title: GBM_11-093

description:
dkfz_11-093
Methylation data from a glioblastoma tumor sample.


title: patient 35, cancer, LCM (copy number analysis)

status: Public on Oct 16 2012

type: genomic

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

hyb_protocol: Using Genome-Wide Human SNP Sty assay kit (Affymetrix), DNA was prepared and was hybridized to each array according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: Copy number analysis was performed using Genotyping Console software (Affymetrix).

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: surgically resected material

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from surgical materials using the QIAamp DNA Micro Kit (Qiagen) for tumor tissue or the QIAamp DNA Mini Kit (Qiagen) for non-cancerous tissue. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

treatment_protocol: Tumor tissue was extracted using laser-capture microdissection. Whole tissue was used for analysis of non-tumor specimens.

tag: metastasis

value: metastasis

tag: Stage

tag: tissue

value: cancer, LCM


title: GBM_11-096

city: Heidelberg

first: Dominik

last: Sturm

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center

description:
dkfz_11-096
Methylation data from a glioblastoma tumor sample.

hyb_protocol: Illumina protocol.

scan_protocol: Illumina iScan System according to the manufacturer's protocol.

data_processing: Data analysis has been carried out using GenomeStudio 2011.1 (methylationmodule 1.9.0) and annotation 1.2. The methylation analysis has been performed as suggested by Illumina with no background subtraction and normalization to internal controls.

label: biotin/DNP

source_name: Primary brain tumor tissue

label_protocol: Illumina protocol.

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride.

value: primary glioblastoma

tag: brain location

tag: age at diagnosis (years)

tag: gender

value: female

tag: h3f3a status

value: WT

tag: idh1 status

tag: dna methylation subgroup

value: RTK II 'classic'


title: GBM_11-048

type: RNA

first: Marcel

last: Kool

address: Im Neuenheimer Feld 580

department: Pediatric Neuro Oncology

description: Gene expression data from a glioblastoma tumor sample

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 = 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).

label: biotin

molecule: total RNA

label_protocol: Affymetrix protocol

extract_protocol: Total RNA from biopsy samples was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using the TRIzol reagent (Invitrogen, Carlsbad, USA), and subsequently passed over a RNeasy Mini Spin Column (Qiagen, Hilden, Germany) for the removal of small fragments. Integrity control and sample quantitation of total extracted RNA was performed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).

tag: tumor location

value: thalamic

tag: subgroup


title: GBM_11-038

value: male

value: RTK II


title: GBM_11-031

value: frontal lobe

value: Mesenchymal


title: patient 33, cancer, LCM (copy number analysis)


title: CTRL_adult CB_02

description:
control_a2
Methylation data from non-neoplastic brain tissue.

source_name: Non-neoplastic adult brain tissue

value: non-neoplastic brain

value: cerebellar

tag: developmental stage

value: adult


title: GBM_11-098

description:
dkfz_11-098
Methylation data from a glioblastoma tumor sample.

value: mesenchymal


title: GBM_11-017

value: temporal lobe


title: GBM_11-092

description:
dkfz_11-092
Methylation data from a glioblastoma tumor sample.


title: GBM_11-013

value: ventricular


title: GBM_11-039

value: MUT

value: IDH


title: CTRL_fetal CB_04

description:
control_f4
Methylation data from non-neoplastic brain tissue.

source_name: Non-neoplastic fetal brain tissue

value: fetus


title: GBM_11-026

value: female


title: patient 32, cancer, LCM (copy number analysis)

value: cancer, LCM


title: CTRL_adult CB_01

description:
control_a1
Methylation data from non-neoplastic brain tissue.


title: GBM_11-014

value: WT

value: RTK I


title: GBM_11-091

description:
dkfz_11-091
Methylation data from a glioblastoma tumor sample.

value: primary glioblastoma

value: thalamic


title: patient 31, cancer, LCM (copy number analysis)


title: GBM_11-040


title: Patient 99, cancer, LCM [NUCKS1 study]

description: Gene expression profile of surgically resected material

hyb_protocol: Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.

data_processing: The data was normalized by robust multichip analysis (RMA) using R statistical software version 2.12.1 and affy library in Bioconductor.

label_protocol: cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).

treatment_protocol: Tumor tissue was extracted using laser-capture microdissection.


title: Patient 97, cancer, LCM [NUCKS1 study]


title: Patient 98, cancer, LCM [NUCKS1 study]

value: metastatic recurrence


title: CTRL_fetal CB_03

description:
control_f3
Methylation data from non-neoplastic brain tissue.


title: CTRL_fetal CB_01

description:
control_f1
Methylation data from non-neoplastic brain tissue.


title: Patient 96, cancer, LCM [NUCKS1 study]


title: patient 27, cancer, LCM (copy number analysis)


title: Patient 95, cancer, LCM [NUCKS1 study]


title: patient 28, cancer, LCM (copy number analysis)


title: Patient 94, cancer, LCM [NUCKS1 study]


title: Patient 88, cancer, LCM [NUCKS1 study]


title: patient 30, cancer, LCM (copy number analysis)


title: patient 26, cancer, LCM (copy number analysis)


title: patient 24, cancer, LCM (copy number analysis)

value: metastasis


title: GBM_11-073

description:
dkfz_11-073
Methylation data from a glioblastoma tumor sample.


title: Patient 90, cancer, LCM [NUCKS1 study]


title: CTRL_fetal CB_02

description:
control_f2
Methylation data from non-neoplastic brain tissue.

value: non-neoplastic brain


title: Patient 86, cancer, LCM [NUCKS1 study]


title: GBM_11-075

description:
dkfz_11-075
Methylation data from a glioblastoma tumor sample.

value: male

value: RTK I 'PDGFRA'

tag: id (schwartzentruber et al. (pmid 22286061))


title: patient 25, cancer, LCM (copy number analysis)


title: Patient 89, cancer, LCM [NUCKS1 study]


title: patient 23, cancer, LCM (copy number analysis)


title: Patient 83, cancer, LCM [NUCKS1 study]


title: GBM_11-074

description:
dkfz_11-074
Methylation data from a glioblastoma tumor sample.


title: GBM_11-072

description:
dkfz_11-072
Methylation data from a glioblastoma tumor sample.

value: parietal lobe


title: Patient 84, cancer, LCM [NUCKS1 study]


title: patient 22, cancer, LCM (copy number analysis)


title: Patient 79, cancer, LCM [NUCKS1 study]


title: GBM_11-071

description:
dkfz_11-071
Methylation data from a glioblastoma tumor sample.

value: mesenchymal


title: Patient 82, cancer, LCM [NUCKS1 study]


title: Patient 81, cancer, LCM [NUCKS1 study]


title: GBM_11-070

description:
dkfz_11-070
Methylation data from a glioblastoma tumor sample.

value: ventricular


title: patient 20, cancer, LCM (copy number analysis)


title: Patient 78, cancer, LCM [NUCKS1 study]


title: Patient 77, cancer, LCM [NUCKS1 study]


title: Patient 73, cancer, LCM [NUCKS1 study]


title: Patient 72, cancer, LCM [NUCKS1 study]


title: Patient 68, cancer, LCM [NUCKS1 study]


title: patient 19, cancer, LCM (copy number analysis)


title: Patient 65, cancer, LCM [NUCKS1 study]


title: Patient 70, cancer, LCM [NUCKS1 study]


title: patient 16, cancer, LCM (copy number analysis)


title: patient 169, cancer, LCM (copy number analysis)


title: Patient 64, cancer, LCM [NUCKS1 study]


title: GBM_11-068

description:
dkfz_11-068
Methylation data from a glioblastoma tumor sample.

value: cerebellopontine angle


title: patient 17, cancer, LCM (copy number analysis)


title: GBM_11-069

description:
dkfz_11-069
Methylation data from a glioblastoma tumor sample.

value: frontal lobe, praecentral


title: Patient 63, cancer, LCM [NUCKS1 study]


title: patient 168, cancer, LCM (copy number analysis)


title: Patient 61, cancer, LCM [NUCKS1 study]


title: Patient 57, cancer, LCM [NUCKS1 study]


title: Patient 59, cancer, LCM [NUCKS1 study]


title: GBM_11-065

description:
dkfz_11-065
Methylation data from a glioblastoma tumor sample.

value: temporal lobe


title: Patient 55, cancer, LCM [NUCKS1 study]


title: Patient 53, cancer, LCM [NUCKS1 study]


title: GBM_11-066

description:
dkfz_11-066
Methylation data from a glioblastoma tumor sample.

value: occipital lobe

value: female


title: Patient 48, cancer, LCM [NUCKS1 study]

value: cancer, LCM


title: patient 166, cancer, LCM (copy number analysis)


title: Patient 46, cancer, LCM [NUCKS1 study]


title: GBM_11-064

description:
dkfz_11-064
Methylation data from a glioblastoma tumor sample.

value: WT


title: patient 161, cancer, LCM (copy number analysis)


title: patient 162, cancer, LCM (copy number analysis)


title: Patient 45, cancer, LCM [NUCKS1 study]


title: patient 164, cancer, LCM (copy number analysis)


title: GBM_11-062

description:
dkfz_11-062
Methylation data from a glioblastoma tumor sample.

value: primary glioblastoma


title: patient 163, cancer, LCM (copy number analysis)


title: GBM_11-063

description:
dkfz_11-063
Methylation data from a glioblastoma tumor sample.

value: frontal lobe


title: GBM_11-067

description:
dkfz_11-067
Methylation data from a glioblastoma tumor sample.


title: GBM_11-060

description:
dkfz_11-060
Methylation data from a glioblastoma tumor sample.

value: MUT

value: IDH


title: Patient 42, cancer, LCM [NUCKS1 study]

description: Gene expression profile of surgically resected material


title: patient 165, cancer, LCM (copy number analysis)

value: metastasis


title: patient 160, cancer, LCM (copy number analysis)


title: Patient 44, cancer, LCM [NUCKS1 study]


title: GBM_11-058

description:
dkfz_11-058
Methylation data from a glioblastoma tumor sample.

value: male


title: GBM_11-055

description:
dkfz_11-055
Methylation data from a glioblastoma tumor sample.

value: RTK II 'classic'


title: Patient 41, cancer, LCM [NUCKS1 study]


title: Patient 38, cancer, LCM [NUCKS1 study]


title: GBM_11-059

description:
dkfz_11-059
Methylation data from a glioblastoma tumor sample.


title: Patient 37, cancer, LCM [NUCKS1 study]


title: Patient 36, cancer, LCM [NUCKS1 study]


title: Patient 52, cancer, LCM [NUCKS1 study]

value: metastatic recurrence


title: patient 158, cancer, LCM (copy number analysis)


title: patient 15, cancer, LCM (copy number analysis)


title: patient 157, cancer, LCM (copy number analysis)


title: patient 156, cancer, LCM (copy number analysis)


title: patient 154, cancer, LCM (copy number analysis)


title: patient 155, cancer, LCM (copy number analysis)


title: GBM_11-056

description:
dkfz_11-056
Methylation data from a glioblastoma tumor sample.


title: GBM_11-057

description:
dkfz_11-057
Methylation data from a glioblastoma tumor sample.


title: GBM_11-061

description:
dkfz_11-061
Methylation data from a glioblastoma tumor sample.

value: parietal lobe

value: RTK I 'PDGFRA'


title: patient 153, cancer, LCM (copy number analysis)


title: Patient 34, cancer, LCM [NUCKS1 study]


title: Patient 35, cancer, LCM [NUCKS1 study]


title: GBM_11-051

description:
dkfz_11-051
Methylation data from a glioblastoma tumor sample.

value: mesenchymal


title: GBM_11-054

description:
dkfz_11-054
Methylation data from a glioblastoma tumor sample.


title: GBM_11-052

description:
dkfz_11-052
Methylation data from a glioblastoma tumor sample.


