitizone Treatment Time Course 1 0h #1
EXPT_ID: 78194
PRINT_ID: 1164

source_name: NHDF vs RZN 0hr (A)


title: Slide 17_hemA_CORM-3_biol rep 1_Cy3 0 Cy5 120

description: The labelling procedure uses equal quantities of RNA from adequate CORM-3/iCORM-3 samples and samples prior to addition of CORM-3/iCORM-3.


title: w1118 replicate 3 vs. nautilus null replicate 3

description: Third biological replicate is dye swaped to avoid any dye bias

hyb_protocol: EXIQON carried out the hybridization using miRCURY LNA Array (v.9.2).

scan_protocol: standard Exiqon protocol

data_processing: standard Exiqon protocol

source_name: nautilus null embryo

label_protocol: After having passed sample QC on bioanalyzer 2100 and RNA measurement on nanodrop instrument, the samples were labeled using the miRCURY Hy3/Hy5 power labeling kit by EXIQON.

growth_protocol: Wild type (w1118) and nautilus null mutant flies were maintained at 25oC and collected embryo for 2 hours. After egg laying the embryo were kept at 6 hours at 25oC.Then isolated total RNA.

treatment_protocol: wild type and mutant embryos were treated same.mutant embryos are homozygous for nautilus gene deletion.

value: nautilus null


title: NHDF vs RZN 0hr (C)

description:
Rosigalitizone Treatment Time Course 1 0h #3
EXPT_ID: 78193
PRINT_ID: 1164

source_name: NHDF vs RZN 0hr (C)

value: cultured normal human dermal fibroblasts


title: Slide 17_hemA_CORM-3_biol rep 1_Cy3 20 Cy5 0


title: nautilus null replicate 2 vs. w1118 replicate 2


title: nautilus null replicate 1 vs. w1118 replicate 1


title: Slide 17_hemA_CORM-3_biol rep 1_Cy3 0 Cy5 40

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM CORM-3 for 40min

value: exposed to 100uM CORM-3 for 40min


title: Slide 17_hemA_CORM-3_biol rep 1_Cy3 0 Cy5 20


title: MLd3-2

city: Yonago

first: Akira

last: Hasegawa

state: Tottori

address: 36-1, Nishimachi

department: Department of Genetic Medicine and Regenerative Therapeutics

country: Japan

institute: Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science,Tottori University

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (Whole Mouse Genome Microarray Kit v1 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

organism: Mus musculus

source_name: mouse Embryonic stem cells, Mono layer day 3, clone #2

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from cells using RNeasy micro kit(Qiagen).

value: Embryonic stem cells


title: EBd3-2

source_name: mouse Embryonic stem cells, Embryoid body day 3, clone #2


title: MLd1-2

source_name: mouse Embryonic stem cells, Mono layer day 1, clone #2


title: EBd4-1

source_name: mouse Embryonic stem cells, Embryoid body day 4, clone #1


title: MLd3-1

source_name: mouse Embryonic stem cells, Mono layer day 3, clone #1


title: MLd1-1

source_name: mouse Embryonic stem cells, Mono layer day 1, clone #1


title: 8-miR cltr null  replicate 1 vs. w1118 replicate 1

source_name: w1118 embryo


title: Slide 17_hemA_CORM-3_biol rep 1_Cy3 0 Cy5 10

source_name: Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM CORM-3 for 10min


title: EBd1-2

source_name: mouse Embryonic stem cells, Embryoid body day 1, clone #2


title: EBd4-2

source_name: mouse Embryonic stem cells, Embryoid body day 4, clone #2


title: EBd1-1

source_name: mouse Embryonic stem cells, Embryoid body day 1, clone #1


title: Ethylene treated cortical cells vs Ethylene untreated cortical cells_rep3_color swap

city: Nagoya

first: Hirokazu

last: Takahashi

state: Aichi

address: Furo-cho, Chikusa

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

description: Gene expression in maize cortical cells between under Ethylene-treated and untreated conditions.

hyb_protocol: Fragmentation and hybridization was carried out with Gene Expression Hybridization Kit (Agilent).  cRNA was hybridized to microarray using hybridization oven G2531A (Agilent), and wash step was performed with Gene Expression Wash Buffer Kit (Agilent). All operations were performed according to manufacturer's protocol.

scan_protocol: Microarrays were scanned using Agilent DNA microarray scanner G2505C  according to manufacturer's instructions.

data_processing: Scanned tiff image files were analyzed with Feature Extraction software version 10.5.1.1 (Agilent). The normalization algorithm is defined by the Agilent Feature Extraction protocol for 2 color gene expression arrays (protocol name: GE2_105_Dec08). Data was normalized using a Linear and LOWESS method in Agilent Feature Extraction software.

organism: Zea mays

source_name: Cortical cells of maize primary root untreated with ethylene

label_protocol: Cy3and Cy5-labeled cRNA were prepared from total RNA using Low RNA Input Linear Amplification Kit (Agilent) in accordance with the manufacturer's protocol with slight modification.

growth_protocol: 8 seeds were placed on moist chromatography paper and rolled up in the paper. The paper was placed in a 2 L gray pot contained with 100 mL deionized water.  After 3 days, the pot was placed in a tightly closed container with or without 1 ppm ethylene gas for 6 hours.

extract_protocol: Total RNA was extracted from the LM-isolated tissues using a PicoPureTM RNA isolation kit (Life Technologies) according to the manufacturer’s instructions.

treatment_protocol: The basal part of the primary root (15-20 mm from the root-shoot junction) was fixed in 75% ethanol: 25% acetic acid. After dehydration in a graded ethanol series, the tissues were embedded in paraffin and sectioned at a thickness of 16 μm. Cortical cells were collected from the root cross sections using a Veritas Laser Microdissection System LCC1704  as described by Takahashi et al., (2010).

tag: inbred line

value: primary root

source_name: Cortical cells of maize primary root treated with ethylene


title: EBd3-1

source_name: mouse Embryonic stem cells, Embryoid body day 3, clone #1


title: TMD231-2 Cell Line

city: PHILADELPHIA

first: Chirayu

middle: Pankaj

last: Goswami

state: PA

address: 110 S 11TH STREET

department: MOLECULAR DIAGNOSTIC LABORATORY

institute: THOMAS JEFFERSON UNIVERSITY HOSPITAL

description:
SAMPLE 19
6260962079_C

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Illumina Genome Studio calculated average intensity values and corresponding signal p values
Probe level data was imported into partek genomics suite for differential expression analysis. Data post processing was done in Partek. ANOVA analysis was performed to identify genes differentially expressed between different cell lines

label_protocol: Microarray with biological triplicates was performed using Illumina HumanHT-12 V4 expression beadchip. Standard Illumina label protocol was used.

growth_protocol: Cells were maintained in MEM and 10% fetal calf serum.

extract_protocol: RNA was prepared using RNeasy kit (Qiagen, Valencia, CA, USA) and cDNA from two μgs of RNA was synthesized using the cDNA Synthesis kit (Bio- Rad, Hercules, CA, USA). qRT-PCR was performed using SyberGreen on a TaqMan 7900HT instrument (Applied Biosystems, Carlsbad, CA, USA).

