title: Sputum from Stage II Moderate, biological replicate 71

city: Stevenage

first: steve

middle: matthew

last: fox

address: Gunnels Wood Road

department: Statistics

institute: GlaxoSmithKline

description: Gene expression data from COPD Stage II Moderate

hyb_protocol: Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on GeneChip HG-U133_plus_2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing: The data was analysed with Rosetta Resolver version 5.0

source_name: Sputum from COPD Stage II Moderate

label_protocol: NuGEN Ovation FLv2 methodology using NuGEN Ovation RNA amplification v2 including C1 spike with Agencourt RNAClean SPIA clean up. FLv2 biotin fragmentation and labelling.

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

tag: age

tag: gender

value: F

tag: gold stage

value: Stage II

tag: group

value: Moderate

tag: plateid

tag: batch

value: B

tag: hyb date


title: A222-RA 1

status: Public on Jun 09 2010

type: genomic

city: Ames

first: Zuo-Wei

last: Wu

state: IA

address: 1113 Veterinary Medicine Bldg

country: USA

institute: Iowa state university

hyb_protocol: Labeled genomic DNA was hybridized to arrays in the NimbleGen Hybridization Buffer for 16 hours at 42oC using a MAUI hybridization system (BioMicro Systems, Inc. Salt Lake City, Utah). Labeled genomic DNA (13ug) from the reference sample LX and from each test sample were co-hybridized to each array. Arrays were washed with NimbleGen wash buffer, and then were spun dry in a microarray high-speed centrifuge (TeleChem International, Inc., Sunnyvale, CA) and stored until scanned.(http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 CGH data extraction.

molecule: genomic DNA

organism: Homo sapiens

source_name: Genomic DNA from the whole blood

label_protocol: Genomic DNA was labeled with a Random prime reaction. DNA (1 ug) was mixed with 1 O.D. of 5’-fluorescence dye labeled random nonamer (Cy3 for 15 patient (RA) and 1 control (Non-RA) and Cy5 for reference Sample (LX) (TriLink Biotechnologies) in 62.5 mM Tris-HCl, 6.25 mM MgCl2 and 0.0875% ß-mercaptoethanol, denatured at 98°C for 5 min, chilled on ice, and incubated with 100 units Klenow fragment (NEB) and dNTP mix (6 mM each in TE) for 2 h at 37°C. Reactions were terminated with 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water. A fifty-fold amplification was typically achieved,(http://www.nimblegen.com/products/lit/lit.html)

extract_protocol: Genomic DNA was extracted using QIAGEN DNA easy kit (Qiagen)

tag: disease state

value: rheumatoid arthritis (RA)

source_name: Reference gDNA from Sample LX (Non-RA) whole blood

value: Non-RA


title: Sputum from Stage II Moderate, biological replicate 70

status: Public on Jun 08 2010

type: RNA

country: United Kingdom

label: Biotin

molecule: total RNA

value: M


title: Sputum from Stage II Moderate, biological replicate 72


title: Sputum from Stage III Severe, biological replicate 59

description: Gene expression data from COPD Stage III Severe

source_name: Sputum from COPD Stage III Severe

value: Stage III

value: Severe


title: MKN7 - 37 cell line study

city: Basel

first: Chia-Huey

last: Ooi

address: Grenzacherstrasse 124

country: Switzerland

institute: F. Hoffmann-La Roche Ltd.

description: Series of 37 (unique) gastric cancer cell lines

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChipÂ® Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS3000 7G.

data_processing: The data were analyzed with R version 2.9.0, package affy. Data processing was performed by RMA normalization and Log 2 transformed.

label: biotin

source_name: gastric cancer cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

growth_protocol: Cancer cell lines were grown as per GC cell lines were obtained either from commercial sources or collaborators and cultured as recommended

extract_protocol: RNeasy mini spin columns (Qiagen) were used according to the manufacturer's instructions.

tag: cell line

tag: cell type

value: gastric cancer


title: Sputum from Stage III Severe, biological replicate 57


title: Sputum from Stage IV Severe, biological replicate 13

description: Gene expression data from COPD Stage IV Severe

source_name: Sputum from COPD Stage IV Severe

value: Stage IV

value: C


title: Sputum from Stage III Severe, biological replicate 58


title: NUGC3 - 37 cell line study

treatment_protocol: Cancer cell lines were grown as per GC cell lines were obtained either from commercial sources or collaborators and cultured as recommended


title: A262-RA 1


title: A289-RA 1


title: Sputum from Stage II Moderate, biological replicate 67


title: Sputum from Stage II Moderate, biological replicate 69


title: Sputum from Stage III Severe, biological replicate 55


title: Sputum from Stage II Moderate, biological replicate 65


title: Sputum from Stage IV Severe, biological replicate 12


title: Sputum from Stage II Moderate, biological replicate 68


title: Sputum from Stage II Moderate, biological replicate 66


title: Sputum from Stage II Moderate, biological replicate 60


title: Sputum from Stage II Moderate, biological replicate 64


title: Sputum from Stage II Moderate, biological replicate 61


title: Sputum from Stage III Severe, biological replicate 52


title: Sputum from Stage III Severe, biological replicate 54


title: Sputum from Stage II Moderate, biological replicate 62


title: Sputum from Stage IV Severe, biological replicate 11


title: Sputum from Stage III Severe, biological replicate 53


title: Sputum from Stage II Moderate, biological replicate 59


title: Sputum from Stage III Severe, biological replicate 46


title: A250-RA 1


title: Sputum from Stage III Severe, biological replicate 45


title: Sputum from Stage III Severe, biological replicate 50


title: Sputum from Stage II Moderate, biological replicate 58


title: Sputum from Stage III Severe, biological replicate 49


title: Sputum from Stage III Severe, biological replicate 51


title: Sputum from Stage III Severe, biological replicate 48


title: Sputum from Stage III Severe, biological replicate 47


title: Sputum from Stage II Moderate, biological replicate 56


title: Sputum from Stage III Severe, biological replicate 56


title: Sputum from Stage II Moderate, biological replicate 57


title: Sputum from Stage III Severe, biological replicate 44


title: SCH - 37 cell line study

value: SCH


title: Sputum from Stage III Severe, biological replicate 42


title: Sputum from Stage III Severe, biological replicate 43


title: Sputum from Stage IV Severe, biological replicate 7


title: Sputum from Stage IV Severe, biological replicate 10


title: Sputum from Stage II Moderate, biological replicate 55


title: Sputum from Stage IV Severe, biological replicate 9


title: Sputum from Stage III Severe, biological replicate 41


title: Sputum from Stage II Moderate, biological replicate 53


title: Sputum from Stage II Moderate, biological replicate 52


title: Sputum from Stage III Severe, biological replicate 40


title: Sputum from Stage II Moderate, biological replicate 54


title: Sputum from Stage IV Severe, biological replicate 8


title: Sputum from Stage III Severe, biological replicate 34

value: A


title: Sputum from Stage III Severe, biological replicate 32


title: Sputum from Stage II Moderate, biological replicate 51


title: Sputum from Stage III Severe, biological replicate 39


title: Sputum from Stage III Severe, biological replicate 30


title: Sputum from Stage III Severe, biological replicate 29


title: Sputum from Stage III Severe, biological replicate 36


title: Sputum from Stage III Severe, biological replicate 37


title: Sputum from Stage III Severe, biological replicate 28


title: Sputum from Stage III Severe, biological replicate 35


title: Sputum from Stage III Severe, biological replicate 33


title: Sputum from Stage II Moderate, biological replicate 50


title: Sputum from Stage IV Severe, biological replicate 6


title: Sputum from Stage III Severe, biological replicate 38


title: Sputum from Stage III Severe, biological replicate 31


title: Sputum from Stage III Severe, biological replicate 27


title: Sputum from Stage II Moderate, biological replicate 49


title: Sputum from Stage III Severe, biological replicate 26


title: Sputum from Stage II Moderate, biological replicate 45


title: Sputum from Stage II Moderate, biological replicate 47


title: Sputum from Stage II Moderate, biological replicate 46


title: Sputum from Stage III Severe, biological replicate 25


title: Sputum from Stage II Moderate, biological replicate 44


title: Sputum from Stage IV Severe, biological replicate 4


title: Sputum from Stage IV Severe, biological replicate 5


title: Sputum from Stage III Severe, biological replicate 19


title: Sputum from Stage II Moderate, biological replicate 48


title: Sputum from Stage III Severe, biological replicate 22


title: Sputum from Stage III Severe, biological replicate 23


title: Sputum from Stage III Severe, biological replicate 24


title: Sputum from Stage III Severe, biological replicate 20


title: Sputum from Stage II Moderate, biological replicate 42


title: Sputum from Stage II Moderate, biological replicate 40


title: Sputum from Stage III Severe, biological replicate 21


title: Sputum from Stage III Severe, biological replicate 17


title: Sputum from Stage II Moderate, biological replicate 39


title: Sputum from Stage II Moderate, biological replicate 43


title: Sputum from Stage II Moderate, biological replicate 37


title: Sputum from Stage II Moderate, biological replicate 38


title: Sputum from Stage II Moderate, biological replicate 36


title: Sputum from Stage II Moderate, biological replicate 35


title: Sputum from Stage III Severe, biological replicate 18


title: Sputum from Stage II Moderate, biological replicate 33


title: Sputum from Stage II Moderate, biological replicate 41


title: Sputum from Stage III Severe, biological replicate 15


title: Sputum from Stage II Moderate, biological replicate 34


title: Sputum from Stage III Severe, biological replicate 16


title: Sputum from Stage II Moderate, biological replicate 32


title: Sputum from Stage II Moderate, biological replicate 31


title: Sputum from Stage IV Severe, biological replicate 3


title: Sputum from Stage III Severe, biological replicate 10


title: Sputum from Stage III Severe, biological replicate 14


title: Sputum from Stage III Severe, biological replicate 13


title: Sputum from Stage III Severe, biological replicate 12


title: Sputum from Stage III Severe, biological replicate 11


title: Sputum from Stage II Moderate, biological replicate 28


title: Sputum from Stage II Moderate, biological replicate 29


title: Sputum from Stage III Severe, biological replicate 8


title: Sputum from Stage II Moderate, biological replicate 25


title: Sputum from Stage II Moderate, biological replicate 22


title: Sputum from Stage II Moderate, biological replicate 27


title: Sputum from Stage II Moderate, biological replicate 24


title: Sputum from Stage II Moderate, biological replicate 23


title: Sputum from Stage IV Severe, biological replicate 2


title: Sputum from Stage II Moderate, biological replicate 19


title: Sputum from Stage II Moderate, biological replicate 17


title: Sputum from Stage II Moderate, biological replicate 20


title: Sputum from Stage III Severe, biological replicate 9


title: Sputum from Stage II Moderate, biological replicate 26


title: Sputum from Stage II Moderate, biological replicate 21


title: Sputum from Stage II Moderate, biological replicate 18


title: Sputum from Stage II Moderate, biological replicate 15


title: Sputum from Stage II Moderate, biological replicate 13


title: Sputum from Stage III Severe, biological replicate 7


title: LBT5

city: Adelaide

first: Naiara

middle: G

last: Bediaga

state: South Australia

address: 4 North Terrace

department: Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences

country: Australia

institute: The University of Adelaide

description:
1954009009_R003_C008
Luminal B tumor

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The average beta values were obtained according to standard protocols using Illumina BeadStudio Methylation software (version 3.2.0).

