title: Patient-17

description:
SAMPLE 17
7878191115_R02C01


title: Patient-22

status: Public on Aug 11 2015

type: genomic

city: Newcastle upon Tyne

first: Alem

middle: Selassie

last: Gabriel

address: Queen Victoria Rd

department: Northern Institute for Cancer Research

country: United Kingdom

institute: Newcastle University

description:
SAMPLE 22
7970368152_R06C01

hyb_protocol: Illumina protocol

scan_protocol: Beadstation GX scanner

data_processing: R-environment (minifi package)

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Bone marrow

label_protocol: Illumina protocol

growth_protocol: Primary cells

extract_protocol: qiagen extraction kit

treatment_protocol: Bone marrow extraction

tag: all cytogenetic subtype

value: HeH

tag: outcome

value: went on to relapse

tag: gender

value: Male


title: Patient-11

description:
SAMPLE 11
6222421026_R05C01

value: Female


title: Patient-14

description:
SAMPLE 14
7878191128_R01C02


title: Patient-15

description:
SAMPLE 15
7878191155_R01C01


title: Patient-6

description:
SAMPLE 6
6222421026_R01C02


title: TET_siTDP43_1 (exon-level)

type: RNA

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
HJAY_r2.pgf
HJAY_r2.full.mps

label: Biotin

molecule: total RNA

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Cells were cultured under DMEM(10%FBS, 1% penicillin-streptomycine). Atmosphere: air, 95%; carbon dioxide (CO2), 5%. Temperature, 37.0°C

extract_protocol: Total RNA extracted using RNeasy Mini Kit (Qiagen) following manufacturer´s instructions

treatment_protocol: Flp-In HEK293 (Invitrogen) carrying  inducible siRNA resistant FLAG-tagged wild type TDP-43, F4L mutant, and TDP43-12XQ/N constructs were induced  (to obtain tagged TDP-43 expression) with 1μg/ml tetracycline (Sigma). Depletion of endogenous TDP-43 was performed by RNA interference using HiPerFect Transfection Reagent (Qiagen) and siRNA specific for TDP-43 (Dharmacon; target sequence 5’-aagcaaagccaagaugagccu-3’).

tag: cell line

tag: genotype/variation

value: siTDP43-treated HEK-293 cells


title: Patient-9

description:
SAMPLE 9
6222421026_R05C02

value: in remission


title: TET_siCTRL_3 (gene-level)

source_name: siCTRL

value: wild-type HEK-293 cells


title: TET_siTDP43_2 (exon-level)


title: Patient-13

description:
SAMPLE 13
7878191128_R01C01


title: Patient-4

description:
SAMPLE 4
6222421026_R06C02


title: Patient-8

description:
SAMPLE 8
6222421026_R04C02


title: Patient-7

description:
SAMPLE 7
6222421026_R03C01


title: Patient-19

description:
SAMPLE 19
7878191115_R03C02


title: TET_siCTRL_3 (exon-level)


title: Patient-1

description:
SAMPLE 1
6222421026_R03C02


title: Patient-5

description:
SAMPLE 5
6222421026_R02C02


title: TET_siCTRL_1 (gene-level)


title: Patient-10

description:
SAMPLE 10
6222421026_R04C01


title: TET_siCTRL_2 (exon-level)


title: TET_siTDP43_3 (exon-level)


title: Patient-2

description:
SAMPLE 2
6222421026_R06C01


title: Patient-3

description:
SAMPLE 3
6222421026_R02C01


title: TDP-WT_TET_siTDP43_2 (gene-level)

source_name: TDP-WT siTDP43

value: siTDP43-treated HEK-293 cells overexpressing a flagged-wildtype TDP-43


title: TDP-WT_TET_siTDP43_3 (exon-level)


title: TET_siCTRL_2 (gene-level)


title: TET_siCTRL_1 (exon-level)


title: TDP-WT_TET_siTDP43_2 (exon-level)


title: TDP-RRM-1-2_TET_siTDP43_3 (gene-level)

source_name: TDP-RRM-1-2 siTDP43

value: siTDP43-treated HEK-293 cells overexpresing a RNA-binding deficient mutant


title: TDP-WT_TET_siTDP43_1 (gene-level)


title: 12-16mm, biological replicate 3

city: New Delhi

first: Archana

last: Sachdev

state: NCR Delhi

address: Pusa campus

department: Biochemistry

country: India

institute: Indian Agricultural Research Institute

description:
Gene expression data from seeds of Glycine max at developmental stage 12-16mm
SAMPLE_4_R3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix Soybean Genome Array

scan_protocol: Genechips were scanned using affymetrix scanner type M10

data_processing: Probe level data was summarized through RMA algorithm, and summarized data was used for differential expression analysis

label: biotin

organism: Glycine max

source_name: Seeds of Glycine max at developmental stage (12-16mm)

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

growth_protocol: Seeds of Glycine max at developmental stages are utilized for the study

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

treatment_protocol: Seeds of Glycine max grown at 28/26°C, 12h light/dark were collected at different developmental stages(0-4, 4-8, 8-12 and 12-16 mm) and analyzed.

tag: cultivar

value: Pusa 16

tag: developmental stage

tag: tissue

value: seed


title: TDP-RRM-1-2_TET_siTDP43_1 (gene-level)


title: GSK126 (set 1)

city: Ann Arbor

first: Ilona

last: Kryczek

address: 1150 W. Medical Center Dr.

country: USA

institute: University of Michigan

hyb_protocol: Following fragmentation, 2.8ug of cDNA were hybridized for 20 hr at 48C on Human Gene ST 2.1 strip arrays using the Affymetrix Gene Atlas system (software version 1.0.4.267)

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system

data_processing: Data was analyzed using the oligo Bioconductor package implemented in the R-statistical environment version 3.0.0. RMA was used to fit log2 transformed expression values

source_name: primary ovarian cancer cells

label_protocol: were prepared according to the NuGen WT-Pico V2 kit protocol from 50 ng total RNA (Ovation PicoSL WTA System V2 P/N 3312). Biotinylated single-stranded cDNA were prepared using the Encore Biotin Module P/N 4200-12, 4200-60, 4200-A01

growth_protocol: Cells were growing in RPMI1640 supplemented with 10% FBS and 1% penicillin/streptomycin solution in a humidified atmosphere with 5% CO2 and 95% air

extract_protocol: RNA were isolated by Rneasy kit according to the manufacturer's protocol

treatment_protocol: Primary ovarian cancer cells were pretreated with GSK126 and stimulated with IFNg for 24 hours

tag: treatment


title: OC8-Control (set 1)

description: OC8 cells expressing non-target shRNA

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol from 400 ng total RNA (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2)

treatment_protocol: Primary ovarian cancer cells were transduced with a shEZH2 lentivirus, and stimulated with IFNg for 24 hours

tag: shRNA

value: Control


title: OC8-shEZH2 (set 2)

description: OC8 cells expressing EZH2 shRNA


title: STARVATION + OXALIPLATIN 1

city: Genova

first: Ulrich

last: Pfeffer

address: L. Benzi 10

country: Italy

institute: IRCCS AOU San Martino - IST

description: STS OXP1.ga.cel

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Expression data were obtained by pre-processing using RMA with quantile normalization in R/BioConductor (R version 3.02, BioConductor 2.12)

label: BIOTIN-STREPTAVIDIN-PHYCOERYTHRIN

organism: Mus musculus

label_protocol: Standard Affymetrix protocol

growth_protocol: CT26  colon cancer cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) and 10% FBS at 37°C and 5% CO2.

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen, Hilden, Germany) following the protocol provided by the supplier

treatment_protocol: Tumor cell lines were cultured in DMEM medium (Euroclone, Milan, Italy) supplemented with 1% L-glutamine, penicillin/streptomycin, nonessential amino acids and 10% fetal bovine serum (FBS) (all from Sigma Aldrich, Milan, Italy) (complete medium). All treatments were performed at 37°C under 5% CO2. Glucose restriction was done by incubating cells in glucose free DMEM (Invitrogen, Monza, Italy) supplemented with either low glucose (0.5 g/L, starvation) or normal glucose (1.0 g/L, control) for 48 hours. Starvation was carried out under serum restriction by incubating cells in DMEM/F12 with  1% (instead of 10% used for controls) FBS for 48 hours. Oxaliplatin (OXP, Hospira, Naples, Italy) treatment was performed 24 hours after STS in a concentration of 10microM.

tag: cell type

value: colon cancer cells

tag: sample group

value: Starvation+Oxaliplatin


title: OXALIPLATIN 1

value: Oxaliplatin


title: OXALIPLATIN 3


title: TDP-WT_TET_siTDP43_1 (exon-level)


title: Control (set 1)


title: OC8-shEZH2 (set 1)

description: OC8 cells expressing EZH2 shRNA


title: TDP-RRM-1-2_TET_siTDP43_2 (gene-level)


title: STARVATION + OXALIPLATIN 2

description: STS OXP2.ga.cel


title: GSK126 (set 2)


title: OXALIPLATIN 2


title: TDP-WT_TET_siTDP43_3 (gene-level)


title: STARVATION 2

value: starvation


title: 12-16mm, biological replicate 2

description:
Gene expression data from seeds of Glycine max at developmental stage 12-16mm
SAMPLE_4_R2


title: Control (set 2)


title: OC8-Control (set 2)

description: OC8 cells expressing non-target shRNA


title: 0-4mm, biological replicate 3

description:
Gene expression data from seeds of Glycine max at developmental stage 0-4mm
SAMPLE_1_R3

source_name: Seeds of Glycine max at developmental stage (0-4mm)


title: STARVATION 3


title: STARVATION 1


title: STARVATION + OXALIPLATIN 3

description: STS OXP3.ga.cel


title: 0-4mm, biological replicate 2

description:
Gene expression data from seeds of Glycine max at developmental stage 0-4mm
SAMPLE_1_R2


title: 0-4mm, biological replicate 1

description:
Gene expression data from seeds of Glycine max at developmental stage 0-4mm
SAMPLE_1_R1


title: TDP-RRM-1-2_TET_siTDP43_3 (exon-level)

value: siTDP43-treated HEK-293 cells overexpressing a RNA-binding deficient mutant


title: TDP-RRM-1-2_TET_siTDP43_1 (exon-level)


title: CONTROL 1

value: control


title: CONTROL 3


title: CONTROL 2


title: 12-16mm, biological replicate 1

description:
Gene expression data from seeds of Glycine max at developmental stage 12-16mm
SAMPLE_4_R1


title: 8-12mm, biological replicate 3

description:
Gene expression data from seeds of Glycine max at developmental stage 8-12mm
SAMPLE_3_R3

source_name: Seeds of Glycine max at developmental stage (8-12mm)


title: TDP-RRM-1-2_TET_siTDP43_2 (exon-level)


title: Young 4

city: Iowa City

first: Thomas

middle: B

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

description: replicate 4

hyb_protocol: 750 ng of this product were mixed with Illumina hybridization buffer, placed onto Illumina MouseRef-8 v2.0 expression beadchip, and incubated at 58º C for 17h, with  rocking, in an Illumina Hybridization Oven. Following hybridization, the arrays  were washed, blocked, then stained with streptavidin-Cy3 (Amersham/GE  Healthcare, Piscataway, NJ) according to the Illumina Whole-Genome Gene  Expression Direct Hybridization Assay protocol.

scan_protocol: Beadchips were scanned with the Illumina iScan System (ID #N0534) and data were collected using the  GenomeStudio software v2011.1.

data_processing: GenomeStudio software v2011.1.