tag: cell line origin

value: TUMOR DERIVATIVE

tag: cell line lineage


title: TMD231-1 Cell Line

description:
SAMPLE 18
6260962064_H


title: Ethylene treated cortical cells vs Ethylene untreated cortical cells_rep2_color swap


title: Ethylene treated cortical cells vs Ethylene untreated cortical cells_rep1_color swap


title: MD231-3 Cell Line

description:
SAMPLE 16
6260962079_E

value: PARENTAL


title: MD231p-3 Cell Line

description:
SAMPLE 17
6260962079_F

value: PARENTAL FOR BrMD231


title: Ethylene treated cortical cells vs Ethylene untreated cortical cells_rep3


title: MD231p-2 Cell Line

description:
SAMPLE 15
6260962064_J


title: MD231p-1 Cell Line

description:
SAMPLE 13
6260962064_C


title: Ethylene treated cortical cells vs Ethylene untreated cortical cells_rep1


title: MD231-1 Cell Line

description:
SAMPLE 12
6260962064_B


title: LIF-2

source_name: mouse Embryonic stem cells, undifferentiated state, clone #2


title: MD231-2 Cell Line

description:
SAMPLE 14
6260962064_I


title: cumulus_cell_replication3

city: Tsukuba

first: Kimiko

last: Inoue

state: Ibaraki

address: 3-1-1 Koyadai

department: Bioresource Engineering Division

institute: BRC, RIKEN

description: Gene expression of cumulus cell used for nuclear donor

hyb_protocol: Cy3 labelled RNA was hybridized to a Whole Mouse Genome oligo DNA microarray (Agilent Technologies) for 16 h at 65 °C according to the manufacturer’s instructions.

scan_protocol: Scanning of microarray slides was performed with a DNA microarray scanner at 5 μm resolution (Agilent Technologies).

data_processing: Scanned image files were processed to give signal intensities using Feature Extraction software (version 9.5.3.1, Agilent Technologies). All raw data were loaded into Gene Spring GX 12.5 software (Agilent Technologies) and normalized by default settings.

source_name: nuclear donor cumulus cell

label_protocol: Amplified RNA was labelled with Cy3 dye (GE Healthcare).

growth_protocol: At 15 h after the hCG injection, cumulus–oocyte complexes were collected from the oviducts and the cumulus cells were dispersed in potassium-enriched simplex optimised medium (KSOM) containing 0.1% bovine testicular hyaluronidase. In vitro fertilized or cloned embryos were cultured with KSOM for 24 hrs at 37°C in a humidified atmosphere containing 6.0% CO2.

extract_protocol: Total RNA was extracted with TRIzol (Life Technologies) from 10 cloned 2-cell embryos cultured for 24 hrs. RNA was subjected to two rounds of linear amplification using TargetAmp Two-Round Aminoallyl-aRNA Amplification Kits (Epicentre) according to the manufacturer’s instructions. For oocytes, control 2-cell embryos and nuclear donor cells, 10 pooled MII oocytes, 10 pooled IVF-derived 2-cell embryos and 500 cumulus cells were all subjected to total RNA extraction and two rounds of RNA amplification.

treatment_protocol: For TSA treatment, 5 nM was added into each culture medium from activation for 8 hrs. Spi-C mRNA was injected by a Piezo-driven micromanipulator into cytoplasts of pronuclear stage embryos.

tag: developmental stage

tag: concentration

tag: no. of embryos/cells


title: Ethylene treated cortical cells vs Ethylene untreated cortical cells_rep2


title: LMD231-1 Cell Line

description:
SAMPLE 10
6260962064_F

tag: cell line

value: LUNG

value: METASTATIC


title: LMD231-3 Cell Line

description:
SAMPLE 11
6260962079_I


title: cumulus_cell_replication2

tag: treatment


title: cumulus_cloned_embryo_with_0.1mg/ml_Spi-C_mRNA_replication3

description: Gene expression of 2-cell stage cumulus cloned embryo cultured for 24hrs after activation, 0.1mg/ml Spi-C mRNA injected at pronuclear stage

source_name: cumulus cloned embryo, 2-cell stage, Spi-C mRNA injected

value: 2-cell stage embryo

value: Spi-C mRNA


title: cumulus_cell_replication4


title: LIF-1

source_name: mouse Embryonic stem cells, undifferentiated state, clone #1

tag: cell type


title: cumulus_cell_replication1


title: cumulus_cloned_embryo_with_0.1mg/ml_Spi-C_mRNA_replication4


title: BrMD231-1 Cell Line

description:
SAMPLE 7
6260962064_D

value: BRAIN


title: cumulus_cloned_embryo_with_0.1mg/ml_Spi-C_mRNA_replication1


title: cumulus_cloned_embryo_with_0.1mg/ml_Spi-C_mRNA_replication2


title: BrMD231-3 Cell Line

description:
SAMPLE 9
6260962079_G


title: BMD231-3 Cell Line

description:
SAMPLE 6
6260962079_H

value: BONE


title: Metastasis medulloblastoma sample_MDT-AP-2014_expression

city: Toronto

first: Xin

last: Wang

state: Ontario

address: 686 Bay Street

department: Laboratory Medicine and Pathobiology

country: Canada

institute: Hospital for Sick Children

hyb_protocol: As directed by Affymetrix.

scan_protocol: As directed by Affymetrix.

data_processing: Normalized expression generated by Expression Console using Affymetrix default analysis settings and Robust Multi-array average (RMA) as normalization method.

source_name: Metastasis human brain tumor sample

label_protocol: As directed by Affymetrix.

extract_protocol: Total RNA was extracted from frozen medulloblastoma tissue using the Trizol method (Invitrogen) as directed by the manufacturer.  RNA integrity was assessed using the Agilent 2100 Bioanalyzer prior to processing for the Gene Array.  Samples with RIN values equal to / greater 7 were included in the study.

tag: sample

tag: sample id

tag: patient id

value: brain

value: medulloblastoma

tag: tumor type

value: metastasis

tag: age

tag: histology

tag: Sex

tag: death

tag: subgroup


title: BrMD231-2 Cell Line

description:
SAMPLE 8
6260962064_K

tag: cell line origin


title: Metastasis medulloblastoma sample_MDT-AP-2305_expression

tag: tissue

value: F


title: Primary medulloblastoma sample_MDT-AP-2305_expression

source_name: Primary human brain tumor sample

value: primary


title: cumulus_cloned_embryo_with_1.0mg/ml_Spi-C_mRNA_replication4

description: Gene expression of 2-cell stage cumulus cloned embryo cultured for 24hrs after activation, 1.0mg/ml Spi-C mRNA injected at pronuclear stage

tag: strain

tag: developmental stage


title: Metastasis medulloblastoma sample_MDT-AP-2126_expression

value: Classic


title: Primary medulloblastoma sample_MDT-AP-2126_expression


title: cumulus_cloned_embryo_with_1.0mg/ml_Spi-C_mRNA_replication2

tag: concentration

tag: no. of embryos/cells


title: BMD231-1 Cell Line

description:
SAMPLE 4
6260962064_E

tag: cell line

tag: cell line lineage


title: ADMD231-2 Cell Line

description:
SAMPLE 2
6260962079_B

value: ADRENAL


title: BMD231-2 Cell Line

description:
SAMPLE 5
6260962064_L


title: Metastasis medulloblastoma sample_MDT-AP-1398_expression

tag: sample

tag: cell type


title: cumulus_cloned_embryo_with_TSA_replication6

description: Gene expression of 2-cell stage cumulus cloned embryo cultured for 24hrs after activation, 5nM TSA treated for 8hrs

source_name: cumulus cloned embryo, 2-cell stage, TSA treated, 8hrs

tag: treatment

value: Trichostatin A


title: cumulus_cloned_embryo_with_1.0mg/ml_Spi-C_mRNA_replication1


title: ADMD231-1 Cell Line

description:
SAMPLE 1
6260962064_G


title: cumulus_cloned_embryo_with_TSA_replication4


title: cumulus_cloned_embryo_with_1.0mg/ml_Spi-C_mRNA_replication3


title: cumulus_cloned_embryo_with_TSA_replication2


title: cumulus_cloned_embryo_with_TSA_replication5


title: ADMD231-3 Cell Line

description:
SAMPLE 3
6260962079_J


title: Melanoma tumor sample from patient 214

city: Lund

first: Göran

last: Jönsson

address: Scheelevägen 8

country: Sweden

institute: Lund University

description:
replicate 1
LuM214

hyb_protocol: Standard protocol for Whole-Genome Expression Direct Hybridization Assay was used (Illumina).

scan_protocol: Arrays were scanned using the iScan Reader (Illumina).

data_processing: The data was normalized using the cubic spline method.