title: Patient 33, cancer, LCM [NUCKS1 study]


title: Patient 31, cancer, LCM [NUCKS1 study]


title: Patient 30, cancer, LCM [NUCKS1 study]


title: patient 152, cancer, LCM (copy number analysis)


title: GBM_11-050

description:
dkfz_11-050
Methylation data from a glioblastoma tumor sample.

value: cerebellar


title: GBM_11-048

description:
dkfz_11-048
Methylation data from a glioblastoma tumor sample.

value: thalamic


title: Patient 32, cancer, LCM [NUCKS1 study]


title: GBM_11-049

description:
dkfz_11-049
Methylation data from a glioblastoma tumor sample.


title: GBM_11-053

description:
dkfz_11-053
Methylation data from a glioblastoma tumor sample.

value: temporal lobe


title: patient 147, cancer, LCM (copy number analysis)


title: Patient 28, cancer, LCM [NUCKS1 study]


title: patient 150, cancer, LCM (copy number analysis)


title: patient 149, cancer, LCM (copy number analysis)


title: patient 148, cancer, LCM (copy number analysis)


title: patient 145, cancer, LCM (copy number analysis)


title: Human Bone_4 [Illumina]

city: Oslo

first: Heidi

middle: Maria

last: Namløs

address: PO Box 4953 Nydalen

department: Institute for cancer research, The Norwegian Radium Hospital

country: Norway

institute: Oslo University Hospital

description: Two normal bone samples from different donors were purchased from Capital Biosciences (Gaithersburg, MD, USA).

hyb_protocol: Synthesis of cDNA, cRNA amplification, and hybridization of cRNA onto the Illumina Human-6 v2.0 Expression BeadChips (San Diego, CA, USA) were performed as per manufacturer's instructions.

scan_protocol: The slides were scanned on a BeadArray Reader (Illumina, Inc.).

data_processing: The data was extracted and quality controlled using the Gene Expression module v3.1.7 of Illumina´s BeadStudio software (v3.1.0.0). Variance-stabilizing transformation (Lin et al., 2008) and quantile normalization on the probe level was carried out using the statistical package R and the Bioconductor package lumi (Du et al., 2008; Gentleman et al., 2004).

source_name: Normal Bone

extract_protocol: RNA was isolated using TRIzol (Invitrogen), followed by RNA clean-up using the QIAGEN Rneasy mini kit with on-column DNAse treatment (Venlo, the Netherlands). RNA quality and concentration were measured using an Agilent 2100 Bioanalyzer (Santa Clara, CA, USA) and Nanodrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA), respectively.

value: Normal bone


title: Patient 27, cancer, LCM [NUCKS1 study]

value: cancer, LCM


title: patient 146, cancer, LCM (copy number analysis)


title: GBM_11-045

description:
dkfz_11-045
Methylation data from a glioblastoma tumor sample.

value: WT


title: Patient 26, cancer, LCM [NUCKS1 study]


title: GBM_11-046

description:
dkfz_11-046
Methylation data from a glioblastoma tumor sample.

value: primary glioblastoma

value: female


title: patient 143, cancer, LCM (copy number analysis)


title: patient 144, cancer, LCM (copy number analysis)


title: Patient 25, cancer, LCM [NUCKS1 study]

description: Gene expression profile of surgically resected material


title: Human Bone_2 [Illumina]

description: Two long bone samples were obtained from amputations of patients without osteosarcoma at the Norwegian Radium Hospital

label_protocol: Synthesis of cDNA, cRNA amplification, and hybridization of cRNA onto the Illumina Human-6 v2.0 Expression BeadChips (San Diego, CA, USA) were performed as per manufacturer's instructions.


title: patient 142, cancer, LCM (copy number analysis)


title: GBM_11-044

description:
dkfz_11-044
Methylation data from a glioblastoma tumor sample.


title: GBM_11-043

description:
dkfz_11-043
Methylation data from a glioblastoma tumor sample.

value: fronto-temporal


title: patient 141, cancer, LCM (copy number analysis)


title: Patient 22, cancer, LCM [NUCKS1 study]


title: Patient 23, cancer, LCM [NUCKS1 study]


title: Human Bone_1 [Illumina]


title: patient 140, cancer, LCM (copy number analysis)


title: Patient 20, cancer, LCM [NUCKS1 study]


title: OS cell line_19 [Illumina]

description: The cell lines were maintained in RPMI 1640 (Invitrogen, Carsbad, CA, USA) supplemented with 10% fetal calf serum, 2 mM L-glutamine (Invitrogen) and 1% Penicillin/Streptomycin (Invitrogen) under standard conditions.

source_name: Osteosarcoma cell line

tag: cell line


title: GBM_11-042

description:
dkfz_11-042
Methylation data from a glioblastoma tumor sample.

value: MUT


title: OS cell line_17 [Illumina]


title: patient 139, cancer, LCM (copy number analysis)


title: Human Bone_3 [Illumina]


title: patient 138, cancer, LCM (copy number analysis)


title: GBM_11-047

description:
dkfz_11-047
Methylation data from a glioblastoma tumor sample.


title: GBM_11-040

description:
dkfz_11-040
Methylation data from a glioblastoma tumor sample.

value: IDH


title: OS cell line_18 [Illumina]

value: U-2 OS


title: GBM_11-041

description:
dkfz_11-041
Methylation data from a glioblastoma tumor sample.


title: GBM_11-039

description:
dkfz_11-039
Methylation data from a glioblastoma tumor sample.


title: GBM_11-038

description:
dkfz_11-038
Methylation data from a glioblastoma tumor sample.

value: male

value: RTK II 'classic'


title: GBM_11-037

description:
dkfz_11-037
Methylation data from a glioblastoma tumor sample.


title: Patient 24, cancer, LCM [NUCKS1 study]

value: metastasis


title: Patient 17, cancer, LCM [NUCKS1 study]

value: metastatic recurrence


title: OS cell line_16 [Illumina]

value: OSA


title: Patient 163, cancer, LCM [NUCKS1 study]


title: patient 136, cancer, LCM (copy number analysis)


title: Patient 162, cancer, LCM [NUCKS1 study]


title: OS cell line_14 [Illumina]

value: MNNG-HOS


title: OS cell line_12 [Illumina]


title: OS cell line_13 [Illumina]

value: MHM


title: Patient 19, cancer, LCM [NUCKS1 study]


title: GBM_11-036

description:
dkfz_11-036
Methylation data from a glioblastoma tumor sample.


title: patient 135, cancer, LCM (copy number analysis)


title: patient 133, cancer, LCM (copy number analysis)


title: GBM_11-035

description:
dkfz_11-035
Methylation data from a glioblastoma tumor sample.

value: parietal lobe

value: mesenchymal


title: Patient 161, cancer, LCM [NUCKS1 study]

value: cancer, LCM


title: OS cell line_15 [Illumina]

value: OHS


title: patient 131, cancer, LCM (copy number analysis)


title: Patient 16, cancer, LCM [NUCKS1 study]


title: GBM_11-034

description:
dkfz_11-034
Methylation data from a glioblastoma tumor sample.

value: primary glioblastoma

value: occipital lobe

value: WT


title: patient 130, cancer, LCM (copy number analysis)


title: patient 134, cancer, LCM (copy number analysis)


title: OS cell line_10 [Illumina]

value: IOR-SARG


title: GBM_11-030

description:
dkfz_11-030
Methylation data from a glioblastoma tumor sample.

value: gyrus cinguli


title: Patient 15, cancer, LCM [NUCKS1 study]


title: GBM_11-032

description:
dkfz_11-032
Methylation data from a glioblastoma tumor sample.

value: brain stem

value: female


title: Patient 160, cancer, LCM [NUCKS1 study]

description: Gene expression profile of surgically resected material


title: OS cell line_11 [Illumina]

value: KPD


title: GBM_11-033

description:
dkfz_11-033
Methylation data from a glioblastoma tumor sample.

value: frontal lobe, praecentral


title: OS cell line_8 [Illumina]


title: Patient 158, cancer, LCM [NUCKS1 study]


title: OS cell line_7 [Illumina]


title: OS cell line_9 [Illumina]


title: Patient 157, cancer, LCM [NUCKS1 study]


title: OS cell line_6 [Illumina]


title: patient 12, cancer, LCM (copy number analysis)


title: patient 129, cancer, LCM (copy number analysis)


title: GBM_11-031

description:
dkfz_11-031
Methylation data from a glioblastoma tumor sample.

value: frontal lobe


title: Patient 156, cancer, LCM [NUCKS1 study]


title: patient 128, cancer, LCM (copy number analysis)

value: metastasis


title: GBM_11-029

description:
dkfz_11-029
Methylation data from a glioblastoma tumor sample.

value: male


title: patient 125, cancer, LCM (copy number analysis)


title: patient 127, cancer, LCM (copy number analysis)


title: patient 124, cancer, LCM (copy number analysis)


title: Patient 154, cancer, LCM [NUCKS1 study]


title: Patient 153, cancer, LCM [NUCKS1 study]


title: GBM_11-024

description:
dkfz_11-024
Methylation data from a glioblastoma tumor sample.

value: thalamic


title: Patient 155, cancer, LCM [NUCKS1 study]

value: metastatic recurrence


title: GBM_11-025

description:
dkfz_11-025
Methylation data from a glioblastoma tumor sample.

value: parietal lobe

value: MUT

value: RTK I 'PDGFRA'


title: OS cell line_5 [Illumina]

description: The cell lines were maintained in RPMI 1640 (Invitrogen, Carsbad, CA, USA) supplemented with 10% fetal calf serum, 2 mM L-glutamine (Invitrogen) and 1% Penicillin/Streptomycin (Invitrogen) under standard conditions.


title: GBM_11-027

description:
dkfz_11-027
Methylation data from a glioblastoma tumor sample.

value: primary glioblastoma

value: mesenchymal


title: patient 123, cancer, LCM (copy number analysis)

value: cancer, LCM


title: OS cell line_4 [Illumina]

value: IOR-MOS


title: GBM_11-023

description:
dkfz_11-023
Methylation data from a glioblastoma tumor sample.

value: temporal lobe

value: WT


title: Patient 152, cancer, LCM [NUCKS1 study]


title: OS cell line_1 [Illumina]


title: GBM_11-026

description:
dkfz_11-026
Methylation data from a glioblastoma tumor sample.

value: female


title: OS cell line_3 [Illumina]

value: HOS


title: OS cell line_2 [Illumina]

value: HAL


title: patient 121, cancer, LCM (copy number analysis)


title: Juvenile replicate 2 vs Mature replicate 2 (dye swap)

city: Bet-Dagan

first: Ron

last: Ophir

address: POB 6

department: Fruit Tree Sciences

country: Israel

institute: Agricultire Research Organization

hyb_protocol: Agilent protocol

scan_protocol: Agilent scanner

data_processing: A lowess normalization within array and Aquantile (limma R-packages) normalization between arrays was performed.