label: Cy3 and Cy5

source_name: Breast cancer tissue

label_protocol: Standard Illumina label protocol

extract_protocol: DNA was extracted with Phenol:clorophorm:ismoamylalcohol, followed by clean-up and bisulfite modification with EZ DNA methylation kit (Zymo Research, Orange, CA, USA) following the manufacturer’s protocol

value: female

tag: tissue

value: Breast cancer tissue

tag: tissue/tumor subtype

value: Luminal B tumor


title: LBT4

description:
1954009009_R003_C007
Luminal B tumor


title: LBT3

description:
1954009009_R002_C003
Luminal B tumor


title: LBT2

description:
1954009009_R001_C007
Luminal B tumor


title: LBT1

description:
1954009009_R001_C006
Luminal B tumor


title: Sputum from Stage II Moderate, biological replicate 16


title: LBS6

description:
1954009009_R008_C006
Luminal B adyacent tissue

source_name: Breast tissue

value: Breast tissue

value: Luminal B adjacent tissue


title: LBT6

description:
1954009009_R004_C003
Luminal B tumor


title: Sputum from Stage II Moderate, biological replicate 14

value: F

value: Stage II

value: Moderate


title: Diffuse Intrinsic Pontine Glioma 11 - Tumour-250knsp

city: Toronto

first: Pawel

last: Buczkowicz

state: Ontario

address: 686 Bay Street

department: Paediatric Laboratory Medicine

country: Canada

institute: Hospital for Sick Children

description: Hybridized to 250K_Nsp

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:
CEL files  were processed using Partek Genome Suite V6.4 and Genotyping Console V2.1 using Segmentation and Hidden-Markov Model Analysis. Tumour samples were normalized to their matched normal. Tumour samples with no corresponding matched normal were normalized using HapMap.
CHP files for samples analyzed on the 250K platform were normalized using BRLMM algorithm. CHP files for samples analyzed on the 6.0 platform were normalized using Birdseed algorithm.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from snap frozen biopsy and autopsy samples from DIPG patients using the acidic phenol-chloroform method. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: DIPG

tag: age at dx (years)

tag: os (months)

tag: symptoms

value: LTS, ataxia, CN

tag: symptom duration (days)

tag: tmz during rt

value: No

tag: tmz post rt

tag: other chemo

value: 99703 then focal radiation1


title: Sputum from Stage II Moderate, biological replicate 30

tag: age

tag: gender

tag: gold stage


title: Sputum from Stage III Severe, biological replicate 6

value: M

value: Stage III

tag: group

value: Severe

tag: plateid

tag: batch


title: Sputum from Stage II Moderate, biological replicate 12

tag: hyb date


title: Sputum from Stage II Moderate, biological replicate 11


title: LBS5

description:
1954009009_R008_C004
Luminal B adyacent tissue


title: Diffuse Intrinsic Pontine Glioma 1 - Normal-250knsp

description: Hybridized to 250K_Nsp

tag: cell type

value: normal brain

value: LTS, CN


title: Diffuse Intrinsic Pontine Glioma 5 - Tumour-250knsp

description: Hybridized to 250K_Nsp

value: Ataxia, CN

value: Yes


title: LBS4

description:
1954009009_R008_C002
Luminal B adyacent tissue

value: female

tag: tissue


title: Diffuse Intrinsic Pontine Glioma 4 - Normal-250knsp

description: Hybridized to 250K_Sty


title: Sputum from Stage II Moderate, biological replicate 10

value: A


title: Diffuse Intrinsic Pontine Glioma 10 - Tumour-250knsp

description: Hybridized to 250K_Nsp

value: CN


title: LAT5

description:
1954009009_R003_C005
Luminal A tumor

value: Breast cancer tissue

tag: tissue/tumor subtype

value: Luminal A tumor


title: Diffuse Intrinsic Pontine Glioma 6 - Normal-250knsp

description: Hybridized to 250K_Sty

tag: age at dx (years)


title: LBS3

description:
1954009009_R006_C004
Luminal B adyacent tissue

value: Breast tissue

value: Luminal B adjacent tissue


title: LAT4

description:
1954009009_R002_C008
Luminal A tumor


title: LAT3

description:
1954009009_R002_C001
Luminal A tumor


title: Sputum from Stage II Moderate, biological replicate 8

value: Stage II

value: Moderate


title: Sputum from Stage II Moderate, biological replicate 9


title: Diffuse Intrinsic Pontine Glioma 3 - Tumour-250knsp

description: Hybridized to 250K_Nsp

value: DIPG

tag: os (months)

value: LTS, ataxia, CN

value: No


title: Diffuse Intrinsic Pontine Glioma 7 - Normal-250knsp

description: Hybridized to 250K_Sty

value: M

tag: symptoms


title: Diffuse Intrinsic Pontine Glioma 7 - Tumour-250knsp

description: Hybridized to 250K_Nsp

tag: symptom duration (days)


title: Sputum from Stage III Severe, biological replicate 4

value: Stage III

value: Severe


title: Sputum from Stage III Severe, biological replicate 3


title: Diffuse Intrinsic Pontine Glioma 4 - Tumour-250knsp

description: Hybridized to 250K_Nsp

tag: tmz during rt


title: LBS1

description:
1954009009_R004_C008
Luminal B adyacent tissue


title: Sputum from Stage III Severe, biological replicate 5

value: F


title: Sputum from Stage II Moderate, biological replicate 7


title: Sputum from Stage III Severe, biological replicate 2


title: LBS2

description:
1954009009_R006_C003
Luminal B adyacent tissue


title: LAT2

description:
1954009009_R001_C004
Luminal A tumor


title: Diffuse Intrinsic Pontine Glioma 6 - Tumour-250knsp

description: Hybridized to 250K_Nsp

value: Ataxia, CN

tag: tmz post rt

value: Yes


title: LAT1

description:
1954009009_R001_C001
Luminal A tumor

value: female


title: LAS4

description:
1954009009_R007_C004
Luminal A adyacent tissue

value: Luminal A adjacent tissue


title: LAS5

description:
1954009009_R007_C007
Luminal A adyacent tissue


title: LAS3

description:
1954009009_R006_C001
Luminal A adyacent tissue


title: Sputum from Stage II Moderate, biological replicate 6

value: A


title: Diffuse Intrinsic Pontine Glioma 3 - Normal-250knsp

description: Hybridized to 250K_Sty

value: normal brain

tag: other chemo


title: Diffuse Intrinsic Pontine Glioma 2 - Tumour-250knsp

description: Hybridized to 250K_Nsp

value: DIPG*

value: LTS, CN


title: Sputum from Stage II Moderate, biological replicate 5

tag: age

value: Stage II


title: Sputum from Stage II Moderate, biological replicate 3

tag: gender

value: Moderate


title: Sputum from Stage II Moderate, biological replicate 4

tag: gold stage


title: Sputum from Stage II Moderate, biological replicate 1

tag: group


title: Sputum from Stage II Moderate, biological replicate 2

tag: plateid


title: Sputum from Stage III Severe, biological replicate 1

tag: batch


title: HT4

description:
1954009009_R004_C004
ERBB2+ tumor

value: Breast cancer tissue

value: ERBB2+ tumor


title: HT5

description:
1954009009_R004_C005
ERBB2+ tumor


title: LAS1

description:
1954009009_R004_C006
Luminal A adyacent tissue

value: Breast tissue


title: HT1

description:
1954009009_R002_C006
ERBB2+ tumor


title: HT3

description:
1954009009_R004_C002
ERBB2+ tumor


title: HT2

description:
1954009009_R003_C002
ERBB2+ tumor


title: HS6

description:
1954009009_R007_C003
ERBB2+ adyacent tissue

value: ERBB2+ adjacent tissue


title: HS4

description:
1954009009_R007_C001
ERBB2+ adyacent tissue


title: HS5

description:
1954009009_R007_C002
ERBB2+ adyacent tissue


title: HS2

description:
1954009009_R005_C007
ERBB2+ adyacent tissue


title: HS3

description:
1954009009_R006_C006
ERBB2+ adyacent tissue


title: HS1

description:
1954009009_R005_C003
ERBB2+ adyacent tissue


title: Sputum from Stage IV Severe, biological replicate 1

description: Gene expression data from COPD Stage IV Severe

value: M

value: Stage IV

tag: hyb date


title: Diffuse Intrinsic Pontine Glioma 1 - Tumour-250knsp

description: Hybridized to 250K_Nsp

tag: cell type

value: F

value: No


title: LCMV-ARM/LCMV-WE infected but not diseased, sample 26

city: Blacksburg

first: kommidi

middle: Reddy

last: Chaitanya

state: VA

address: Virginia Tech

institute: VBI

description: Gene expression analysis of liver sample.

hyb_protocol: Standard Affymetrix method.

scan_protocol: Standard Affymetrix method. Model 7g.

data_processing: GC-RMA using R2.10.

organism: Macaca mulatta

source_name: LCMV-ARM and LCMV-WE infected but not diseased

label_protocol: Standard Affymetrix method.

growth_protocol: Twenty healthy adult rhesus macaques, five to nine years of age, were used for a terminal study. Liver tissue samples were obtained on the day of euthanasia from uninfected controls and infected animals. Before euthanasia, blood was taken for clinical chemistry and hematology; tissues were processed for RNA extraction within 15 minutes after collection.

extract_protocol: RNA was extracted using Trizol (Gibco-BRL) followed by a Qiagen RNeasy kit to clean the RNA.

treatment_protocol: Briefly, animals were either uninfected or infected intravenously (i.v.) with LCMV-ARM (non-virulent strain) and/or LCMV-WE (virulent strain) using 103 plaque-forming units (pfu) virus. LCMV-WE alone, at 103 pfu i.v., is uniformly lethal. Four animals infected with both LCMV-ARM and LCMV-WE (103 pfu each) did not develop symptoms and were classified as "infected-but-not-diseased". Infection in macaques was monitored by plaque assay of infectious particles in plasma, by infectious center assay of PBMC and liver tissues, and by RT-PCR to detect viral RNA in tissues.

tag: developmental stage

value: adult

tag: tissue

value: liver

tag: infection

value: LCMV-ARM and LCMV-WE

tag: time

value: day 30

tag: diseased

value: no


title: LCMV-ARM/LCMV-WE infected but not diseased, sample 15


title: LCMV-ARM/LCMV-WE infected but not diseased, sample 22


title: LCMV-ARM/LCMV-WE infected but not diseased, sample 11


title: LCMV-ARM infected but not diseased, day 5, sample 5

value: LCMV-ARM

value: day 5


title: LCMV-ARM infected but not diseased, day 3, sample 3

value: day 3


title: LCMV-WE infected, day 11, sample 11

source_name: LCMV-WE infected, day 11

value: LCMV-WE

value: day 11

value: yes


title: BT8

description:
1954009009_R003_C001
Basal-like tumor

value: female

value: Breast cancer tissue

tag: tissue/tumor subtype

value: Basal-like tumor


title: BT9

description:
1954009009_R003_C003
Basal-like tumor


title: LCMV-WE infected, day 12, sample 12

source_name: LCMV-WE infected, day 12

value: day 12


title: BT7

description:
1954009009_R002_C007
Basal-like tumor


title: BT5

description:
1954009009_R002_C004
Basal-like tumor


title: BT4

description:
1954009009_R002_C002
Basal-like tumor


title: LCMV-WE infected, day 7, sample 10

source_name: LCMV-WE infected, day 7

value: day 7


title: LCMV-WE infected, day 6, sample 9

source_name: LCMV-WE infected, day 6

value: day 6


title: BT2

description:
1954009009_R001_C005
Basal-like tumor


title: BT12

description:
1954009009_R004_C001
Basal-like tumor


title: BT3

description:
1954009009_R001_C008
Basal-like tumor


title: LCMV-WE infected, day 4, sample 7

source_name: LCMV-WE infected, day 4

value: adult

value: day 4


title: LCMV-WE infected, day 6, sample 8

value: liver


title: BT6

description:
1954009009_R002_C005
Basal-like tumor


title: BT11

description:
1954009009_R003_C006
Basal-like tumor


title: BT10

description:
1954009009_R003_C004
Basal-like tumor


title: LCMV-WE infected, day 3, sample 5

source_name: LCMV-WE infected, day 3


title: LCMV-WE infected, day 1, sample 2

source_name: LCMV-WE infected, day 1

value: day 1


title: BS9

description:
1954009009_R006_C005
Basal-like adyacent tissue

value: Breast tissue

value: Basal-like adjacent tissue


title: BT1

description:
1954009009_R001_C003
Basal-like tumor


title: LCMV-WE infected, day 1, sample 1


title: uninfected control, sample 9

source_name: uninfected control

value: uninfected

value: no


title: uninfected control, sample 7


title: BS8

description:
1954009009_R006_C002
Basal-like adyacent tissue


title: LCMV-WE infected, day 4, sample 6

value: LCMV-WE


title: MM94

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

hyb_protocol: Arrays were hybridizedaccording to Illuminas recommendations

scan_protocol: Arrays were scanned according to Illuminas recommendations

data_processing: Images were analysed using Beadstudio v3 and normalized using the cubic-spline method. VALUE represents Beadstudio processed, cubic spline normalised intensity data from Refseq genes that were used in subsequent analyses.