source_name: CD11c cells (lungs)

label_protocol: DNA microarray sample processing. RNA sample preparation for hybridization  and the subsequent hybridization to the Illumina beadchips were performed at  the University of Iowa DNA Facility using the manufacturer’s recommended  protocol. Briefly, 100 nanograms total RNA was converted to amplified Biotin- aRNA using the Epicentre TargetAmp-Nano Labeling Kit for Illumina Expression  BeadChip (Illumina, Inc., San Diego, CA, Cat. #TAN07924) according to the  manufacturer’s recommended protocol. The amplified Biotin-aRNA product was  purified through a QIAGEN RNeasy MinElute Cleanup column (QIAGEN Cat  #74204) according to modifications from Epicentre.

extract_protocol: Pulmonary CD11 cells separated using magnetic beads (miltenyi). Total RNA from CD11c cells extracted using mirVana kit (Life Technologies) according to manufacturer's protocol. Quality checked using agilent Bioanalyzer.

tag: strain

value: Lungs

value: CD11c cells

tag: cell age

value: 6-8 weeks


title: 8-12mm, biological replicate 2

description:
Gene expression data from seeds of Glycine max at developmental stage 8-12mm
SAMPLE_3_R2


title: NT 3

city: Oslo

first: Ian

last: Mills

address: Gaustadalleen 21

department: Centre for Molecular Medicine Norway

country: Norway

institute: University of Oslo

description: SAMPLE 7

hyb_protocol: Hybridization of cRNA onto the Illumina HumanHT-12 v.4 Expression BeadChips (Illumina Inc, California, USA) was carried out as per manufacturer's instructions

scan_protocol: After scanning, the iScan software extracts signal intensities and saves all files for each BeadChip. Raw data is imported to Illumina’s GenomeStudio software V2011.1, Gene Expression module v. 1.9.0. Here the quality of each array and scan is investigated, and text files with both non-normalized and quantile normalized data exported.

data_processing: Data extraction, quantile normalization and initial quality control of the bead summary raw data were performed using GenomeStudio v2011.1 from Illumina and the Gene Expression module v1.9.0. The data were annotated using the HumanHT-12_V4_0_R2_15002873_B.bgx annotation file from Illumina.

source_name: NT

label_protocol: Labelling was performed with Illumina® TotalPrep™-96 RNA Amplification Kit according to manufacturer's instructions

growth_protocol: Panc03.27 pancreatic adenocarcinoma cells were obtained from ATCC and cultured in RPMI (Sigma-Aldrich) containing 10% FBS (Invitrogen), 2 mmol/L glutamine, penicillin/streptomycin (BioWhittaker), and 500µl ITS (Sigma-Aldrich) at 37°C in a humidified atmosphere of 5% CO2

extract_protocol: Total RNA of four biological replicates for each cell line was extracted using the RNeasy kit (Qiagen) according to manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Panc03.27 5-FU resistant cell lines were generated by continuous exposure of the tumor cells to 5-FU (Sigma-Aldrich) over a 6 month period. Incubation began with 0.5µg/ml 5-FU and increased to 1µg/ml over time.  After stable, proliferating lines resistant to 1µg/ml 5-FU was created, clones were selected through limited dilution and clones derived from single cells were isolated and expanded over the next 3-4 months.

value: 5-FU sen Panc03.27


title: 4-8mm, biological replicate 3

description:
Gene expression data from seeds of Glycine max at developmental stage 4-8mm
SAMPLE_2_R3

source_name: Seeds of Glycine max at developmental stage (4-8mm)


title: 4-8mm, biological replicate 1

description:
Gene expression data from seeds of Glycine max at developmental stage 4-8mm
SAMPLE_2_R1


title: Young 2

description: replicate 2


title: 8-12mm, biological replicate 1

description:
Gene expression data from seeds of Glycine max at developmental stage 8-12mm
SAMPLE_3_R1


title: Young 1

description: replicate 1


title: NT 1

description: SAMPLE 5


title: 4-8mm, biological replicate 2

description:
Gene expression data from seeds of Glycine max at developmental stage 4-8mm
SAMPLE_2_R2


title: NT 4

description: SAMPLE 8


title: 5-FU res BiV 3

description: SAMPLE 3

value: 5-FU res Panc03.27


title: 5-FU res BiV 4

description: SAMPLE 4


title: Young 3

description: replicate 3


title: 5-FU res BiV 2

description: SAMPLE 2


title: Middle-aged 4

description: replicate 4

value: 10-13 months


title: NT 2

description: SAMPLE 6


title: 5-FU res BiV 1

description: SAMPLE 1


title: Middle-aged 2

description: replicate 2


title: Middle-aged 3

description: replicate 3


title: Middle-aged 1

description: replicate 1


title: endocervix n9-12

status: Public on Aug 10 2015

city: San Francisco

first: Linda

last: Giudice

state: CA

address: 513 Parnassus Ave. HSE 1619

department: OBGYN and RS

institute: University of California, San Francisco

description: 68_cx_28_bx1 n9.CEL

hyb_protocol: Microarrays were hybridized, washed, stained, and scanned according to the protocol described in the WT sense target labeling assay manual from Affymetrix (version 4; FS450_0007).

scan_protocol: Microarrays were hybridized, washed, stained, and scanned according to the protocol described in WT Sense Target Labeling Assay Manual from Affymetrix (Version 4; FS450_0007) at the UCSF Gladstone Genomics Core Facility.

data_processing: GeneSpringGX 11, Microarray Technology: Affymetrix.ExonExprChip.HuGene-1_0-st-v1, Summarization Algorithm: ExonRMA16, Normalization: Quantile, Baseline Transformation: median of all samples

label_protocol: RNA was reverse transcribed/amplified into cDNA using the NuGEN FFPE kit, and sense-strand cDNA targets were created using the NuGEN WT-Ovation Exon Module, followed by fragmentation and labeling using NuGEN Encore Biotin Module for hybridization to Affymetrix Human Gene 1.0 ST arrays.

extract_protocol: RNA is extracted using the Magery Nagel Nucleospin RNA II kit.

treatment_protocol: After an initial screening and enrollment visit, participants were instructed in study procedures as follows.  Participants were asked to use vaginal products (Conceptrol N-9 gel or UPG) or no product during a menstrual cycle and to return after each exposure period, for collection of clinical samples to assess treatment effects. Treated cycles were followed by 'washout' menstrual cycles during which no study intervention or biological sampling occurred. Early in the study, volunteers were randomized to either N9 then UPG or the reverse sequence. The 'no product or applicator' cycle was introduced to the study protocol part-way through the study, and women who had participated prior to this modification were invited back for a third study cycle.

tag: tissue and passage

value: endocervix

tag: endometrial cycle phase

value: mid-secretory endometrium (MSE)

tag: product used

value: Nonoxynol-9 (n9)


title: endocervix n9-9

description: 61_cx_20_bx3 n9.CEL


title: endocervix n9-3

description: 22_Cx_5_bx1 n9.CEL


title: endocervix n9-4

description: 27_Cx_10_bx2 n9.CEL


title: endocervix n9-7

description: 52_cx_16_bx2 n9.CEL


title: endocervix gel-8

description: 60_cx_20_bx2 gel.CEL

value: Universal Placebo Gel (UPG)


title: endocervix n9-10

description: 62_cx_21_bx1 n9.CEL


title: endocervix gel-7

description: 58_cx_19_bx1 gel.CEL


title: endocervix n9-8

description: 54_cx_17_bx1 n9.CEL


title: endocervix gel-1

description: 14_Cx_1_bx_1 gel.CEL


title: endocervix n9-5

description: 30_Cx_14_bx1 n9.CEL


title: endocervix n9-6

description: 50_cx_13_bx2 n9.CEL


title: endocervix n9-1

description: 15_Cx_1_bx_2 n9.CEL


title: endocervix control-12

description: 71_cx_30_bx1 none.CEL

value: none (control)


title: endocervix n9-11

description: 67_cx_27_bx2 n9.CEL


title: endocervix n9-2

description: 18_Cx_2_bx_2 n9.CEL


title: endocervix gel-2

description: 17_Cx_2_bx_1 gel.CEL


title: endocervix gel-9

description: 65_cx_26_bx1 gel.CEL


title: endocervix gel-4

description: 29_Cx_11_bx_2 gel.CEL


title: endocervix gel-5

description: 53_cx_16_bx3 gel.CEL


title: endocervix control-11

description: 70_cx_29_bx1 none.CEL


title: endocervix gel-6

description: 57_cx_18_bx3 gel.CEL


title: endocervix gel-3

description: 24_Cx_8_bx2 gel.CEL


title: endocervix control-9

description: 59_cx_20_bx1 none.CEL


title: endocervix control-8

description: 56_cx_18_bx1 none.CEL


title: endocervix control-10

description: 69_cx_28_bx2 none.CEL


title: endocervix control-6

description: 49_cx_11_bx3 none.CEL


title: endocervix control-5

description: 28_Cx_10_bx3 none.CEL


title: endocervix control-7

description: 51_cx_16_bx1 none.CEL


title: endometrium n9-9

description: 41_endo_21_bx1 n9.CEL

value: endometrium


title: endocervix control-3

description: 21_Cx_4_bx3 none.CEL


title: endocervix control-1

description: 16_Cx_1_bx3 none.CEL


title: endometrium n9-8

description: 38_endo_17_bx1 n9.CEL


title: endometrium n9-4

description: 07_Endo_6_bx1 n9.CEL


title: endometrium n9-6

description: 32_endo_13_bx2 n9.CEL


title: endometrium n9-2

description: 03_Endo_4_bx1 n9.CEL


title: endometrium gel-7

description: 45_endo_26_bx1 gel.CEL


title: endocervix control-2

description: 19_Cx_2_bx3 none.CEL


title: endometrium n9-5

description: 12_Endo_12_bx1 n9.CEL


title: endometrium n9-7

description: 36_endo_16_bx2 n9.CEL


title: endometrium gel-1

description: 01_Endo_1_bx1 gel.CEL


title: endometrium n9-1

description: 02_Endo_1_bx2 n9.CEL


title: endometrium gel-6

description: 40_endo_19_bx1 gel.CEL


title: endocervix control-4

description: 23_Cx_7_bx3 none.CEL


title: endometrium control-4

description: 11_Endo_10_bx3 none.CEL


title: endometrium gel-3

description: 31_endo_4bx4 gel.CEL


title: endometrium control-7

description: 43_endo_22_bx1 none.CEL


title: endometrium control-5

description: 34_endo_15_bx2 none.CEL


title: endometrium gel-4

description: 33_endo_15_bx1 gel.CEL


title: endometrium n9-3

description: 06_Endo_5_bx1 n9.CEL


title: endometrium control-8

description: 47_endo_30_bx1 none.CEL


title: endometrium gel-5

description: 37_endo_16_bx3 gel.CEL


title: endometrium control-3

description: 10_Endo_7a_bx3 none.CEL


title: endometrium control-6

description: 35_endo_16_bx1 none.CEL


title: endometrium gel-2

description: 08_Endo_6_bx2 gel.CEL


title: endometrium control-2

description: 09_Endo_6_bx3 none.CEL


title: endometrium gel-8

description: 48_endo_31_bx1 gel.CEL


title: endometrium control-1

description: 05_Endo_4_bx3 none.CEL


title: Brain_Carrier_3dpi_rep2

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

country: Canada

institute: The University of Victoria

hyb_protocol: Samples and reference were combined, fragmented, then hybridized to randomized-order cGRASP 4x44k salmonid arrays (Agilent eArray AMADID: 025055) as per manufacturers’ instructions with the added stabilization solution step to prevent ozone-related problems (Agilent). Slides were kept in the dark in a low ozone atmosphere until scanned.

scan_protocol: Slides were scanned on a ScanArray® Express (Perkin Elmer) at 5 µm resolution with constant PMT settings (Cy5:75; Cy3:80) that had been optimized to obtain 1% of all spots saturated.