source_name: Malignant melanoma

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

extract_protocol: Total RNA was extracted using the Allprep kit (DNA/RNA mini kit) from Qiagen in accordance with the prescribed protocol provided with the kit. Quality control was performed using a Bioanalyser (Agilent).

tag: gender

value: Male

tag: tumor stage

value: Regional

value: Lymph node

tag: distant metastasis free survival in days

tag: distant metastasis free survival (1=death, 0=alive)

tag: disease specific survival in days

tag: disease specific survival (1=death, 0=alive)


title: Primary medulloblastoma sample_MDT-AP-1398_expression

tag: sample id

tag: patient id

tag: tumor type

tag: age

tag: histology

tag: Sex

tag: death

tag: subgroup


title: cumulus_cloned_embryo_without_TSA_replication7

description: Gene expression of 2-cell stage cumulus cloned embryo cultured for 24hrs after activation

source_name: cumulus cloned embryo, 2-cell stage

tag: strain

tag: developmental stage

tag: concentration

tag: no. of embryos/cells


title: Melanoma tumor sample from patient 212

description:
replicate 1
LuM212

tag: gender

value: Female

tag: tumor stage

tag: tissue


title: Primary medulloblastoma sample_MDT-AP-0586_expression

tag: sample

tag: cell type

value: LCA

value: M


title: Metastasis medulloblastoma sample_MDT-AP-0586_B_expression

tag: sample id


title: cumulus_cloned_embryo_with_TSA_replication1

value: 2-cell stage embryo

tag: treatment


title: Primary medulloblastoma sample_MDT-AP-1323_expression

tag: patient id

tag: tumor type


title: Metastasis medulloblastoma sample_MDT-AP-1323_expression

tag: age

tag: histology


title: cumulus_cloned_embryo_with_TSA_replication3


title: cumulus_cloned_embryo_without_TSA_replication8


title: cumulus_cloned_embryo_without_TSA_replication5


title: Metastasis medulloblastoma sample_MDT-AP-0527_A_expression

tag: Sex

tag: death


title: Melanoma tumor sample from patient 209

description:
replicate 1
LuM209

value: In-transit

tag: distant metastasis free survival in days

tag: distant metastasis free survival (1=death, 0=alive)

tag: disease specific survival in days

tag: disease specific survival (1=death, 0=alive)


title: Melanoma tumor sample from patient 213

description:
replicate 1
LuM213

tag: gender


title: Metastasis medulloblastoma sample_MDT-AP-0586_A_expression

tag: subgroup


title: cumulus_cloned_embryo_without_TSA_replication6

tag: strain

tag: developmental stage

tag: concentration

tag: no. of embryos/cells


title: Melanoma tumor sample from patient 210

description:
replicate 1
LuM210

tag: tumor stage

tag: tissue


title: Metastasis medulloblastoma sample_MDT-AP-0527_B_expression

tag: sample

tag: sample id

tag: patient id

tag: cell type

tag: tumor type


title: Melanoma tumor sample from patient 211

description:
replicate 1
LuM211

tag: age

tag: distant metastasis free survival in days


title: cumulus_cloned_embryo_without_TSA_replication4

tag: treatment


title: Melanoma tumor sample from patient 207

description:
replicate 1
LuM207

tag: distant metastasis free survival (1=death, 0=alive)

tag: disease specific survival in days

tag: disease specific survival (1=death, 0=alive)


title: Melanoma tumor sample from patient 208

description:
replicate 1
LuM208

tag: gender

value: Cutaneous


title: Metastasis medulloblastoma sample_MDT-AP-0522_A_expression

value: brain

tag: histology

tag: Sex

tag: death

tag: subgroup


title: Primary medulloblastoma sample_MDT-AP-0527_expression

tag: tissue

value: medulloblastoma


title: Melanoma tumor sample from patient 205

description:
replicate 1
LuM205

tag: tumor stage


title: Melanoma tumor sample from patient 206

description:
replicate 1
LuM206

value: Subcutaneous


title: Metastasis medulloblastoma sample_MDT-AP-0522_B_expression

tag: sample

tag: sample id

value: metastasis


title: Melanoma tumor sample from patient 204

description:
replicate 1
LuM204

value: General


title: Metastasis medulloblastoma sample_MDT-AP-0586_C_expression

tag: patient id

tag: cell type


title: cumulus_cloned_embryo_without_TSA_replication1

tag: strain

tag: developmental stage

tag: concentration

tag: no. of embryos/cells


title: cumulus_cloned_embryo_without_TSA_replication3

tag: treatment


title: Melanoma tumor sample from patient 203

description:
replicate 1
LuM203

tag: age

tag: distant metastasis free survival in days

tag: distant metastasis free survival (1=death, 0=alive)

tag: disease specific survival in days

tag: disease specific survival (1=death, 0=alive)


title: cumulus_cloned_embryo_without_TSA_replication2


title: Primary medulloblastoma sample_MDT-AP-0522_expression

tag: tumor type

value: primary

tag: histology

tag: Sex

tag: death

tag: subgroup


title: in_vitro_fertilized_embryo_replication5

description: Gene expression of 2-cell stage in vitro fertilized embryo cultured for 24 hrs after insemination

source_name: in vitro fertilized embryo, 2-cell stage


title: in_vitro_fertilized_embryo_replication6


title: Melanoma tumor sample from patient 202

description:
replicate 1
LuM202

tag: gender

tag: tumor stage

tag: tissue


title: in_vitro_fertilized_embryo_replication2

tag: strain

tag: developmental stage


title: Melanoma tumor sample from patient 201

description:
replicate 1
LuM201


title: Metastasis medulloblastoma sample_MDT-AP-0321_expression

tag: sample

tag: sample id

tag: patient id

tag: cell type

value: Classic

value: F


title: in_vitro_fertilized_embryo_replication4

tag: treatment

tag: concentration

tag: no. of embryos/cells


title: Primary medulloblastoma sample_MDT-AP-0321_expression

tag: tumor type

tag: age


title: in_vitro_fertilized_embryo_replication3


title: in_vitro_fertilized_embryo_replication1


title: Melanoma tumor sample from patient 198

description:
replicate 1
LuM198

value: Male

tag: distant metastasis free survival in days

tag: distant metastasis free survival (1=death, 0=alive)

tag: disease specific survival in days

tag: disease specific survival (1=death, 0=alive)


title: Primary medulloblastoma sample_MDT-AP-2014_expression

tag: histology

tag: Sex

tag: death

tag: subgroup


title: Melanoma tumor sample from patient 196

description:
replicate 1
LuM196

tag: gender

tag: tumor stage

tag: tissue

value: Visceral


title: Melanoma tumor sample from patient 200

description:
replicate 1
LuM200

value: Regional

value: Lymph node


title: LS411N-5FU-R+VA 0nM_2

city: Augusta

first: Kebin

last: Liu

state: GA

address: 1410 Laney Walker Blvd

department: Biochemistry and Molecular Biology

institute: Medical College of Georgia

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: GC-RMA

label_protocol: Biotinylated cDNAs were prepared according to the standard Ambion and Affymetrix protocol from 250 ng total RNA (The Ambion WT Expression Kit and GeneChip Terminal Labeling Kit, Affymetrix).

growth_protocol: Cells were cultured in RPMI medium plus 10% FBS for 3 days in a CO2 incubator before RNA isolation