molecule: polyA RNA

organism: Eucalyptus grandis

source_name: Juvenile

label_protocol: Agilent labeling kit

extract_protocol: RNA extraction was carried out as previously described (Southerton et al. 1998), with some modifications. Three gr of tissue were ground in liquid nitrogen to a fine powder using a mortar and pestle, and then 10 ml of extraction buffer pre-heated to 65°C were added, and the tubes were shaken thoroughly and incubated for 5 min at 65°C. The extraction buffer contained 2% cetyl-trimethyl-ammonium bromide (CTAB), 2% polyvinyl pyrrolidone (PVP) 40, 100 mM Tris-HCl, pH 8.0, 25 mM EDTA, 2 M NaCl, 0.5 g/l spermidine, and 2% beta-mercaptoethanol. All reagents were freshly prepared. Two steps of chloroform extraction were employed, followed by centrifugation at 10,000g for 15 min after each step. The upper phase was mixed with 0.25 volume of 10 M LiCl, and the RNA was precipitated overnight at 4°C. Following centrifugation at 10,000g for 20 min, the RNA pellet was dissolved in 500 ul of SSTE buffer, and then extracted with an equal volume of chloroform.  The SSTE buffer contained 0.5% SDS, 1 M NaCl, 10 mM Tris-HCl, pH 8.0, and 1 mM EDTA. The RNA was then precipitated by the addition of 2 volumes of ethanol, placed at -70°C for 1 h, and then pelleted by centrifugation at 10,000g in a microcentrifuge at 4°C. The pellet was dried and then dissolved in RNAse free water. The RNA sample was further purified by using Qiagen RNeasy mini kit and DNAse treatment using RNAse free DNAse1 from Qiagen

value: cuttings

source_name: Mature


title: patient 11, cancer, LCM (copy number analysis)

value: metastasis


title: Patient 150, cancer, LCM [NUCKS1 study]


title: patient 117, cancer, LCM (copy number analysis)


title: patient 115, cancer, LCM (copy number analysis)


title: GBM_11-021

description:
dkfz_11-021
Methylation data from a glioblastoma tumor sample.

value: male

value: IDH


title: Patient 148, cancer, LCM [NUCKS1 study]


title: Juvenile replicate 1 vs Mature replicate 1 (dye swap)


title: GBM_11-028

description:
dkfz_11-028
Methylation data from a glioblastoma tumor sample.


title: GBM_11-022

description:
dkfz_11-022
Methylation data from a glioblastoma tumor sample.

value: RTK II 'classic'


title: GBM_11-019

description:
dkfz_11-019
Methylation data from a glioblastoma tumor sample.

value: DIPG


title: Mature replicate 2 vs Juvenile replicate 2


title: Patient 146, cancer, LCM [NUCKS1 study]


title: Patient 149, cancer, LCM [NUCKS1 study]


title: patient 119, cancer, LCM (copy number analysis)


title: Patient 147, cancer, LCM [NUCKS1 study]


title: Patient 145, cancer, LCM [NUCKS1 study]


title: GBM_11-018

description:
dkfz_11-018
Methylation data from a glioblastoma tumor sample.


title: patient 118, cancer, LCM (copy number analysis)


title: Patient 144, cancer, LCM [NUCKS1 study]


title: patient 116, cancer, LCM (copy number analysis)


title: V720_PD0332991_rep2

city: Boston

first: Takaomi

last: Sanda

address: 450 Brookline Ave

country: USA

institute: Dana-Farber Cancer Institute

hyb_protocol: Standard Affymetrix 3' array hybridyzation protocol.

scan_protocol: Standard Affymetrix confocal laser scanner protocol.

data_processing: The data was normalized and analyzed by dChip software.

organism: Mus musculus

source_name: Breast cancer V720 cells

label_protocol: Standard Affymetrix biotin label protocol.

growth_protocol: V720 cells were cultured in DMEM medium supplemented with 10% fetal calf serum (Hyclone) and Pen/Strep (100U/ml, Invitrogen).

extract_protocol: Total RNA was harvested by Trizol followed by a column purification using RNeasy Mini kit (Qiagen) following manufacturer's instruction.

treatment_protocol: V720 cells were treated with vehicle (VO) or 1 microM PD 0332991 (PD) for 24 hrs.

value: Mammary epithelium

tag: agent

value: CDK4/6 inhibitor PD 0332991


title: V720_PD0332991_rep3


title: V720_PD0332991_rep1


title: Patient 142, cancer, LCM [NUCKS1 study]


title: Patient 141, cancer, LCM [NUCKS1 study]


title: Patient 143, cancer, LCM [NUCKS1 study]


title: GBM_11-020

description:
dkfz_11-020
Methylation data from a glioblastoma tumor sample.

value: primary glioblastoma

value: frontal lobe, praecentral


title: patient 109, cancer, LCM (copy number analysis)

value: cancer, LCM


title: V720_vehicle_rep2

value: vehicle


title: GBM_11-016

description:
dkfz_11-016
Methylation data from a glioblastoma tumor sample.

value: parietal lobe

value: RTK I 'PDGFRA'


title: V720_vehicle_rep3


title: patient 111, cancer, LCM (copy number analysis)


title: patient 88, cancer, LCM (copy number analysis)

value: metastatic recurrence


title: patient 113, cancer, LCM (copy number analysis)


title: GBM_11-013

description:
dkfz_11-013
Methylation data from a glioblastoma tumor sample.

value: ventricular

value: female

value: WT


title: Patient 140, cancer, LCM [NUCKS1 study]

description: Gene expression profile of surgically resected material


title: patient 106, cancer, LCM (copy number analysis)


title: GBM_11-015

description:
dkfz_11-015
Methylation data from a glioblastoma tumor sample.

value: frontal lobe


title: Patient 139, cancer, LCM [NUCKS1 study]


title: BreastTumor_FishOilTamoxifen_rep3

city: Barretos

first: Lucas

middle: Tadeu

last: Bidinotto

state: SP

address: Antenor Duarte Vilela, 1331

country: Brazil

institute: Barretos Cancer Hospital

description: Gene expression array of cribriform tumors after 8 weeks of treatment

hyb_protocol: 1.65 ug of labeled cRNA was hybridized to microarray slides (Whole rat genome-4X44K oligo microarrays-G4112F, Agilent Technologies) at 65°C for 17 hours. Slides were then washed and scanned following Agilent’s recommendations.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, extended dynamic range, Dye channel is set to Green, Green PMT Hi 100% and Green PMT lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software v9.5.3.1 using the default protocol (GE1-v5_95_Feb07 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: Cribriform mammary tumor, Fish oil and tamoxifen treated rats, replicate 3

label_protocol: 200 ng of total RNA from three cribriform tumors per group were processed for microarray hybridization using Quick Amp Labeling Kit-one color (Agilent Technologies, Palo Alto, CA) following the manufacturer’s protocol, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from cribriform tumors using RNeasy Mini Kit (Qiagen Inc., Valencia, CA) following manufacture’s protocol. After DNase I treatment, RNA concentration was measured using NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). RNA quality was assessed using capillary electrophoresis using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: Sex

value: Female

value: Cribriform tumor

tag: age

value: 11 weeks

tag: strain

value: Sprague-Dawley


title: GBM_11-017

description:
dkfz_11-017
Methylation data from a glioblastoma tumor sample.

value: temporal lobe

value: male


title: BreastTumor_FishOilTamoxifen_rep2

source_name: Cribriform mammary tumor, Fish oil and tamoxifen treated rats, replicate 2


title: GBM_11-011

description:
dkfz_11-011
Methylation data from a glioblastoma tumor sample.

value: primary glioblastoma


title: GBM_11-012

description:
dkfz_11-012
Methylation data from a glioblastoma tumor sample.


title: patient 103, cancer, LCM (copy number analysis)

tag: metastasis

tag: Stage


title: patient 104, cancer, LCM (copy number analysis)

value: metastasis

tag: tissue


title: BreastTumor_FishOilTamoxifen_rep1

source_name: Cribriform mammary tumor, Fish oil and tamoxifen treated rats, replicate 1


title: GBM_11-008

description:
dkfz_11-008
Methylation data from a glioblastoma tumor sample.

tag: brain location

value: thalamic

tag: age at diagnosis (years)


title: Patient 136, cancer, LCM [NUCKS1 study]

value: cancer, LCM


title: V720_vehicle_rep1

value: Mammary epithelium

value: vehicle


title: patient 102, cancer, LCM (copy number analysis)


title: GBM_11-009

description:
dkfz_11-009
Methylation data from a glioblastoma tumor sample.

tag: gender

tag: h3f3a status

value: MUT

value: IDH


title: Patient 134, cancer, LCM [NUCKS1 study]


title: Patient 135, cancer, LCM [NUCKS1 study]


title: Patient 138, cancer, LCM [NUCKS1 study]


title: BreastTumor_FishOil_rep3

source_name: Cribriform mammary tumor, Fish oil treated rats, replicate 3


title: patient 101, cancer, LCM (copy number analysis)


title: patient 100, cancer, LCM (copy number analysis)


title: GBM_11-010

description:
dkfz_11-010
Methylation data from a glioblastoma tumor sample.

tag: idh1 status

tag: dna methylation subgroup

value: mesenchymal


title: Mature replicate 1 vs Juvenile replicate 1

value: cuttings


title: GBM_11-006

description:
dkfz_11-006
Methylation data from a glioblastoma tumor sample.

value: WT


title: BreastTumor_CornOilTamoxifen_rep3

source_name: Cribriform mammary tumor, Corn oil and tamoxifen treated rats, replicate 3

value: Female


title: Patient 129, cancer, LCM [NUCKS1 study]


title: BreastTumor_FishOil_rep2

source_name: Cribriform mammary tumor, Fish oil treated rats, replicate 2

value: Cribriform tumor


title: Non-phagocytic population replicate 3

city: Burlington

first: Adam

last: Sateriale

state: VT

address: 320 Stafford Hall

department: Medicine

institute: University of Vermont

description: Non-phagocytic population replicate 3

hyb_protocol: GeneChip Hybridization Oven 640. 45°C for 16hrs rotating at 60rpm.

scan_protocol: Image acquired uding manufacturer's protocols; 7G Affymetrix GeneChip Scanner and GCOS software.

data_processing: R using Bioconductor and with LIMMA and AFFY packages.

organism: Entamoeba histolytica

source_name: Total RNA

label_protocol: Biotinylation

growth_protocol: Glass culture tubes using TYI-S-33 growth medium and harvested mid-log phase.

extract_protocol: Trizol (Qiagen)

treatment_protocol: M280 Streptavidin Dynabeads (Invitrogen) were labeled with 20ug/mL biotinylated Human C1q (Quidel). Entamoeba histolytica (strain HM1) were washed twice with PBS then resuspended with the labeled beads at a 10:1 ratio of beads to trophozoites. Samples were  incubated at 37°C for 45 minutes, washed twice with agitation to remove adherent beads, then resuspended in MACS buffer. Samples were loaded into magnetic columns (Miltenyi Biotec) and trophozoites were seperated according to manufacturer's protocols.

tag: phenotype

value: Non-phagocytic


title: Subject D3, P cells

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

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 arbitrarily set to 100.

source_name: Bone marrow

label_protocol: Standard Affymetrix protocol.

extract_protocol: Total RNA was isolated from FACS sorted (described in accompanying PMID 16741228) bone marrow cells from DBA patients and control individuals using an RNA isolation kit (Qiagen) according to the manufacturer's instructions. The mRNA fractions were reverse transcribed into cDNA and amplified by One-step reverse transcription-polymerase chain reaction (RT-PCR) kit (Qiagen) using primers that flanked the beginning and the end of the coding region.

tag: subject id

value: Male

value: 42 year old

tag: cell type

value: multipotential P, CD34+, CD71−, CD45RA−

tag: disease status

value: Diamond Blackfan anemia


title: BreastTumor_CornOilTamoxifen_rep1

source_name: Cribriform mammary tumor, Corn oil and tamoxifen treated rats, replicate 1

value: 11 weeks

value: Sprague-Dawley


title: Patient 12, cancer, LCM [NUCKS1 study]

source_name: surgically resected material

value: cancer, LCM


title: Patient 133, cancer, LCM [NUCKS1 study]


title: BreastTumor_CornOilTamoxifen_rep2

source_name: Cribriform mammary tumor, Corn oil and tamoxifen treated rats, replicate 2


title: Phagocytic population replicate 1

description: Phagocytic population replicate 1

value: Phagocytic


title: BreastTumor_FishOil_rep1

source_name: Cribriform mammary tumor, Fish oil treated rats, replicate 1


title: Patient 130, cancer, LCM [NUCKS1 study]


title: Phagocytic population replicate 3

description: Phagocytic population replicate 3


title: Subject D3, E cells

value: erythroid E, CD34+, CD71 hi, CD45RA−


title: Subject D2, P cells

value: 30 year old


title: Subject D3, M cells

value: myeloid M, CD34+, CD71 low, CD45RA+


title: BreastTumor_CornOil_rep3

source_name: Cribriform mammary tumor, Corn oil treated rats, replicate 3


title: Patient 131, cancer, LCM [NUCKS1 study]

value: metastasis


title: Patient 128, cancer, LCM [NUCKS1 study]


title: GBM_11-007

description:
dkfz_11-007
Methylation data from a glioblastoma tumor sample.

