title: EBV-LCL_10Gy4hr_11_RS7

status: Public on May 02 2011

city: East Melbourne

first: Jason

last: Li

address: St Andrews Pl

country: Australia

institute: Peter MacCallum Cancer Centre

hyb_protocol: Followed the exact prodedure of the 'GeneChip Whole Transcript (WT) Sense Target labelling assay Manual' (Affymetrix).

scan_protocol: Chips were scanned with a Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using aroma.affymetrix (R package). RMA background correction were applied to probe intensities, gene level expression were quantile normalized. Only the Core probesets have been used for analysis.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: Blood sample

growth_protocol: EBV-transformed lymphoblast cell lines were grown in RPMI medium and fibroblasts in DMEM medium, both supplemented with 10% FBS and gentamicin and incubated in a 5% CO2 humidified incubator at 37oC.

extract_protocol: Cells were grown to a density of 1 x 107, pelleted, resuspended in 3 ml PBS and an equal volume of Trizol (Invitrogen, Carlsbad, CA, USA) was added, mixed and the aqueous layer was mixed with and equal volume of 70 percent ethanol and added onto a RNeasy column (Qiagen, Venlo, The Netherlands). The RNA extraction was continued by using the RNeasy method as per manufactures recommendation except starting with the addition of the sample of Buffer RW1. RNA concentration and integrity was determined by analysing on a bioanalyzer (Agilent, Santa Clara, CA, USA). RNA was determined to be high enough quality if a minimum RIN of 8.5 was obtained.

treatment_protocol: Approximately 1x 108  lymphoblast cells or 1x107 primary fibroblasts were irradiated with 0 Gy, 2 Gy or 10 Gy IR at RT using a Cs137 source with a dose rate of 1.7min/Gy

value: LCL

tag: individual

tag: control or radiosensitive

value: RS

tag: dose

tag: hour


title: EBV-LCL_5Gy4hr_10

type: RNA

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Followed the exact prodedure of the 'GeneChip Whole Transcript (WT) Sense Target labelling assay Manual' (Affymetrix).

tag: cell type


title: EBV-LCL_0Gy4hr_11_RS7


title: EBV-LCL_0Gy4hr_9


title: EBV-LCL_1Gy4hr_10


title: EBV-LCL_10Gy8hr_10


title: EBV-LCL_5Gy4hr_8


title: EBV-LCL_10Gy4hr_11_RS44


title: EBV-LCL_0Gy4hr_11_RS44


title: EBV-LCL_2Gy4hr_8


title: EBV-LCL_10Gy48hr_10


title: EBV-LCL_10Gy4hr_10


title: EBV-LCL_20Gy4hr_8


title: EBV-LCL_20Gy4hr_10


title: EBV-LCL_2Gy4hr_10


title: EBV-LCL_10Gy8hr_8


title: EBV-LCL_10Gy4hr_9


title: EBV-LCL_10Gy48hr_8


title: EBV-LCL_10Gy2hr_8


title: EBV-LCL_0Gy4hr_10


title: EBV-LCL_10Gy24hr_10


title: EBV-LCL_10Gy2hr_10


title: EBV-LCL_10Gy4hr_8


title: Ependymoma 29

status: Public on Aug 15 2011

city: Houston

first: Stephen

middle: Mack

last: Christopher

state: TX

address: 1102 Bates Avenue C1030.02

department: Pediatrics

country: USA

institute: Baylor College of Medicine

description: PLIER expression value derived from Expression Console (v1.1) software, core-gene level analysis

hyb_protocol: Samples were hybridized to the Affymetrix Exon 1.0ST arrays at the London Regional Genomics Centre (London, Ontario)

scan_protocol: Array scanning was performed according to manufacturers instructions (Affymetrix).

data_processing: Raw data were processed with Affymetrix Expression Console (version 1.1). Gene Level (CORE content) analysis was performed using the following settings: PLIER summarization, PM-GCBG background correction, Quantile (sketch) normalization. Probesets were then annotated using the human genome (HG19) build within Expression Console.