data_processing: Images were quantified in Imagene 8.1 (Biodiscovery). Poor and control spots were flagged for downstream filtering, and the median background intensity was subtracted from the median signal value for each probe. Samples were loaded into GeneSpring 11.5.1 (Agilent). Negative raw values were set at 1.0, each array was normalized by an intensity-dependent Lowess, and a baseline to median transformation of normalized expression values was performed per gene. Control spots, and any probes not passing the following were removed: raw values ≥ 500 in both channels, and no poor quality flags in at least 65% of the samples in any one condition. A two-way ANOVA (p ≤ 0.01; no multiple test correction) was performed in GeneSpring (Agilent) to identify differentially expressed genes influenced by IHNV status (naïve, survivor, or carrier), poly(I:C)-injection (control or injected), or an interaction of both factors. Probes with a significant interaction effect were removed from the main effect lists. Probes with a significant effect of IHNV status were additionally filtered by fold change (FC), finding those probes with a 1.5-fold difference between survivor and control groups, or carrier and control groups concurrently in both poly(I:C) injected and non-injected groups. Probes with a significant effect of poly(I:C) injection were additionally filtered by fold change to identify probes different between the poly(I:C)-injected and the non-injected control groups (FC ≥ 1.5) consistently in all of the following three comparisons: poly(I:C)-naïve vs. non-injected-naïve; poly(I:C)-survivor vs. non-injected-survivor; and poly(I:C)-carrier vs. non-injected-carrier. Probes with a significant interaction between IHNV status and poly(I:C)-injection were filtered by fold change to retain probes that were differentially expressed by 1.5-fold between any two groups.

organism: Oncorhynchus nerka

label_protocol: cDNA synthesis and cRNA amplification was performed on 200 ng input total RNA using the Low Input Quick Amp system (Agilent Technologies; v6.5) with Cy5- or Cy3-CTP (Perkin Elmer). Experimental groups were labeled with Cy5-CTP (Perkin Elmer) and these consisted of naïve (n = 7), survivors (n = 7), and carriers (n = 5), as well as poly(I:C)-injected naïve (n = 7), poly(I:C)-injected survivors (n = 7), and poly(I:C)-injected carriers (n = 2). A reference pool was generated by synthesizing Cy3-labeled cRNA from two individuals from each of the six conditions (total in reference = 12 samples). Equimolar concentrations of each synthesized Cy3-cRNA sample (n = 12) was pooled to create a common reference used to hybridize to each array alongside sample Cy5-cRNA. All cRNA samples were quality checked for specific activity as per manufacturers’ protocol (Agilent) and kept at -80 °C in the dark until hybridization.

growth_protocol: In June 2011 Sockeye Salmon fry (1000 fish from Sakinaw Lake stock, brood year 2010) were transferred from Rosewall Creek hatchery, Fanny Bay, British Columbia (B.C.) to the Pacific Biological Station, Nanaimo, B.C.. Fish were reared in 2.7 m3 tanks and 5 °C (± 1 °C) freshwater under a natural photoperiod.

extract_protocol: Samples were randomized and total RNA was extracted from brain samples using TRIzol (Invitrogen) by physical disruption with a TissueLyser II (Retsch). The remainders of each sample were then purified by treatment with DNase I (Qiagen) and subsequently column-purified using the RNeasy® MinElute® Cleanup kit (Qiagen) following manufacturer instructions.  Total RNA was quantified and quality checked by spectrophotometry (NanoDrop-1000) and 1% agarose gel electrophoresis, then stored at -80 °C.

treatment_protocol: In November 2011 Sockeye Salmon (600 fry, average weight = 5.5 g) were immersed for one hour in a 85 L static, aerated, 5°C freshwater bath containing IHNV (Okanagan 2000 isolate, U genogroup; K. Garver, unpublished) at a dose of 1.98 x 103 pfu ml-1. After the one hour exposure to virus, the fish along with bath water were transferred into a 700 L tank. Sockeye Salmon from a separate tank that were not handled or exposed to IHNV served as control fish (naïve fish). Challenged and naïve fish were maintained in freshwater in one tank each, and monitored daily for signs of disease and morbidity for a period of nine months. To mimic temperature changes that would be normally experienced in freshwater, fish were held for four months at 5 °C (± 1 °C) followed by a slow transition over several days to 9 °C (± 1 °C) for the remaining five months. At the end of the study (nine months post challenge), naïve and surviving Sockeye Salmon had similar average weights of 23 g and 20 g, respectively. At 271 dpc, 240 surviving fish from each of the challenge and naïve groups were reassigned into smaller 400 L tanks (120 fish per tank; total of four tanks) supplied with the same source of water. Shortly after the transfer, one group each of the challenged and naïve fish received an intraperitoneal (ip) injection of poly(I:C) (Sigma-Aldrich) dissolved in saline solution at a dose of 10 µg per g fish. For controls, a group each of challenged and naïve fish were transferred without injection. A sample of 39 fish were removed from each tank at 3 (274 dpc), 7 (278 dpc) and 10 (281 dpc) days after poly(I:C) injection/transfer. At sampling fish were euthanized in an overdose of buffered tricaine methanesulfonate (TMS) and brain tissues were aseptically removed, individually flash-frozen in liquid N2 and transferred to -80 °C until RNA extraction.

value: brain

tag: ihnv status

tag: polyic treatment

source_name: pool of 2 samples from each experimental conditions (total = 12 samples), containing equimolar sample(s) per condition

tag: sample tpe

value: reference pool


title: female liver_Nucleophosmin_genome tiling

city: Seattle

first: Xinxian

last: Deng

state: WA

address: 1959 NE Pacific St.

department: Laboratory Medicine and Pathology

institute: University of Washington

description: NimbleGen genome tiling array 2007-07-27_MM8_TILE_ChIP_10_HX1

hyb_protocol: Standard NimbleGen protocol

scan_protocol: Standard NimbleGen protocol

data_processing: Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy5/Cy3 were computed. The supplementary GFF files contain the bi-weight mean adjusted log base 2 ratios in MM8 coordinates

source_name: Nucleophosmin ChIP DNA from mouse female adult liver

label_protocol: Amplified ChIP or input DNA were labeled by Cy5 or Cy3 respectively using standard NimbleGen protocol.

extract_protocol: Several million cells were fixed with 1% formaldehyde and lysed in 1 ml of IP buffer (150mM NaCl, 50 mM Tris pH7.5, 5 mM EDTA, 0.5% NP-40, 1.0% Triton X-100). The nuclear pellet was sheared to an average size of 0.5-1 kb by sonication. A 10% of chromatin was saved as the input fraction. ChIP was performed using 5ug antibody. Pull-down chromatin by protein A sepharose beads and input were treated with 0.2M NaCl at 65°C overnight to remove crosslinks. DNA was purified using Qiaquick® PCR purification kit (Qiagen) and amplified using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma) prior to labeling.

tag: genotype

value: wild type

value: liver

tag: gender

value: female

tag: chip antibody

value: Nucleophosmin Abcam (ab10530)

source_name: ChIP input DNA

value: wildtype


title: Brain_Survivor_3dpi_rep6


title: Brain_Survivor-polyIC_3dpi_rep6

value: polyIC


title: Brain_Naïve-polyIC_3dpi_rep2


title: Brain_Survivor_3dpi_rep1


title: Brain_Carrier_7dpi_rep5


title: Brain_Survivor_3dpi_rep3


title: Brain_Survivor_3dpi_rep4


title: Brain_Naïve-polyIC_3dpi_rep5


title: Brain_Naïve-polyIC_3dpi_rep7


title: Brain_Naïve_3dpi_rep3


title: Brain_Survivor-polyIC_3dpi_rep3


title: Brain_Naïve-polyIC_3dpi_rep3


title: Brain_Survivor-polyIC_3dpi_rep5


title: Brain_Naïve_3dpi_rep1


title: Brain_Naïve_3dpi_rep7


title: Brain_Naïve_3dpi_rep2


title: Brain_Survivor-polyIC_3dpi_rep4


title: Brain_Survivor-polyIC_3dpi_rep1


title: Brain_Carrier_3dpi_rep1


title: Brain_Naïve_3dpi_rep5


title: Brain_Survivor_3dpi_rep5


title: Brain_Naïve-polyIC_3dpi_rep4


title: Brain_Carrier_7dpi_rep4


title: Brain_Naïve_3dpi_rep6


title: Brain_Naïve-polyIC_3dpi_rep1


title: Brain_Survivor_3dpi_rep7


title: Brain_Survivor-polyIC_3dpi_rep7


title: male liver_Nucleophosmin_genome tiling

source_name: Nucleophosmin ChIP DNA from mouse male adult liver

value: male


title: Brain_Naïve-polyIC_3dpi_rep6


title: Brain_Survivor-polyIC_3dpi_rep2


title: Brain_Carrier_3dpi_rep3


title: Brain_Carrier-polyIC_3dpi_rep2


title: Brain_Naïve_3dpi_rep4


title: Brain_Carrier-polyIC_3dpi_rep1


title: P427

first: Bernett

last: Lee

address: 8A Biomedical Grove #03-06 Immunos

country: Singapore

institute: Singapore Immunology Network

hyb_protocol: 750ng of labelled cRNAs were hybridized to the Illumina Human HT12 V4.0 arrays for 16 hours at 58°C and the arrays were washed and stained according to the Illumina Wash Protocol.

scan_protocol: The human chips were scanned using BeadArray Scanner 500GX and the images were analyzed using GenomeStudio Gene Expression v 1.9.0.

data_processing: The data were normalised using quantile normalisation with lumi in R.

source_name: Isolated neutrophils

label_protocol: Biotinylated cRNA was prepared according to the Illumina® Ambion TotalPrep™ 96 RNA Amplification kit using 40ng of RNA.

growth_protocol: No growth protocol was used. Isolated neutrophils were directly processed for RNA isolation.

extract_protocol: Total RNA was extracted following the double extraction protocol using Trizol and mirVana™ miRNA Isolation Kit. Total RNA integrity was assessed by Agilent Bioanalyzer.

treatment_protocol: No treatment of neutrophils was performed.

value: neutrophils

value: M

tag: age

value: 20 yr

tag: disease status

value: healthy

tag: ethnicity

value: Chinese


title: P454


title: P456

value: 21 yr


title: Brain_Survivor_3dpi_rep2

tag: tissue


title: P430

tag: cell type

value: F

value: 19 yr


title: P447

value: 22 yr


title: P462

value: 18 yr


title: A84

value: 24 yr


title: P426


title: P304

value: 23 yr


title: P431


title: P39


title: P282

value: 29 yr


title: A92


title: P289


title: P41


title: P298


title: A75


title: A77


title: A71


title: A66


title: P42


title: A5


title: P458


title: P328


title: A4


title: A299


title: A295


title: A293


title: A281


title: A287


title: A276


title: A271


title: A278


title: A268


title: A286


title: A259


title: A262


title: A249


title: A294


title: A246


title: A283


title: A253


title: A263


title: A260


title: A273


title: A265


title: A252


title: A257


title: A292


title: A26


title: A244


title: A245


title: A261


title: A248


title: A264


title: A241


title: A231


title: A240


title: A24


title: A234


title: A229

value: 0 yr


title: A224


title: A219


title: A217


title: A223


title: A218


title: A220


title: A210


title: A226


title: A208


title: patient 4BV, sample 14, liver metastasis

city: Baltimore

first: Szilvia

last: Solyom

state: MD

address: 733 North Broadway

department: Institute for Genomic Medicine

institute: Johns Hopkins University School of Medicine

hyb_protocol: Incubate 200ul cocktail for 16hrs at 50° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing:
CEL files were imported and processed for allele intensities with Partek GS v6.6 using default settings.  Copy number was determined using paired samples, where the tumor samples were compared to the same patient's normal tissue.  Amplified/deleted regions were examined using Partek's segmentation analysis protocol.
Allele intensities from Partek GS v6.6, adjusted for fragment length and probe sequence, without normalization are included in the file "Ptk-Signals.txt " available on the series record.