source_name: Primary brain tumor tissue

value: primary glioblastoma

value: male

value: mesenchymal

tag: id (schwartzentruber et al. (pmid 22286061))


title: patient 08, cancer, LCM (copy number analysis)


title: Phagocytic population replicate 2

description: Phagocytic population replicate 2


title: patient 06, cancer, LCM (copy number analysis)

value: metastatic recurrence


title: GBM_11-003

description:
dkfz_11-003
Methylation data from a glioblastoma tumor sample.

value: fronto-temporal

value: WT

value: MUT

value: IDH


title: Human Bone_4 [Agilent]

description: Two normal bone samples from different donors were purchased from Capital Biosciences (Gaithersburg, MD, USA).

hyb_protocol: Cy3 labelled RNA was resuspended in 18 ul nuclease-free water, 4.5 ul 10x GE Blocking Agent and 22.5 ul 2x Hi-RPM Hybridization Buffer following the manufacturer’s instructions. The samples were hybridized to Agilent Human miRNA Microarrays (version 2, G4470B) for 20 hours at 55˚C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minutes at room temperature with GE Wash Buffer 1(Agilent) and 5 minutes with 37˚C Wash Buffer 2 (Agilent), and finally in acetonitrile 1 minute at room temperature (no stabilization and drying solution should be used). Protocol: miRNA Microarray System with miRNA Complete Labeling and Hyb Kit Version 2.0 (Agilent, USA). P/N G4170-90011.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B). Scan Area 61x21.6 mm, Scan resolution 5um, single pass. Dye channel is set to Green and with XDR Hi 100% and XDR Lo 5%.

data_processing: The images were preprocessed using the Feature Extraction software package v9.5.1 (Agilent Technology) using default parameters (protocol miRNA-v1_95_May07 and Grid 019118_D_20080214). The data files were imported to Agilent GeneSpring GX10 for preprosessing and further statistical analysis. The intensity values were log2 transformed and quantile normalized.

source_name: Normal Bone

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 100 ng total RNA using the miRNA Microarray System with miRNA Complete Labeling and Hyb Kit Version 2.0 (Agilent, USA) (P/N G4170-90011) according to the manufacturer's instructions

extract_protocol: Total RNA, including small RNAs, from cell lines and bones was extracted using the Qiagen miRNeasy Mini kit (Qiagen, California, USA) according to the manufacturer's protocol. RNA purity and quantity was measured on a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, Delaware, USA), and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA).

value: Normal bone


title: Human Bone_3 [Agilent]


title: GBM_11-014

description:
dkfz_11-014
Methylation data from a glioblastoma tumor sample.

value: frontal lobe

value: female

value: RTK I 'PDGFRA'


title: BreastTumor_CornOil_rep2

source_name: Cribriform mammary tumor, Corn oil treated rats, replicate 2

tag: Sex

value: Female

value: Cribriform tumor

value: 11 weeks

value: Sprague-Dawley


title: GBM_11-002

description:
dkfz_11-002
Methylation data from a glioblastoma tumor sample.

value: cerebellar


title: Human Bone_2 [Agilent]

description: Two long bone samples were obtained from amputations of patients without osteosarcoma at the Norwegian Radium Hospital


title: Human Bone_1 [Agilent]


title: GBM_11-005

description:
dkfz_11-005
Methylation data from a glioblastoma tumor sample.

value: primary glioblastoma

value: thalamic


title: OS cell line_19 [Agilent]

description: The cell lines were maintained in RPMI 1640 (Invitrogen, Carsbad, CA, USA) supplemented with 10% fetal calf serum, 2 mM L-glutamine (Invitrogen) and 1% Penicillin/Streptomycin (Invitrogen) under standard conditions.

source_name: Osteosarcoma cell line

tag: cell line


title: Non-phagocytic population replicate 1

description: Non-phagocytic population replicate 1

value: Non-phagocytic

tag: strain


title: GBM_11-004

description:
dkfz_11-004
Methylation data from a glioblastoma tumor sample.

value: mesenchymal


title: Patient 127, cancer, LCM [NUCKS1 study]

description: Gene expression profile of surgically resected material

tag: metastasis

value: cancer, LCM


title: BreastTumor_CornOil_rep1

description: Gene expression array of cribriform tumors after 8 weeks of treatment

source_name: Cribriform mammary tumor, Corn oil treated rats, replicate 1

tag: age


title: Patient 121, cancer, LCM [NUCKS1 study]

value: metastasis

tag: Stage

tag: tissue


title: Subject D2, E cells

value: Male

value: 30 year old

value: erythroid E, CD34+, CD71 hi, CD45RA−

value: Diamond Blackfan anemia


title: Non-phagocytic population replicate 2

description: Non-phagocytic population replicate 2


title: Subject C6, M cells

value: between 25  and 40 years old

value: myeloid M, CD34+, CD71 low, CD45RA+

value: Control


title: Patient 123, cancer, LCM [NUCKS1 study]


title: Subject D1, P cells

value: Female

value: 46 year old

value: multipotential P, CD34+, CD71−, CD45RA−


title: Subject D1, M cells


title: Subject D1, E cells


title: OS cell line_18 [Agilent]

value: U-2 OS


title: Patient 124, cancer, LCM [NUCKS1 study]


title: OS cell line_17 [Agilent]


title: Patient 11, cancer, LCM [NUCKS1 study]


title: OS cell line_16 [Agilent]

value: OSA


title: Patient 119, cancer, LCM [NUCKS1 study]


title: OS cell line_15 [Agilent]

value: OHS


title: Subject C6, E cells


title: OS cell line_14 [Agilent]

value: MNNG-HOS


title: Subject C5, M cells


title: OS cell line_13 [Agilent]

value: MHM


title: Subject C5, P cells


title: Subject C5, E cells


title: OS cell line_12 [Agilent]


title: splenic RNA from mice infected with YopM-deficient strain (M') after 16hr, Replicate 3

city: Chapel Hill

first: June

last: Brickey

state: NC

address: 450 West Drive

institute: UNC

description: Biological replicate 3 of 3. Splenic cells fromYopM mutant-infected mice at 16hr

hyb_protocol: Cy-labeled experimental (Red, Cy5) and Universal reference (Cy3, Green) probes were combined in hybridization buffer (40% formamide in SSC, poly(dA) oligo, COT-1 DNA), heated, and samples were applied to microarrays enclosed by Maui Mixer (SC, BioMicroSystems). After 18 hour hybridization at 42C with constant mixing, slides were washed briefly in SSC-SDS buffers.

scan_protocol: Scanned on a GenePix 4000B scanner (Molecular Dynamics). Images were quantified using GenePix Pro Software (version 6.0).

data_processing: Global normalization based on Lowess curve fitting; R Bioconductor analysis using a non-parametric permutation test (1000 permutations with FDR of 0.1) to identify statistically differentially expressed genes

label_protocol: 100 ng of total RNA were amplified and labeled using Oligo dT primer, SuperScriptIII reverse transcriptase, and aminoallyl-UTP using TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit 101 according to manufacturer's instructions (Epicentre). Amplified aa-RNA probes were coupled to Cy5 or Cy3 dyes (GE HealthCare) and RNeasy column purified (Qiagen).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions (Invitrogen) and cleaned over the RNEasy column (Qiagen).

treatment_protocol: 16hr with YopM-deficient strain

tag: infection

value: YopM-deficient strain (M')

tag: post-infection time

value: splenic cells

source_name: Universal Mouse Reference RNA

tag: sample type

value: reference -Stratagene (#740100)

value: Cell lines (11):embryo, fibroblast,kidney, hepatocyte, lung macrophage, B and T lymphocytes, mammary gland, myoblast, skin, testis


title: Subject C6, P cells


title: Subject C4, M cells


title: Patient 117, cancer, LCM [NUCKS1 study]

value: metastatic recurrence

value: cancer, LCM


title: Patient 118, cancer, LCM [NUCKS1 study]

value: metastasis


title: Patient 116, cancer, LCM [NUCKS1 study]


title: Patient 115, cancer, LCM [NUCKS1 study]


title: OS cell line_11 [Agilent]

value: KPD


title: Patient 125, cancer, LCM [NUCKS1 study]


title: Subject C4, E cells

value: between 25  and 40 years old

value: erythroid E, CD34+, CD71 hi, CD45RA−

value: Control


title: Subject C3, P cells

value: Female

value: multipotential P, CD34+, CD71−, CD45RA−


title: Subject C4, P cells


title: GBM_11-001

description:
dkfz_11-001
Methylation data from a glioblastoma tumor sample.

value: primary glioblastoma

tag: brain location

value: temporal lobe

tag: age at diagnosis (years)

tag: gender

value: male

tag: h3f3a status

tag: idh1 status

value: WT


title: Patient 113, cancer, LCM [NUCKS1 study]


title: OS cell line_10 [Agilent]

value: IOR-SARG


title: OS cell line_9 [Agilent]


title: Patient 110, cancer, LCM [NUCKS1 study]


title: splenic RNA from mice infected with YopM-deficient strain (M') after 16hr, Replicate 2

description: Biological replicate 2 of 3. Splenic cells from YopM mutant-infected mice at 16hr

value: YopM-deficient strain (M')

tag: cell type

value: splenic cells


title: Patient 109, cancer, LCM [NUCKS1 study]


title: OS cell line_8 [Agilent]


title: Patient 111, cancer, LCM [NUCKS1 study]


title: OS cell line_7 [Agilent]


title: Subject C2, P cells

tag: subject id

value: Male

tag: disease status


title: splenic RNA from mice infected with YopM-deficient strain (M') after 1hr, Replicate 3

description: Biological replicate 3 of 3. Splenic cells from YopM mutant-infected mice at 1hr

treatment_protocol: 1hr with YopM-deficient strain

value: reference -Stratagene (#740100)

value: Cell lines (11):embryo, fibroblast,kidney, hepatocyte, lung macrophage, B and T lymphocytes, mammary gland, myoblast, skin, testis


title: splenic RNA from mice infected with YopM-deficient strain (M') after 16hr, Replicate 1

description: Biological replicate 1 of 3. Splenic cells from YopM mutant-infected mice at 16hr


title: splenic RNA from mice infected with YopM-deficient strain (M') after 1hr, Replicate 2

description: Biological replicate 2 of 3. Splenic cells from YopM mutant-infected mice at 1hr


title: OS cell line_6 [Agilent]

tag: cell line


title: splenic RNA from mice infected with YopM-deficient strain (M') after 1hr, Replicate 1

description: Biological replicate 1 of 3. Splenic cells from YopM mutant-infected mice at 1hr

tag: strain


title: Subject C3, E cells

tag: Sex


title: Patient 107, cancer, LCM [NUCKS1 study]

tag: metastasis

value: cancer, LCM


title: Patient 108, cancer, LCM [NUCKS1 study]

tag: Stage


title: Subject C2, M cells

tag: age

value: myeloid M, CD34+, CD71 low, CD45RA+


title: Subject C3, M cells

value: between 25  and 40 years old


title: OS cell line_5 [Agilent]


title: Subject C1, P cells


title: OS cell line_4 [Agilent]

value: IOR-MOS


title: splenic RNA from mice infected with YopM-competent strain (D27) after 16hr, Replicate 2

description: Biological replicate 2 of 3. Splenic cells from D27-infected mice at 16hr