source_name: Brain Tumor

label_protocol: 2 micrograms of RNA was used for single-strand cDNA synthesis then labeling using the Affymetrix WT sense target labeling assay all performed according to Affymetrix manufacturers instructions.

extract_protocol: Fresh frozen tumors were immersed in liquid nitrogen, then pulverized into a powder using a mortar and pestle. RNA was then extracted using the Trizol (Invitrogen) method according to manufacturers directions. Concentration of mRNA was determined using a NanoDrop. Quality of mRNA and assessment of DNA contamination was determined by analysis of 50-200ng RNA on the Agilent Bioanalyzer.

tag: tissue

value: Ependymoma brain tumor

tag: age

tag: gender

value: M

tag: location

value: Spinal Cord


title: EBV-LCL_10Gy4hr_6


title: EBV-LCL_0Gy4hr_8


title: EBV-LCL_0Gy4hr_6


title: EBV-LCL_10Gy4hr_5

value: CL


title: EBV-LCL_10Gy4hr_7


title: EBV-LCL_1Gy4hr_8


title: EBV-LCL_0Gy4hr_7


title: EBV-LCL_0Gy4hr_4


title: EBV-LCL_10Gy8hr_3


title: EBV-LCL_1Gy4hr_3


title: EBV-LCL_0Gy4hr_5


title: EBV-LCL_5Gy4hr_3


title: EBV-LCL_10Gy4hr_4


title: EBV-LCL_2Gy4hr_3


title: EBV-LCL_10Gy48hr_3


title: EBV-LCL_0Gy4hr_3_CL32


title: EBV-LCL_10Gy4hr_3_CL25


title: EBV-LCL_20Gy4hr_3


title: EBV-LCL_10Gy4hr_3


title: EBV-LCL_10Gy24hr_3_CL32


title: EBV-LCL_10Gy2hr_3


title: EBV-LCL_10Gy4hr_3_CL22


title: EBV-LCL_0Gy4hr_3_CL25


title: EBV-LCL_0Gy4hr_3_CL22


title: EBV-LCL_5Gy4hr_2


title: EBV-LCL_20Gy4hr_2


title: EBV-LCL_2Gy4hr_2


title: EBV-LCL_10Gy2hr_2


title: Primary fibroblast_2Gy4hr_12

source_name: Skin punch biopsy

value: Fibroblast


title: EBV-LCL_10Gy24hr_8


title: EBV-LCL_10Gy4hr_2


title: EBV-LCL_10Gy8hr_2


title: Primary fibroblast_2Gy4hr_11


title: Primary fibroblast_10Gy4hr_12


title: EBV-LCL_10Gy48hr_2


title: Primary fibroblast_0Gy4hr_12


title: Primary fibroblast_1Gy4hr_10


title: Primary fibroblast_10Gy4hr_11


title: Primary fibroblast_10Gy8hr_10


title: EBV-LCL_1Gy4hr_2


title: Primary fibroblast_2Gy4hr_10b


title: EBV-LCL_0Gy4hr_1


title: Primary fibroblast_2Gy4hr_10


title: Primary fibroblast_5Gy4hr_10


title: EBV-LCL_10Gy4hr_1


title: Primary fibroblast_20Gy4hr_10


title: EBV-LCL_10Gy24hr_2


title: EBV-LCL_0Gy4hr_2


title: Primary fibroblast_0Gy4hr_11


title: Primary fibroblast_10Gy48hr_10


title: Primary fibroblast_10Gy24hr_10


title: Primary fibroblast_0Gy4hr_10


title: Sphere1

status: Public on Jun 09 2011

city: Bangalore

first: Sudhir

last: Krishna

state: Karnataka

address: UAS-GKVK Campus, Bellary Road

country: India

institute: National Centre for Biological Sciences, TIFR

description: Gene expression from cell line grown in sphere medium

hyb_protocol: 1650ng of cy3 labeled samples for  4x44k arrays and 600 ng  cy3 labeled samples for 8x15 arrays were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned on an Agilent Technologies G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 9.5.1.1  and 10.5.1.1)

data_processing: The normalization was done using GeneSpring GX 11 Software.