source_name: surgical pathology, liver tissue

label_protocol: Following standard Affymetrix Cytogenetics Copy Number Assay Protocol, DNA was StyI and NspI digested and biotin labeled.

growth_protocol: none, surgical pathology specimens

extract_protocol: DNA from these tissues was extracted using the AllPrep DNA/RNA Mini kit (Qiagen) after tissue disruption and homogenization with a rotor-stator homogenizer.

treatment_protocol: fresh-frozen tissues, dissected

tag: tumor status

value: metastasis

value: liver


title: patient 4BV, sample 12, colorectal adenoma

source_name: surgical pathology, colorectal tissue

value: adenoma

value: colorectal


title: A206

value: neutrophils

value: M


title: A204

value: healthy


title: patient 4BV, sample 13, primary colorectal cancer

value: primary cancer


title: A201

value: 21 yr

value: Chinese


title: A209

value: 19 yr


title: A195

value: F


title: A203


title: A199


title: A212

value: 22 yr


title: patinet 4BV, sample 11, normal colon

value: normal


title: A198


title: patient 3BV, ample 10/1, adenoma with high grade dysplasia

value: adenoma with high grade dysplasia


title: A190


title: A183


title: A181

value: 24 yr


title: A180


title: A18

value: 20 yr


title: A189


title: A192


title: A193


title: patient 2BV, sample 7, liver metastasis

value: metastasis


title: patient 3BV, sample 15, normal colon


title: A194


title: A185


title: A165


title: A285


title: patient 2BV, sample 5, colorectal adenoma


title: patient 1BV, sample 3/1,  primary colorectal cancer


title: A99


title: patient 1BV, sample 1, normal colon


title: patient 2BV, sample 6/1, primary colorectal cancer


title: patient 2BV, sample 20, normal liver

value: liver


title: A149


title: A155


title: A143


title: A145


title: A157


title: A140

value: 23 yr


title: A154


title: A118


title: A122


title: A116


title: A141


title: A111


title: A103


title: A11


title: A102


title: A227


title: 48h_r2

city: Palaiseau

first: Adeline

last: SIMON

address: 22 place de l'agronomie

institute: INRAE

description: This sample is of wild-type Botrytis cinerea B0510, cultured on mature grapevines at 48h. It is the second of three 48h biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization on microarrays were done by PartnerChip (Evry, France) using the procedures established by NimbleGen (Roche)  and the reagents from Invitrogen (Life technologies, France).

scan_protocol: Scanning was performed by PartnerChip (Evry, France) using NimbleScan.

data_processing: The raw data (.pair file) were subjected to RMA background correction (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), and quantile normalization (Bolstad et al. Bioinformatics 19(2):185), as implemented in the ANAIS website (http://anais.versailles.inra.fr/). Probe data were summarized by gene.

organism: Botrytis cinerea B05.10

source_name: Botrytis cinerea B0510_wild-type

label_protocol: Synthesis of double-stranded cDNA and Cy3-labeling were done by PartnerChip (Evry, France) using the procedures established by NimbleGen (Roche) and the reagents from Invitrogen (Life technologies, France)

growth_protocol: The equatorial areas of berries were inoculated with B. cinerea conidia. The inoculated berries were kept in clear plastic boxes in 100% relative humidity in a growth chamber with fluorescent light tubes. Peel samples were collected at 16h, 24h, 48h. For the mycelium control, B. cinerea was cultivated on minimal media during 48h with the same light conditions that for the infected berries.

extract_protocol: Total RNA was extracted according to the total RNA isolation protocol described by Reid et al. (2006), but with 10M rather than 8M LiCl, and resuspended in RNAse/DNAse-free water. The total RNA was then treated with a DNA-freeTM kit to remove any trace of DNA (Ambion – Applied Biosystems).

value: wild-type

tag: growth condition

value: 48h on mature grapevine berries (Marselan cultivar)


title: 48h_r1

description: This sample is of wild-type Botrytis cinerea B0510, cultured on mature grapevines at 48h. It is the first of three 48h biological replicates used in this experiment, each from separate cultures.


title: 48h_r3

description: This sample is of wild-type Botrytis cinerea B0510, cultured on mature grapevines at 48h. It is the third of three 48h biological replicates used in this experiment, each from separate cultures.


title: 16h_r4

description: This sample is of wild-type Botrytis cinerea B0510, cultured on mature grapevines at 16h. It is the third of three 16h biological replicates used in this experiment, each from separate cultures.

value: 16h on mature grapevine berries (Marselan cultivar)


title: 24h_r2

description: This sample is of wild-type Botrytis cinerea B0510, cultured on mature grapevines at 24h. It is the second of three 24h biological replicates used in this experiment, each from separate cultures.

value: 24h on mature grapevine berries (Marselan cultivar)


title: A117

value: neutrophils

value: healthy


title: A76

value: Chinese


title: 24h_r1

description: This sample is of wild-type Botrytis cinerea B0510, cultured on mature grapevines at 24h. It is the first of three 24h biological replicates used in this experiment, each from separate cultures.


title: 24h_r3

description: This sample is of wild-type Botrytis cinerea B0510, cultured on mature grapevines at 24h. It is the third of three 24h biological replicates used in this experiment, each from separate cultures.


title: A13

value: M

value: 21 yr


title: 16h_r3

description: This sample is of wild-type Botrytis cinerea B0510, cultured on mature grapevines at 16h. It is the second of three 16h biological replicates used in this experiment, each from separate cultures.


title: Myc_r2

description: This sample is of wild-type Botrytis cinerea B0510, cultured on static liquid minimal medium. It is the second of four mycelium (Myc) biological replicates used in this experiment, each from separate cultures.

value: static liquid minimal medium


title: hNAG-1 Tg WAT replicate 1

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from abdominal WAT from hNAG-1 transgenic mice

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: Abdominal WAT from hNAG-1 transgenic mice, replicate 1

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Total RNA was extracted using QIAzol Lysis Reagent from Qiagen following the manufacture's instruction, a total of about 150mg of fat was used for each sample to yeild enough total RNA.

value: female

tag: strain

value: 30 wk

value: abdominal WAT


title: Myc_r1

description: This sample is of wild-type Botrytis cinerea B0510, cultured on static liquid minimal medium. It is the first of four mycelium (Myc) biological replicates used in this experiment, each from separate cultures.


title: hNAG-1 Tg WAT replicate 2

source_name: Abdominal WAT from hNAG-1 transgenic mice, replicate 2


title: Myc_r4

description: This sample is of wild-type Botrytis cinerea B0510, cultured on static liquid minimal medium. It is the fourth of four mycelium (Myc) biological replicates used in this experiment, each from separate cultures.


title: hNAG-1 Tg WAT replicate 3

source_name: Abdominal WAT from hNAG-1 transgenic mice, replicate 3


title: hNAG-1 Wt WAT replicate 2

description: Gene expression from abdominal WAT from WT mice

source_name: Abdominal WAT from WT mice, replicate 2

value: wildtype


title: Myc_r3

description: This sample is of wild-type Botrytis cinerea B0510, cultured on static liquid minimal medium. It is the fhird of four mycelium (Myc) biological replicates used in this experiment, each from separate cultures.


title: hNAG-1 Wt WAT replicate 1

source_name: Abdominal WAT from WT mice, replicate 1


title: HCAEC_si_RNF1

city: Fukuoka

first: Kazuhiro

last: Ohkubo

state: Fukuoka

address: 3-1-1, Maidashi, Higashi-ku

department: Department of Pediatrics

country: Japan

institute: Graduate School of Medical Sciences, Kyushu University

description: Gene expression upon treatment with siRNF213

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray SurePrint G3 Human GE Microarray Kit 8x60K v2 ; 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 four samples were normalized by the quantile algorithm with the Bioconductor.

source_name: Human coronary artery endothelial cell, siRNF213, replicate1

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

growth_protocol: HCAECs were cultured in EGM-2MV (Lonza) containing 10% fetal calf serum. All cell cultures were maintained at 37˚C in normoxic environments with 5% CO2 and 100% humidity.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

treatment_protocol: Transfection of siRNA was conducted using Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer’s protocol.

value: coronary artery endothelial cell

tag: condition


title: HCAEC_si_negative_control1

description: Gene expression upon treatment with control siRNA

source_name: Human coronary artery endothelial cell, control siRNA, replicate1

value: control siRNA


title: hNAG-1 Wt WAT replicate 3

source_name: Abdominal WAT from WT mice, replicate 3


title: HCAEC_si_RNF2

source_name: Human coronary artery endothelial cell, siRNF213, replicate2


title: A115

value: 23 yr


title: HCAEC_si_negative_control2

source_name: Human coronary artery endothelial cell, control siRNA, replicate2


title: 16h_r2

description: This sample is of wild-type Botrytis cinerea B0510, cultured on mature grapevines at 16h. It is the first of three 16h biological replicates used in this experiment, each from separate cultures.

value: wild-type


title: A160


title: wt_2

status: Public on Aug 09 2015

first: Charlie

last: Kim

address: 1001 Potrero Ave

department: Medicine

hyb_protocol: 600 ng of each Cy3-labeled aaRNA hybridized to a SurePrint G3 Custom Gene Expression 8x60K microarray (Agilent) as per manufacturers protocol.

scan_protocol: Arrays were scanned on an Agilent scanner, 3 um resolution, 20-bit tiff

data_processing: Gene expression values were quantile normalized using the aroma.light R package and median centered across samples.

organism: Drosophila melanogaster

source_name: insc-Gal4 >mCD8-GFP  neuroblasts, dpn overexpression

label_protocol: 1.5 ug of aRNA coupled to Cy3 in 0.1 M sodium bicarbonate pH 9 buffer and purified over spin columns

growth_protocol: Total  RNA extraction from FACS-isolated neuroblasts marked with insc

extract_protocol: RNA was isolated from 20,000-40,000 cells (RNAqueous Micro, Life Technologies).  Purified RNA was amplified (MessageAmp II , Life Technologies) with minor modifications to manufacturer’s instructions to generate amino-allyl incorporated amplified RNA.

treatment_protocol: Wild type or eag mutant Drosophila brains were dissociated with trypsin and FACS sorted

value: dpn overexpression

value: insc-Gal4>mCD8-GFP neuroblasts


title: eag_1

source_name: insc-Gal4 >mCD8-GFP  neuroblasts, dpn overexpression, eag mutant

value: eag mutant, dpn overexpression


title: wt_1


title: eag_2


title: ZT=4-(1/8/03)-MMAE49

city: Stanford

first: David

last: Strick

address: 300 Pasteur Dr

institute: Stanford University

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51752.gif

hyb_protocol: not provided

scan_protocol: scanner model: GenePix 4000B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Common reference-whole eye

label_protocol: not provided

extract_protocol: not provided

value: whole eye

value: RPE/choroid/sclera tissues

value: male

value: 2 months

tag: time

value: 4 h


title: A12

source_name: Isolated neutrophils

value: neutrophils

value: healthy

value: Chinese


title: ZT=16-(1/10/03)-MMAE232

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51766.gif


title: LightMelanocytes_24h_KCM+_rep6

status: Public on Aug 08 2015

city: London

first: Saioa

last: Lopez

address: Gower Street

institute: UCL

hyb_protocol: The hybridization step was performed using SureHyb hybridization chamber (Agilent Technologies) and 600 ng of labeled cRNA samples, for 17 hours at 65ºC and 10,000 rpms in an hybridization oven. Microarrays were stabilized with ozone-barrier slide covers (Agilent).

scan_protocol: Image processing of the microarrays was performed by using Agilent Feature Extraction software v10.7.3.1.