treatment_protocol: 16hr with parental strain

tag: infection

value: YopM-competent strain (D27)

tag: tissue


title: Patient 104, cancer, LCM [NUCKS1 study]

value: metastasis


title: splenic RNA from mice infected with YopM-competent strain (D27) after 16hr, Replicate 1

description: Biological replicate 1 of 3. Splenic cells from D27-infected mice at 16hr

tag: post-infection time

tag: sample type


title: OS cell line_3 [Agilent]

value: HOS


title: splenic RNA from mice infected with YopM-competent strain (D27) after 1hr, Replicate 3

description: Biological replicate 3 of 3. Splenic cells from D27-infected mice at 1hr

treatment_protocol: 1hr with parental strain


title: Patient 106, cancer, LCM [NUCKS1 study]

value: metastatic recurrence


title: OS cell line_2 [Agilent]

value: HAL


title: splenic RNA from mice infected with YopM-competent strain (D27) after 1hr, Replicate 2

description: Biological replicate 2 of 3. Splenic cells from D27-infected mice at 1hr


title: Subject C1, M cells

value: Female

value: Control


title: splenic RNA from mice infected with YopM-competent strain (D27) after 16hr, Replicate 3

description: Biological replicate 3 of 3. Splenic cells from D27-infected mice at 16hr


title: Subject C2, E cells

value: erythroid E, CD34+, CD71 hi, CD45RA−


title: OS cell line_1 [Agilent]


title: Patient 101, cancer, LCM [NUCKS1 study]


title: Subject C1, E cells


title: Subject D2, M cells

value: 30 year old

value: Diamond Blackfan anemia


title: Patient 100, cancer, LCM [NUCKS1 study]


title: HUVEC_Ezh2- vs. control-siRNA_replicate 3

city: Berlin

first: Henryk

last: Dreger

address: Charitéplatz 1

department: Cardiology and Angiology

institute: Charité - Universitätsmedizin Berlin

description: Gene expression log ratio in HUVEC transfected with siRNA directed against Ezh2 and control siRNA, respectively. Replicate 3.

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 825 ng of the corresponding Cy3- and Cy5-labeled fragmented cRNA were combined and hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% Nlauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated 0.06x SSPE

scan_protocol: Fluorescence signals of the hybridized Agilent Oligo Microarrays were detected using Agilent’s DNA microarray scanner (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolverâ gene expression data analysis system (Rosetta Biosoftware). Log 2 ratios were calculated using Microsoft Excel 2010.

label: Cy3 (Intensity1)

source_name: HUVEC - control

label_protocol: RNA samples were amplified and labeled using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: HUVEC were isolated by collagenase type II (Biochrom KG, Berlin, Germany) digestion of human umbilical veins and cultured at 37°C with 5% CO2 in EC medium (MCDB 131, Gibco BRL, Life Technologies GmbH, Karlsruhe, Germany) with the following supplements: 20 μg/mL Endothelial Cell Growth Supplement (PromoCell, Heidelberg, Germany), 1 ng/mL fibroblast growth factor (Biomol, Hamburg, Germany), 0.1 ng/mL endothelial growth factor (Biomol), 2% fetal calf serum (Biochrom), 2 mmol/L L-glutamine (Gibco), 1 μg/mL hydrocortisone (Sigma-Aldrich, Hamburg, Germany), 1 IU/mL heparin (Biochrom), 5 IU/mL penicillin and 5 μg/mL streptomycin (Biochrom).

extract_protocol: 72 hours after transfection, mRNA was extracted using Trizol according to the manufacturer's recommendations.

treatment_protocol: HUVEC were transfected with 25 nmol/L of control small interfering RNA (siRNA) (Silencer Select Negative Control Ambion, Austin, TX) or siRNA directed against Ezh2 (s4918; Ambion) using Oligofectamine (Invitrogen).

value: human umbilical vein endothelial cells (HUVEC)

tag: genotype/variation

value: control siRNA

label: Cy5 (Intensity2)

source_name: HUVEC - Ezh2 knock down

value: Ezh2 siRNA


title: Patient 102, cancer, LCM [NUCKS1 study]

value: cancer, LCM


title: HUVEC_Ezh2- vs. control-siRNA_replicate 2

description: Gene expression log ratio in HUVEC transfected with siRNA directed against Ezh2 and control siRNA, respectively. Replicate 2.


title: HUVEC_Ezh2- vs. control-siRNA_replicate 1

description: Gene expression log ratio in HUVEC transfected with siRNA directed against Ezh2 and control siRNA, respectively. Replicate 1.


title: Patient 08, cancer, LCM [NUCKS1 study]

description: Gene expression profile of surgically resected material


title: Patient 06, cancer, LCM [NUCKS1 study]


title: PE-0069-del

status: Public on Oct 15 2012

city: Rochester

first: Zhifu

last: Sun

state: MN

address: 200 1st ST SW

department: HSR-BSI

institute: Mayo Clinic

description:
Bisulfite-modified DNA.
VG0069P002

ArrayID: 1009701107

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27 Beadchips using the standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner settings.

data_processing: Illumina GenomeStudio (version 2010.2) was used to process the raw data. Average Beta and detection p-values from GenomeStudio are without normalization. Technical replicates were averaged. CpGs detected in less than 95% of samples were excluded.

label: Cy3 and Cy5

source_name: maternal leukocytes, delivery

label_protocol: Bisulfite modification was performed using the EZ DNA Methylation Kit (Zymo Research, Orange, CA).

extract_protocol: Genomic DNA was extracted using the QIAgen Flexigene Reagent kit and AutoGenFlex DNA purification kit from the frozen buffy coats, which were collected in a 10 ml EDTA tube, quantified with a NanoDrop spectrophotometer, normalized with standard PicoGreen methodology, and plated in 1000 ng aliquots.

value: maternal leukocytes

tag: pregnancy status

value: delivery


title: PE-0066-del

description:
Bisulfite-modified DNA.
VG0066P002

ArrayID: 1009701106


title: splenic RNA from mice infected with YopM-competent strain (D27) after 1hr, Replicate 1

description: Biological replicate 1 of 3. Splenic cells from D27-infected mice at 1hr

value: splenic cells

value: reference -Stratagene (#740100)

value: Cell lines (11):embryo, fibroblast,kidney, hepatocyte, lung macrophage, B and T lymphocytes, mammary gland, myoblast, skin, testis


title: PE-0034-del

description:
Bisulfite-modified DNA.
VG0034P002

ArrayID: 1009701101


title: PE-0073-del

description:
Bisulfite-modified DNA.
VG0073P002

ArrayID: 1009701108


title: PE-0060-del

description:
Bisulfite-modified DNA.
VG0060P002

ArrayID: 1009701103


title: PE-0046-del

description:
Bisulfite-modified DNA.
VG0046P002

ArrayID: 1009701102


title: PE-0012-del

description:
Bisulfite-modified DNA.
VG0012P002

ArrayID: 1010904563


title: PE-0028-del

description:
Bisulfite-modified DNA.
VG0028P002

ArrayID: 1009701100
This Sample represents 2 technical replicates.


title: PE-0001-del

description:
Bisulfite-modified DNA.
VG0001P002

ArrayID: 1009701096


title: NL-0215-pp

description:
Bisulfite-modified DNA.
LP0215P008

ArrayID: 1009701095

source_name: maternal leukocytes, postpartum

value: postpartum

tag: individual identifier


title: NL-0215-early

description:
Bisulfite-modified DNA.
LP0215P002

ArrayID: 1009701092

source_name: maternal leukocytes, early

value: early


title: PE-0007-del

description:
Bisulfite-modified DNA.
VG0007P002

ArrayID: 1009701097


title: NL-0215-mid

description:
Bisulfite-modified DNA.
LP0215P004

ArrayID: 1009701093

source_name: maternal leukocytes, middle

value: middle


title: PE-0064-del

description:
Bisulfite-modified DNA.
VG0064P002

ArrayID: 1009701104


title: NL-0158-early

description:
Bisulfite-modified DNA.
LP0158P002

ArrayID: 1009701088
This Sample represents 2 technical replicates.


title: NL-0158-mid

description:
Bisulfite-modified DNA.
LP0158P004

ArrayID: 1009701089


title: PE-0065-del

description:
Bisulfite-modified DNA.
VG0065P002

ArrayID: 1009701105


title: NL-0158-pp

description:
Bisulfite-modified DNA.
LP0158P008

ArrayID: 1009701091


title: PE-0074-del

description:
Bisulfite-modified DNA.
VG0074P002

ArrayID: 1010904564


title: NL-0128-del

description:
Bisulfite-modified DNA.
LP0128P006

ArrayID: 1010904562
This Sample represents 2 technical replicates.


title: NL-0152-del

description:
Bisulfite-modified DNA.
LP0152P006

ArrayID: 1009701086


title: NL-0152-early

description:
Bisulfite-modified DNA.
LP0152P002

ArrayID: 1009701084


title: NL-0215-del

description:
Bisulfite-modified DNA.
LP0215P006

ArrayID: 1009701094


title: PE-0008-del

description:
Bisulfite-modified DNA.
VG0008P002

ArrayID: 1009701098


title: NL-0152-mid

description:
Bisulfite-modified DNA.
LP0152P004

ArrayID: 1009701085
This Sample represents 2 technical replicates.


title: NL-0128-pp

description:
Bisulfite-modified DNA.
LP0128P008

ArrayID: 1009701083


title: NL-0158-del

description:
Bisulfite-modified DNA.
LP0158P006

ArrayID: 1009701090
This Sample represents 2 technical replicates.


title: NL-0122-del

description:
Bisulfite-modified DNA.
LP0122P006

ArrayID: 1009701078


title: NL-0128-early

description:
Bisulfite-modified DNA.
LP0128P002

ArrayID: 1009701080
This Sample represents 2 technical replicates.


title: NL-0122-pp

description:
Bisulfite-modified DNA.
LP0122P008

ArrayID: 1009701079


title: Patient 103, cancer, LCM [NUCKS1 study]

description: Gene expression profile of surgically resected material


title: NL-0080-pp

description:
Bisulfite-modified DNA.
LP0080P008

ArrayID: 1009701071


title: NL-0105-pp

description:
Bisulfite-modified DNA.
LP0105P008

ArrayID: 1009701075
This Sample represents 2 technical replicates.