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

treatment_protocol: Cells were cultured in the absence (control) or presence of 50 nM verticillin A for 3 days

tag: cell line


title: unfertilized_oocyte_replication6

description: Gene expression of metaphase II unfertilized oocytes used for recipient

source_name: unfertilized oocyte

tag: strain

tag: developmental stage

value: metaphase II oocyte

tag: treatment


title: unfertilized_oocyte_replication7

tag: concentration

tag: no. of embryos/cells


title: Melanoma tumor sample from patient 199

description:
replicate 1
LuM199

tag: age

tag: distant metastasis free survival in days


title: LS411N-5FU-R+VA 50nM_2

value: verticillin A


title: HVL31

city: Pittsburgh

first: Velpandi

last: Ayyavoo

address: 130 Desoto street, University

institute: Velpandi Ayyavoo

data_processing:
Each run was exported separately using an auto detection threshold. The data were then uploaded to RealTime StatMiner software (Integromics, PA) for further analysis. Detectability threshold for miRNA assays was set to Ct value less than or equal to 35 and at least 25% of all samples in each group. We used Grubbs method to eliminate outliers within technical replicates and Genorm method to select endogenous control that is U6-snRNA/mammU6 for normalization based on stability scoring across the samples in each group. Differentially expressed miRNA between different groups were identified using parametric t-test or LIMMA (one factor analysis) and were then sorted using Benjamini-Hochberg false discovery rate (FDR) method with adjusted p-value <0.05. The fold changes were obtained using linear RQ values.
The fold change worksheet reports low viral load/control, high viral/control, and high viral load/load viral load ratios.

label: FAM

source_name: PBMC, High viral load

label_protocol: Reverse transcription was performed using the Taqman MicroRNA Reverse Transcription kit (Applied Biosystems) following the manufacturer's instructions. Quantitative Real Time PCR was performed using Microfluidic Cards-Human MicroRNA card set v3.0 (Applied Biosystems) using the ViiA 7 Real Time PCR system, following the manufacturer's instructions and using the comparative CT and standard settings.

extract_protocol: Total RNA from PBMCs was extracted with MirVana isolation kit (Applied Biosystems)

value: PBMC

tag: hiv status

value: High viral load


title: unfertilized_oocyte_replication4


title: Melanoma tumor sample from patient 194

description:
replicate 1
LuM194

value: Female

tag: distant metastasis free survival (1=death, 0=alive)

tag: disease specific survival in days

tag: disease specific survival (1=death, 0=alive)


title: unfertilized_oocyte_replication5


title: HVL30


title: HVL29


title: Melanoma tumor sample from patient 193

description:
replicate 1
LuM193


title: Melanoma tumor sample from patient 195

description:
replicate 1
LuM195

value: Primary

value: Cutaneous


title: Melanoma tumor sample from patient 191

description:
replicate 1
LuM191

value: Subcutaneous


title: Melanoma tumor sample from patient 190

description:
replicate 1
LuM190


title: unfertilized_oocyte_replication3


title: Melanoma tumor sample from patient 197

description:
replicate 1
LuM197


title: unfertilized_oocyte_replication2


title: Melanoma tumor sample from patient 189

description:
replicate 1
LuM189


title: Melanoma tumor sample from patient 192

description:
replicate 1
LuM192


title: Melanoma tumor sample from patient 188

description:
replicate 1
LuM188


title: LS411N-5FU-R+VA 0nM_1


title: LS411N-5FU-R+VA 50nM_1


title: HVL26


title: unfertilized_oocyte_replication1


title: HVL25


title: HVL24


title: ES_cells_Control_8hours.5

city: Maastricht

first: Kasper

last: Derks

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Center

description:
Quality Control: Approved
Control.3

hyb_protocol: Amplified materials were hybridized to Mouse Genome HT MG-430 PM Affymetrix for 16 hours at 45°C, subsequently washed and stained with the HWS Kit (#901530)

scan_protocol: Samples were finally scanned using the GeneChip Scanner 3000-7G (Affymetrix Inc., Santa Clara, CA, USA). Image generation and feature extraction were performed using Affymetrix GCOS Software v1.4.0.036.

data_processing: The data were analyzed with Affy and Limma packages from the Bioconductor project for the R statistical languaje. RMA was used to correct background, normalize and summarize expression values per each probe set. Mixed linear model with coeficients was used to identify the differentially expressed genes, false discovery rate correction was perfomed using the Benjamini and Hochberg methodology.

label_protocol: mRNA was amplified and labeled with the 3'IVT-Express Labeling Kit (#901229) according to the manufacturer’s instructions  (Affymetrix Inc., Santa Clara, CA, USA).

growth_protocol: Cells were grown for 2 passages on feeder coated plates and 1 pasage on gelatin coated plates before taken into experiment

extract_protocol: miRNeasy kit (qiagen) used to extract Total RNA

treatment_protocol: 2.5uM of Cisplatin or DMSO (volume equal of 100%) was added to the medium.

value: Control DMSO

tag: time

value: 8 hr

tag: cell type

value: HPRT deficient ES cells

tag: passage


title: Melanoma tumor sample from patient 187

description:
replicate 1
LuM187

tag: gender

tag: tumor stage


title: ES_cells_Control_8hours.6

description:
Quality Control: Approved
Control.4


title: HVL21

tag: tissue


title: Melanoma tumor sample from patient 186

description:
replicate 1
LuM186


title: HVL22


title: ES_cells_Control_8hours.4

description:
Quality Control: Approved
Control.2

tag: strain


title: Melanoma tumor sample from patient 184

description:
replicate 1
LuM184


title: ES_cells_Cisplatin_8hours.5

description:
Quality Control: Approved
Cisplatin.3

value: Cisplatin


title: MammaryTissue_HFRS.P4_HF.P3_4065_cy3

city: Saint-genes-champanelle

first: Anne

last: de la Foye

address: INRA-UMRH

country: France

institute: INRA

description:
HFRS.P4_HF.P3_4065_cy3
Biological replicate 8 of 8 and technical replicate 2 of 2. Control diet vs supplemented diet from the same cow

hyb_protocol: Hybridizations were performed with 40 pmol of incorporated Cy3 for the mammary mRNA of one control cow (HF or LF) and 40 pmol of incorporated Cy5 for the mammary mRNA of the same cow receiving the lipid-supplemented diet (HF-RS or LF-SO). Each RNA sample was also labeled with the dyes swapped to eliminate artifacts resulting from variation in the incorporation of the different dyes in the experimental and control samples. Each slide was prepared with RNA extracted from an individual cow receiving one basal diet (e.g. LF) during one period and the same cow with the same basal diet supplemented in lipid (e.g. LF-SO) during another period. Thus, a total of 46 microarrays (12 HF vs. HF-RS and 11 LF vs. LF-SO comparisons in a dye-swapped manner) were run. Hybridization of the microarrays with fluorescently labeled cDNA was conducted in a Ventana hybridization system (Ventana Medical Systems, S.A, Illkirch, France) at 42°C for 8 h,

scan_protocol: The fluorescence intensity was scanned at 10 µm using an Agilent G2505B Microarray Scanner (Agilent Technologies, Inc., Santa Clara, CA, USA).

data_processing: background corrected data (normexp + offset method according to Ritchie 2007), LOWESS normalized,  block-effect corrected via the subtraction of the median by block, inter-arrays normalized via Median Absolute Deviation scali ng

organism: Bos taurus

source_name: mammary gland_HF

label_protocol: 5µg of total RNA was used to synthesize fluorescently labeled cDNA in the presence of either Cy3- or Cy5-dCTP (GE Healthcare Europe GmbH, Orsay, France) using the Pronto ChipShot™ Direct Labeling Kit (Corning, Avon, France). The labeled cDNA was purified through application to an equilibrated filter cartridge using the ChipShot™ Membrane Clean-Up System (Promega, Madison, WI, USA). The quantity and labeling efficiency of the labeled cDNA were determined by measuring the absorbance at 260, 550 and 650 nm using a NanoDrop™ spectrophotometer.

growth_protocol: Twelve cows were studied at midlactation stage,

extract_protocol: Total RNA was prepared through homogenization of approximately 80-100 mg of mammary tissue in 1 ml of TRIzol Reagent (Invitrogen Life Technologies, Cergy Pontoise, France), followed by isolation using the Promega total RNA isolation system of (Promega, Charbonnières, France). Potential contaminating genomic DNA was removed through a DNase treatment step.