data_processing: Raw data were processed with GeneSpring GX software v11.5.1 (Agilent). Feature extraction flags were transformed as follows: if feature was not positive and significant, not uniform, not well above background or was a population outlier: compromised; if feature was saturated: not detected. our data were subjected to a DDHF (Data-Driven Haar-Fisz) transformation for variance stabilization with the R package DDHFm (Motakis et al, 2006). Data were transformed to log base 2 and normalized following the quantile method (Bolstad et al, 2003). Flag spot information in data files was used to filter probe sets. Entities in which more than 50% of samples in 1 out of any 7 conditions (0h, 6h KCM-, 12h KCM-, 24h KCM, 6h KCM+, 12h KCM+ and 24h KCM+) had “detected” flags were maintained for the analysis.

label_protocol: 100 ng RNA were labelled with the Low input Quick Amp Labeling kit, one color (Agilent)

growth_protocol: Human epidermal keratinocytes were cultured in EpiLife Medium supplemented with human keratinocyte growth supplement (HKGS). Human epidermal melanocytes were cultivated in Medium 254 supplemented with 1% human melanocyte growth supplement (HMGS). All the cell lines were maintained in an incubator under an atmosphere of 5% CO2 at 37ºC. Media were refreshed every two days.

extract_protocol: RNA extraction kit from Ambion

treatment_protocol: Keratinocyte supernatants were harvested from both non-irradiated (hereinafter KCM-) and irradiated keratinocytes (24 hours after treatment) (hereinafter KCM+) and kept frozen at -80ºC until use. Subconfluent melanocyte cultures were cultivated in Medium 254 supplemented with HMGS and KCM+ or KCM- Medium in a proportion 1:1. The following day they were irradiated with 75 mJ/cm2 of UVB, and harvested at 6, 12 and 24 hours post irradiation. We used non-irradiated control cultures that were covered by aluminium foil during irradiation (Fig 1).

value: skin

value: epidermal keratinocytes

tag: pigmentation level

value: light

tag: media

value: KCM+

tag: hours post irradiation


title: ZT=0.5-(1/9/03)-MMAE215

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51757.gif


title: ZT=13-(1/10/03)-MMAE245

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51781.gif


title: ZT=23-(1/9/03)-MMAE214

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51756.gif


title: ZT=23-(1/10/03)-MMAE233

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51768.gif


title: ZT=13-(1/8/03)-MMAE212

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51754.gif


title: ZT=11-(1/9/03)-MMAE224

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51763.gif


title: LightMelanocytes_24h_KCM+_rep1


title: ZT=16-(1/9/03)-MMAE213

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51755.gif


title: ZT=1.5-(1/10/03)-MMAE236

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51775.gif


title: LightMelanocytes_24h_KCM+_rep5


title: ZT=4-(1/9/03)-MMAE223

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51761.gif


title: LightMelanocytes_24h_KCM+_rep3


title: LightMelanocytes_24h_KCM+_rep4


title: DarkMelanocytes_24h_KCM+_rep6

value: dark


title: ZT=23-(1/11/03)-MMAE247

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51785.gif


title: LightMelanocytes_24h_KCM+_rep2


title: ZT=11-(1/8/03)-MMAE211

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51753.gif


title: ZT=16-(1/11/03)-MMAE246

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51783.gif


title: ZT=-0.5-(1/10/03)-MMAE234

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51770.gif


title: DarkMelanocytes_24h_KCM+_rep4


title: ZT=0.5-(1/8/03)-MMAE52

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51745.gif


title: ZT=1-(9/8/02)-MMAE221

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51758.gif

value: 1 h


title: ZT=4-(1/10/03)-MMAE243

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51777.gif


title: ZT=1.5-(1/8/03)-MMAE50

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51750.gif


title: ZT=1.5-(1/9/03)-MMAE222

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51759.gif


title: DarkMelanocytes_24h_KCM+_rep1


title: DarkMelanocytes_24h_KCM+_rep2


title: LightMelanocytes_12h_KCM+_rep6


title: LightMelanocytes_12h_KCM+_rep5


title: LightMelanocytes_12h_KCM+_rep4


title: DarkMelanocytes_12h_KCM+_rep4


title: LightMelanocytes_12h_KCM+_rep3


title: DarkMelanocytes_12h_KCM+_rep5


title: DarkMelanocytes_12h_KCM+_rep6


title: LightMelanocytes_12h_KCM+_rep1


title: LightMelanocytes_6h_KCM+_rep6


title: LightMelanocytes_6h_KCM+_rep5


title: ZT=11-(1/10/03)-MMAE244

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51779.gif


title: DarkMelanocytes_12h_KCM+_rep3


title: LightMelanocytes_6h_KCM+_rep4


title: LightMelanocytes_12h_KCM+_rep2


title: DarkMelanocytes_12h_KCM+_rep2


title: DarkMelanocytes_24h_KCM+_rep5


title: LightMelanocytes_6h_KCM+_rep3


title: ZT=1-(9/7/02)-MMAE51

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51746.gif


title: LightMelanocytes_6h_KCM+_rep2


title: ZT=13-(1/9/03)-MMAE225

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51764.gif


title: DarkMelanocytes_12h_KCM+_rep1


title: DarkMelanocytes_6h_KCM+_rep5


title: DarkMelanocytes_6h_KCM+_rep4


title: ZT=1- (9/9/02)-MMAE235

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51772.gif


title: DarkMelanocytes_6h_KCM+_rep6


title: DarkMelanocytes_6h_KCM+_rep1


title: LightMelanocytes_24h_KCM-_rep3

value: KCM-


title: LightMelanocytes_6h_KCM+_rep1


title: LightMelanocytes_24h_KCM-_rep5


title: DarkMelanocytes_6h_KCM+_rep2


title: LightMelanocytes_24h_KCM-_rep2


title: DarkMelanocytes_24h_KCM-_rep4


title: DarkMelanocytes_24h_KCM-_rep2


title: LightMelanocytes_24h_KCM-_rep6


title: DarkMelanocytes_24h_KCM-_rep3


title: LightMelanocytes_24h_KCM-_rep1


title: LightMelanocytes_12h_KCM-_rep3


title: LightMelanocytes_12h_KCM-_rep5


title: DarkMelanocytes_24h_KCM-_rep5


title: LightMelanocytes_12h_KCM-_rep4


title: DarkMelanocytes_12h_KCM-_rep6


title: LightMelanocytes_12h_KCM-_rep1


title: DarkMelanocytes_24h_KCM-_rep6


title: DarkMelanocytes_12h_KCM-_rep5


title: DarkMelanocytes_12h_KCM-_rep2


title: LightMelanocytes_12h_KCM-_rep6


title: DarkMelanocytes_24h_KCM-_rep1


title: LightMelanocytes_12h_KCM-_rep2


title: LightMelanocytes_6h_KCM-_rep6


title: DarkMelanocytes_12h_KCM-_rep3


title: DarkMelanocytes_12h_KCM-_rep1


title: DarkMelanocytes_24h_KCM+_rep3


title: DarkMelanocytes_12h_KCM-_rep4


title: LightMelanocytes_6h_KCM-_rep4


title: LightMelanocytes_6h_KCM-_rep3


title: LightMelanocytes_6h_KCM-_rep1


title: DarkMelanocytes_6h_KCM-_rep6


title: LightMelanocytes_6h_KCM-_rep2


title: DarkMelanocytes_6h_KCM-_rep2


title: DarkMelanocytes_6h_KCM-_rep5


title: DarkMelanocytes_6h_KCM-_rep4


title: DarkMelanocytes_6h_KCM-_rep3


title: LightMelanocytes_0h_rep4


title: LightMelanocytes_0h_rep6


title: LightMelanocytes_0h_rep1


title: LightMelanocytes_0h_rep5


title: DarkMelanocytes_6h_KCM-_rep1


title: DarkMelanocytes_0h_rep6


title: DarkMelanocytes_6h_KCM+_rep3


title: DarkMelanocytes_0h_rep5


title: relA_0.2%glu_rep2

city: Wuhan

first: Lu

last: Li

email: sakura.tree@163.com, xuzf@mail.hzau.edu.cn, xuzhuofei@sohu.com, kobe2071@tom.com

state: Hubei

address: Shizishan Street 1

country: China

institute: Huazhong Agricultural University

description:
Gene expression in exponential growth phase
relA_5
R11

hyb_protocol: After fragmentation of the Cy3-cRNA, hybridization was performed using Gene Expression Hybridization Kit (Agilent Technologies, Beijing, China).

scan_protocol: Arrays were scanned by Agilent Microarray Scanner System with resolution of 5 μm, The signal intensities were normalized using Feature Extraction Software (Agilent Technologies) and transformed into log2 values.

data_processing: Data were analyzed using GeneSpring Software 5.0 (Silicon Genetics, CA, USA)

organism: Streptococcus suis

source_name: relA mutant strain cultured in 0.2% glucose CDM, replicate 2

label_protocol: 2 μg RNA was reverse-transcribed into cDNA, and then the cDNA was transcribed into aaUTP labeled cRNA and purified. 4 μg cRNA was labeled with Cy3 NHS ester (GE healthcare) and purified.

growth_protocol: Cells were growth in chemical defined medium (CDM) at 37°C

extract_protocol: Total RNA were isolated and purified using QIAGEN RNeasy Mini Kit (Qiagen, Shanghai, China) according to the manufacturer’s instructions.

treatment_protocol: Overnight cultured cells were washed with CDM for three times and resuspended in CDM containing 0.2% glucose and CDM containing 1% glucose to the density of OD600≈0.1 respectively. After 6 hours further incubation, cells in exponential growth period were collected for microarray analysis

value: relA mutant

tag: growth protocol

value: 0.2% glucose

tag: growth stage

value: exponential growth phase


title: relA_0.2%glu_rep3

description:
Gene expression in exponential growth phase
relA_6
R12

source_name: relA mutant strain cultured in 0.2% glucose CDM, replicate 3


title: LightMelanocytes_0h_rep2


title: relA_0.2%glu_rep1

description:
Gene expression in exponential growth phase
relA_4
R10

source_name: relA mutant strain cultured in 0.2% glucose CDM, replicate 1


title: DarkMelanocytes_0h_rep3


title: DarkMelanocytes_0h_rep4


title: DarkMelanocytes_0h_rep2


title: relA_1%glu_rep3

description:
Gene expression in exponential growth phase
relA_3
R3

source_name: relA mutant strain cultured in 1% glucose CDM, replicate 3

value: 1% glucose


title: LightMelanocytes_0h_rep3


title: relA_1%glu_rep2

description:
Gene expression in exponential growth phase
relA_2
R2

source_name: relA mutant strain cultured in 1% glucose CDM, replicate 2


title: relA_1%glu_rep1

description:
Gene expression in exponential growth phase
relA_1
R1

source_name: relA mutant strain cultured in 1% glucose CDM, replicate 1


title: DarkMelanocytes_0h_rep1


title: Berry_VB_Bc_48hpi_rep_c

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

institute: University of Verona

description: Grapevine berry at veraison stage 48h post inoculation with Botrytis cinerea B05-10

hyb_protocol: Samples were hybridised to slides using a NimbleGen hybridization system.

scan_protocol: The slide was scanned using an Axon GenePix® 4000A scanner, after which resulting images were imported into NimbleScan software for grid alignment and expression data analyses.

data_processing: The data were normalized using quantile normalization and gene calls generated using a robust multi-chip average (RMA) algorithm (Irizarry). The statistically significant transcripts from the grapevine microarray data were detected using ANAIS with the FDR-test for multiple tests correction of ANOVA p-values (Simon & Biot, 2010).

organism: Vitis vinifera

source_name: berry

label_protocol: cDNA samples were labeled with Cy3 using a NimbleGen One-Color DNA labeling kit

growth_protocol: All grapevine berries used in this study belongs to the cultivar Marselan and were collected from one experimental INRA vineyard near Bordeaux between 2009 and 2011. The B. cinerea inoculum was produced by growing the strain B05-10 (Quidde et al., 1998) on solid medium (1.5 % malt extract, 0.5 % glucose, 0.1 % tryptone, 0.1 % casein hydrolysate, 0.1 % yeast extract and 0.02 % tRNA) first for five days in the dark, followed by five days under black light (300–400 nm) to promote fungal sporulation (OSRAM L36-73; 10 h/14 h day/night).