title: NL-0152-pp

description:
Bisulfite-modified DNA.
LP0152P008

ArrayID: 1009701087


title: NL-0070-pp

description:
Bisulfite-modified DNA.
LP0070P008

ArrayID: 1009701067


title: NL-0122-early

description:
Bisulfite-modified DNA.
LP0122P002

ArrayID: 1009701076


title: NL-0122-mid

description:
Bisulfite-modified DNA.
LP0122P004

ArrayID: 1009701077


title: NL-0128-mid

description:
Bisulfite-modified DNA.
LP0128P004

ArrayID: 1009701081


title: NL-0045-pp

description:
Bisulfite-modified DNA.
LP0045P008

ArrayID: 1009701063


title: NL-0070-mid

description:
Bisulfite-modified DNA.
LP0070P004

ArrayID: 1009701065


title: NL-0045-del

description:
Bisulfite-modified DNA.
LP0045P006

ArrayID: 1009701062


title: NL-0070-early

description:
Bisulfite-modified DNA.
LP0070P002

ArrayID: 1010904560


title: NL-0070-del

description:
Bisulfite-modified DNA.
LP0070P006

ArrayID: 1009701066


title: NL-0105-del

description:
Bisulfite-modified DNA.
LP0105P006

ArrayID: 1010904561


title: NL-0080-early

description:
Bisulfite-modified DNA.
LP0080P002

ArrayID: 1009701068


title: NL-0080-del

description:
Bisulfite-modified DNA.
LP0080P006

ArrayID: 1009701070


title: NL-0105-early

description:
Bisulfite-modified DNA.
LP0105P002

ArrayID: 1009701072


title: NL-0105-mid

description:
Bisulfite-modified DNA.
LP0105P004

ArrayID: 1009701073


title: NL-0045-early

description:
Bisulfite-modified DNA.
LP0045P002

ArrayID: 1009701060


title: NL-0045-mid

description:
Bisulfite-modified DNA.
LP0045P004

ArrayID: 1009701061


title: NL-0043-pp

description:
Bisulfite-modified DNA.
LP0043P008

ArrayID: 1009701059


title: NL-0043-del

description:
Bisulfite-modified DNA.
LP0043P006

ArrayID: 1009701058


title: NL-0031-mid

description:
Bisulfite-modified DNA.
LP0031P004

ArrayID: 1009701053


title: NL-0043-early

description:
Bisulfite-modified DNA.
LP0043P002

ArrayID: 1009701056


title: NL-0043-mid

description:
Bisulfite-modified DNA.
LP0043P004

ArrayID: 1009701057


title: NL-0030-early

description:
Bisulfite-modified DNA.
LP0030P002

ArrayID: 1009701048


title: NL-0031-del

description:
Bisulfite-modified DNA.
LP0031P006

ArrayID: 1009701054


title: NL-0031-pp

description:
Bisulfite-modified DNA.
LP0031P008

ArrayID: 1009701055


title: NL-0030-pp

description:
Bisulfite-modified DNA.
LP0030P008

ArrayID: 1009701051


title: NL-0080-mid

description:
Bisulfite-modified DNA.
LP0080P004

ArrayID: 1009701069


title: NL-0031-early

description:
Bisulfite-modified DNA.
LP0031P002

ArrayID: 1009701052


title: NL-0030-mid

description:
Bisulfite-modified DNA.
LP0030P004

ArrayID: 1009701049


title: NL-0028-mid

description:
Bisulfite-modified DNA.
LP0028P004

ArrayID: 1009701045


title: NL-0030-del

description:
Bisulfite-modified DNA.
LP0030P006

ArrayID: 1009701050


title: NL-0008-pp

description:
Bisulfite-modified DNA.
LP0008P008

ArrayID: 1009701043


title: NL-0028-del

description:
Bisulfite-modified DNA.
LP0028P006

ArrayID: 1009701046


title: NL-8-Null

description:
Bisulfite-modified DNA.
Biobank8

ArrayID: 1013101087

source_name: maternal leukocytes, nulligravid

value: nulligravid


title: NL-0008-early

description:
Bisulfite-modified DNA.
LP0008P002

ArrayID: 1009701040


title: NL-3-Null

description:
Bisulfite-modified DNA.
Biobank3

ArrayID: 1013101089


title: NL-7-Null

description:
Bisulfite-modified DNA.
Biobank7

ArrayID: 1013101088


title: NL-0008-mid

description:
Bisulfite-modified DNA.
LP0008P004

ArrayID: 1009701041


title: NL-0028-early

description:
Bisulfite-modified DNA.
LP0028P002

ArrayID: 1009701044


title: NL-4-Null

description:
Bisulfite-modified DNA.
Biobank4

ArrayID: 1013101085


title: NL-6-Null

description:
Bisulfite-modified DNA.
Biobank6

ArrayID: 1013101081


title: NL-0008-del

description:
Bisulfite-modified DNA.
LP0008P006

ArrayID: 1009701042


title: NL-2-Null

description:
Bisulfite-modified DNA.
Biobank2

ArrayID: 1013101080


title: NL-5-Null

description:
Bisulfite-modified DNA.
Biobank5

ArrayID: 1013101082


title: NL-9-Null

description:
Bisulfite-modified DNA.
Biobank9

ArrayID: 1013101090


title: NL-13-Null

description:
Bisulfite-modified DNA.
Biobank13

ArrayID: 1008200833


title: NL-0028-pp

description:
Bisulfite-modified DNA.
LP0028P010

ArrayID: 1009701047


title: PAO1-3

city: Syracuse

first: Christopher

last: Nomura

state: NY

address: 1 Forestry Dr.

department: Chemistry

institute: SUNY-ESF

description: Gene expression from mid-exponential cells grown in rich media

hyb_protocol: Following fragmentation, 5 ug of cDNA were hybridized for 16 hr at 50C 60 rpm on GeneChip P. aeruginosa Genome Array with rotation at 60 rpm. GeneChips were processed with an Affymetrix Fluidics Station 450 using the modified Flex FS450_0002 P. aeruginosa array protocol (as specified in the Affymetrix GeneChip Expression Analysis Technical Manual), using stains from the Affymetrix Hybridization, Wash, and Stain Kit.

scan_protocol: Arrays were scanned with the Affymetrix GeneChip Scanner 7G Plus

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.

organism: Pseudomonas aeruginosa PAO1

source_name: Cells harvested at OD 600 nm of 0.5

label_protocol: Samples were processed according to the Prokaryotic Target Preparation Protocol in Affymetrix GeneChip Expression Analysis Technical Manual.  Briefly, 10 ug of RNA was used to synthesize cDNA via random primers and SuperScript II reverse transcriptase.  cDNA was purified using Qiagen MinElute PCR purification columns.  The resulting cDNA was fragmented and labeled with biotin.

growth_protocol: P. aeruginosa PAO1-UW or PW5126 was grown in 50-mL of peptone broth (per liter: 20 grams peptone derived from gelatin, 10 g K2SO4, and 1.5 MgSO4) at 37 C, 200 rpm, until an OD 600 of 0.5 was reached.

extract_protocol: RNA was isolated using the enzymatic lysis and proteinase K digestion method of Qiagen Rneasy with on-column DNA digestion.

treatment_protocol: At an OD 600 nm of 0.5, 0.5 mL of culture was treated with 1.0 mL of RNAprotect Bacterial reagent (Qiagen).

tag: genotype

value: wild-type PAO1


title: NL-11-Null

description:
Bisulfite-modified DNA.
Biobank11

ArrayID: 1013101086
This Sample represents 2 technical replicates.

tag: cell type


title: PAO1-4


title: PW5126-1

organism: Pseudomonas aeruginosa


title: PW5126-3


title: NL-10-Null

description:
Bisulfite-modified DNA.
Biobank10

ArrayID: 1013101079


title: PW5126-2


title: PW5126-4


title: NL-1-Null

description:
Bisulfite-modified DNA.
Biobank1

ArrayID: 1013101084
This Sample represents 2 technical replicates.


title: NL-14-Null

description:
Bisulfite-modified DNA.
Biobank14

ArrayID: 1006001637


title: PAO1-1


title: NL-12-Null

description:
Bisulfite-modified DNA.
Biobank12

ArrayID: 1013700422


title: PAO1-2


title: Cb016_117_E00029027_No

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

country: United Kingdom

institute: Institute of Cancer Research

description: Gene expression profile for blood from advanced castraction resistant PrCa patient

hyb_protocol: cDNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 Array. Microarrays were washed, stained, and scanned according to standard procedures.

scan_protocol: Standard Affymetrix protocols were used.

data_processing: Expression signal estimates were derived from CEL files using the robust multiarray analysis (RMA) algorithm.

source_name: 2.5ml peripheral venous blood

label_protocol: Fifty nanograms of purified RNA were amplified, fragmented and labelled using the Ovation™ Whole Blood Solution (NuGen Technologies, San Carlos, CA), which preserves globin transcripts.

growth_protocol: Peripheral venous blood was collected in a 5 mL PAXgeneTM tubes (PreAnalytiX)

extract_protocol: Whole blood RNA was isolated and purified using the PAXgeneTM Blood RNA Kit (PreAnalytiX) according to the manufacturer’s instructions

tag: patient

value: Advanced castration resistant

tag: centre

value: Beatson

tag: plate

tag: replicate

value: No


title: Cb016_114_E00019027_Technical

description: Gene expression profile for blood from a good prognosis PrCa patient

value: Good prognosis

value: RMH

value: Technical


title: Cb016_103_E00019040_No


title: Cb016_115_E00019045_No


title: Cb016_104_E00019029_Technical


title: Cb016_102_E00019024_No


title: Cb016_113_E00019016_No


title: Cb016_106_E00019027_No


title: Cb016_116_E00019061_No


title: Cb016_112_E00019027_Biological

value: Biological


title: Cb016_110_E00029029_No


title: Cb016_109_E00029028_No


title: Cb016_111_E00019017_No


title: Cb016_118_E00019008_No


title: Cb016_105_E00029019_Biological


title: Cb016_108_E00029008_No


title: Cb016_107_E00019057_No


title: Cb016_100_E00029020_Technical


title: Cb016_099_E00019037_Technical


title: Cb016_096_E00019067_No


title: Cb016_097_E00019050_No


title: Cb016_098_E00019009_No


title: Cb016_092_E00019063_No


title: Cb016_101_E00019043_No


title: Cb016_090_E00029005_No


title: Cb016_093_E00029020_No


title: Cb016_088_E00019047_No


title: Cb016_087_E00029003_No


title: Cb016_091_E00029031_No


title: Cb016_094_E00019032_No


title: Cb016_095_E00019006_No


title: Cb016_089_E00029020_Biological


title: Cb016_085_E00029011_No


title: Cb016_084_E00019068_No


title: Cb016_080_E00019054_No


title: Cb016_075_E00019011_No


title: Cb016_076_E00019042_No


title: Cb016_073_E00019038_No


title: Cb016_078_E00029012_Biological


title: Cb016_072_E00019023_No


title: Cb016_074_E00029012_No


title: Cb016_082_E00019048_No


title: Cb016_081_E00019020_No


title: Cb016_086_E00029004_No


title: Cb016_077_E00019002_No


title: Cb016_070_E00019007_No


title: Cb016_071_E00029030_No


title: Cb016_069_E00019026_No


title: rss3 0 mM NaCl, replicate 3

city: nagoya

first: yosuke

last: toda

state: aichi-ken

address: furo-cho chikusa-ku

institute: nagoya university

hyb_protocol: Agilent protocol G4140-90050. 825 ng of each Cy-5- and Cy-3-labeled cRNAs were used for hybridization.

scan_protocol: Using Agilent scanner model G2505B.

data_processing: The scanned images were analyzed with Feature Extraction Software v10.5.1.1 (Agilent) to obtain background-subtracted and spatially-detrended Processed Signal intensities. All of the raw Cy-5 and Cy-3 signals (gBGSubSignal and rBGSubSignal, respectively) were normalized by variance stabilization normalization method using R software (http://www.r-project.org/). After normalization, the relative expression levels of genes were calculated by subtracting the Cy-5 values by Cy-3 values (reference). Relative log2 expressions were Z-scaled with R software.

organism: Oryza sativa

source_name: rss3 0 mM NaCl

label_protocol: 400 ng RNAs were labeled by Low RNA input Linear Amplification/Labeling Kit (Agilent).

growth_protocol: Wild type and rss3 seedlings were grown on the MS medium in the absence or prescence of 100 mM NaCl for 3 days.

extract_protocol: RNAs were extracted from 1-mm root tips by RNeasy mini kit (Qiagen).