source_name: cell line grown in sphere medium

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the  samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: The primary cancer samples (PS-M1) were used without culturing. The CaSki spheres were grown for 14days in non-adherent condition in sphere medium and the adherent weregrwon in DMEM with serum.

extract_protocol: Qiagen mini kit for CaSki adherent and sphere following the manufacturer's recommendations. Trizol method for patient samples.RNA was quantified using NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell line

value: CaSki

value: cell line derived from metastatic lesion


title: Primary fibroblast_10Gy2hr_10


title: Primary fibroblast_2Gy5hr_9


title: Primary fibroblast_10Gy4hr_10


title: Primary fibroblast_10Gy8hr_9


title: Primary fibroblast_5Gy4hr_9


title: Primary fibroblast_10Gy4hr_9b


title: Primary fibroblast_10Gy48hr_9


title: Primary fibroblast_10Gy4hr_8


title: Primary fibroblast_10Gy4hr_9


title: Primary fibroblast_2Gy5hr_5


title: Primary fibroblast_1Gy4hr_9


title: Primary fibroblast_0Gy4hr_8


title: Primary fibroblast_20Gy4hr_9


title: Primary fibroblast_2Gy4hr_9


title: Primary fibroblast_10Gy24hr_9


title: Primary fibroblast_5Gy4hr_5


title: Primary fibroblast_10Gy2hr_9


title: Primary fibroblast_0Gy4hr_7


title: Primary fibroblast_2Gy4hr_7


title: Primary fibroblast_10Gy4hr_7


title: Primary fibroblast_10Gy4hr_6


title: Primary fibroblast_0Gy4hr_9


title: Primary fibroblast_0Gy0hr_9


title: Primary fibroblast_2Gy4hr_6


title: Primary fibroblast_2Gy4hr_8


title: Primary fibroblast_2Gy4hr_5


title: Primary fibroblast_10Gy48hr_5


title: Primary fibroblast_20Gy4hr_5


title: Primary fibroblast_0Gy4hr_6


title: Primary fibroblast_10Gy4hr_5


title: Primary fibroblast_1Gy4hr_5


title: Primary fibroblast_10Gy24hr_5


title: Primary fibroblast_10Gy4hr_3


title: Primary fibroblast_2Gy5hr_2


title: Primary fibroblast_10Gy2hr_2


title: Primary fibroblast_0Gy4hr_4


title: Primary fibroblast_10Gy4hr_2


title: Primary fibroblast_10Gy4hr_2b


title: Primary fibroblast_0Gy4hr_3


title: Primary fibroblast_1Gy4hr_2


title: Primary fibroblast_0Gy4hr_2


title: Primary fibroblast_0Gy4hr_5


title: Primary fibroblast_10Gy48hr_2


title: Primary fibroblast_10Gy4hr_4


title: Primary fibroblast_2Gy4hr_2


title: Primary fibroblast_5Gy4hr_2


title: Primary fibroblast_10Gy2hr_5


title: Primary fibroblast_2Gy4hr_4


title: Primary fibroblast_10Gy8hr_5


title: Primary fibroblast_2Gy4hr_3


title: Primary fibroblast_10Gy8hr_2


title: Primary fibroblast_2Gy4hr_1


title: Primary fibroblast_10Gy24hr_2


title: Primary fibroblast_20Gy4hr_2


title: Primary fibroblast_10Gy4hr_1


title: Primary fibroblast_0Gy0hr_2


title: Blood_P16_CMLonTKI_49mos

status: Public on Mar 15 2011

type: genomic

city: Kuala Lumpur

first: Veera Sekaran

last: Nadarajan

address: Lembah Pantai

department: Pathology

country: Malaysia

institute: University Malaya

hyb_protocol: The purified labeled samples were mixed with 50 μg of human Cot-1 DNA (Invitrogen) and Agilent 10X Blocking Agent and Agilent 2X Hybridization Buffer. The hybridization mixtures were denatured at 95°C for 3 min and incubated at 37°C for 30 min. Samples were then applied to the microarrays enclosed in Agilent SureHyb-enabled hybridization chambers for 24 h at 65°C. After hybridization, slides were washed sequentially.