extract_protocol: RNA was extracted with a modified Reid et al. (2006) protocol. Pre-warmed (60ºC) extraction buffer consisting of 300 mM Tris-HCl (pH 8), 25 mM EDTA, 2 M NaCl, 1 mM aurintricarboxylic acid, 2 % (m/v) hexadecyl-trimethyl-ammonium bromide, 2 % (m/v) polyvinylpolypyrrolidone, 0.05 % (m/v) spermidine trihydrochloride, and 2 % (v/v) ß-mercaptoethanol was added to frozen berry peel powder at 15 mL/g and shaken vigorously. Samples were incubated in a 60ºC water bath for 10 min and shaken every 2 min. An equal volume of chloroform/3-methyl-1-butanol (24:1) was added and samples were mixed vigorously, followed by centrifugation at 3500 g for 15 min at 4ºC. The water phase was collected and subjected to a repeated chloroform extraction. Nucleic acids in the water phase were precipitated in 0.3 M sodium acetate (pH 5.2) and by adding 0.6 vol of isopropyl alcohol. After 1 h at -20ºC the precipitates were pelleted by centrifugation at 3500 g for 30 min at 4ºC and the pellet was dissolved in 1 mL TE buffer (10 mM Tris-HCl, pH 8; 1 mM EDTA). LiCl was added to 2.5 M and large RNAs were precipitated overnight at 4ºC, pelleted by centrifugation at 20 000 g for 30 min at 4ºC. The pellet was washed with 70% ethanol and dissolved in water. Remaining traces of DNA were removed by DNaseI treatment (DNA-free, Invitrogen) and the RNA quality was analyzed using a RNA 6000 nano kit (Agilent Technologies, Waldbronn, Germany).

treatment_protocol: The equatorial area of each berry was inoculated with 3 inoculum droplets spotted in triangle, each of 10 µl with 5000 conidia in potato dextrose browth

value: berry

tag: developmental stage

value: veraison stage

tag: hours post inoculation


title: SC-19_1%glu_rep1

description:
Gene expression in exponential growth phase
SC-19_1
S1

source_name: SC-19 strain cultured in 1% glucose CDM, replicate 1

value: parental SC-19


title: SC-19_1%glu_rep2

description:
Gene expression in exponential growth phase
SC-19_2
S2

source_name: SC-19 strain cultured in 1% glucose CDM, replicate 2


title: SC-19_0.2%glu_rep1

description:
Gene expression in exponential growth phase
SC-19_4
S10

source_name: SC-19 strain cultured in 0.2% glucose CDM, replicate 1


title: SC-19_0.2%glu_rep2

description:
Gene expression in exponential growth phase
SC-19_5
S11

source_name: SC-19 strain cultured in 0.2% glucose CDM, replicate 2


title: SC-19_0.2%glu_rep3

description:
Gene expression in exponential growth phase
SC-19_6
S12

source_name: SC-19 strain cultured in 0.2% glucose CDM, replicate 3


title: Berry_VB_Bc_48hpi_rep_a


title: Berry_VB_Bc_24hpi_rep_c

description: Grapevine berry at veraison stage 24h post inoculation with Botrytis cinerea B05-10


title: SC-19_1%glu_rep3

description:
Gene expression in exponential growth phase
SC-19_3
S3

source_name: SC-19 strain cultured in 1% glucose CDM, replicate 3


title: +Ky-2_salt_rep3

city: Nara

first: Kaori

last: Sako

state: Nara

address: 3327-204, Nakamachi

department: Department of Advanced Bioscience

institute: Kindai University

description: with Ky-4

hyb_protocol: 600 ng of cRNAs was hybridized to the microarray (GPL20781) at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer  (Agilent), and then dried immediately by brief centrifugation.

scan_protocol: The microarray was scanned by Agilent DNA Microarray Scanner G2539A ver. C and  raw data was extracted using Feature Extraction program ver 9.1.

data_processing: RMA normalization was performed for signals of microarray probes using limma package on R program.

organism: Arabidopsis thaliana

label_protocol: 200 ng of each RNA sample was used to prepare for Cy3-labeled cRNA, using Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: four-day-old wild-type plants (Arabidopsis thaliana ecotype Columbia) were grown on 1/2 MS, 0.1 % Agar medium.

extract_protocol: Total RNA was extracted from whole plants using RNeasy Plant Mini Kit  (QIAGEN).

treatment_protocol: The plants were treated 1 M Ky-2 for 24 hours and supplied 100 mM NaCl for two hours.

value: whole plant

tag: ecotype

value: Columbia

value: salinity stress

tag: treatment

value: 1 M Ky-2 for 24 hours


title: Berry_VB_Bc_48hpi_rep_b


title: Berry_VB_Bc_24hpi_rep_b


title: +Ky-2_salt_rep1

description: with Ky-2


title: -Ky-2_salt_rep3

description: without Ky-4

value: without Ky-2


title: +Ky-2_salt_rep2

description: with Ky-3


title: +Ky-2_con_rep3

description: with Ky-4

value: unstress


title: -Ky-2_salt_rep1

description: without Ky-2


title: Berry_VB_0hpi_rep_a

description: Grapevine berry at veraison stage


title: Berry_MB_Bc_48hpi_rep_c

description: Grapevine berry at harvesting stage 48h post inoculation with Botrytis cinerea B05-10

value: harvesting stage


title: JHH7_4h_AtRA

city: Yokohama

first: Xian-Yang

last: Qin

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

institute: RIKEN Center for Integrative Medical Sciences

description: Gene expression after 4h  1μM AtRA treatment

hyb_protocol: Oligonucleotide microarray experiments were performed using Affymetrix HG-U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA, USA).

scan_protocol: The arrays were scanned using an GenePix 4000B microarray scanner (Axon Instruments, Union City, CA, USA).

data_processing: data normalization and analysis was performed with GeneSpring GX13.0 (Agilent Technologies)

source_name: JHH7, 4h, AtRA

label_protocol: RNA was amplified into cRNA and labeled with Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technologies).

growth_protocol: JHH7 were maintained in maintained in Dulbecco's Modified Eagle Medium (DMEM; Wako Industries) containing 10% fetal bovine serum (FBS, Mediatech, Herndon, VA, USA), 100 U/ml penicillin/streptomycin and 2 mmol/L L-glutamine (Mediatech, Herndon, VA, USA) and grown at 37°C in a 5% CO2 humidified incubator.

extract_protocol: Total RNA was isolated from the culture cells using an RNeasy Kit (Qiagen, Valencia, CA) in accordancewith the manufacturer’s instructions. Quantification and quality assessment of theisolated RNA samples were performed and verified using a NanoDrop spectrophotometer (NanoDrop products, Wilmington, DE) in accordancewith the manufacturer’s instructions.

value: liver tumor

tag: gender

value: Male


title: Berry_VB_0hpi_rep_b

description: Grapevine berry at veraison stage

tag: tissue


title: Berry_MB_Bc_48hpi_rep_b


title: JHH7_1h_AtRA

description: Gene expression after 1h  1μM AtRA treatment

source_name: JHH7, 1h, AtRA


title: Berry_VB_Bc_24hpi_rep_a


title: Berry_VB_0hpi_rep_c

description: Grapevine berry at veraison stage


title: -Ky-2_salt_rep2

description: without Ky-3


title: Berry_MB_Bc_48hpi_rep_a


title: JHH7_1h_ACR

description: Gene expression after 1h  10μM ACR treatment

source_name: JHH7, 1h, ACR


title: Berry_MB_Bc_24hpi_rep_c

description: Grapevine berry at harvesting stage 24h post inoculation with Botrytis cinerea B05-10


title: Berry_MB_Bc_24hpi_rep_b


title: Berry_MB_Bc_24hpi_rep_a


title: Pla2g10-Tg, skin_Rep2

city: Setagaya

first: Kei

last: Yamamoto

state: Tokyo

address: 2-1-6 kamikitazawa

department: Lipid Metabolism Project

institute: Tokyo Metropolitan Institute of Medical Science

description: gene expression profile in skin tissue of Pla2g10-overexpressing transgenic mouse

hyb_protocol: 1.5 µg of Cy3 or Cy5-labeled cRNA was fragmented using the Agilent Gene Expression Hybridization Kit protocol. Hybridizations were performed for 17 hours at 65ºC at 5 rpm in a rotating hybridization oven.

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

data_processing:
GenePix Software (Molecular Devices) was used for background subtraction and normalization.
Values represent normalized log10 ratio (Cy5/Cy3).

label_protocol: 500 ng of total RNA was amplified and labeled using the Agilent Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

growth_protocol: Pla2g10-Tg/+ mice and littermate controls (C57BL/6 background) were housed in climate-controlled (23 oC) pathogen-free facilities with a 12 h light-dark cycle, with free access to standard LFD (CE2; CLEA Japan) and water.

extract_protocol: Total RNA was extracted from skin of 25 days-old mouse and purified using the RNeasy Mini Kit (Qiagen). The quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

value: 25-day old skin

tag: genotype

source_name: Control

value: Control


title: JHH7_0h

description: Gene expression at 0h

source_name: JHH7, 0h


title: Pla2g10-Tg, skin_Rep1


title: +Ky-2_con_rep2

description: with Ky-3


title: JHH7_4h_ACR

description: Gene expression after 4h  10μM ACR treatment

source_name: JHH7, 4h, ACR


title: -Ky-2_con_rep1

description: without Ky-2


title: Berry_MB_0hpi_rep_c

description: Grapevine berry at harvesting stage


title: +Ky-2_con_rep1

description: with Ky-2


title: -Ky-2_con_rep3

description: without Ky-4


title: Berry_MB_0hpi_rep_a

description: Grapevine berry at harvesting stage


title: Berry_MB_0hpi_rep_b

description: Grapevine berry at harvesting stage


title: Pla2g2f-Tg, skin_Rep1

description: gene expression profile of Pla2g2f-overexpressing transgenic mouse skin

hyb_protocol: 0.75 µg of Cy3 or Cy5-labeled cRNA was fragmented using the Agilent Gene Expression Hybridization Kit protocol. Hybridizations were performed for 17 hours at 65ºC at 5 rpm in a rotating hybridization oven.

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

growth_protocol: Pla2g2f-Tg/+ mice and littermate controls (C57BL/6 background) were housed in climate-controlled (23 oC) pathogen-free facilities with a 12 h light-dark cycle, with free access to standard LFD (CE2; CLEA Japan) and water.


title: Pla2g2f-Tg, skin_Rep2


title: Pla2g2f-/- keratinocye_Control

description: gene expression profile in mouse keratinocytes (Pla2g2f-/-) treated without calcium

hyb_protocol: 1.65 µg of Cy3-labeled cRNA was fragmented using the Agilent Gene Expression Hybridization Kit protocol. Hybridizations were performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with SureScan Microarray Scanner (Agilent Technologies) using a scan resolution of 5µm and dye channel of Green with PMT set to 100%.