tag: cultivar

value: Nipponbare

value: rss3 mutant

value: day 3

value: 1 mm long root tip

source_name: WT 0 mM NaCl (reference)

value: Nipponbarre

value: wild type


title: rss3 100 mM NaCl, replicate 3

source_name: rss3 100 mM NaCl


title: WT 100 mM NaCl, replicate 3

source_name: WT 100 mM NaCl


title: Cb016_068_E00019036_No


title: Cb016_065_E00019033_No


title: Cb016_066_E00029010_No


title: Cb016_063_E00029021_No


title: rss3 100 mM NaCl, replicate 2


title: Cb016_067_E00019025_Biological


title: Cb016_061_E00019025_No


title: Cb016_064_E00019070_No


title: Cb016_062_E00029022_No


title: WT 0 mM NaCl, replicate 3

source_name: WT 0 mM NaCl


title: rss3 0 mM NaCl, replicate 2


title: Cb016_057_E00029026_No


title: Cb016_060_E00019015_No


title: Cb016_059_E00029025_No


title: WT 0 mM NaCl, replicate 1


title: rss3 0 mM NaCl, replicate 1


title: WT 0 mM NaCl, replicate 2


title: WT 100 mM NaCl, replicate 2


title: SCI subject 3 after FES exercise training

city: Nijmegen

first: Gerwen

last: Lammers

address: PO Box 9101

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

description: Gene expression after FES exercise training (1 SCI subject)

hyb_protocol: According to the Affymetrix GeneChip whole transcript sense target labelling assay

scan_protocol: According to the Affymetrix GeneChip Expression Wash, Stain and Scan User Manual

data_processing: The Affymetrix CEL files were imported into Genomic Suite software (Version 6.4, Partek, St. Louis, MO, USA). Probe sets were normalised using the Robust Multiarray Analysis (RMA) algorithm including background correction for probe GC content. Transcript summaries were calculated using the mean intensities of the corresponding probe sets, representing the quantitative gene expression levels.

source_name: vastus lateralis muscle, SCI subject, 8 weeks FES exercise training

extract_protocol: Frozen muscle biopsy samples were ground using a mortar and pestle, placed in RNA-Bee, which contains phenol and guanidine thiocyanate (Tel-test, Friendswood, TX, USA), and homogenised using an T25 ultra-turrax dispenser (IKA, Staufen, Germany). RNA was isolated using phenol/chloroform extraction, and purified according to the RNeasy mini kit clean-up protocol including an on-column DNase digestion (Qiagen, Hilden, Germany). The RNA concentration and purity were measured with a Nanodrop spectrophotometer (Thermo Scientific, Waltham, MA, USA) and RNA integrity was analysed on an Agilent Bioanalyser (Santa Clara, CA, USA).

treatment_protocol: Local aneasthesia with 1% (w/v) lidocaine, incision of the skin and fascia, ~100 mg mucle tissue needle biopsy ~15 cm above the knee according to the Bergström technique, immediately frozen in liquid nitrogen and stored at -80°C

tag: subject

value: SCI

tag: intervention

value: FES

tag: timepoint

value: after


title: Cb016_056_E00019029_Biological

tag: Stage


title: Cb016_058_E00019013_No


title: Cb016_083_E00029004_Biological


title: rss3 100 mM NaCl, replicate 1

tag: age

tag: tissue


title: WT 100 mM NaCl, replicate 1


title: Cb016_055_E00029023_No


title: SCI subject 2 after FES exercise training

label_protocol: According to the Affymetrix GeneChip whole transcript sense target labelling assay


title: SCI subject 2 before FES exercise training

description: Gene expression after long-term deconditioning (1 SCI subject)

source_name: vastus lateralis muscle, SCI subject, baseline

value: before


title: SCI subject 1 after FES exercise training


title: Healthy subject 3 after limb suspension

description: Gene expression after local deconditioning (1 subject)

source_name: vastus lateralis muscle, healthy subject, 8 weeks ULLS deconditioning

value: Healthy

value: ULLS


title: SCI subject 1 before FES exercise training


title: Cb016_054_E00029009_No

value: Advanced castration resistant

value: Beatson

value: No


title: Healthy subjects 4, 5, and 6 (pooled RNA) after limb suspension

description: Gene expression after local deconditioning (2 subject)


title: Cb016_049_E00019019_No

value: RMH


title: Cb016_051_E00019029_No

value: Good prognosis


title: Healthy subject 2 before limb suspension

description: Gene expression at baseline (1 subject)

source_name: vastus lateralis muscle, healthy subject, baseline


title: Blood normal, biological rep 2

city: Vancouver

first: Scott

last: Tebbutt

state: BC

address: Room 166, 1081 Burrard Street

country: Canada

institute: University of British Columbia

hyb_protocol: Hybridation was performed according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol.

data_processing: The data were analyzed with Partek Genomics Suite 6.5 using Partek default analysis settings.

source_name: normal

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

growth_protocol: blood were frozen at -80C

extract_protocol: Qiagen RNeasy mini kits were used for total RNA extraction from Paxgene blood tube samples; Trizol extraction of total RNA from EDTA blood tube was performed according to the manufacturer's instructions.

tag: sample type

value: normal

value: blood

tag: disease state

tag: treatment

value: untreated


title: Healthy subject 1 before limb suspension

description: Gene expression at baseline (1 subject)


title: Healthy subjects 4, 5, and 6 (pooled RNA) before limb suspension

description: Gene expression at baseline (1 subject)


title: SCI subject 3 before FES exercise training


title: Cb016_053_E00019069_No


title: Healthy subject 2 after limb suspension


title: Cb016_050_E00019041_No


title: Healthy subject 1 after limb suspension


title: Cb016_046_E00019049_No


title: Cb016_052_E00019062_No


title: Cb016_045_E00019039_No


title: Blood normal, biological rep 4


title: Blood normal, biological rep 1


title: Cb016_034_E00019034_No


title: Cb016_039_E00029015_No


title: Cb016_033_E00019051_No


title: Cb016_048_E00019058_No


title: Cb016_042_E00019022_No


title: Blood normal, biological rep 3


title: Cb016_032_E00019021_No


title: Cb016_038_E00019044_No


title: Cb016_079_E00019060_No


title: Cb016_023_E00019012_No


title: Blood pre EDTA, biological rep 4

source_name: Blood pre challenge with EDTA blood tube

value: EDTA tube blood

value: asthma

value: pre-allergen challenge


title: Cb016_027_E00029002_No


title: Blood pre depleted, biological rep 4

source_name: Blood pre challenge non-globin depleted with Paxgene blood tube

value: Globin depleted PAXgene tube blood


title: Healthy subject 3 before limb suspension

description: Gene expression at baseline (1 subject)


title: Blood pre EDTA, biological rep 5


title: Blood post EDTA, biological rep 1

source_name: Blood post challenge with EDTA blood tube

value: post-allergen challenge


title: Blood post EDTA, biological rep 3


title: Blood pre EDTA, biological rep 2


title: Blood post depleted, biological rep 4

source_name: Blood post challenge non-globin depleted with Paxgene blood tube


title: Cb016_022_E00019035_No


title: Cb016_018_E00019005_No


title: Cb016_025_E00019059_No


title: Cb016_020_E00029016_No


title: Cb016_019_E00019030_No


title: Cb016_024_E00019037_Biological

value: Biological


title: Cb016_029_E00019071_No


title: Blood post EDTA, biological rep 5


title: Blood pre EDTA, biological rep 1


title: Blood pre depleted, biological rep 3


title: Blood post EDTA, biological rep 2


title: Blood post depleted, biological rep 3


title: Cb016_021_E00019018_No


title: Blood post depleted, biological rep 2


title: Cb016_026_E00029017_No


title: Cb016_017_E00029019_No


title: Cb016_015_E00019037_No


title: Blood pre depleted, biological rep 2


title: Cb016_028_E00019072_No


title: Cb016_016_E00019010_No


title: Blood pre non-depleted, biological rep 4

value: Globin non-depleted PAXgene tube blood


title: Cb016_012_E00019055_No


title: Cb016_010_E00019031_No


title: Blood post non-depleted, biological rep 4


title: Blood pre depleted, biological rep 1


title: Blood post non-depleted, biological rep 3


title: Cb016_014_E00029014_No


title: Cb016_009_E00029013_No


title: Blood post depleted, biological rep 1


title: Cb016_013_E00019031_Biological


title: Blood pre non-depleted, biological rep 3


title: Cb016_008_E00019046_No


title: Cb016_007_E00019064_No


title: Blood pre EDTA, biological rep 3


title: Blood post non-depleted, biological rep 2


title: Cb016_006_E00019056_No


title: Blood pre non-depleted, biological rep 2


title: Cb016_004_E00019001_No


title: Blood pre non-depleted, biological rep 1


title: 14.6

city: Brussels

first: Claudia

last: Spits

address: Laarbeeklaan 103

department: Research Group of Reproduction and Genetics

country: Belgium

institute: Vrije Universiteit Brussel

description:
G14
_GE2-NonAT_95_Feb07_nodetrend.txt

hyb_protocol: Array-CGH was carried out as described previously (Le Caignec et al., 2006, Nucleic Acids Res. 34, e68 ) with minor modifications using BAC/PAC arrays of 1MB resolution (www.microarrays.be)

scan_protocol: The slides were  scanned using an Agilent dual laser DNA microarray scanner G2566AA (Agilent technologies, Palo Alto, CA, USA). The scan images were processed with Agilent Feature Extraction Software v9.5.

data_processing: The scan images were processed with Agilent Feature Extraction Software v9.5. The raw log2Ratios are preprocessed by channel clone normalization method as described by Cheng et al. (2011, Genome Biol. 12, R80).

source_name: blastomere 6 from embryo 14

extract_protocol: Blastomeres were collected and amplified by multiple displacement amplification (MDA) as described by Spits et al. (2006,Nat. Protocols. 1, 1965-1970).

treatment_protocol: We used surplus embryos donated for research from couples who had achieved a live birth from the same IVF cycle and where the woman was less than 35 years of age at the time of oocyte collection. Fourteen embryos inseminated by ICSI and cryopreserved on day 2 of development were thawed using standard methods (Jericho et al., 2003,Hum Reprod. 18(3), 568-71 ). Embryos were cultured overnight and, in accordance with the law of the state of Victoria, allowed to succumb by being left for 24 hours at room temperature.

tag: day of embryo development

value: day 3 embryo

tag: number of blastomeres in embryo

value: embryo with seven blastomeres

source_name: Control genomic DNA

tag: gender

value: female


title: 14.4

description:
G11
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 4 from embryo 14

label_protocol: Array-CGH was carried out as described previously (Le Caignec et al., 2006, Nucleic Acids Res. 34, e68 ) with minor modifications using BAC/PAC arrays of 1MB resolution (www.microarrays.be)


title: 14.3

description:
G7
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 3 from embryo 14


title: Blood post non-depleted, biological rep 1


title: 14.2

description:
G5
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 2 from embryo 14


title: 14.7

description:
G18
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 7from embryo 14


title: Cb016_001_E00029024_No

source_name: 2.5ml peripheral venous blood

tag: patient

value: Advanced castration resistant

value: Beatson


title: 14.1

description:
G3
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 1 from embryo 14


title: 13.4

description:
G12
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 4 from embryo 13


title: 13.5

description:
G16
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 5 from embryo 13


title: Cb016_002_E00019065_No

tag: centre

value: RMH

value: No


title: Cb016_005_E00019066_No

tag: plate


title: Cb016_003_E00019004_No

tag: replicate


title: 13.6

description:
G19
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 6 from embryo 13


title: 13.3

description:
G8
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 3 from embryo 13


title: 13.7

description:
G20
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 7 from embryo 13


title: 13.2

description:
G6
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 2 from embryo 13


title: 13.1

description:
G1
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 1 from embryo 13


title: MM line transfected with shERK5, rep 1

first: Arti

last: Shukla

address: 89 Beaumont Avenue

department: Pathology

description: Gene expression data in ERK5 inhibited epithelioid mesothelioma cell line

hyb_protocol: Biotin-labeled cDNA fragments that were hybridized to the probe array at 45 oC for 16 h.

scan_protocol: The probe array were scanned (Affymetrix GeneArray Scanner, GS3000) to quantify the fluorescence intensity associated with each oligonucleotide probe

data_processing: A human U133A 2.0 array was scanned twice, the images overlaid, and the average intensities of each probe cell compiled. Microarray data were analyzed using GeneSifter software (VizX Labs, Seattle, WA) by RMA method. Data were log transformed.