scan_protocol: Slides were scanned on an Agilent G2505B scanner. Microarray images were processed using Agilent Feature Extraction Software (version 9.5.31).

data_processing:
Linear normalized background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.
Normalized log2ratio (Cy5/Cy3) or (Cy3/Cy5) representing CML/ref is provided in the data matrix.

molecule: genomic DNA

source_name: CML, accelerated phase on IM

label_protocol: 1.0µg of total genomic DNA (gDNA) of the test sample (patient) and a references sample with concentration at least 50ng/µL were digested with 5U of AluI and RsaI for 2h at 37°C followed by incubation for 20 minutes at 65°C to inactivate the enzymes. The purified restricted samples were labeled with Cy5-dUTP or Cy3-dUTP by using the Agilent genomic DNA labeling kit PLUS (Agilent p/n 5188-5309) as per manufacturers instructions. Both purified labeled genomic DNA were combined.

extract_protocol: Total genomic DNA was extracted from archived samples using QIAGEN AllPrep® DNA/RNA/Protein Mini Kit, as recommended by the manufacturer.

value: Blood

tag: patient

tag: age (years)

tag: sex

value: Male

tag: disease status

value: CML

tag: cml stage

value: accelerated

tag: therapy

value: treated with imatinib mesylate (IM) for 49mos

source_name: Human male genomic DNA (Promega P/N G1471)

tag: reference

value: Promega P/N G1471


title: Blood_P16_CMLonTKI_19mos

value: treated with imatinib mesylate (IM) for 19mos


title: Blood_P14_CMLonTKI_35mos

value: treated with imatinib mesylate (IM) for 35mos


title: Primary fibroblast_0Gy4hr_1

tag: individual


title: Blood_P13_CMLonTKI_40mos

source_name: CML, chronic phase on IM

value: chronic

value: treated with imatinib mesylate (IM) for 40mos


title: Blood_P16_CMLonTKI_37mos

value: treated with imatinib mesylate (IM) for 37mos


title: Blood_P15_CMLonTKI_49mos


title: Blood_P14_CMLonTKI_47mos

value: treated with imatinib mesylate (IM) for 47mos


title: Blood_P15_CMLonTKI_55mos

value: treated with imatinib mesylate (IM) for 55mos


title: Blood_P16_CMLonTKI_31mos

value: treated with imatinib mesylate (IM) for 31mos


title: Blood_P14_CMLonTKI_23mos

value: treated with imatinib mesylate (IM) for 23mos


title: Blood_P14_CMLonTKI_41mos

value: treated with imatinib mesylate (IM) for 41mos


title: Blood_P13_CMLonTKI_32mos

value: treated with imatinib mesylate (IM) for 32mos


title: Blood_P13_CMLonTKI_11mos

value: Blood

value: treated with imatinib mesylate (IM) for 11mos


title: Blood_P13_CMLonTKI_19mos

value: Male

value: CML


title: Blood_P13_CMLonTKI_25mos

value: treated with imatinib mesylate (IM) for 25mos


title: Blood_P13_CMLonTKI_4mos

value: treated with imatinib mesylate (IM) for 4mos

value: Promega P/N G1471


title: Blood_P12_CMLonTKI_52mos

value: treated with imatinib mesylate (IM) for 52mos


title: Blood_P12_CMLonTKI_58mos

value: chronic

value: treated with imatinib mesylate (IM) for 58mos


title: Blood_P9_CMLonTKI_7mos

value: Female

value: treated with imatinib mesylate (IM) for 7mos

source_name: Human female genomic DNA (Promega P/N G1521)