treatment_protocol: 4 experimental diets (Low Forage (LF); High forage (HF); HF + 13.9 g/100g of DM of whole intact rapeseeds (HF-RS); LF + 4 g/100g of DM of sunflowers oil (LF-SO)  distributed according to a 4x4 latin square design,

tag: physiological stage

value: mid lacationa stage

tag: diet

value: HF

value: mammary gland

source_name: mammary gland_HFRS

value: HFRS


title: MammaryTissue_HFRS.P4_HF.P3_4044_cy3

description:
HFRS.P4_HF.P3_4044_cy3
Biological replicate 7 of 8 and technical replicate 2 of 2. Control diet vs supplemented diet from the same cow


title: Melanoma tumor sample from patient 183

description:
replicate 1
LuM183

value: Male

value: Regional

value: Lymph node


title: Melanoma tumor sample from patient 180

description:
replicate 1
LuM180


title: Melanoma tumor sample from patient 182

description:
replicate 1
LuM182


title: MammaryTissue_HFRS.P4_HF.P3_4065_cy5

description:
HFRS.P4_HF.P3_4065_cy5
Biological replicate 8 of 8 and technical replicate 1 of 2. Control diet vs supplemented diet from the same cow


title: HVL19

value: PBMC


title: HVL20

value: High viral load


title: MammaryTissue_HFRS.P4_HF.P3_4044_cy5

description:
HFRS.P4_HF.P3_4044_cy5
Biological replicate 7 of 8 and technical replicate 1 of 2. Control diet vs supplemented diet from the same cow


title: ES_cells_Control_8hours.3

description:
Quality Control: Approved
Control.1

tag: treatment


title: Melanoma tumor sample from patient 181

description:
replicate 1
LuM181

value: Local


title: ES_cells_Cisplatin_8hours.3

description:
Quality Control: Approved
Cisplatin.1


title: Melanoma tumor sample from patient 179

description:
replicate 1
LuM179


title: Melanoma tumor sample from patient 178

description:
replicate 1
LuM178

value: Female


title: HVL23


title: HVL18


title: HVL17


title: Melanoma tumor sample from patient 177

description:
replicate 1
LuM177


title: MammaryTissue_HFRS.P3_HF.P2_4055_cy3

description:
HFRS.P3_HF.P2_4055_cy3
Biological replicate 6 of 8 and technical replicate 2 of 2. Control diet vs supplemented diet from the same cow


title: HVL14


title: HVL13


title: HVL16


title: ES_cells_Cisplatin_8hours.6

description:
Quality Control: Approved
Cisplatin.4


title: HVL12


title: HVL11


title: HVL15


title: HVL10


title: HVL9


title: MammaryTissue_HFRS.P2_HF.P1_4056_cy3

description:
HFRS.P2_HF.P1_4056_cy3
Biological replicate 2 of 8 and technical replicate 2 of 2. Control diet vs supplemented diet from the same cow


title: HVL8


title: MammaryTissue_HFRS.P3_HF.P2_4035_cy5

description:
HFRS.P3_HF.P2_4035_cy5
Biological replicate 5 of 8 and technical replicate 1 of 2. Control diet vs supplemented diet from the same cow


title: ES_cells_Cisplatin_8hours.4

description:
Quality Control: Approved
Cisplatin.2


title: MammaryTissue_HFRS.P1_HF.P4_4050_cy5

description:
HFRS.P1_HF.P4_4050_cy5
Biological replicate 4 of 8 and technical replicate 2 of 2. Control diet vs supplemented diet from the same cow


title: MammaryTissue_HFRS.P1_HF.P4_4043_cy5

description:
HFRS.P1_HF.P4_4043_cy5
Biological replicate 3 of 8 and technical replicate 2 of 2. Control diet vs supplemented diet from the same cow


title: MammaryTissue_HFRS.P3_HF.P2_4055_cy5

description:
HFRS.P3_HF.P2_4055_cy5
Biological replicate 6 of 8 and technical replicate 1 of 2. Control diet vs supplemented diet from the same cow


title: Melanoma tumor sample from patient 175

description:
replicate 1
LuM175


title: MammaryTissue_HFRS.P1_HF.P4_4050_cy3

description:
HFRS.P1_HF.P4_4050_cy3
Biological replicate 4 of 8 and technical replicate 1 of 2. Control diet vs supplemented diet from the same cow


title: HVL7


title: MammaryTissue_HFRS.P3_HF.P2_4035_cy3

description:
HFRS.P3_HF.P2_4035_cy3
Biological replicate 5 of 8 and technical replicate 2 of 2. Control diet vs supplemented diet from the same cow


title: Melanoma tumor sample from patient 166

description:
replicate 1
LuM166


title: Melanoma tumor sample from patient 171

description:
replicate 1
LuM171


title: Melanoma tumor sample from patient 176

description:
replicate 1
LuM176


title: MammaryTissue_LFSO.P4_LF.P3_4041_cy3

description:
LFSO.P4_LF.P3_4041_cy3
Biological replicate 9 of 9 and technical replicate 2 of 2. Control diet vs supplemented diet from the same cow

source_name: mammary gland_LF

value: LF

source_name: mammary gland_LFSO

value: LFSO


title: MammaryTissue_HFRS.P1_HF.P4_4043_cy3

description:
HFRS.P1_HF.P4_4043_cy3
Biological replicate 3 of 8 and technical replicate 1 of 2. Control diet vs supplemented diet from the same cow


title: MammaryTissue_HFRS.P2_HF.P1_4056_cy5

description:
HFRS.P2_HF.P1_4056_cy5
Biological replicate 2 of 8 and technical replicate 1 of 2. Control diet vs supplemented diet from the same cow


title: MammaryTissue_HFRS.P2_HF.P1_4041_cy3

description:
HFRS.P2_HF.P1_4041_cy3
Biological replicate 1 of 8 and technical replicate 2 of 2. Control diet vs supplemented diet from the same cow


title: Melanoma tumor sample from patient 173

description:
replicate 1
LuM173


title: Melanoma tumor sample from patient 170

description:
replicate 1
LuM170

value: General

value: Visceral


title: Melanoma tumor sample from patient 174

description:
replicate 1
LuM174

value: Cutaneous


title: Melanoma tumor sample from patient 168

description:
replicate 1
LuM168


title: Melanoma tumor sample from patient 172

description:
replicate 1
LuM172


title: HVL5


title: MammaryTissue_HFRS.P2_HF.P1_4041_cy5

description:
HFRS.P2_HF.P1_4041_cy5
Biological replicate 1 of 8 and technical replicate 1 of 2. Control diet vs supplemented diet from the same cow


title: Melanoma tumor sample from patient 169

description:
replicate 1
LuM169


title: HVL4


title: HVL3


title: Melanoma tumor sample from patient 167

description:
replicate 1
LuM167


title: HVL28


title: HVL2


title: HVL1


title: LVL32

source_name: PBMC, Low viral load

value: Low viral load


title: MammaryTissue_LFSO.P3_LF.P2_4016_cy3

description:
LFSO.P3_LF.P2_4016_cy3
Biological replicate 8 of 9 and technical replicate 2 of 2. Control diet vs supplemented diet from the same cow

value: mid lacationa stage


title: LVL30


title: MammaryTissue_LFSO.P3_LF.P2_4043_cy5

description:
LFSO.P3_LF.P2_4043_cy5
Biological replicate 6 of 9 and technical replicate 1 of 2. Control diet vs supplemented diet from the same cow


title: MammaryTissue_LFSO.P3_LF.P2_4050_cy5

description:
LFSO.P3_LF.P2_4050_cy5
Biological replicate 7 of 9 and technical replicate 1 of 2. Control diet vs supplemented diet from the same cow


title: MammaryTissue_LFSO.P4_LF.P3_4041_cy5

description:
LFSO.P4_LF.P3_4041_cy5
Biological replicate 9 of 9 and technical replicate 1 of 2. Control diet vs supplemented diet from the same cow


title: Melanoma tumor sample from patient 165

description:
replicate 1
LuM165


title: LVL29


title: Melanoma tumor sample from patient 185

description:
replicate 1
LuM185


title: Melanoma tumor sample from patient 163

description:
replicate 1
LuM163


title: MammaryTissue_LFSO.P3_LF.P2_4016_cy5

description:
LFSO.P3_LF.P2_4016_cy5
Biological replicate 8 of 9 and technical replicate 1 of 2. Control diet vs supplemented diet from the same cow