source_name: Melanoma metastasis

label_protocol: RNA was amplified and labelled according to Illuminas recommendations

extract_protocol: Total RNA was isolated using qiazol followed by Qiagen RNAeasy kit

value: Melanoma metastasis

tag: os (days)

tag: event (0=alive, 1=dead)

tag: sex

value: Female

tag: age at metastases

tag: type of metastases

value: Lymphnode

tag: age at primary diagnosis

tag: localization of primary melanoma

value: Lower extremity

tag: type

value: SSM

tag: breslow

tag: clark

tag: stage

value: IV

tag: braf/nras

tag: cdkn2a (hd=homozygous deletion, *=germline)

tag: molecular subtype

value: Pigmentation

tag: cd3 immunohistochemistry

value: non-brisk

tag: cd20 immunohistochemistry


title: LCMV-WE infected, day 2, sample 3

source_name: LCMV-WE infected, day 2

tag: developmental stage

value: adult

tag: tissue

tag: infection

tag: time

value: day 2

tag: diseased

value: yes


title: uninfected control, sample 8

value: liver


title: MM93

tag: os (days)

tag: event (0=alive, 1=dead)

tag: sex

value: Male

tag: age at metastases

tag: type of metastases

value: Trunk

value: HD

value: absent


title: MM88

value: Subcutaneous

tag: age at primary diagnosis

tag: localization of primary melanoma

value: Lower extremity, acral

tag: type

tag: breslow

tag: clark

value: Normal-like


title: BS7

description:
1954009009_R005_C012
Basal-like adyacent tissue

tag: gender

value: female

value: Breast tissue

tag: tissue/tumor subtype

value: Basal-like adjacent tissue


title: BS6

description:
1954009009_R005_C011
Basal-like adyacent tissue


title: BS12

description:
1954009009_R008_C001
Basal-like adyacent tissue


title: BS13

description:
1954009009_R008_C005
Basal-like adyacent tissue


title: BS11

description:
1954009009_R007_C006
Basal-like adyacent tissue


title: BS10

description:
1954009009_R007_C005
Basal-like adyacent tissue


title: BS5

description:
1954009009_R005_C006
Basal-like adyacent tissue


title: BS4

description:
1954009009_R005_C004
Basal-like adyacent tissue


title: MM95

value: Melanoma metastasis

value: Lymphnode

value: SSM

tag: stage

value: IV

tag: braf/nras

tag: cdkn2a (hd=homozygous deletion, *=germline)

tag: molecular subtype

value: Proliferative

tag: cd3 immunohistochemistry

tag: cd20 immunohistochemistry


title: BS3

description:
1954009009_R005_C002
Basal-like adyacent tissue

tag: tissue


title: MM82

tag: os (days)

tag: event (0=alive, 1=dead)

tag: sex

value: Lower extremity

value: p16INK4A methylation


title: MM83

value: Female

tag: age at metastases

tag: type of metastases

tag: age at primary diagnosis

value: Pigmentation

value: brisk


title: MM81

tag: localization of primary melanoma

value: Upper extremity

tag: type

tag: breslow


title: BS2

description:
1954009009_R005_C001
Basal-like adyacent tissue

tag: gender

tag: tissue/tumor subtype


title: MM86

value: Male

value: Trunk

value: NMM

tag: clark

tag: stage

tag: braf/nras


title: MM73

value: Subcutaneous

tag: cdkn2a (hd=homozygous deletion, *=germline)

tag: molecular subtype

value: Normal-like

tag: cd3 immunohistochemistry

value: non-brisk


title: BS1

description:
1954009009_R004_C007
Basal-like adyacent tissue

value: female

tag: tissue

value: Breast tissue

value: Basal-like adjacent tissue


title: MM78

value: Melanoma metastasis

tag: os (days)

tag: event (0=alive, 1=dead)

value: Lymphnode

value: SSM

value: III

value: High-immune response

tag: cd20 immunohistochemistry


title: MM80

tag: sex

value: Female

tag: age at metastases

tag: type of metastases

value: IV


title: MM64

tag: age at primary diagnosis

tag: localization of primary melanoma

value: Upper extremity

tag: type

value: absent


title: MM68

value: Male

value: Trunk

tag: breslow

value: brisk


title: BP1

description:
1954009009_R006_C007
Basal-like peritumoral

tag: gender

tag: tissue/tumor subtype

value: Basal-like peritumoral


title: BP3

description:
1954009009_R008_C007
Basal-like peritumoral


title: MM60

tag: clark

tag: stage

tag: braf/nras

value: Proliferative

value: non-brisk


title: LAS2

description:
1954009009_R005_C005
Luminal A adyacent tissue

value: female

value: Breast tissue

value: Luminal A adjacent tissue


title: MM61

value: Melanoma metastasis

value: Subcutaneous

tag: cdkn2a (hd=homozygous deletion, *=germline)

tag: molecular subtype

value: Pigmentation

tag: cd3 immunohistochemistry


title: MM55

tag: tissue

tag: os (days)

tag: event (0=alive, 1=dead)

value: No primary detected

value: NMM


title: MM58

tag: sex

tag: age at metastases

value: Head

value: SSM

value: IV

value: p16INK4A A148T*

tag: cd20 immunohistochemistry


title: MM51

value: Male

tag: type of metastases

tag: age at primary diagnosis

tag: localization of primary melanoma

value: Trunk

value: p16INK4A methylation

value: Normal-like

value: absent


title: MM71

value: Lymphnode

tag: type

tag: breslow

value: High-immune response

value: non-brisk


title: MM53

value: Melanoma metastasis

value: Female

tag: clark


title: MM45

tag: stage

value: III

value: Pigmentation


title: MM50

value: Subcutaneous

value: Head and eye

tag: braf/nras


title: MM44

value: No primary detected

tag: cdkn2a (hd=homozygous deletion, *=germline)


title: MM42

value: SSM

value: IV

tag: molecular subtype

value: brisk


title: MM43

value: Trunk

value: BRAF- V600E

value: HD

tag: cd3 immunohistochemistry


title: MM57

tag: tissue

value: NMM

value: Normal-like


title: MM40

tag: os (days)

value: Male

value: Lymphnode

value: High-immune response


title: MM52

value: Melanoma metastasis

tag: event (0=alive, 1=dead)

value: Female

value: non-brisk

value: absent


title: MM47

tag: sex

value: Subcutaneous

value: p16INK4A methylation

value: Pigmentation


title: MM38

tag: age at metastases

value: SSM

value: IV


title: MM41

value: No primary detected

tag: cd20 immunohistochemistry


title: Scerev_Sparad_F2_hybrid P5D2

city: Stanford

first: Gavin

last: Sherlock

state: CA

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80509.gif

hyb_protocol: not provided

scan_protocol: Agilent

data_processing: Agilent Feature Extraction

organism: Saccharomyces cerevisiae

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: S.cerevisiae+S.paradoxus genomic DNA

source_name: P5D2 gDNA

tag: genotype


title: F2 random spores pool 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80525.gif

source_name: F2 random spores pool 2 gDNA


title: MM37

tag: type of metastases

tag: age at primary diagnosis

tag: localization of primary melanoma

value: Trunk


title: reference vs reference control

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80515.gif

value: control


title: Scerev_Sparad_F2_hybrid P5A10

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80488.gif

source_name: P5A10 gDNA


title: F2 random spores pool 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80524.gif

source_name: F2 random spores pool 1 gDNA


title: Scerev_Sparad_F2_hybrid P6C2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80501.gif

source_name: P6C2 gDNA


title: Scerev_Sparad_F2_hybrid P5B6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80520.gif

source_name: P5B6 gDNA


title: Scerev_Sparad_F2_hybrid P6C1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80500.gif

source_name: P6C1 gDNA


title: MM24

tag: type

tag: breslow

tag: clark

value: HD

value: Proliferative


title: MM31

value: Male

tag: stage

tag: braf/nras

tag: cdkn2a (hd=homozygous deletion, *=germline)


title: MM30

tag: tissue

value: Lymohnode

value: Lower extremity

value: NMM

tag: molecular subtype

tag: cd3 immunohistochemistry

value: brisk


title: MM27

value: Melanoma metastasis

tag: os (days)

tag: event (0=alive, 1=dead)

tag: sex

value: non-brisk

value: absent


title: MM34

value: Female

tag: age at metastases

value: Subcutaneous

value: Head

value: p16INK4A methylation

value: High-immune response

tag: cd20 immunohistochemistry


title: Scerev_Sparad_F2_hybrid P6A1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80480.gif

tag: reference

value: S.cerevisiae+S.paradoxus genomic DNA

source_name: P6A1 gDNA

tag: genotype


title: MM25

tag: type of metastases

tag: age at primary diagnosis

tag: localization of primary melanoma

value: IV

value: p16INK4A  A148T*, HD


title: MM22

value: Upper extremity

tag: type

tag: breslow

tag: clark

value: Proliferative


title: Scerev_Sparad_F2_hybrid P5C7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80506.gif

source_name: P5C7 gDNA


title: Scerev_Sparad_F2_hybrid P5C10

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80508.gif

source_name: P5C10 gDNA


title: Scerev_Sparad_F2_hybrid P5B4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80519.gif

source_name: P5B4 gDNA


title: Scerev_Sparad_F2_hybrid P5A4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80477.gif

source_name: P5A4 gDNA


title: Scerev_Sparad_F2_hybrid P6C3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80502.gif

source_name: P6C3 gDNA


title: Scerev_Sparad_F2_hybrid P6A4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80491.gif

source_name: P6A4 gDNA


title: MM21

value: Male

value: No primary detected

tag: stage

tag: braf/nras

tag: cdkn2a (hd=homozygous deletion, *=germline)


title: MM16

tag: tissue

value: Lymphnode

value: III

value: HD

tag: molecular subtype

tag: cd3 immunohistochemistry


title: MM19

value: Melanoma metastasis

tag: os (days)

tag: event (0=alive, 1=dead)

tag: sex

value: Trunk

value: SSM

value: Pigmentation

value: non-brisk


title: Scerev_Sparad_F2_hybrid P5C6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80505.gif