value: Promega P/N G1521


title: Blood_P11_CMLonTKI_27mos

value: treated with imatinib mesylate (IM) for 27mos


title: Blood_P8_CMLonTKI_45mos

value: treated with imatinib mesylate (IM) for 45mos


title: Blood_P10_CMLonTKI_6mos

source_name: CML, blast crisis on IM

value: blast crisis

value: treated with imatinib mesylate (IM) for 6mos


title: Blood_P9_CMLonTKI_22mos

value: Blood

value: treated with imatinib mesylate (IM) for 22mos


title: Blood_P8_CMLonTKI_32mos

value: Male

value: treated with imatinib mesylate (IM) for 32mos


title: Blood_P6_CMLonTKI_0mos

value: CML

value: treated with imatinib mesylate (IM) for 0mos


title: Blood_P12_CMLonTKI_33mos

value: treated with imatinib mesylate (IM) for 33mos

value: Promega P/N G1471


title: Blood_P6_CMLonTKI_6mos

value: chronic


title: Blood_P8_CMLonTKI_39mos

value: treated with imatinib mesylate (IM) for 39mos


title: Blood_P7_CMLonTKI_48mos

value: accelerated

value: treated with imatinib mesylate (IM) for 48mos


title: Blood_P5_CMLonTKI_29mos

value: treated with imatinib mesylate (IM) for 29mos


title: Blood_P9_CMLonTKI_20mos

value: Female

value: treated with imatinib mesylate (IM) for 20mos

value: Promega P/N G1521


title: Blood_P7_CMLonTKI_15mos

value: treated with imatinib mesylate (IM) for 15mos


title: Blood_P3_CMLonTKI_28mos

value: Blood

value: treated with imatinib mesylate (IM) for 28mos


title: Blood_P5_CMLonTKI_17mos

value: Male

value: treated with imatinib mesylate (IM) for 17mos


title: Blood_P1_CMLonTKI_54mos

value: CML

value: treated with imatinib mesylate (IM) for 54mos


title: Blood_P5_CMLonTKI_0mos

value: treated with imatinib mesylate (IM) for 0mos


title: Blood_P2_CMLonTKI_42mos

value: treated with imatinib mesylate (IM) for 42mos

value: Promega P/N G1471


title: Blood_P3_CMLonTKI_18mos

value: chronic

value: treated with imatinib mesylate (IM) for 18mos


title: Blood_P1_CMLonTKI_45mos

value: treated with imatinib mesylate (IM) for 45mos


title: MDS tumor cells patient 88

status: Public on Jan 30 2011

city: Duesseldorf

first: Brigitte

last: Royer-Pokora

address: Universitätsstr. 1

country: Germany

institute: Institute of Human Genetics and Anthropology, Heinrich-Heine-University Duesseldorf

description:
Agilent Feature Extraction file: sample_88.txt
MDS tumor cells

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Feature Extraction Software (version 10.7.1.1) was used for background subtraction and LOWESS normalization.

source_name: MDS tumor cells, patient 88

label_protocol: Protocol Version 5.0, June 2007, Agilent.Same gender reference/control DNA was purchased from Promega as pool.

growth_protocol: Bone marrow cells were cultured unstimulated 24, 48 or 72 hrs in RPMI or Marrow Max Medium and 10% FCS. Colcemid was used to arrest cell cycle in metaphases.

extract_protocol:
For samples marked Qiagen: DNA was extracted from methanol-acetic acid fixed cells with QIAamp DNA Blood Midi Kit (Qiagen).
For samples marked PC: DNA was extracted from methanol-acetic acid fixed cells with Proteinase K, SDS and Phenol-Chloroform.

treatment_protocol: Hypotonic treatment to eliminate red blood cells and fixation with methanol-acetic acid (3:1) of white blood cells.

value: F

tag: International Prognostic Scoring System (IPSS)

tag: extract protocol

value: Qiagen

source_name: control DNA

value: Pooled, same gender reference/control DNA (Promega)


title: MDS tumor cells patient 103

description:
Agilent Feature Extraction file: sample_103.txt
MDS tumor cells

hyb_protocol: Protocol Version 5.0, June 2007, Agilent.