title: Melanoma tumor sample from patient 164

description:
replicate 1
LuM164


title: MammaryTissue_LFSO.P1_LF.P4_4055_cy5

description:
LFSO.P1_LF.P4_4055_cy5
Biological replicate 5 of 9 and technical replicate 2 of 2. Control diet vs supplemented diet from the same cow


title: Melanoma tumor sample from patient 158

description:
replicate 1
LuM158


title: Melanoma tumor sample from patient 160

description:
replicate 1
LuM160


title: LVL28


title: MammaryTissue_LFSO.P3_LF.P2_4050_cy3

description:
LFSO.P3_LF.P2_4050_cy3
Biological replicate 7 of 9 and technical replicate 2 of 2. Control diet vs supplemented diet from the same cow


title: Melanoma tumor sample from patient 157

description:
replicate 1
LuM157


title: Melanoma tumor sample from patient 161

description:
replicate 1
LuM161


title: LVL31


title: Melanoma tumor sample from patient 162

description:
replicate 1
LuM162


title: LVL27


title: Melanoma tumor sample from patient 156

description:
replicate 1
LuM156

value: Primary


title: MammaryTissue_LFSO.P1_LF.P4_4051_cy3

description:
LFSO.P1_LF.P4_4051_cy3
Biological replicate 4 of 9 and technical replicate 1 of 2. Control diet vs supplemented diet from the same cow

value: mammary gland


title: Melanoma tumor sample from patient 155

description:
replicate 1
LuM155


title: LVL26


title: LVL25


title: MammaryTissue_LFSO.P3_LF.P2_4043_cy3

description:
LFSO.P3_LF.P2_4043_cy3
Biological replicate 6 of 9 and technical replicate 2 of 2. Control diet vs supplemented diet from the same cow


title: LVL24


title: LVL23


title: LVL22


title: LVL21


title: MammaryTissue_LFSO.P1_LF.P4_4055_cy3

description:
LFSO.P1_LF.P4_4055_cy3
Biological replicate 5 of 9 and technical replicate 1 of 2. Control diet vs supplemented diet from the same cow


title: Melanoma tumor sample from patient 154

description:
replicate 1
LuM154


title: LVL20


title: LVL19


title: HVL6


title: LVL18


title: MammaryTissue_LFSO.P2_LF.P1_4044_cy5

description:
LFSO.P2_LF.P1_4044_cy5
Biological replicate 1 of 9 and technical replicate 1 of 2. Control diet vs supplemented diet from the same cow


title: MammaryTissue_LFSO.P1_LF.P4_4035_cy3

description:
LFSO.P1_LF.P4_4035_cy3
Biological replicate 3 of 9 and technical replicate 2 of 2. Control diet vs supplemented diet from the same cow


title: Melanoma tumor sample from patient 159

description:
replicate 1
LuM159


title: MammaryTissue_LFSO.P2_LF.P1_4065_cy3

description:
LFSO.P2_LF.P1_4065_cy3
Biological replicate 2 of 9 and technical replicate 2 of 2. Control diet vs supplemented diet from the same cow


title: MammaryTissue_LFSO.P1_LF.P4_4051_cy5

description:
LFSO.P1_LF.P4_4051_cy5
Biological replicate 4 of 9 and technical replicate 2 of 2. Control diet vs supplemented diet from the same cow


title: MammaryTissue_LFSO.P2_LF.P1_4044_cy3

description:
LFSO.P2_LF.P1_4044_cy3
Biological replicate 1 of 9 and technical replicate 2 of 2. Control diet vs supplemented diet from the same cow


title: MammaryTissue_LFSO.P2_LF.P1_4065_cy5

description:
LFSO.P2_LF.P1_4065_cy5
Biological replicate 2 of 9 and technical replicate 1 of 2. Control diet vs supplemented diet from the same cow


title: HVL27


title: LVL16


title: Melanoma tumor sample from patient 153

description:
replicate 1
LuM153


title: Melanoma tumor sample from patient 151

description:
replicate 1
LuM151

value: In-transit

value: Subcutaneous


title: Melanoma tumor sample from patient 152

description:
replicate 1
LuM152

value: Male

value: Regional


title: Melanoma tumor sample from patient 149

description:
replicate 1
LuM149


title: Melanoma tumor sample from patient 146

description:
replicate 1
LuM146


title: LVL17

value: PBMC


title: MammaryTissue_LFSO.P1_LF.P4_4035_cy5

description:
LFSO.P1_LF.P4_4035_cy5
Biological replicate 3 of 9 and technical replicate 1 of 2. Control diet vs supplemented diet from the same cow


title: Melanoma tumor sample from patient 147

description:
replicate 1
LuM147

value: Lymph node


title: Melanoma tumor sample from patient 150

description:
replicate 1
LuM150


title: LVL14


title: Melanoma tumor sample from patient 144

description:
replicate 1
LuM144


title: Melanoma tumor sample from patient 145

description:
replicate 1
LuM145


title: LVL13


title: Transcriptome of aha1-7 mutant

city: Madison

first: Miyoshi

last: Haruta

state: WI

address: 425 Henry Mall

department: Biotechnology Center

institute: University of Wisconsin Madison

hyb_protocol: Ten microgram of aRNA was hybridized to the ATH-1 Affymetrix expression array at 45C for 16 hours in Affymetrix 640 hybridization oven. Hybridization cocktail was prepared according to protocols provided in the Affymetrix Expression Analysis Technical Manual.

scan_protocol: Gene Chip was scanned on Affymetrix GC3000 G7 scanner using the Affymetrix Command Console v2.0 software.

data_processing: Data was extracted from the images scanned with GC3000 G7 using the Affymetrix Expression Console v1.1 software.

organism: Arabidopsis thaliana

source_name: aha1 mutant

label_protocol: RNA was labeled using Ambion MessageAmp Biotin II-Enhanced IVT kit. 14 hour IVT reaction at 37C.

growth_protocol: Seedlings were vertically grown on one-half strength Murashige and Skoog media

extract_protocol: QIAGEN RNeasy Plant kit was used to extract total RNA

treatment_protocol: Seedlings were grown for five days under ideal growth condition

tag: ecotype background

value: Col

tag: genotype/variation

value: aha1-7 mutant

value: five days old,

value: light grown seedlings


title: LVL15


title: Transcriptome of aha2-4 mutant replicate

source_name: aha2 mutant

value: aha2-4 mutant

tag: age


title: Transcriptome of aha1-6 mutant replicate

value: aha1-6 mutant


title: Melanoma tumor sample from patient 142

description:
replicate 1
LuM142

tag: distant metastasis free survival in days


title: Melanoma tumor sample from patient 143

description:
replicate 1
LuM143

tag: distant metastasis free survival (1=death, 0=alive)


title: Transcriptome of aha2-5 mutant

value: aha2-5 mutant


title: LVL12

tag: hiv status

value: Low viral load


title: Melanoma tumor sample from patient 148

description:
replicate 1
LuM148

value: Female

tag: disease specific survival in days

tag: disease specific survival (1=death, 0=alive)


title: LVL11


title: Transcriptome of Col WT

description: Col WT061709

source_name: wild type

value: wild type


title: Transcriptome of Col WT replicate

description: Col WT03082010


title: Melanoma tumor sample from patient 141

description:
replicate 1
LuM141

value: General


title: Melanoma tumor sample from patient 140

description:
replicate 1
LuM140


title: Mo CD34+ [Sousa_8_GFW2]

city: London

first: Stephen

last: Henderson

address: Paul O'Gorman Building

department: Cancer Institute

institute: UCL

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 Scanner

data_processing: The data were preprocessed and normalised using the Bioconductor 'oligo' package and the 'robust multiarray average' (RMA) algorithm

source_name: G-CSF treated C57Bl/6 mice

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

growth_protocol: MDSC were propgated from bone marrow in G-CSF, GM-CSF and IL-13 [Highfill et al. Blood 2010, 116:5738-5747); Lin-CD11b+ CD34+ cells were grown in presence of Stemspan  and Flt3 ligand and SCF.  All other cell populations were isolated directly from mice.