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.5.1.1) with set to default for all parameters.

source_name: Pla2g2f-/- keratinocye_Control

label_protocol: 200 ng of total RNA was amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer's protocol.

growth_protocol: Keratinocytes were isolated from whole skin of C57BL/6 newborn mice (Pla2g2f+/+ or Pla2g2f-/-) using 0.05% collagenase A and cultured for 3 days.

extract_protocol: Total RNA was extracted from keratinocytes and purified using the RNeasy Mini Kit (Qiagen). Samples are pooled from keratinocytes from 6 mice for each genotype. The quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Keratinocytes were treated with or without 1 mM CaCl2 for 48 h.

tag: cell

value: keratinocyte

tag: agent

value: control


title: Pla2g2f+/+ keratinocye_CaCl2

description: gene expression profile in mouse keratinocytes (Pla2g2f+/+) treated with calcium

source_name: Pla2g2f+/+ keratinocye_CaCl2

value: calcium


title: BrCaLine_HCC1187_Rep_3

status: Public on Aug 07 2015

city: North Chicago

first: Xin

last: Lu

state: IL

address: 1 North Waukegan Rd

department: Oncology Discovery

institute: Abbvie

description: Gene expression data of cultured cell line

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133A 2.0 chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 following recommended Affymetrix protocols.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000.

data_processing: The data were analyzed with Partek software using GCRMA algorithm

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Breast cancer cell lines obtained from the ATCC or DSMZ were cultured in the recommended media containing 10% FBS (Invitrogen Corporation, Carlsbad, CA, USA) and 10mM L-glutamine.

extract_protocol: Total RNA was extracted from cell lines using Qiazol lysis reagent and the RNeasy 96 universal tissue kit (Qiagen)

treatment_protocol: Untreated

tag: cell line

value: Breast Cancer cell line HCC-1187


title: BrCaLine_HCC1187_Rep_2


title: Pla2g2f-/- keratinocye_CaCl2

description: gene expression profile in mouse keratinocytes (Pla2g2f-/-) treated with calcium

source_name: Pla2g2f-/- keratinocye_CaCl2


title: Pla2g2f+/+ keratinocye_Control

description: gene expression profile in mouse keratinocytes (Pla2g2f+/+) treated without calcium

source_name: Pla2g2f+/+ keratinocye_Control


title: BrCaLine_HCC1187_Rep_1


title: BrCaLine_HCC202_Rep_1

value: Breast Cancer cell line HCC-202


title: BrCaLine_HCC1599_Rep_2

value: Breast Cancer cell line HCC-1599


title: BrCaLine_HCC202_Rep_3


title: BrCaLine_HCC1599_Rep_1


title: BrCaLine_HCC202_Rep_2


title: -Ky-2_con_rep2

description: without Ky-3

value: whole plant

tag: condition


title: BrCaLine_ZR7530_Rep_1

value: Breast Cancer cell line ZR-7530


title: BrCaLine_ZR7530_Rep_3


title: BrCaLine_BT474_Rep_3

value: Breast Cancer cell line BT474


title: BrCaLine_BT474_Rep_1


title: BrCaLine_MDAMB175VII_Rep_1

value: Breast Cancer cell line MDA-MB-175(VII)


title: BrCaLine_ZR7530_Rep_2


title: BrCaLine_MDAMB175VII_Rep_3


title: BrCaLine_MDAMB175VII_Rep_2


title: BrCaLine_CAMA1_Rep_2

value: Breast Cancer cell line CAMA-1


title: BrCaLine_BT474_Rep_2


title: BrCaLine_UACC812_Rep_3

value: Breast Cancer cell line UACC-812


title: BrCaLine_UACC812_Rep_1


title: BrCaLine_CAMA1_Rep_3


title: BrCaLine_CAMA1_Rep_1


title: BrCaLine_MDAMB453_Rep_1

value: Breast Cancer cell line MDA-MB-453


title: BrCaLine_ZR751_Rep_3

value: Breast Cancer cell line ZR751


title: BrCaLine_ZR751_Rep_1


title: BrCaLine_MDAMB453_Rep_2


title: BrCaLine_HCC1143_Rep_1

value: Breast Cancer cell line HCC-1143


title: BrCaLine_HCC1143_Rep_3


title: BrCaLine_UACC812_Rep_2


title: BrCaLine_T47D_Rep_3

value: Breast Cancer cell line T47D


title: BrCaLine_T47D_Rep_2


title: BrCaLine_MDAMB453_Rep_3


title: BrCaLine_MDAMB231_Rep_2

value: Breast Cancer cell line MDA-MB-231


title: BrCaLine_ZR751_Rep_2


title: BrCaLine_SKBR3_Rep_2

value: Breast Cancer cell line SKBR3


title: BrCaLine_SKBR3_Rep_3


title: BrCaLine_MDAMB231_Rep_3


title: BrCaLine_MDAMB231_Rep_1


title: BrCaLine_T47D_Rep_1


title: BrCaLine_MDAMB468_Rep_2

value: Breast Cancer cell line MDA-MB-468


title: BrCaLine_MCF7_Rep_3

value: Breast Cancer cell line MCF-7(Luc)


title: BrCaLine_MCF7_Rep_2


title: BrCaLine_MDAMB361_Rep_2

value: Breast Cancer cell line MDA-MB-361


title: BrCaLine_MDAMB361_Rep_3


title: BrCaLine_HCC1395_Rep_2

value: Breast Cancer cell line HCC-1395


title: BrCaLine_HCC2218_Rep_1

value: Breast Cancer cell line HCC-2218


title: BrCaLine_DU4475_Rep_1

value: Breast Cancer cell line DU-4475


title: BrCaLine_MDAMB468_Rep_1


title: BrCaLine_SKBR3_Rep_1


title: BrCaLine_HCC2218_Rep_2


title: BrCaLine_MCF7_Rep_1


title: BrCaLine_DU4475_Rep_3


title: BrCaLine_HCC2218_Rep_3


title: BrCaLine_DU4475_Rep_2


title: BrCaLine_MDAMB361_Rep_1


title: BrCaLine_HCC1419_Rep_2

value: Breast Cancer cell line HCC-1419


title: BrCaLine_HCC1419_Rep_1


title: BrCaLine_HCC1937_Rep_2

value: Breast Cancer cell line HCC-1937


title: BrCaLine_HCC1500_Rep_3

value: Breast Cancer cell line HCC-1500


title: BrCaLine_HCC1395_Rep_1


title: BrCaLine_HCC1419_Rep_3


title: BrCaLine_HCC1954_Rep_3

value: Breast Cancer cell line HCC-1954


title: BrCaLine_HCC1954_Rep_2


title: BrCaLine_HCC1500_Rep_1


title: BrCaLine_HCC1954_Rep_1


title: BrCaLine_HCC1500_Rep_2


title: BrCaLine_HCC1806_Rep_1

value: Breast Cancer cell line HCC-1806


title: BrCaLine_HCC1806_Rep_3


title: BrCaLine_BT20_Rep_2

value: Breast Cancer cell line BT-20


title: BrCaLine_BT20_Rep_3


title: BrCaLine_HCC1428_Rep_3

value: Breast Cancer cell line HCC-1428


title: BrCaLine_BT20_Rep_1


title: BrCaLine_BT549_Rep_3

value: Breast Cancer cell line BT-549


title: BrCaLine_BT549_Rep_2


title: BrCaLine_HCC1806_Rep_2


title: BrCaLine_HCC1569_Rep_1

value: Breast Cancer cell line HCC-1569


title: BrCaLine_HCC1569_Rep_2


title: BrCaLine_HCC1569_Rep_3


title: BrCaLine_HCC1428_Rep_1


title: BrCaLine_HCC1428_Rep_2


title: BrCaLine_HCC38_Rep_3

value: Breast Cancer cell line HCC-38


title: BrCaLine_HCC38_Rep_2


title: BrCaLine_HCC70_Rep_1

value: Breast Cancer cell line HCC-70


title: BrCaLine_Hs578T_Rep_1

value: Breast Cancer cell line HS-578T


title: BrCaLine_HCC70_Rep_3


title: BrCaLine_HCC70_Rep_2


title: BrCaLine_HCC38_Rep_1


title: STF_2

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

country: Germany

institute: Institute for Biomedical Engineering

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the Affymetrix Power Tools (APT) Software Package. Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).

source_name: STF-expanded

label_protocol: biotin

extract_protocol: RNeasy kit (Quiagen)

treatment_protocol: Human CB samples were obtained from the Department for Gynecology and Obstetrics, University Clinic Würzburg after informed consent approved by the local Ethical Committee of the University of Würzburg. CD34+ progenitors were obtained by immunomagnetic bead selection using either CD34 progenitor cell isolation or Diamond CD34 isolation kits (Miltenyi Biotec, Bergisch-Gladbach, Germany). The purities of CD34+ progenitor samples were determined flow cytometry (Immunophenotype of CD34+ cells: 91% CD34; 86,9% CD133; 33% CD38; 98% CD45; immunophenotype of CD34- cells: 1% CD34; 1,2% CD133; 46,8% CD38; 58% CD45). For expansion, CD34+ progenitor cells were seeded at a concentration of 2E+05 cells/ml into StemSpan serum-free medium (StemCell Technologies Inc., Vancouver, Canada) supplemented with 1% penicillin and streptomycin (Gibco Invitrogen Corporation, Paisley, UK) and heparin (10 ng/mL, Ratiopharm, Ulm, Germany) plus either STF (stem cell factor (SCF, 10 ng/mL, Peprotech, London, UK), recombinant human thrombopoetin (TPO, 20 ng/mL, Peprotech), recombinant human fibroblast growth factor-1 (FGF-1, 10 ng/mL, Peprotech), or STFIA (STF plus angiopoietin like-5 (Angptl-5, 500 ng/mL, Tebu-Bio, Taipei, Taiwan) and insulin-like growth factor binding-protein 2 (IGFBP2, 100 ng/mL, R&D Systems, Minneapolis, USA)) cocktails (Zhang et al., 2008). For EZH2 inhibitor treatment, CD34+ cells in STF culture were co-incubated with either GSK343 (kindly provided from the SGC, University of Toronto) or GSK126 EZH2 inhibitors (Chemie Tek, Indianapolis, USA) at 1 mM. Cells were cultured in 4-well polystyrene plates (Nunc, Roskilde, Denmark). Fresh medium was added every second day and cell densities were maintained at 2×105 cells/ml.

tag: cell type

value: STF-expanded


title: STFIA_2

source_name: STFIA-expanded CD34+ cells

value: STFIA-expanded CD34+ cells


title: BrCaLine_Hs578T_Rep_3


title: NT-PGC-1α [4B]

city: Baton Rouge

first: Ji Suk

last: Chang

state: LA

address: 6400 Perkins Rd.

department: Gene Regulation and Metabolism

institute: Pennington Biomedical Research Center

description: immortalized cells

hyb_protocol: Ten micrograms of digoxigenin-11-UTP-labeled (Roche Diagnostics) cRNA was fragmented using the Applied Biosystems Chemiluminescent Detection Kit protocol. Pooled samples were hybridized onto ABI Mouse Genome Survey arrays.

scan_protocol: The microarray slides were scanned and gridded, and the images were digitized and analyzed using an Applied Biosystems 1700 Chemiluminescent Microarray Analyzer.

data_processing:
Data files were analyzed using the package ABarray v1.36.0 (Applied Biosystems, Foster City, CA), the statistical program R v.2.2.1 (http://www.r-project.org) and the quantile-quantile method for normalization across arrays (http://www.bioconductor.org). Parameters for feature control were set at signal/noise ratio ≥3 and quality flags <5,000 in order to generate fold changes for features.
The Sample table contains quantile normalized signal, SN-signal to noise ratio and flag-flagged defect in the array oligonucleotide spot.  The RawData Matrix contains non-normalized data exported from the package ABarray v1.36.0. 1A and 1B represent technical replicates of control samples (empty vector) and 4A and 4B of NT-PGC-1α-expressing samples.

source_name: brown adipocytes

label_protocol: One microgram of RNA was amplified and labeled using the NanoAmp IVT-Amplification Kit (Applied Biosystems).

growth_protocol: Immortalized brown preadipocytes were transduced with lentivirus expressing NT-PGC-1α or empty vector. Preadipocytes were grown to become confluent in growth mediem (DMEM+FBS) and differentiation was induced for 2 days in the growth medium containing 20 nM insulin, 1 nM triiodothyronine, 0.5 mM isobutylmethlyxanthine, 2 µg/ml dexamethasone and 250 µM indomethacin. Thereafter, cells were maintained in the growth medium containing 20 nM insulin and 1 nM triiodothyronine for additional 5 days (Zhang Y et al, 2009, JBC 284(47):32813).