tag: reference

source_name: P5C6 gDNA


title: MM20

source_name: Melanoma metastasis

tag: age at metastases

value: Subcutaneous

value: Lower extremity

value: NMM

value: p16INK4A methylation

tag: cd20 immunohistochemistry


title: MM17

value: Female

tag: type of metastases

tag: age at primary diagnosis

value: IV

value: absent


title: Scerev_Sparad_F2_hybrid P5A6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80479.gif

value: S.cerevisiae+S.paradoxus genomic DNA

source_name: P5A6 gDNA

tag: genotype


title: MM13

value: Male

tag: localization of primary melanoma

tag: type

tag: breslow

value: Proliferative


title: MM14

value: Upper extremity

tag: clark

tag: stage

tag: braf/nras


title: Scerev_Sparad_F2_hybrid P6A8

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80492.gif

source_name: P6A8 gDNA


title: Scerev_Sparad_F2_hybrid P6A6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80483.gif

source_name: P6A6 gDNA


title: MM18

tag: tissue

value: No primary detected

tag: cdkn2a (hd=homozygous deletion, *=germline)

tag: molecular subtype

value: High-immune response


title: Scerev_Sparad_F2_hybrid P5D3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80510.gif

source_name: P5D3 gDNA


title: Scerev_Sparad_F2_hybrid P3A10

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80450.gif

source_name: P3A10 gDNA


title: Scerev_Sparad_F2_hybrid B5B10

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80494.gif

source_name: B5B10 gDNA


title: Scerev_Sparad_F2_hybrid P3D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80469.gif

source_name: P3D4 gDNA


title: MM12

value: Melanoma metastasis

tag: os (days)

tag: event (0=alive, 1=dead)

value: Head

value: Normal-like

tag: cd3 immunohistochemistry


title: Scerev_Sparad_F2_hybrid P5A5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80478.gif

tag: reference

source_name: P5A5 gDNA


title: MM11

tag: sex

tag: age at metastases

value: Lymphnode

tag: cd20 immunohistochemistry


title: reference vs reference control 1 (F1)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80443.gif

source_name: cc155xGSY147 (F1 gDNA)

tag: genotype


title: MM10

tag: type of metastases

value: Subcutaneous

tag: age at primary diagnosis

tag: localization of primary melanoma

value: Trunk

value: SSM

value: non-brisk


title: Scerev_Sparad_F2_hybrid P6A5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80482.gif

source_name: P6A5 gDNA


title: Scerev_Sparad_F2_hybrid P5C4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80498.gif

source_name: P5C4 gDNA


title: MM08

tag: type

value: NMM

tag: breslow

tag: clark

value: Pigmentation


title: Scerev_Sparad_F2_hybrid P6C6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80511.gif

source_name: P6C6 gDNA


title: MM09

tag: tissue

value: Upper extremity, acral

tag: stage

value: IV

tag: braf/nras

value: p16INK4A A127S*

value: brisk


title: Scerev_Sparad_F2_hybrid P5A9

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80487.gif

value: S.cerevisiae+S.paradoxus genomic DNA

source_name: P5A9 gDNA


title: Scerev_Sparad_F2_hybrid P2B6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74241.gif

source_name: P2B6 gDNA


title: Scerev_Sparad_F2_hybrid P2A1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74235.gif

source_name: P2A1 gDNA


title: Scerev_Sparad_F2_hybrid P1G8

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74228.gif

source_name: P1G8 gDNA


title: Scerev_Sparad_F2_hybrid 1000 spores 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80470.gif

source_name: F2 random spores pool 4 gDNA


title: Scerev_Sparad_F2_hybrid P5B9

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80493.gif

source_name: P5B9 gDNA


title: Scerev_Sparad_F2_hybrid P2B7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74242.gif

source_name: P2B7 gDNA


title: Scerev_Sparad_F2_hybrid P3C3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80461.gif

source_name: P3C3 gDNA


title: Scerev_Sparad_F2_hybrid P6C5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80504.gif

source_name: P6C5 gDNA


title: MM06

source_name: Melanoma metastasis

tag: os (days)

value: Male

value: Lower extremity

tag: cdkn2a (hd=homozygous deletion, *=germline)

value: p16INK4A methylation

tag: molecular subtype


title: MM04

value: Melanoma metastasis

tag: event (0=alive, 1=dead)

value: Female

value: HD

value: Proliferative

tag: cd3 immunohistochemistry

value: absent


title: Scerev_Sparad_F2_hybrid P5B3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80518.gif

tag: reference

source_name: P5B3 gDNA


title: Scerev_Sparad_F2_hybrid P6C4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80503.gif

source_name: P6C4 gDNA


title: Scerev_Sparad_F2_hybrid P6B10

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80499.gif

source_name: P6B10 gDNA


title: Scerev_Sparad_F2_hybrid P3A3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80445.gif

source_name: P3A3 gDNA


title: MM03

tag: sex

tag: age at metastases

value: Subcutaneous

value: Head

value: SSM

value: p16INK4A A148T*

value: High-immune response

tag: cd20 immunohistochemistry


title: Scerev_Sparad_F2_hybrid P3D3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80468.gif

source_name: P3D3 gDNA

tag: genotype


title: Scerev_Sparad_F2_hybrid P2A8

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74239.gif

source_name: P2A8 gDNA


title: Scerev_Sparad_F2_hybrid P5A8

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80486.gif

source_name: P5A8 gDNA


title: Scerev_Sparad_F2_hybrid P6A10

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80484.gif

source_name: P6A10 gDNA


title: msh2 F2 random spores pool 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80526.gif

source_name: msh2 F2 random spores pool 3 gDNA


title: msh2 F2 random spores pool 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80527.gif

source_name: msh2 F2 random spores pool 4 gDNA


title: msh2 F2 random spores pool 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80517.gif

source_name: msh2 F2 random spores pool 2 gDNA


title: Scerev_Sparad_F2_hybrid P1H8

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74234.gif

source_name: P1H8 gDNA


title: Scerev_Sparad_F2_hybrid P6A3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80475.gif

source_name: P6A3 gDNA


title: Scerev_Sparad_F2_hybrid P5C9

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80507.gif

source_name: P5C9 gDNA


title: MM02

tag: type of metastases

tag: age at primary diagnosis

tag: localization of primary melanoma

value: NMM

value: IV

value: Pigmentation

value: non-brisk


title: MM01

value: Male

value: Lymphnode

value: Trunk

tag: type

tag: breslow

tag: clark

value: p16INK4A P114L

value: brisk


title: Scerev_Sparad_F2_hybrid P2C4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80437.gif

value: S.cerevisiae+S.paradoxus genomic DNA

source_name: P2C4 gDNA


title: Scerev_Sparad_F2_hybrid P3C5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80463.gif

source_name: P3C5 gDNA


title: Scerev_Sparad_F2_hybrid P5A1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80472.gif

source_name: P5A1 gDNA


title: Scerev_Sparad_F2_hybrid P6B2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80523.gif

source_name: P6B2 gDNA


title: Scerev_Sparad_F2_hybrid P5A3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80474.gif

source_name: P5A3 gDNA


title: Scerev_Sparad_F2_hybrid P3B5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80457.gif

source_name: P3B5 gDNA


title: Scerev_Sparad_F2_hybrid P1H3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74231.gif

source_name: P1H3 gDNA


title: Scerev_Sparad_F2_hybrid P3B4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80456.gif

source_name: P3B4 gDNA


title: HUVEC_Ad-CCM1_48hrs_rep1

city: Mannheim

first: Andreas

last: Fischer

address: Ludolf-Krehl-Str. 13-17

department: Joint Research Division Vascular Biology

country: Germany

institute: German Cancer Research Center and Medical Faculty Mannheim, Heidelberg University

description: biological replicate2

hyb_protocol: Hybridization is performed at 58°C, in GEX-HCB buffer (Illumina Inc.) at a concentration of 50 ng cRNA/µl, unsealed in a wet chamber for 20 h. Spike-in controls for low, medium and highly abundant RNAs were added, as well as mismatch control and biotinylation control oligonucleotides. Microarrays were washed twice in E1BC buffer (Illumina Inc.) at room temperature for 5 minutes. After blocking for 5 min in 4 ml of 1% (wt/vol) Blocker Casein in phosphate buffered saline Hammarsten grade (Pierce Biotechnology, Inc., Rockford, IL), array signals are developed by a 10-min incubation in 2 ml of 1 µg/ml Cy3-streptavidin (Amersham Biosciences, Buckinghamshire, UK) solution and 1% blocking solution. After a final wash in E1BC, the arrays are dried and scanned.

scan_protocol: Microarray scanning was done using a Beadstation array scanner, setting adjusted to a scaling factor of 1 and PMT settings at 430. Data extraction was done for all beads individually, and outliers are removed when > 2.5 MAD (median absolute deviation). All remaining data points are used for the calculation of the mean average signal for a given probe, and standard deviation for each probe was calculated.

data_processing: The data were normalised using quantile normalisation with Illumina BeadStudio v. 3. For analysis duplicates were averaged and the expression fold change of CCM1 expressing cells to the GFP expressing control was calculated

label_protocol: Biotin-labeled cRNA were prepared according to Illumina's recommended sample labeling procedure based on the modified Eberwine protocol (Proc. Natl. Acad. Sci. U. S. A. (1992) 89:3010–3014). In brief, 250 ng total RNA was used for complementary DNA (cDNA) synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA according to the MessageAmp II aRNA Amplification kit (Ambion, Inc., Austin, TX). Biotin-16-UTP was purchased from Roche Applied Science, Penzberg, Germany. The cRNA was column purified according to TotalPrep RNA Amplification Kit, and eluted in 60 µl of water. Quality of cRNA was controlled using the RNA Nano Chip Assay on an Agilent 2100 Bioanalyzer and spectrophotometrically quantified (NanoDrop).

growth_protocol: Human umbilical vein endothelial cells (HUVEC) were cultured in gelatine coated 6-well plates with ECGM2 medium including Supplement Mix (PromoCell) and 10% FCS. Cells were grown as a confluent monolayer and transduced with adenovirus with an MOI of 50.

extract_protocol: RNA was isolated using the Rneasy kit (Qiagen) according to the instructions of the manufacturer. Optional steps of the protocol were skipped and no optional supplements to the buffers were used. The quality of total RNA was checked by gel analysis using the total RNA Nano chip assay on an Agilent 2100 Bioanalyzer (Agilent Technologies). All samples had RNA index values greater than 8.5. RNA concentrations were determined using the NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE).

tag: cell type


title: Scerev_Sparad_F2_hybrid P3D2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80467.gif

source_name: P3D2 gDNA


title: HUVEC_Ad-GFP_48hrs_rep2

description: biological replicate1

source_name: GFP

value: Human umbilical vein endothelial cells (HUVEC)


title: HUVEC_Ad-CCM1_48hrs_rep2

description: biological replicate2


title: Scerev_Sparad_F2_hybrid P2A2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74236.gif

source_name: P2A2 gDNA


title: Scerev_Sparad_F2_hybrid P5C2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80496.gif

source_name: P5C2 gDNA


title: Scerev_Sparad_F2_hybrid P5C3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80497.gif

source_name: P5C3 gDNA


title: Scerev_Sparad_F2_hybrid P1H2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74230.gif

source_name: P1H2 gDNA


title: Scerev_Sparad_F2_hybrid P2H10

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80442.gif

source_name: P2H10 gDNA


title: MM65

hyb_protocol: Arrays were hybridized according to Illuminas recommendations

data_processing: Images were analysed using Beadstudio v3 and normalized using the cubic-spline method. VALUES are Genomestudio processed, cubic spline normalised intensity data.