treatment_protocol: Lin-CD11b+CD34+ cells were isolated from G-CSF treated C57Bl/6 mice or iNOS knockout mice.

tag: cell type

value: Spleen Lin- (CD4-CD8-Ly6G-B220-Ter119-) CD11b+CD34+ cells


title: LVL10


title: Transcriptome of aha2-4 mutant


title: Transcriptome of aha1-6 mutant


title: Melanoma tumor sample from patient 139

description:
replicate 1
LuM139


title: LVL9


title: LVL8


title: Melanoma tumor sample from patient 138

description:
replicate 1
LuM138

value: Local

value: Other


title: Mo CD34+ [Sousa_9_GFW3]


title: Mo CD34+ ko [Sousa_6_GFK3]

source_name: G-CSF treated iNOS knockout mice


title: Mo CD34+ [Sousa_7_GFW1]


title: LVL7


title: Melanoma tumor sample from patient 137

description:
replicate 1
LuM137

value: Male

value: Primary

value: Cutaneous


title: LVL6

value: PBMC


title: Melanoma tumor sample from patient 136

description:
replicate 1
LuM136

value: Regional

value: Lymph node


title: Mo CD34+ ko [Sousa_5_GFK2]


title: Melanoma tumor sample from patient 135

description:
replicate 1
LuM135


title: Melanoma tumor sample from patient 134

description:
replicate 1
LuM134


title: Melanoma tumor sample from patient 133

description:
replicate 1
LuM133

value: Subcutaneous


title: Mo CD34+ ko [Sousa_4_GFK1]


title: LVL5


title: Mo CD34+ ex [Sousa_3_GFE3]

value: Spleen Lin- (CD4-CD8-Ly6G-B220-Ter119-) CD11b+CD34+ cells cultured in Flt3 ligand and SCF


title: Mo CD34+ ex [Sousa_2_GFE2]


title: Mo CD34+ ex [Sousa_1_GFE1]


title: Melanoma tumor sample from patient 132

description:
replicate 1
LuM132


title: LVL4


title: LVL3


title: LVL2


title: Mo LY6C+ [JS_9_PBS3]

source_name: C57Bl/6 mice

value: Spleen Lin- (CD3-, CD19-, B220-, NK1.1-, Ly6G-) CD11b+CD115+Ly6C+ monocytes


title: LVL1


title: CT36

source_name: PBMC, Control

value: Seronegative


title: Mo LY6C+ [JS_8_PBS2]


title: Mo CD34+ [JS_6_RB3]


title: Melanoma tumor sample from patient 127

description:
replicate 1
LuM127

source_name: Malignant melanoma


title: Mo CD34+ [JS_5_RB2]


title: CT35


title: Melanoma tumor sample from patient 129

description:
replicate 1
LuM129


title: Melanoma tumor sample from patient 130

description:
replicate 1
LuM130

value: In-transit


title: Mo LY6C+ [JS_7_PBS1]


title: Melanoma tumor sample from patient 131

description:
replicate 1
LuM131


title: Melanoma tumor sample from patient 128

description:
replicate 1
LuM128


title: Melanoma tumor sample from patient 126

description:
replicate 1
LuM126


title: CT34


title: CT33


title: CT32


title: MDSC [G32_MDSC2]

value: Myeloid-derived suppressor cells (Ly6C+CD11b+ cells derived from G-CSF, GM-CSF and IL-13 cultured bone marrow)


title: MDSC [G32_MDSC3]


title: Mo CD34+ [JS_4_RB1]


title: Mo LY6C+ [G32_PBS1]


title: Melanoma tumor sample from patient 124

description:
replicate 1
LuM124


title: Melanoma tumor sample from patient 123

description:
replicate 1
LuM123

value: Female


title: Melanoma tumor sample from patient 122

description:
replicate 1
LuM122


title: Melanoma tumor sample from patient 125

description:
replicate 1
LuM125


title: MDSC [G32_MDSC1]


title: Mo LY6C- [G32_LY6Cpool]

value: Spleen Lin- (CD3-, CD19-, B220-, NK1.1-, Ly6G-) CD11b+CD115+Ly6C- monocytes


title: CT31


title: Melanoma tumor sample from patient 121

description:
replicate 1
LuM121


title: CT30


title: CT29


title: Mo LY6C- [G32_LY6Cnew]


title: Melanoma tumor sample from patient 120

description:
replicate 1
LuM120


title: CT28


title: CT27


title: Sample23

type: genomic

city: Cleveland

first: Bartlomiej

last: Przychodzen

address: 9600 Euclid Avenue

department: THOR

institute: Cleveland Clinic

description: Hybridized to GenomeWideSNP_6

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

scan_protocol: not provided

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) and Affymetrix Genotyping Console Software (GCOS 4.0.0).

label: Biotin

molecule: genomic DNA

source_name: AML

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Standard protocol

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using the Qiagen DNA Blood Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, Qubit and 2% agarose gel electrophoresis.

tag: diagnosis

value: acute myeloid leukemia (AML)


title: Sample35

description: Hybridized to GenomeWideSNP_6


title: CMOP [G32_CMOP3]

value: Bone marrow Lin- (CD3-, CD19-, B220-, NK1.1-, Ly6G-) CD117+CD115+CD135-Ly6C+CD11b- common monocyte progenitors


title: Melanoma tumor sample from patient 117

description:
replicate 1
LuM117

tag: gender


title: Sample21

description: Hybridized to GenomeWideSNP_6


title: Melanoma tumor sample from patient 119

description:
replicate 1
LuM119

tag: tumor stage

value: General

value: Visceral


title: Sample22

description: Hybridized to GenomeWideSNP_6


title: Sample19

description: Hybridized to GenomeWideSNP_6


title: Sample34

description: Hybridized to GenomeWideSNP_6


title: CMOP [G32_CMOP1]


title: IL-17 low Sample 12 rep2

first: Daniel

last: De Carvalho

state: ON

address: 101 College Street, room 9-302

institute: Ontario Cancer Institute

description: replicate 2

data_processing: The data were normalised using quantile normalisation with Matlab

source_name: breast cancer biopsy

label_protocol: RNA was amplified using the Illumina TotalPrep RNA Amplification Kit according to the manufacturer’s instructions

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment. Quality control was performed with Agilent Bioanalyser.

tag: il17 status

value: low

tag: tissue

value: breast cancer biopsy


title: IL-17 low Sample 15

description: replicate 1


title: Melanoma tumor sample from patient 116

description:
replicate 1
LuM116

value: Male


title: Melanoma tumor sample from patient 115

description:
replicate 1
LuM115

value: Regional


title: CT26

value: PBMC


title: CT24


title: Mo LY6C- [G32_LY6C2]

tag: strain


title: CT23


title: CT25


title: Melanoma tumor sample from patient 113

description:
replicate 1
LuM113


title: Sample18

description: Hybridized to GenomeWideSNP_6


title: Sample20

description: Hybridized to GenomeWideSNP_6


title: Melanoma tumor sample from patient 114

description:
replicate 1
LuM114

value: Primary

value: Cutaneous


title: CT22


title: IL-17 low Sample 11 rep2

description: replicate 2


title: Sample17

description: Hybridized to GenomeWideSNP_6


title: Sample14

description: Hybridized to GenomeWideSNP_6


title: Melanoma tumor sample from patient 112

description:
replicate 1
LuM112

value: Lymph node


title: FL.G-CSF : Flt3L and G-CSF induced monocytes [JS_6_RB3]

description: Gene expression data from primary monocytes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mogene 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were preprocessed and normalised initially using the Bioconductor oligo package (RMA algorithm). (In Publication data were further merged with other public datasets and renormalised)

growth_protocol: Not applicable

extract_protocol: Extraction of total RNA was performedusing the RNAeasy Microkit (Qiagen, UK)

treatment_protocol: Monocytes populations were purified fromCD11c-DTR mice which were injected with PBS or diphtheria toxin 48 hours previously. Common monocyte progenitors (cMoP) were isolated from untreated C57BL/6 mice.