extract_protocol: Total RNA was isolated using Tri-Reagent (Molecular Research Center) with modifications to remove DNA using Qiagen RNAeasy columns.

tag: strain

value: FVB


title: NT-PGC-1α [4A]

description: immortalized cells


title: CD34-

source_name: fresh CD34- cells

value: fresh CD34- cells


title: CD34+

source_name: fresh CD34+ cells

value: fresh CD34+ cells


title: empty vector [1A]

description: immortalized cells


title: empty vector [1B]

description: immortalized cells


title: P3

city: La Jolla

first: Maike

last: Sander

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

hyb_protocol: 1.65 μg of cRNA was fragmented and hybridized to the array for 17 hr. at 65°C then washed.

scan_protocol: Arrays were scanned with the AgilentTechnologies Scanner G2505B US23502332 using protocol version GE1-v5_95_Feb07

data_processing: Mean foreground intensities were obtained for each spot and imported into the mathematical software package “R”, which is used for all data input, diagnostic plots, normalization and quality checking steps of the analysis process using scripts developed in-house by Peter White specifically for this analysis. In outline, the Cy3 (green) intensities were not background corrected (this has been shown to only introduce noise), and corrected for the scanner offset (40 was subtracted for each intensity). The dataset was filtered to remove positive control elements and any elements that had been flagged as bad. Using the negative controls on the arrays, the background threshold was determined and all values less than this value were set to the threshold value. Finally, the data was normalized using the Limma Quantile Normalization package in “R” (Smyth 2004, Bolstad et al., 2003).

label_protocol: Approximately 250 ng of total RNA was amplified and labeled with Cy3 using the Low RNA Input Linear Amp Kit PLUS, One-Color (Agilent Technologies, Santa Clara, CA). This labeling reaction produces 0.25 – 2.0 μg of Cy3-labeled cRNA (anti-sense), by first converting mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT and then amplifying the sample using T7 RNA Polymerase in the presence of Cy3-CTP.

growth_protocol: All animal experiments described herein were approved by the University of California, Irvine and San Diego Institutional Animal Care and Use Committees. For timed matings, noon on the day of vaginal plug appearance was designated e0.5.

extract_protocol: E12.5 dorsal pancreatic epithelia were manually microdissected and stored in 50 μl of RLT lysis buffer (QIAGEN, Valencia, CA) in the –80°C freezer. Each individual RNA sample was collected from three dorsal pancreata (i.e. three embryos) as per the manufacturer's instructions. We prepared RNA samples in ~12 μl of DEPC-treated water. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: dorsal pancreatic epithelia

tag: age

value: Embryonic day 12

tag: genotype/variation


title: S3


title: BrCaLine_HCC1143_Rep_2

value: Breast Cancer cell line HCC-1143


title: STFIA_1


title: DH2


title: DH1


title: S2


title: P1


title: P2


title: STF_1

source_name: STF-expanded CD34+ cells

value: STF-expanded CD34+ cells


title: DH3&4


title: NEW 056A

first: Alice

last: Gao

state: London

address: 237 Fulham Road

department: Breast Cancer Now

institute: The Institute of Cancer Research

description: pre-treatment

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were transformed and normalized using variance-stabilizing transformation and robust spline normalization method in the Lumi package in R

source_name: breast tumour

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

extract_protocol: mRNA from treated cells was extracted with RNeasy Mini Kit (Qiagen), as per the manufacturer's instructions, and quantification performed using the Agilent 2100 Bioanalyzer (Expert Software version B.02.03) with RNA Nano LabChip Kits (Agilent Technologies).

tag: rmh lab code

value: NEW 056

tag: Sex

value: female

tag: trtlong

value: Faslodex 250mg

value: pre-treatment

value: breast tumour


title: S1


title: NEW 025A

description: pre-treatment

value: NEW 025


title: NEW 055A

description: pre-treatment

value: NEW 055


title: NEW 056B

description: on-treatment

value: on-treatment


title: NEW 025B.2

description: on-treatment


title: BrCaLine_HCC1937_Rep_1

value: Breast Cancer cell line HCC-1937


title: NEW 007A

description: pre-treatment

value: NEW 007


title: NEW 050B

description: on-treatment

value: NEW 050


title: NEW 050A

description: pre-treatment


title: NEW 007B

description: on-treatment


title: NEW 019B

description: on-treatment

value: NEW 019


title: Sample 71M

city: San Francisco

first: Alan

middle: Hunter

last: Shain

address: 555 MISSION BAY SOUTH BLVD RM 282 # 3118

department: Pathology and Dermatology

institute: University of California San Francisco

hyb_protocol: Agilent Oligo aCGH hybridization kit. Manufacturer's instructions.

scan_protocol: Feature Extraction version 9.1 (Agilent Technologies)

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

source_name: Sample 71M

label_protocol: Bioprome aCGH genomic labeling kit. Manufacturer's instructions.

extract_protocol: Qiagen Dneasy. Manufacturer's instructions.

tag: Stage

value: Primary Tumor

value: Fresh Frozen Desmoplastic Melanoma Tumor

source_name: Pooled Normal male genomic DNA

value: Male

value: Blood


title: NEW 019A

description: pre-treatment


title: NEW 014B.2

description: on-treatment

value: NEW 014


title: NEW 014A

description: pre-treatment


title: BrCaLine_Hs578T_Rep_2

value: Breast Cancer cell line HS-578T


title: NEW 033B

description: on-treatment

value: NEW 033

value: female


title: Sample 11M

source_name: Sample 11M


title: NEW 009A

description: pre-treatment

value: NEW 009

value: Faslodex 250mg

value: pre-treatment


title: NEW 039B

description: on-treatment

value: NEW 039

value: breast tumour


title: NEW 039A

description: pre-treatment


title: NEW 033A

description: pre-treatment


title: NEW 055B.2

description: on-treatment

value: NEW 055

value: on-treatment


title: Sample 35M

source_name: Sample 35M


title: NEW 037A

description: pre-treatment

value: NEW 037


title: NEW 028A

description: pre-treatment

value: NEW 028


title: NEW 024B

description: on-treatment

value: NEW 024


title: NEW 037B

description: on-treatment


title: NEW 028B

description: on-treatment


title: BrCaLine_HCC1937_Rep_3

value: Breast Cancer cell line HCC-1937


title: Sample 53M

source_name: Sample 53M

value: Primary Tumor

value: Fresh Frozen Desmoplastic Melanoma Tumor

value: Male


title: Sample 46M

source_name: Sample 46M

value: Blood


title: Sample 12M

source_name: Sample 12M


title: Sample 49M

source_name: Sample 49M


title: BrCaLine_BT549_Rep_1

value: Breast Cancer cell line BT-549


title: Sample 37M

source_name: Sample 37M


title: NEW 024A

description: pre-treatment

value: female


title: NEW 015A

description: pre-treatment

value: NEW 015


title: NEW 008A

description: pre-treatment

value: NEW 008

value: Faslodex 500mg


title: NEW 008B

description: on-treatment


title: Sample 19M

source_name: Sample 19M


title: NEW 034A

description: pre-treatment

value: NEW 034

value: pre-treatment


title: NEW 041A

description: pre-treatment

value: NEW 041

value: Faslodex 250mg

value: breast tumour


title: NEW 020A

description: pre-treatment

value: NEW 020


title: NEW 031A

description: pre-treatment

value: NEW 031


title: NEW 041B

description: on-treatment

value: on-treatment


title: NEW 018A

description: pre-treatment

value: NEW 018


title: NEW 015B

description: on-treatment


title: Sample 40M

source_name: Sample 40M

value: Primary Tumor

value: Fresh Frozen Desmoplastic Melanoma Tumor


title: NEW 058A

description: pre-treatment

value: NEW 058


title: NEW 018B

description: on-treatment


title: NEW 030B

description: on-treatment

value: NEW 030


title: HCC1428

description: Genomic copy number of cultured cell line

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

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

data_processing: The data were analyzed with Partek software, controled by pooling of all HapMap normal tissues, and segment smoothed

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Total DNA was extracted from cell lines using using the DNeasy Blood and Tissue kit (Qiagen Cat#69506) per manufacture’s protocol, except DNA was eluted in DNA Suspension buffer (Teknova).

value: Breast Cancer cell line HCC1428


title: NEW 062A

description: pre-treatment

value: NEW 062

value: female


title: NEW 009B

description: on-treatment

value: NEW 009


title: NEW 059B

description: on-treatment

value: NEW 059

value: Faslodex 500mg


title: NEW 030A

description: pre-treatment

value: pre-treatment


title: NEW 051B

description: on-treatment

value: NEW 051


title: NEW 044A

description: pre-treatment

value: NEW 044

value: breast tumour


title: Sample DM15

source_name: Sample DM15

value: FFPE

value: Male

value: Blood


title: NEW 054B

description: on-treatment

value: NEW 054

value: on-treatment


title: Sample DM21

source_name: Sample DM21

value: Primary Tumor


title: NEW 051A

description: pre-treatment


title: Sample DM68

source_name: Sample DM68


title: Sample DM13

source_name: Sample DM13


title: NEW 057A

description: pre-treatment

value: NEW 057


title: NEW 042A

description: pre-treatment

value: NEW 042


title: Sample DM05

source_name: Sample DM05


title: NEW 042B

description: on-treatment

source_name: breast tumour


title: NEW 040A

description: pre-treatment

value: NEW 040


title: NEW 040B.2

description: on-treatment

value: female


title: NEW 029A.2

description: pre-treatment

value: NEW 029


title: NEW 044B.2

description: on-treatment


title: NEW 010A

description: pre-treatment

value: NEW 010


title: NEW 062B

description: on-treatment

value: NEW 062

value: Faslodex 500mg


title: Sample DM79

source_name: Sample DM79


title: NEW 010B

description: on-treatment


title: Sample DM65

source_name: Sample DM65

source_name: Pooled Normal male genomic DNA


title: NEW 057B

description: on-treatment


title: Sample DM8

source_name: Sample DM8


title: NEW 029B

description: on-treatment


title: Sample DM6

source_name: Sample DM6


title: Sample DM74

source_name: Sample DM74


title: Sample DM100

source_name: Sample DM100


title: Sample DM64

source_name: Sample DM64


title: Sample DM77

source_name: Sample DM77


title: NEW 049A

description: pre-treatment

value: NEW 049

value: pre-treatment


title: NEW 058B

description: on-treatment

value: NEW 058

value: breast tumour


title: Sample DM58

source_name: Sample DM58

value: FFPE

value: Male


title: NEW 054A

description: pre-treatment

value: NEW 054


title: Sample DM55

source_name: Sample DM55

value: Blood


title: Sample DM59

source_name: Sample DM59

value: Primary Tumor


title: NEW 005A

description: pre-treatment

value: NEW 005


title: Sample DM49

source_name: Sample DM49


title: MDAMB231

value: Breast Cancer cell line MDAMB231


title: NEW 006B

description: on-treatment

value: NEW 006

value: on-treatment


title: Sample DM42

source_name: Sample DM42


title: Sample DM34

source_name: Sample DM34


title: Sample DM48

source_name: Sample DM48


title: Sample DM45

source_name: Sample DM45


title: Sample DM51

source_name: Sample DM51


title: NEW 005B

description: on-treatment

source_name: breast tumour

value: female


title: Sample DM37

source_name: Sample DM37

source_name: Pooled Normal male genomic DNA


title: Sample DM36

source_name: Sample DM36


title: Sample DM43

source_name: Sample DM43


title: NEW 034B

description: on-treatment

value: NEW 034


title: Sample DM31

source_name: Sample DM31


title: Sample DM29

source_name: Sample DM29


title: NEW 049B

description: on-treatment


title: Sample DM28

source_name: Sample DM28


title: Sample DM26

source_name: Sample DM26