source_name: Melanoma metastasis

tag: tissue

value: Melanoma metastasis

tag: os (days)

value: Female

value: liver

value: Acral

tag: stage

tag: braf/nras

value: wt


title: Scerev_Sparad_F2_hybrid P3B3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80455.gif

source_name: P3B3 gDNA


title: Scerev_Sparad_F2_hybrid P2C10

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80438.gif

source_name: P2C10 gDNA


title: HUVEC_Ad-GFP_48hrs_rep1

description: biological replicate1


title: Scerev_Sparad_F2_hybrid P6B1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80522.gif

source_name: P6B1 gDNA


title: Scerev_Sparad_F2_hybrid P5A7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80485.gif

source_name: P5A7 gDNA


title: Scerev_Sparad_F2_hybrid P2D1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80439.gif

source_name: P2D1 gDNA


title: Scerev_Sparad_F2_hybrid P3C2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80460.gif

source_name: P3C2 gDNA


title: Scerev_Sparad_F2_hybrid P2A5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74238.gif

source_name: P2A5 gDNA


title: MM76_2

tag: event (0=alive, 1=dead)

value: SSM

tag: cdkn2a (hd=homozygous deletion, *=germline)

tag: molecular subtype

value: High-immune response

tag: cd3 immunohistochemistry


title: MM90

tag: sex

tag: age at metastases

value: IV

value: HD

tag: cd20 immunohistochemistry


title: MM49

tag: type of metastases

tag: age at primary diagnosis

value: Head


title: Scerev_Sparad_F2_hybrid P3C10

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80465.gif

tag: reference

source_name: P3C10 gDNA

tag: genotype


title: Scerev_Sparad_F2_hybrid P3B10

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80459.gif

source_name: P3B10 gDNA


title: Scerev_Sparad_F2_hybrid P3B2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80454.gif

source_name: P3B2 gDNA


title: Scerev_Sparad_F2_hybrid P3C7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80464.gif

source_name: P3C7 gDNA


title: reference vs reference control 2 (F1)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80444.gif

source_name: cc154xGSY145 (F1 gDNA)


title: BPH_adrenal_rep3

city: La Jolla

first: Ryan

last: Friese

institute: University of California San Diego

description: Gene expression data from BPH mouse adrenal gland.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on MG-U74Av2 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 2500.

organism: Mus musculus

source_name: BPH hypertensive mouse strain, adrenal gland

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

extract_protocol: Total RNA was extracted from isolated adrenal glands from BPL (n=3) and BPH (n=3) mice with the RNAzol (guanidinium thiocyanate) kit (TelTest, Friendswood, TX), followed by RNase-free DNase I (Qiagen, Valencia, CA) treatment to eliminate residual genomic DNA.

tag: strain

value: BPH hypertensive mouse strain (Schlager 1974)

value: Male

tag: age

value: Adrenal gland


title: BPH_adrenal_rep2

tag: tissue


title: Scerev_Sparad_F2_hybrid P3D1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80466.gif

source_name: P3D1 gDNA


title: BPH_adrenal_rep1


title: Scerev_Sparad_F2_hybrid P5B8

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80521.gif

source_name: P5B8 gDNA


title: Scerev_Sparad_F2_hybrid P5B7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80490.gif

source_name: P5B7 gDNA


title: Scerev_Sparad_F2_hybrid P6C10

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80514.gif

source_name: P6C10 gDNA


title: MM85

source_name: Melanoma metastasis

tag: os (days)

tag: localization of primary melanoma

value: Trunk

tag: type

tag: breslow

tag: clark

value: p16INK4A methylation

value: Pigmentation


title: Scerev_Sparad_F2_hybrid P5C1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80495.gif

value: S.cerevisiae+S.paradoxus genomic DNA

source_name: P5C1 gDNA


title: Scerev_Sparad_F2_hybrid P6C9

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80513.gif

source_name: P6C9 gDNA


title: Scerev_Sparad_F2_hybrid P3A6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80447.gif

source_name: P3A6 gDNA


title: Scerev_Sparad_F2_hybrid P6C8

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80512.gif

source_name: P6C8 gDNA


title: MM32

value: Melanoma metastasis

tag: event (0=alive, 1=dead)

value: abdominal node

tag: stage

tag: braf/nras

tag: cdkn2a (hd=homozygous deletion, *=germline)

value: p16INK4A P114L*

tag: molecular subtype


title: Scerev_Sparad_F2_hybrid P5B1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80489.gif

source_name: P5B1 gDNA


title: BPL_adrenal_rep3

description: Gene expression data from BPL mouse adrenal gland.

source_name: BPL hypotensive mouse strain, adrenal gland

value: BPL hypotensive mouse strain (Schlager 1974)

tag: sex


title: BPL_adrenal_rep2


title: Scerev_Sparad_F2_hybrid P3B1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80452.gif

source_name: P3B1 gDNA


title: MM67

tag: age at metastases

tag: type of metastases

value: liver

tag: age at primary diagnosis

value: GI tractus

value: wt

tag: cd3 immunohistochemistry

tag: cd20 immunohistochemistry


title: Scerev_Sparad_F2_hybrid P1G3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74010.gif

tag: reference

tag: genotype


title: BPL_adrenal_rep1

tag: strain

tag: age

tag: tissue


title: HIV 16.1 V+,S-, Tube 15 (251508710514)

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: Four subpopulations were collected from clones 5.1 and 16.1 of the HIV cell line as such: V-, S+; V+, S+; V-, S-; V-, S+, where V = Venus expression and S = SSEA 1 expression.

hyb_protocol: Slides were hybridized according to manufacturers protocol (Two-Color Microarray-Based Genr Expression Analysis Protocol,  Product # G4140-90050, Version 5.0.1, August 2006)

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing: Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.

source_name: Pre-Primitive Endoderm with V+ S-

label_protocol: Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.

extract_protocol: Total RNA was extracted using Trizol according to Invitrogen's protocol.  Cells were pelleted and 1mL Trizol reagent was added to the cell pellet.

treatment_protocol: HIV cell line clone 16 was plated at a density of 200000 cells/ml. Following growth under self-renewing conditions in the presence of LIF for 24 hours, cells were separated by flow cytometry on the basis of venus and SSEA1 expression.

tag: ES cells

tag: Strain

tag: Genetic modification

value: gene knock in

tag: Individual Identifier

source_name: Universal Mouse Reference Cell Line Pool

label_protocol: Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts

tag: Universale Mouse Reference


title: Scerev_Sparad_F2_hybrid P2B3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74004.gif


title: MM35

tag: os (days)

tag: event (0=alive, 1=dead)

tag: localization of primary melanoma

value: No primary

tag: type

tag: breslow

tag: clark

tag: stage

value: IV

tag: braf/nras

tag: cdkn2a (hd=homozygous deletion, *=germline)

tag: molecular subtype

value: Proliferative


title: Scerev_Sparad_F2_hybrid P6A2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80481.gif

tag: reference

source_name: P6A2 gDNA

tag: genotype


title: Scerev_Sparad_F2_hybrid P2D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80440.gif

source_name: P2D4 gDNA


title: MM23_2

tag: tissue

tag: sex

value: Female

tag: age at metastases

tag: type of metastases

tag: age at primary diagnosis

value: NMM

value: HD

tag: cd3 immunohistochemistry

tag: cd20 immunohistochemistry


title: Scerev_Sparad_F2_hybrid P3A7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80448.gif

source_name: P3A7 gDNA


title: HIV 16.1 V-,S-, Tube 13 (251508710514)

source_name: Pre-Primitive Endoderm with V- S-

tag: ES cells

tag: Strain

tag: Genetic modification

tag: Individual Identifier

tag: Universale Mouse Reference


title: Scerev_Sparad_F2_hybrid cc261

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74003.gif


title: MM66

tag: os (days)

tag: event (0=alive, 1=dead)

value: Male

tag: localization of primary melanoma

value: Trunk

tag: type

value: SSM

tag: breslow

tag: clark

tag: stage

tag: braf/nras

value: High-immune response


title: HIV 16.1 V+,S+, Tube 11 (251508710514)

source_name: Pre-Primitive Endoderm with V+ S+


title: Scerev_Sparad_F2_hybrid P2B9

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74243.gif

tag: reference

value: S.cerevisiae+S.paradoxus genomic DNA

source_name: P2B9 gDNA

tag: genotype


title: Scerev_Sparad_F2_hybrid P1F8

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74009.gif


title: Scerev_Sparad_F2_hybrid P1H5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74233.gif

source_name: P1H5 gDNA


title: Scerev_Sparad_F2_hybrid P1G9

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74002.gif


title: Scerev_Sparad_F2_hybrid P2B8

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74007.gif


title: Scerev_Sparad_F2_hybrid P2H9

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80441.gif

source_name: P2H9 gDNA


title: MM54

source_name: Melanoma metastasis

tag: tissue

value: Melanoma metastasis

tag: sex

tag: age at metastases

tag: type of metastases

tag: age at primary diagnosis

value: Eye

tag: cdkn2a (hd=homozygous deletion, *=germline)

tag: molecular subtype

tag: cd3 immunohistochemistry


title: Scerev_Sparad_F2_hybrid P2C2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80435.gif

source_name: P2C2 gDNA


title: HIV 16.1 V-,S+, Tube 9 (251508710514)

source_name: Pre-Primitive Endoderm with V- S+

tag: ES cells

tag: Strain

tag: Genetic modification

tag: Individual Identifier

tag: Universale Mouse Reference


title: MM23_1

tag: os (days)

tag: event (0=alive, 1=dead)

value: liver

tag: localization of primary melanoma

tag: type

tag: breslow

tag: clark

tag: stage

value: Pigmentation

tag: cd20 immunohistochemistry


title: HIV 5.1 V+,S-, Tube 7 (251508710513)

treatment_protocol: HIV cell line clone 5 was plated at a density of 200000 cells/ml. Following growth under self-renewing conditions in the presence of LIF for 24 hours, cells were separated by flow cytometry on the basis of venus and SSEA1 expression.


title: MM39

tag: tissue

tag: sex

tag: age at metastases

tag: type of metastases

tag: age at primary diagnosis

tag: braf/nras

value: wt


title: Scerev_Sparad_F2_hybrid P2C5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74006.gif

tag: reference

tag: genotype


title: Scerev_Sparad_F2_hybrid 1000 spores 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80471.gif

source_name: F2 random spores pool 3 gDNA


title: HIV 5.1 V+,S+, Tube 3 (251508710513)

tag: ES cells

tag: Strain

tag: Genetic modification

value: gene knock in

tag: Individual Identifier

tag: Universale Mouse Reference


title: HIV 5.1 V-,S-, Tube 5 (251508710513)


title: MM48

tag: os (days)

tag: event (0=alive, 1=dead)

tag: localization of primary melanoma

tag: type

tag: breslow

tag: cdkn2a (hd=homozygous deletion, *=germline)

tag: molecular subtype

tag: cd3 immunohistochemistry


title: MM77

tag: tissue

tag: sex

tag: age at metastases

tag: type of metastases

value: lymphnode

tag: age at primary diagnosis

tag: clark

tag: stage

value: p16INK4A methylation

tag: cd20 immunohistochemistry


title: MM60

value: Mucosa, head

value: IV

tag: braf/nras

value: Proliferative


title: 251404310002_A_88

description: Image: http://smd.stanford.edu/MicroArray/gifs//85963.gif

tag: reference

source_name: GSY#88 (F1 gDNA)

tag: genotype


title: 251404310001_B_control

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-12/85962.gif

source_name: S. paradoxus genomic DNA

value: S. paradoxus genomic DNA

source_name: S. cerevisiae genomic DNA

value: control


title: Scerev_Sparad_F2_hybrid P1F9

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74001.gif


title: Scerev_Sparad_F2_hybrid P2A4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74237.gif

source_name: P2A4 gDNA


title: MM36

tag: os (days)

tag: event (0=alive, 1=dead)

value: Male

tag: localization of primary melanoma

value: p16INK4A A148T*


title: MM87

value: Trunk

tag: type

value: NMM

tag: breslow

tag: cdkn2a (hd=homozygous deletion, *=germline)

value: p16INK4A E88Ter*

value: High-immune response


title: Scerev_Sparad_F2_hybrid P3C4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80462.gif

value: S.cerevisiae+S.paradoxus genomic DNA

source_name: P3C4 gDNA


title: MM69

tag: tissue

value: Melanoma metastasis

value: Female

value: liver

value: GI tractus

tag: molecular subtype

value: Pigmentation

tag: cd3 immunohistochemistry


title: HIV 5.1 V-,S+, Tube 1 (251508710513)

description: Four subpopulations were collected from clones 5.1 and 16.1 of the HIV cell line as such: V-, S+; V+, S+; V-, S-; V-, S+, where V = Venus expression and S = SSEA 1 expression.