value: spleen

value: monocyte

value: 8-12 weeks


title: Sample15

description: Hybridized to GenomeWideSNP_6


title: Sample13

description: Hybridized to GenomeWideSNP_6


title: Melanoma tumor sample from patient 111

description:
replicate 1
LuM111

value: Female


title: CT19

value: Seronegative


title: CT20


title: IL-17 low Sample 12 rep1

description: replicate 1


title: Melanoma tumor sample from patient 109

description:
replicate 1
LuM109

value: Local


title: Sample12

description: Hybridized to GenomeWideSNP_6

value: acute myeloid leukemia (AML)


title: CT18


title: FL.G-CSF : Flt3L and G-CSF induced monocytes [JS_4_RB1]


title: Melanoma tumor sample from patient 110

description:
replicate 1
LuM110


title: Sample10

description: Hybridized to GenomeWideSNP_6


title: DT LY6C+ : DT injected LY6C+ monocytes [JS_2_DT2]

source_name: DT LY6C+ : DT injected LY6C+ monocytes


title: IL-17 low Sample 11 rep1

description: replicate 1


title: IL-17 low Sample 14

description: replicate 1


title: IL-17 low Sample 20

description: replicate 1


title: DT LY6C+ : DT injected LY6C+ monocytes [JS_3_DT3]


title: Melanoma tumor sample from patient 108

description:
replicate 1
LuM108


title: IL-17 high Sample 22 rep2

description: replicate 2

value: high


title: CT17


title: CT21


title: Melanoma tumor sample from patient 107

description:
replicate 1
LuM107

value: General

value: Visceral


title: Sample9

description: Hybridized to GenomeWideSNP_6


title: Sample8

description: Hybridized to GenomeWideSNP_6


title: CT16


title: CMOP [G32_CMOP2]

value: Bone marrow Lin- (CD3-, CD19-, B220-, NK1.1-, Ly6G-) CD117+CD115+CD135-Ly6C+CD11b- common monocyte progenitors


title: CT15


title: IL-17 high Sample 17 rep2

description: replicate 2

value: breast cancer biopsy


title: Sample16

description: Hybridized to GenomeWideSNP_6


title: DT LY6C+ : DT injected LY6C+ monocytes [JS_1_DT1]


title: CT14


title: Melanoma tumor sample from patient 118

description:
replicate 1
LuM118


title: CT13


title: IL-17 high Sample 17 rep1

description: replicate 1


title: Melanoma tumor sample from patient 106

description:
replicate 1
LuM106

value: Male

value: Regional


title: Melanoma tumor sample from patient 105

description:
replicate 1
LuM105


title: PBS LY6C- : PBS injected LY6C- monocytes [G32_LY6Cnew]


title: Sample3

description: Hybridized to GenomeWideSNP_6


title: CT12

value: PBMC


title: Melanoma tumor sample from patient 104

description:
replicate 1
LuM104


title: IL-17 high Sample 13

description: replicate 1


title: Sample2

description: Hybridized to GenomeWideSNP_6


title: IL-17 high Sample 19

description: replicate 1


title: PBS LY6C- : PBS injected LY6C- monocytes [G32_LY6C2]


title: IL-17 high Sample 18

description: replicate 1


title: CT11


title: DT LY6C+ : DT injected LY6C+ monocytes [G32_DT1]


title: IL-17 high Sample 22 rep1

description: replicate 1


title: CT10


title: CT9


title: Melanoma tumor sample from patient 103

description:
replicate 1
LuM103


title: CT8


title: Sample4

description: Hybridized to GenomeWideSNP_6


title: Melanoma tumor sample from patient 101

description:
replicate 1
LuM101


title: IL-17 high Sample 16

description: replicate 1


title: Sample1

description: Hybridized to GenomeWideSNP_6


title: Melanoma tumor sample from patient 100

description:
replicate 1
LuM100


title: CT7


title: Sample24

description: Hybridized to GenomeWideSNP_6


title: IL-17 high Sample 21

description: replicate 1


title: FL.G-CSF : Flt3L and G-CSF induced monocytes [JS_5_RB2]


title: Melanoma tumor sample from patient 99

description:
replicate 1
LuM99

value: Subcutaneous


title: cMoP : common monocyte progenitor [G32_CMOP3]

source_name: cMoP : common monocyte progenitor

value: bone marrow


title: cMoP : common monocyte progenitor [G32_CMOP1]


title: cMoP : common monocyte progenitor [G32_CMOP2]


title: Untreated-Mdr2/KO Liver vs Tumor (Spon4F)

city: Jerusalem

last: Goldenberg

address: Ein Kerem

department: Gene therapy

country: Israel

institute: Hadassah medical center

hyb_protocol: According to manufacturer protocol (Affymetrix)

data_processing:
The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities and ratios (including background subtraction and normalization), rejects outliers, and calculates statistical confidences (p-values).   Further analysis and visualization of the hybridization results was performed with the Agilent CGH Analytics software (V 3.5). Here, the following aberration filter settings have been used:  (i) Minimum number of probes present in an aberrant region = 2 (ii) Minimum absolute average log2 ratio for region = 0.3 corresponds to a fold change of 1.23.  (iii) The statistical analysis of aberrant regions was based on the aberrations detection method ADM-2
We used ADM-2 algorithm, the score represents the deviation of the weighted average of the normalized log ratios from its expected value of zero and incorporates quality information about each probe measurement.

source_name: Liver, Non Tumor, Untreated

growth_protocol: Regular growth on normal diet

extract_protocol: Tri-reagent

treatment_protocol: 70% PHx of both male and female Mdr2-KO mice at the age of either 3 or 6 months

value: Untreated

tag: genotype

value: liver, non-tumor

source_name: Mdr2/KO-Untreated, Tumor

value: liver, tumor


title: HSC3+AzC 4d rep 2

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

description:
replicate 2
HSC3 + AzC(2)

data_processing: Data analysis was performed with GeneSpring GX software (Agilent Technologies). Quantile normalization was performed. Differentially expressed gene lists were generated by using Fold Change analysis tool.

source_name: oral tumor

label_protocol: 500ng total RNA was converted into cDNA using biotinylated random nonamers, oligodeoxythymidine 18 primers and Illumina-supplied reagents, according to Illumina manufacturer's instructions.

growth_protocol: Oral cancer cell lines, such as OC3, SAS, SCC-15, and HSC3, were cultured with or without 10 uM of 5-aza-2’-deoxycytidine (AzC) for 4 days.

extract_protocol: Total RNA was isolated using an RNeasy mini kit (Qiagen) according to the manufacturer's instruction.

value: male

tag: cell line

value: epithelia

tag: treatment

value: AzC


title: Melanoma tumor sample from patient 98

description:
replicate 1
LuM98

value: In-transit


title: Untreated-Mdr2/KO Liver vs Tumor (Spon3F)

scan_protocol: According to manufacturer protocol (Affymetrix)

value: Female


title: HSC3+AzC 4d rep 1

description:
replicate 2
HSC3 + AzC (1)


title: Melanoma tumor sample from patient 102

description:
replicate 1
LuM102

value: Lymph node


title: CT6

value: Seronegative


title: HSC3 rep 1

description:
replicate 1
HSC3 (1)

value: mock


title: HSC3 rep 2

description:
replicate 1
HSC3 (2)


title: Melanoma tumor sample from patient 96

description:
replicate 1
LuM96


title: Melanoma tumor sample from patient 97

description:
replicate 1
LuM97

value: Primary

value: Cutaneous


title: CT4


title: CT3


title: CT5


title: CT2


title: CT1


title: SCC-15 rep 2

description:
replicate 1
SCC-15 (2)