source_name: Stable transfection with shERK5 SureSilencing plasmid

label_protocol: RNA was synthesized to ds cDNA which was then converted to amplified ss cDNA using a Nugen Ovation V2 system. ss cDNA was Biotinylated using TdT end label.

growth_protocol: All cells were incubated at 37oC and 5% CO2 and grown to approximately 80-90% confluency in DMEM/F12 medium at a 1:1 ratio containing 10% fetal bovine serum (FBS), 0.1 ug/ml hydrocortisone, 2.5 ug/ml insulin, 2.5 ug/ml transferrin and 2.5 ng/ml sodium selenite and penicillin-streptomycin (50 U/ml penicillin G, 50 ug/ml streptomycin sulfate)

extract_protocol: Total RNA was extracted from cells using an RNeasy Plus Mini kit according to the manufacturer's protocol (Qiagen, Valencia, CA). RNA was dissolved in RNAs free water and quantified using the NanoDrop spectrophotometer.

treatment_protocol: In order to achieve inhibition of ERK5, mesothelioma cells (HMESO) were stably transfected with  shERK5 plasmid from SABiosciences using Lipofectamine 2000. After selection in G418 (400ug/ml) medium for 14 days, limited dilution was performed to get pure clones of more than 70% inhibited ERK5.

tag: cell line

value: HMESO

tag: cell type

value: epithelioid malignant mesothelioma (MM)

tag: transfection

tag: property

value: ERK5>70% inhibited


title: MM line transfected with shERK5, rep 3


title: 12.6

description:
G17
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 6 from embryo 12

value: embryo with six blastomeres


title: MM line transfected with shERK5, rep 2


title: Blood post EDTA, biological rep 4

source_name: Blood post challenge with EDTA blood tube

value: EDTA tube blood

value: blood

value: asthma


title: 12.4

description:
G10
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 4 from embryo 12

source_name: Control genomic DNA


title: 12.2

description:
G4
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 2 from embryo 12


title: 12.5

description:
G15
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 5 from embryo 12


title: 9.1

description:
F1
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 1 from embryo 9

value: embryo with eight blastomeres


title: 10.5

description:
F13
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 5 from embryo 10


title: 10.6

description:
F16
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 6 from embryo 10


title: 9.2

description:
F4
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 2 from embryo 9


title: 11.2

description:
F5
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 2 from embryo 11

value: embryo with five blastomeres


title: 8.4

description:
D23
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 4 from embryo 8


title: 11.3

description:
F7
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 3 from embryo 11


title: 8.5

description:
D24
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 5 from embryo 8


title: 11.5

description:
F15
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 5 from embryo 11


title: 8.3

description:
D19
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 3 from embryo 8


title: 8.6

description:
D29
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 6 from embryo 8


title: 12.1

description:
G2
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 1 from embryo 12


title: 10.3

description:
F8
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 3 from embryo 10


title: 9.6

description:
F17
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 6 from embryo 9


title: 9.5

description:
F14
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 5 from embryo 9

source_name: Control genomic DNA


title: 9.3

description:
F11
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 3 from embryo 9


title: 8.1

description:
D14
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 1 from embryo 8


title: 7.6

description:
D27
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 6 from embryo 7


title: 8.2

description:
D16
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 2 from embryo 8


title: 7.4

description:
D20
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 4 from embryo 7


title: 7.2

description:
D12
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 2 from embryo 7


title: 7.1

description:
D8
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 1 from embryo 7


title: 6.2

description:
D15
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 2 from embryo 6


title: 6.3

description:
D28
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 3 from embryo 6


title: 7.3

description:
D17
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 3 from embryo 7


title: 6.1

description:
D5
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 1 from embryo 6


title: 5.5

description:
D26
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 5 from embryo 5


title: 5.3

description:
D13
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 3 from embryo 5


title: 1.4

description:
C10
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 4 from embryo 1


title: 3.5

description:
C17
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 5 from embryo 3


title: 3.7

description:
C22
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 7 from embryo 3


title: 4.5

description:
D7
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 5 from embryo 4

source_name: Control genomic DNA


title: 3.3

description:
C11
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 3 from embryo 3


title: 3.2

description:
C9
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 2 from embryo 3


title: 4.1

description:
D1
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 1 from embryo 4


title: 4.4

description:
D6
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 4 from embryo 4


title: 1.2

description:
C5
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 2 from embryo 1


title: 3.1

description:
C7
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 1 from embryo 3


title: 4.6

description:
D9
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 6 from embryo 4


title: 1.1

description:
C1
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 1 from embryo 1


title: 3.4

description:
C16
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 4 from embryo 3


title: 5.2

description:
D11
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 2 from embryo 5


title: 5.4

description:
D18
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 4 from embryo 5


title: 2.5

description:
C14
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 5 from embryo 2


title: 2.6

description:
C18
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 6 from embryo 2


title: 1.3

description:
C6
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 3 from embryo 1


title: 2.4

description:
C13
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 4 from embryo 2


title: 3.6

description:
C20
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 6 from embryo 3


title: 1.6

description:
C19
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 6 from embryo 1

source_name: Control genomic DNA


title: 1.5

description:
C15
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 5 from embryo 1


title: 2.2

description:
C4
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 2 from embryo 2


title: 2.3

description:
C8
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 3 from embryo 2


title: 2.1

description:
C3
_GE2-NonAT_95_Feb07_nodetrend.txt

source_name: blastomere 1 from embryo 2


title: Xen_StageVI_mat_6

status: Public on Oct 14 2012

city: Rennes

first: Julien

last: Bobe

address: Campus de Beaulieu

country: France

institute: Institut National de la Recherche Agronomique

description: Gene expression in stade VI xenopus ovulatory follicles in which oocytes have undergone maturation (metaphase II oocytes awaiting fertilization) and are developmentally fully competent.

hyb_protocol: 1.65 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 25x fragmentation buffer and 10x blocking agent following the manufacturers instructions (Agilent Technologies, Santa Clara, CA) . On completion of the fragmentation reaction, 55 µl of 2x GEx Hybridization Buffer HI-RPM (Agilent provided) was added to the fragmentation mixture and hybridized to Agilent Bovine Oligo Microarray (G2519F AMADID 015066) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2566AA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 015066_D_20060913) to obtain background subtracted and spatially detrended Processed Signal intensities.  Poor quality features that were either saturated or non-uniform were flagged using Genespring Agilent software. Only features with a signal-to-noise ratio (SNR) of up to 2.6 and significantly different from the local background (two sided t-test) were used for further analysis. Entities were then filtered based on these flag values: at least 80% of the values in any 2 out of 3 conditions must have acceptable values. Expression values were then log2-transformed and submitted to a scale normalisation

organism: Xenopus laevis

source_name: xenopus follicles, stage VI, mature in vitro, metaphase II, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.35µg RNA using the One-Color Microarray based gene Expression kit (Quick Amp Labeling, Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Sexually mature adult Xenopus laevis females (>3 year-old) were used for sampling immature vitellogenic (stage IV) and post-vitellogenic (stage VI) ovarian follicles. Mature follicles were obtained by incubating immature post-vitellogenic follicles for 15 h at room temperature in OR2 buffer (83 mM NaCl, 2.5 mM KCl, 1 mM CaCl2, 1 mM MgCl2, 1 mM Na2HPO4, 5 mM HEPES, pH 7.4) supplemented with 40 IU/mL of human chorionic gonadotropin.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen, Cergy Pontoise, France). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The monolayers of follicular cells (=granulosa cells) surrounding the oocytes  were manually recovered after a 30-min treatment with collagenase in calcium-free OR2 buffer and washed in PBS. Cell pellets  were snap-frozen in liquid nitrogen after addition of TRIzol reagent and stored at -70°C until RNA extraction.

value: stage VI ovarian follicles

tag: Stage

tag: meiotic stage

value: metaphase II

tag: development capacity

value: developmentally fully competent


title: OM_Mat_T25

description: Gene expression in rainbow trout ovulatory follicles in which oocytes have undergone maturation (metaphase II oocytes awaiting fertilization) and are developmentally fully competent.

hyb_protocol: 1.65 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 25x fragmentation buffer and 10x blocking agent following the manufacturers instructions (Agilent Technologies, Santa Clara, CA) . On completion of the fragmentation reaction, 55 µl of 2x GEx Hybridization Buffer HI-RPM (Agilent provided) was added to the fragmentation mixture and hybridized to Agilent Bovine Oligo Microarray (G2514F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 016320_D_F_20070321) to obtain background subtracted and spatially detrended Processed Signal intensities.  Poor quality features that were either saturated or non-uniform were flagged using Genespring Agilent software. Only features with a signal-to-noise ratio (SNR) of up to 2.6 and significantly different from the local background (two sided t-test) were used for further analysis. Entities were then filtered based on these flag values: at least 80% of the values in any 3 out of 4 conditions must have acceptable values. Expression values were then log2-transformed and submitted to a scale normalisation

organism: Oncorhynchus mykiss

source_name: rainbow trout ovarian follicles, mature, metaphase II, sample 25

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.35 µg RNA using the One-Color Microarray based gene Expression kit (Quick Amp Labeling, Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Samples were collected from 3-year old rainbow trout females during reproductive season during late-vitellogenesis (NC1 samples), post-vitellogenesis (C1 samples) and after meiosis resumption (C2 samples).

treatment_protocol: Individual follicles were isolated and the follicular layers dissected out using forceps in trout mineral medium.

tag: tissue

value: ovarian follicles

tag: stage of oogenesis

value: Mature, germinal vesicle breakdown completed

value: developmentally competent


title: Xen_StageVI_mat_15

source_name: xenopus follicles, stage VI, mature in vitro, metaphase II, replicate 2


title: Cow_Mat_Vivo_27

description: Gene expression in cow ovulatory follicles in which oocytes have undergone maturation (metaphase II oocytes awaiting fertilization) and are developmpentally fully competent. These ovulatory follicles were collected by ovum pick-up (OPU) in vivo

hyb_protocol: 1.65 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 25x fragmentation buffer and 10x blocking agent following the manufacturers instructions (Agilent Technologies, Santa Clara, CA) . On completion of the fragmentation reaction, 55 µl of 2x GEx Hybridization Buffer HI-RPM (Agilent provided) was added to the fragmentation mixture and hybridized to Agilent Bovine Oligo Microarray (G2519F AMADID 015354) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 015354_D_20061130) to obtain background subtracted and spatially detrended Processed Signal intensities.  Poor quality features that were either saturated or non-uniform were flagged using Genespring Agilent software. Only features with a signal-to-noise ratio (SNR) of up to 2.6 and significantly different from the local background (two sided t-test) were used for further analysis. Entities were then filtered based on these flag values: at least 80% of the values in any 2 out of 3 conditions must have acceptable values. Expression values were then log2-transformed and submitted to a scale normalisation

organism: Bos taurus

source_name: Cow follicles, mature in vivo, metaphase II, sample 27, replicate 2

growth_protocol: Holstein adult non-lactating cows 3-5 years old were used for sampling of mature COC (cumulus-oocyte complexes) after basic superovulation protocol. Adult cows of different ages and 3-6 months-old calves were used for recovery of immature COC.

treatment_protocol: Cumulus cells were separated from the oocytes in TCM199 culture medium (Sigma), washed in PBS and kept in TriZol reagent at -80°C prior to extraction.


title: Xen_StageVI_mat_18

source_name: xenopus follicles, stage VI, mature in vitro, metaphase II, replicate 3


title: OM_Mat_T30

source_name: rainbow trout ovarian follicles, mature, metaphase II, sample 30


title: OM_PV_T9

description: Gene expression in rainbow trout follicles in which prophase I oocytes are meiotically competent and developmentally competent after meiosis resumption

source_name: rainbow trout ovarian follicles, post-vitellogenesis, prophase I, poorly responsive to hormone stimulation, sample 9

value: post-vitellogenesis

value: prophase I