tag: ES cells

tag: Strain

tag: Genetic modification

value: gene knock in

tag: Individual Identifier

source_name: Universal Mouse Reference Cell Line Pool

tag: Universale Mouse Reference


title: Scerev_Sparad_F2_hybrid P2A9

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74240.gif

source_name: P2A9 gDNA


title: Scerev_Sparad_F2_hybrid P1G2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74000.gif


title: MM76_1

tag: sex

tag: age at metastases

tag: type of metastases

tag: age at primary diagnosis

value: SSM

tag: clark

tag: stage

value: IV

tag: braf/nras

value: wt

tag: cd20 immunohistochemistry


title: Scerev_Sparad_F2_hybrid P2C3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80436.gif

tag: reference

source_name: P2C3 gDNA

tag: genotype


title: Scerev_Sparad_F2_hybrid P1H1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74229.gif

source_name: P1H1 gDNA


title: MM59

tag: tissue

tag: os (days)

tag: event (0=alive, 1=dead)

value: abdominal node

tag: localization of primary melanoma

value: Genital

tag: type

tag: breslow

tag: cdkn2a (hd=homozygous deletion, *=germline)

value: p16INK4A methylation

tag: molecular subtype


title: MM15

tag: sex

value: Male

tag: age at metastases

value: Acral

value: AMM

tag: cd3 immunohistochemistry


title: Sorted monocytes rep3 (MO MAC DC)

status: Public on Jun 07 2010

city: Regensburg

first: Maja

last: Klug

address: Franz-Josef-Strauss-Allee 11

department: Hematology

institute: University Hospital Regensburg

description: gender: male

hyb_protocol: Samples were hybridized for 16h at 65°C using a stringent protocol according to the manufacture's instructions (Agilent).  Arrays were disassembled and washed for 1 minute in Agilent gene Expression (GE)  wash buffer 1 followed by washing 1 minute in prewarmed (37°C) GE wash buffer 2.

scan_protocol: Images were scanned immediately after washing using a DNA microarray scanner (Agilent) at 5 µm resolution.

data_processing: Data was processed using Feature Extraction Software (Agilent) and further analyzed using GeneSpring GX software version 10.0.2 (worksheet1: DC_kinetic) or version 7 (worksheet 2: MO_MAC_DC). Data were normalized to the 75 th percentile and baseline transformed to the median of freshly isolated monocytes. The sorted CD14+ cells (DC kinetic and MO MAC DC) and the elutriated monocytes (MO MAC DC) were considered as one monocyte population).

source_name: Monocytes sorted from peripheral blood mononuclear cells

label_protocol: Labeling and hybridization were performed using the Agilent Gene Expression system according to the manufacturer’s instructions. In brief, 200 ng to 1000 ng of high-quality RNA were amplified and Cyanine 3-CTP labeled with the One Color Low RNA Input Linear Amplification Kit (Agilent). Labeling efficiency was controlled using the NanoDrop spectrophotometer.

growth_protocol: Monocyte-derived dendritic cells (DC) were obtained by culturing elutriated monocytes with 20U/ml IL-4, 280U/ml GM-CSF and 10% FCS; monocyte-derived macrophages (MAC) were obtained by culturing elutriated monocytes with 2% AB serum

extract_protocol: Total cellular RNA of the different cell types (monocytes, macrophages dendritic cells) was isolated after different time points (6h, 18h, 27h, 42h, 51h, 66h, day7) using the RNeasy Kit (Qiagen). RNA concentration was measured with a ND-1000 Spectrophotometer (NanoDrop, Thermo Fisher Scientific) and quality was controlled on agarose gels or using the Agilent Bioanalyzer.

treatment_protocol: Peripheral blood mononuclear cells were obtained from healthy donors by leukapheresis; elutriated monocytes were obtained form peripheral blood mononuclear cells by counter current elutriation; CD14+ sorted monocytes were isolated from peripheral blood mononuclear cells with the FACS_ARIA system

tag: gender

value: male

tag: sample type

value: primary cells

tag: disease state

value: healthy donor

tag: cell type


title: Scerev_Sparad_F2_hybrid P5A2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80473.gif

tag: reference

value: S.cerevisiae+S.paradoxus genomic DNA

source_name: P5A2 gDNA


title: Sorted monocytes rep2 (MO MAC DC)

description: gender: male

value: Monocytes sorted from peripheral blood mononuclear cells


title: Sorted monocytes rep1 (MO MAC DC)

description: gender: male


title: NTera2: Undiff [mRNA]

city: West Point

first: Michele

last: Cleary

state: PA

address: 770 Sumneytown Pike

department: Genetics and Pharmacogenomics

institute: Merck and Co., Inc.

description: Recent advances in the study of human embryonic stem cells (hESCs) and induced-pluripotent stem cells (iPS) highlight their importance as both model systems for basic research and avenues for therapeutic applications.  To gain better insight into the molecular properties and developmental capabilities of these cells, a clearer understanding of their molecular properties is crucial.  In this study, we analyze changes in the expression profile of microRNAs (miRNAs) and mRNAs in nine different, National Institutes of Health (NIH)-approved hESC lines.  By examining both undifferentiated hESCs and cells exposed to an undirected differentiation scheme at early stages found those miRNAs and mRNAs enriched in the hESC lines, and those miRNAs and mRNAs initially regulated upon commitment.  In comparing these profiles with those of an embryonal carcinoma (EC) cell line, NTera-2, we observed distinct patterns of miRNA expression in hESCs.  Furthermore, this analysis demonstrates that some previously identified hESC-enriched miRNAs, such as the miR-302 family and miR-17-92 miRNA cluster, are regulated at very early stages of commitment.  Additionally, we identify other early response miRNAs, not previously identified as hESC-enriched, and describe a large cluster of hESC-enriched miRNAs located on chromosome 19, whose expression changes rapidly in response to differentiation cues.  Examination of changes in mRNA expression during early commitment further reveals that many differentiation-regulated genes are possible candidates for regulation by these hESC-enriched miRNAs.

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

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

data_processing: Data were loaded into the Rosetta Resolver system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).  Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.  The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

label: Biotin is incorporated during the amplification.  This binds a streptavidin-conjugated phycoerythrin during the post-hybridization staining process that provides the measurable signal.

source_name: embryonal carcinoma cell line

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cRNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

tag: cell line/type

value: NTera2 Undiff


title: NTera2: Diff [mRNA]

value: NTera2 Diff


title: Scerev_Sparad_F2_hybrid P1G7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74011.gif

tag: genotype


title: Elutriated monocytes rep7 (MO MAC DC)

description: gender: male

source_name: Monocytes obtained after counter current centrifugal elutriation

value: primary cells, CD14+


title: Elutriated monocytes rep4 (MO MAC DC)

description: gender: male

value: Monocytes obtained after counter current centrifugal elutriation


title: 251404310001_A_control

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-12/85961.gif

value: S. cerevisiae genomic DNA

value: control


title: Elutriated monocytes rep2 (MO MAC DC)

description: gender: male


title: Scerev_Sparad_F2_hybrid P3B9

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80458.gif

source_name: P3B9 gDNA


title: Scerev_Sparad_F2_hybrid P3A5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80446.gif

source_name: P3A5 gDNA


title: Dendritic cells day7 rep2 (MO MAC DC)

description: gender: male

source_name: Monocyte-derived dendritic cell

value: Monocyte-derived dendritic cell


title: Macrophages day7 rep2 (MO MAC DC)

description: gender: male

source_name: Monocyte-derived macrophages

value: Monocyte-derived macrophages


title: Macrophages day7 rep6 (MO MAC DC)

description: gender: male


title: Dendritic cells day7 rep6 (MO MAC DC)

description: gender: male


title: BG01: Diff [mRNA]

source_name: human embryonic stem cell line

value: BG01 Diff


title: Scerev_Sparad_F2_hybrid P1H4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74232.gif

source_name: P1H4 gDNA


title: Scerev_Sparad_F2_hybrid P2C8

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74008.gif


title: HSF6: Diff [mRNA]

value: HSF6 Diff


title: H7: Undiff [mRNA]

value: H7 Undiff


title: Elutriated monocytes rep5 (MO MAC DC)

description: gender: male


title: Dendritic cells 6h rep3 (DC kinetic)

value: primary cells; healthy donor


title: H7: Diff [mRNA]

value: H7 Diff


title: Dendritic cells day7 rep1 (DC kinetic)

value: male

value: primary cells


title: Sorted monocytes rep2 (DC kinetic)


title: Dendritic cells 42h rep3 (DC kinetic)


title: HSF6: Undiff [mRNA]

value: HSF6 Undiff


title: Sorted monocytes rep3 (DC kinetic)

value: Monocytes sorted from peripheral blood mononuclear cells


title: Dendritic cells 18h rep3 (DC kinetic)


title: Dendritic cells 42h rep1 (DC kinetic)


title: BG03: Diff [mRNA]

value: BG03 Diff


title: BG01: Undiff [mRNA]

value: BG01 Undiff


title: H14: Undiff [mRNA]

value: H14 Undiff


title: H9: Diff [mRNA]

value: H9 Diff


title: BG03: Undiff [mRNA]

value: BG03 Undiff


title: H1: Diff [mRNA]

value: H1 Diff


title: H9: Undiff [mRNA]

value: H9 Undiff


title: Elutriated monocytes rep3 (DC kinetic)

value: primary cells; CD14+; healthy donor

value: primary cells, CD14+

value: Monocytes obtained after counter current centrifugal elutriation


title: H14: Diff [mRNA]

value: H14 Diff


title: Dendritic cells 27h rep1 (DC kinetic)

value: primary cells; healthy donor

value: Monocyte-derived dendritic cell


title: Elutriated monocytes rep2 (DC kinetic)

value: male


title: Scerev_Sparad_F2_hybrid P1G10

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74005.gif

value: S.cerevisiae+S.paradoxus genomic DNA


title: H1: Undiff [mRNA]

value: H1 Undiff


title: H13: Undiff [mRNA]

value: H13 Undiff


title: Dendritic cells 27h rep2 (DC kinetic)

value: primary cells


title: Dendritic cells 27h rep3 (DC kinetic)


title: BG02: Diff [mRNA]

value: BG02 Diff


title: Dendritic cells 6h rep2 (DC kinetic)


title: Dendritic cells 66h rep1 (DC kinetic)


title: Dendritic cells 18h rep1 (DC kinetic)


title: Dendritic cells 51h rep2 (DC kinetic)


title: SCP2 with hypoxia for 24h, repeat A

city: Princeton

first: Yibin

last: Kang

state: NJ

address: LTL 254, Washington Road

department: Molecular Biology

institute: Princeton University

description: 1% O2 level, 24h

hyb_protocol: Labeled cRNA (mixed Cy5-labeled and Cy3-labeled) was incubated with Blocking agent and Fragmentation buffer (Agilent Gene Expression Hybridization Kit) for 30min at 60°C. GEx Hybridization Buffer HI-RPM was then added to the mixture. Samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized for 16h. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2565AA scanner.Images were quantified using Agilent Feature Extraction Software (version 9.1.3).

data_processing: The data were analyzed with Genespring GX 7.3 Expression Analysis using Per Spot (divide by control channel), Per Chip (normalize to 50th percentile) and Per Gene (normalize to median) normalization methods.

source_name: SCP2 with hypoxia for 24h, repeat A

label_protocol: 325ng of total RNA were primed with T7 promoter primer at 65°C for 10 min, then reversed transcribed to cDNA at 40°C for 2h with MMLV RT, and transcribed to cRNA with T7 RNA polymerase with dATP, dTTP, dGTP and Cy5-CTP(test) or Cy3-CTP (reference) at 40°C for 2. Labeled cRNA was purified with Qiagen RNeasy mini kit.

growth_protocol: These sublines were maintained in DMEM with 10% FBS and antibiotics.

extract_protocol: Total RNA extracted using Qiagen RNeasy mini kit following manufacturer's instructions.

treatment_protocol: Low oxygen (1%) was applied by placed the cells in an oxygen chamber in tissue culture incubator (37-degree) for designated period (6h or 24h). The control was cultured in the tissue culture incubator (21% oxygen, 37-degree).

tag: cell line

value: breast cancer cell MDA-MB-231

tag: subline

tag: treatment

value: 1% O2 in oxygen chamber

tag: stress

value: hypoxia

tag: time

source_name: Universal Human Reference RNA (Stratagene)

value: 10 human cell lines


title: Dendritic cells 42h rep2 (DC kinetic)


title: SCP2 with hypoxia for 24h, repeat B

description: 1% O2 level, 24h

source_name: SCP2 with hypoxia for 24h, repeat B


title: Dendritic cells 18h rep2 (DC kinetic)


title: Dendritic cells 51h rep1 (DC kinetic)


title: Dendritic cells 66h rep2 (DC kinetic)


title: Dendritic cells day7 rep2 (DC kinetic)


title: Diffuse Intrinsic Pontine Glioma 8 - Normal-6.0

description: Hybridized to 6.0

value: normal brain

value: F

tag: age at dx (years)

tag: os (months)

tag: symptoms

value: CN

tag: symptom duration (days)

tag: tmz during rt

value: Yes

tag: tmz post rt


title: Elutriated monocytes rep1 (DC kinetic)

value: primary cells; CD14+; healthy donor

tag: gender

tag: sample type

value: primary cells, CD14+

value: Monocytes obtained after counter current centrifugal elutriation


title: Dendritic cells 6h rep1 (DC kinetic)

tag: disease state

value: primary cells; healthy donor

value: male

tag: cell type

value: Monocyte-derived dendritic cell


title: Dendritic cells 66h rep3 (DC kinetic)


title: SCP2 with hypoxia for 6h, repeat B

description: 1% O2 level, 6h

source_name: SCP2 with hypoxia for 6h, repeat B


title: Dendritic cells 51h rep3 (DC kinetic)


title: SLK5dpi_H3K27me3

city: Hamburg

first: Thomas

last: Guenther

department: Mechanisms of Antiviral Defense

institute: Heinrich-Pette-Institut

description: Analysis of H3K27me3 patterns in de novo infected SLK cells at 5 days post-infection

hyb_protocol: Labelled input and ChIP samples were blocked using Agilent blocking solution and human cot-1 DNA (Invitrogen), and hybridized using the Agilent Oligo aCGH/ChIP-on-chip Hybridization Kit at 65°C for 24 hrs in a rotating oven. Arrays were washed once with Oligo aCGH/ChIP-on-chip Wash Buffer 1 (Agilent 5188-5221) at RT for 5 min and in Oligo aCGH/ChIP-on-chip Wash Buffer 2 (Agilent 5188-5222) at 37°C for 1 min.

scan_protocol: Microarrays were scanned using a GenePix Personal 4100A scanner (Axon Instruments)

data_processing: Primary array analysis and data normalization was carried out using GenePix®Pro 6.0 software (Axon Instruments). All ChIP datasets were normalized using the adenovirus type 5 DNA that was added as a spike-in prior to labeling, hence correcting for errors during labelling, hybridization or scanning of the samples (probes Ad5f/r_K_475 to _590 were excluded due to a sequence deletion). To eliminate false positive spots, we hybridized DNA from KSHV-negative SLK cells and identified all probes which exhibited high levels of background hybridization (i.e., fluorescence levels that exceeded the mean value plus 1x the standard deviation of all KSHV-specific spots on the negative control array). These probes (which mapped almost exclusively to repeat regions) were permanently flagged in all datasets and not used for further analysis. While our arrays carry probes specific for the M and P types of the KSHV genome, the KSHV genomes from the BCBL1 and AP3 lines have not been fully sequenced and thus may deviate from the reference genomes at a few locations. To control for such sequence differences, we flagged all spots which exhibited fluorescence levels which did not exceed a background fluorescence treshold in the input channel, which was set to the mean fluorescence plus twice the standard deviation of all negative control features (i.e. empty array features as well as spots containing irrelevant sequences, corresponding to all Agilent probes in the datasets which are labeled with NC2_ and (-)3xSLv1). Note that, if sequence diversification leads to only a reduction of hybridization efficiency (e.g. due to single nucleotide polymorphism, which will not abolish hybridization), this will not falsify our results as the hybridization efficiency will be reduced in input as well as the immunoprecipitated sample; the ratio will thus be unaffected. In addition to above quality controls, in each dataset we flagged all probes which exhibited more than 30 % variance between duplicate spots. The 30% treshold corresponds to the mean variance plus twice the standard deviation exhibited by all KSHV-specific probes in all ChIP experiments, thus removing all probes which show a significantly increased variance between individual spot repeats. After normalization, an enrichment score was calculated for each of the probes, represented by the ratio of fluorescence signal intensities in the immunoprecipitated samples relative to the input control.

source_name: H3K27me3 ChIP DNA from de novo infected SLK cells at 5 days post-infection

label_protocol: 500 ng of amplified ChIP-input controls and 500 ng of amplified immunoprecipitated ChIP material were labeled with Cy3 and Cy5 using Agilent Genomic DNA Labeling Kit PLUS according to Agilents recommendations. For normalization purposes, 0.1 ng of Adenovirus Type 5 DNA were added to each samples prior to the labeling procedure. After labeling, samples were purified using Microcon YM-30 filter columns (Milipore).

growth_protocol: established cell line; grown under standard conditions

extract_protocol: ChIP analysis was performed as described by Si et al. (J Virol. 2006 Sep;80(18):9017-30) and recommended by the array manufacturer (Agilent Mammalian ChIP-on-chip protocol V10.0, May 2008), with some modifications. For chromatin immunoprecipitation, protein from 5x10^6 to 2x10^7 cells was cross-linked to DNA with 1 % formaldehyde in PBS for 10 min (adherent cells) or 20 min (suspension cells) at room temperature. The reaction was quenched by adding 1/20th volume 2.5 M glycine, cells were washed with PBS, scraped off the dish and collected. Cells were washed twice with ice cold PBS. All following steps were performed at 4°C. Lysis and wash buffers contained 1x protease inhibitor cocktail (Roche) and 1 mM Pefabloc® SC-Protease Inhibitor (Roth). Nuclei were isolated by incubation of cross-linked cells with 1 ml buffer I (50 mM Hepes-KOH, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) for 10 min on ice and pelleted by centrifugation (1,350 x g 5 min). The nuclei were subsequently washed with 1 ml buffer II (10 mM Tris-HCl, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), pelleted again and resuspended in 1 ml buffer III (1% SDS, 10 mM EDTA, 50 mM Tris-HCL). Chromatin was fragmented by sonication using a BioruptorTM (Diagenode) to an average length if 100-500 bp. After addition of 100 µl 10% Triton X-100, cell debris was pelleted by centrifugation (20,000 x g, 4°C) and supernatants were collected. For each individual IP, chromatin from 1x106 cells in a maximum volume of 200µl was diluted with dilution buffer (0.01 % SDS, 1.1 % Triton X-100, 1.2 mM EDTA, 16,7 mM Tris-HCl, 167 mM NaCl) to a final volume of 2 ml. To reduce non-specific background, chromatin was pre-incubated with 60 µl salmon-sperm DNA protein-A agarose beads (Upstate). Antibodies (2 to 10 µg, depending on the antibody) specific for the histone modifications H3K9/K14-Ac (Upstate: #06-599), H3K4-me3 (Upstate: #04-745), H3K9-me3 (Upstate: #17-625) or H3K27-me3 (Upstate: #07-449) were added and incubated for 16 hrs at 4°C on a rotating wheel. 60 µl agarose beads were added to precipitate the chromatin-immunocomplexes for 1 hr at 4°C. Beads were washed once with low-salt buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, 150 mM NaCl), once with high-salt buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, 500 mM NaCl), once with LiCl-wash buffer (0.25 M LiCl, 1 % Nonidet P-40, 1 % Na-deoxycholate, 1 mM EDTA, 10 mM Tris-HCl) and twice with TE buffer. Chromatin was eluted from the beads in 210 µl elution-buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1 % SDS) for 30 min at 65°C. 8 µl of a 5 M NaCl solution were added to 200 µl of the supernatant, and chromatin was de-crosslinked overnight at 65°C. Samples were diluted by adding 200 µl TE and RNA was degraded with 8 µl RNAseA (10 mg/ml) for 2 hrs at 37°C. For degradation of protein, 7 µl of CaCl2 solution (300 mM CaCl2 in 10 mM Tris-HCl) and 4 µl ProteinaseK (20 mg/ml Peqlab) were added and samples were incubated for 1h at 55°C. DNA was purified two times by phenol-chloroform extraction followed by a single chloroform extraction. DNA (400 µl in total) was precipitated with 1055 µl ethanol (100 %), 24 µl NaCl (5 M) and 3 µl glycogen (10 mg/ml) at -80°C for at least 30 min. After centrifugation (20.000 x g, 4°C, 15 min), pellets were washed once with ethanol (70 %) centrifuged again and dried in a vacuum centrifuge. DNA was resuspended in 70 µl of 10 mM Tris-HCl. For preparation of input controls, 1/4th of the amount of chromatin that was used in the immunopreciptations was employed. Input samples were diluted in dilution buffer to a final volume of 200 µl and were treated identical to IP samples, starting with the decrosslinking step. Both samples were subsequenctly subjected to whole genome amplification and labeling using a linker mediated PCR protocol (Agilent Mammalian ChIP-on-chip protocol V10.0, May 2008), followed by microarray hybridization.

treatment_protocol: Cultures were infected with KSHV 5 days prior to DNA extraction

value: SLK

tag: antibody

value: biological sample

value: endothelial cells

source_name: Input DNA from de novo infected SLK cells at 5 days post-infection


title: SCP2 with hypoxia for 6h, repeat A

description: 1% O2 level, 6h

source_name: SCP2 with hypoxia for 6h, repeat A

value: breast cancer cell MDA-MB-231


title: BG02: Undiff [mRNA]

tag: cell line/type

value: BG02 Undiff


title: Sorted monocytes rep1 (DC kinetic)

source_name: Monocytes sorted from peripheral blood mononuclear cells

value: primary cells


title: SLK5dpi_H3K4me3

description: Analysis of H3K4me3 patterns in de novo infected SLK cells at 5 days post-infection

source_name: H3K4me3 ChIP DNA from de novo infected SLK cells at 5 days post-infection

tag: cell line


title: SLK5dpi_H3K9me3

description: Analysis of H3K9me3 patterns in de novo infected SLK cells at 5 days post-infection

source_name: H3K9me3 ChIP DNA from de novo infected SLK cells at 5 days post-infection


title: Diffuse Intrinsic Pontine Glioma 9 - Normal-6.0

description: Hybridized to 6.0

value: M

value: LTS, ataxia, CN


title: SLKP_H3K27me3

description: Analysis of H3K27me3 patterns in SLKP cells (long-term KSHV infected SLK cells)

source_name: H3K27me3 ChIP DNA from SLKP cells (long-term KSHV infected SLK cells)

value: SLKP

source_name: Input DNA from SLKP cells (long-term KSHV infected SLK cells)


title: SCP2 with hypoxia for 0h, repeat B

description: 21% O2 level

source_name: SCP2 with hypoxia for 0h, repeat B

tag: subline

value: 1% O2 in oxygen chamber

value: 0h (without treatment)

value: 10 human cell lines


title: Diffuse Intrinsic Pontine Glioma 8 - Tumour-6.0

description: Hybridized to 6.0

value: DIPG

value: F

value: CN

value: Yes


title: SCP2 with hypoxia for 0h, repeat A

description: 21% O2 level

source_name: SCP2 with hypoxia for 0h, repeat A

tag: treatment


title: SLK_Input

description: The Cy3 channel of this sample was used as a negative control to permanently flag spots which exhibit cross-hybridization with cellular DNA; there is no ratio data for this sample.

hyb_protocol: Labelled input and MeDIP samples were blocked using Agilent blocking solution and human cot-1 DNA (Invitrogen), and hybridized using the Agilent Oligo aCGH/ChIP-on-chip Hybridization Kit at 65°C for 24 hrs in a rotating oven. Arrays were washed once with Oligo aCGH/ChIP-on-chip Wash Buffer 1 (Agilent 5188-5221) at RT for 5 min and in Oligo aCGH/ChIP-on-chip Wash Buffer 2 (Agilent 5188-5222) at 37°C for 1 min.

scan_protocol: Microarrays were scanned with a GenePix Personal 4100A scanner (Axon Instruments)

data_processing: Primary array analysis and data normalization was carried out using GenePix®Pro 6.0 software (Axon Instruments). All MeDIP datasets were normalized using the methylated pCR2.1 plasmid which had been added to the samples prior to the immunoprecipitation, thus controlling for differences in MeDIP efficiency as well as labelling and array hybridization. Both channels were adjusted such that the average ratio of input vs. MeDIP signals across all pCR2.1-specific spots was 1. To eliminate false positive spots, we hybridized DNA from KSHV-negative SLK cells and identified all probes which exhibited high levels of background hybridization (i.e., fluorescence levels that exceeded the mean value plus 1x the standard deviation of all KSHV-specific spots on the negative control array). These probes (which mapped almost exclusively to repeat regions) were permanently flagged in all datasets and not used for further analysis. While our arrays carry probes specific for the M and P types of the KSHV genome, the KSHV genomes from the BCBL1 and AP3 lines have not been fully sequenced and thus may deviate from the reference genomes at a few locations. To control for such sequence differences, we flagged all spots which exhibited fluorescence levels which did not exceed a background fluorescence treshold in the input channel, which was set to the mean fluorescence plus twice the standard deviation of all negative control features (i.e. empty array features as well as spots containing irrelevant sequences, corresponding to all Agilent probes in the datasets which are labeled with NC2_ and (-)3xSLv1). Note that, if sequence diversification leads to only a reduction of hybridization efficiency (e.g. due to single nucleotide polymorphism, which will not abolish hybridization), this will not falsify our results as the hybridization efficiency will be reduced in input as well as the immunoprecipitated sample; the ratio will thus be unaffected. In addition to above quality controls, in each dataset we flagged all probes which exhibited more than 30 % variance between duplicate spots. The 30% treshold corresponds to the mean variance plus twice the standard deviation exhibited by all KSHV-specific probes in all MeDIP experiments, thus removing all probes which show a significantly increased variance between individual spot repeats. MeDIP data were furthermore corrected by subtracting from each probe-specific signal the value observed in the negative control, i.e. the MeDIP sample representing the unmethylated KSHV bacmid in the background of cellular DNA. After normalization, an enrichment score was calculated for each of the probes, represented by the ratio of fluorescence signal intensities in the immunoprecipitated samples relative to the input control.

source_name: DNA from KSHV-negative SLK cells

label_protocol: 500 ng of MeDIP-input and all of the MeDIP material were labeled with Cy3 and Cy5 using Agilent Genomic DNA Labeling Kit PLUS according to Agilents recommendations. After labeling, samples were purified using Microcon YM-30 filter columns (Milipore).

extract_protocol: Highly pure genomic DNA serving as input for MeDIP was prepared by proteinase K digestion, followed by phenol chloroform extraction and ethanol precipitation. Negative and positive controls were prepared by mixing genomic DNA from SLK cells with unmethylated or in vitro methylated KSHV bacmid DNA (Zhou et al., J Virol. 2002 Jun;76(12):6185-96), respectively. The ratio of viral vs. cellular DNA was selected such that it mimics the episome content typically seen in KSHV-infected PEL cell lines and the SLKp line (approx. 30-40 copies per cell). The control DNA or DNA from KSHV-infected cells was resuspended in TE containing RNAseA and incubated for at least 2 hrs at 37°C to degrade RNA. DNA was sonicated to an average fragment size of 100-500 bp using a BioruptorTM (Diagenode). In order to allow quantification and normalization across multiple samples, 0.2 ng of in vitro methylated pCR2.1 plasmid (described at the end of this section) were added to 5 µg of sheared DNA and diluted in TE to a final volume of 250 µl. 50 µl (1 µg) of the dilution were saved as an input control, and another 250 µl TE were added to the remaining 200 µl. Denaturing of DNA was performed by incubation at 98°C for 10 min, followed by incubation on ice for 10 min. Subsequently, 51 µl 10x IP-buffer (100 mM Na-phosphate buffer, pH 7.0, 1.4 mM NaCl, 0.5 % Triton X-100) were added. Immunoprecipitation was performed by addition of 2.5 µg of a 5´-methylcytidine specific antibody (MAb-5MECYT-100, Diagenode) and incubation for 2 hrs on a rotating wheel at 4°C. 50 µl Dynabeads® M-280 Sheep anti-Mouse IgG (Invitrogen) were washed once with 0.1 % BSA in PBS, resuspended in 50 µl 1x IP-buffer, added to the DNA-antibody complexes and incubated for 2 hrs. Samples were washed three times with 1x IP-buffer for 10 min. Beads were resuspended in 150 µl elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 0.5 % SDS) and 3.5 µl proteinase K were added. Samples were incubated shaking at 55°C for 15 min followed by 2 min at 65°C. Eluate was collected, elution was repeated once and the eluates were combined. DNA was purified twice by phenol-chloroform extraction, followed by a single chloroform extraction. DNA (300 µl in total) was precipitated with 810 µl ethanol (100 %), 24 µl NaCl (5 M) and 3 µl glycogen (10 mg/ml) at -80°C for at least 30 min. After centrifugation (20.000 x g, 4°C, 15 min), pellets were washed once with ethanol (70 %) centrifuged again, dried in a speedvac and resuspended in 15.5 µl H2O. Input controls were prepared by adding 250 µl water to 50 µl of the sheared DNA input samples and treated identical to the IP samples, starting with the ethanol precipitation step. The samples were subsequently analyzed by qPCR or microarray hybridization. For control and normalization purposes, we prepared in vitro methylated DNA from a bacmid containing the complete KSHV genome and the pCR2.1 vector (Invitrogen). DNA was methylated by incubating 15 µg of DNA with 40 units of the CpG methyltransferase M.SssI (NEB) for 2 hrs in 1x NEBuffer 2 containing 160 µM S-adenosylmethionine (SAM). Fresh SAM was added and reactions were incubated for another 2 hrs. DNA was purified and the reaction was repeated once to ensure complete methylation. Quantitative methylation was confirmed by restriction analysis using methylation sensitive enzymes (HpaII and MspI, Fermentas), and/or bisulfite sequencing of specific loci.

value: spot performance control


title: SLKP_H3K9me3

description: Analysis of H3K9me3 patterns in SLKP cells (long-term KSHV infected SLK cells)

source_name: H3K9me3 ChIP DNA from SLKP cells (long-term KSHV infected SLK cells)


title: SLKP_H3K4me3

description: Analysis of H3K4me3 patterns in SLKP cells (long-term KSHV infected SLK cells)

source_name: H3K4me3 ChIP DNA from SLKP cells (long-term KSHV infected SLK cells)


title: BCBL1_H3K27me3

description: Analysis of H3K27me3 patterns in the PEL-derived cell line BCBL1

source_name: H3K27me3 ChIP DNA from BCBL1 cells

value: B cells

source_name: Input DNA from BCBL1 cells


title: SLK_Bac_neg_control_MeDIP

description: MeDIP negative control sample: prior to MeDIP, unmethylated KSHV bacmid Bac36 DNA was spiked into genomic SLK DNA and adjusted via real time PCR to mimic KSHV copy numbers as seen in BCBL1 and SLKP cells. This dataset was used to perform MeDIP specific background correction for all other datasets and is thus not represented by its own 'MeDIP to input' ratio.

source_name: MeDIP of DNA from KSHV-negative SLK cells spiked with unmethylated KSHV Bacmid (Bac36) DNA

value: SLK

value: negative control

source_name: Input, DNA from KSHV-negative SLK cells spiked with unmethylated KSHV Bacmid (Bac36) DNA


title: SLKP_H3K9/14Ac

description: Analysis of H3K9/14Ac patterns in SLKP cells (long-term KSHV infected SLK cells)

source_name: H3K9/14Ac ChIP DNA from SLKP cells

value: biological sample

value: endothelial cells

source_name: Input DNA from SLKP cells


title: LM2 with hypoxia for 6h, repeat A

description: 1% O2 level, 6h

source_name: LM2 with hypoxia for 6h, repeat A

value: breast cancer cell MDA-MB-231

tag: stress

value: hypoxia

source_name: Universal Human Reference RNA (Stratagene)


title: HBL6_MeDIP

description: Analysis of DNA methylation patterns in the PEL-derived cell line HBL6

source_name: MeDIP of DNA from PEL-derived HBL6 cells

source_name: Input, DNA from PEL-derived HBL6 cells


title: BCBL1_H3K9me3

description: Analysis of H3K9me3 patterns in the PEL-derived cell line BCBL1

source_name: H3K9me3 ChIP DNA from BCBL1 cells


title: BCBL1_H3K4me3

description: Analysis of H3K4me3 patterns in the PEL-derived cell line BCBL1

source_name: H3K4me3 ChIP DNA from BCBL1 cells


title: LM2 with hypoxia for 0h, repeat A

description: 21% O2 level

source_name: LM2 with hypoxia for 0h, repeat A

tag: time