source_name: MDS tumor cells, patient 103


title: MDS tumor cells patient 89

description:
Agilent Feature Extraction file: sample_89.txt
MDS tumor cells

source_name: MDS tumor cells, patient 89


title: MDS tumor cells patient 100

description:
Agilent Feature Extraction file: sample_100.txt
MDS tumor cells

source_name: MDS tumor cells, patient 100


title: MDS tumor cells patient 93

description:
Agilent Feature Extraction file: sample_93.txt
MDS tumor cells

source_name: MDS tumor cells, patient 93

value: M


title: MDS tumor cells patient 86

description:
Agilent Feature Extraction file: sample_86.txt
MDS tumor cells

source_name: MDS tumor cells, patient 86


title: cell line SW480, 10 cells, replicate C

status: Public on Oct 01 2010

city: Barcelona

first: Victoria

last: Core

address: Baldiri Reixac, 10

department: Functional Genomics Core

country: Spain

institute: Institute for Research in Biomedicine

description: Gene expression data from 100 pg total RNA

hyb_protocol: Affymetrix GeneChip Human Gene 1.0ST arrays were hybridized with 10 ug of labeled, amplified dsDNA, washed, stained and scanned according to the protocol  described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics  protocol FS450_007)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003)

source_name: ATCC: CCL-228

label_protocol: The indicated starting amount of total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and subsequently labeled using GeneChip Mapping 10K Xba Assay Kit (Affymetrix; catalog # 900441), according to manufacturer's instructions.

extract_protocol: ATCC protocol

tag: protocol

value: Pico profiling


title: MDS tumor cells patient 78

description:
Agilent Feature Extraction file: sample_78.txt
MDS tumor cells

source_name: MDS tumor cells, patient 78


title: MDS tumor cells patient 64

description:
Agilent Feature Extraction file: sample_64.txt
MDS tumor cells

source_name: MDS tumor cells, patient 64


title: MDS tumor cells patient 95

description:
Agilent Feature Extraction file: sample_95.txt
MDS tumor cells

source_name: MDS tumor cells, patient 95


title: MDS tumor cells patient 83

description:
Agilent Feature Extraction file: sample_83.txt
MDS tumor cells

source_name: MDS tumor cells, patient 83


title: MDS tumor cells patient 63

description:
Agilent Feature Extraction file: sample_63.txt
MDS tumor cells

source_name: MDS tumor cells, patient 63


title: MDS tumor cells patient 37

description:
Agilent Feature Extraction file: sample_37.txt
MDS tumor cells

source_name: MDS tumor cells, patient 37


title: Non-malignant bone_NB04_replicate 2

status: Public on Aug 30 2010

city: Woolloongabba

first: Liliana

middle: Beatriz

last: Endo-Munoz

state: Queensland

address: TRI, 37 Kent St

department: Diamantina Institute

institute: University of Queensland

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers, as described by the manufacturer. Washing was performed following solutions and protocols recommended by Agilent.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: LOWESS normalized, background subtracted data obtained from log of ratio of processed test signal/processed reference signal using GeneSpring version 7.2.

source_name: Total RNA from non-malignant bone labelled with AlexFluor647

label_protocol: 20 ug of total RNA incubated with 5 ug anchored oligo(dT)12-18 primer 70oC/10 min. Reverse transcription performed at 42oC/2 h with 0.65 uL aminoallyl dNTP - 25 mM dATP, dGTP, dCTP, 7.5 mM dTTP, 15 mM aminoallyl d-UTP, and 400 U Superscript II. The RNA was labelled at room temperature/1 hour with AlexaFluor555 or AlexaFluor647 in the presence of 0.3M NaHCO3 and DMSO.

extract_protocol: Total RNA extracted from 100 mg of tumour biopsy with 900 uL Trizol and 100 uL 2M acetic acid.

treatment_protocol: Biopsies were removed from patients and immediately frozen in dry ice, before long-term storage at -80oC.

tag: Female, 75 years, femur head

source_name: Total RNA pooled from 8 cancer cell lines

tag: HDF, COLO-16, LNCap, DU145, SK-BR3, U2OS, HT29, DG75


title: MDS tumor cells patient 61

description:
Agilent Feature Extraction file: sample_61.txt
MDS tumor cells

source_name: MDS tumor cells, patient 61


title: Non-malignant bone_NB06_replicate 3

tag: Male, 71 years


title: Non-malignant bone_NB03_replicate 1

tag: Female, 49 years


title: Non-malignant bone_NB09_replicate 5

tag: Male, 79 years


title: Biopsy_non-metastatic_NM07_rep 1

source_name: Total RNA from osteosarcoma biopsy of non-metastatic patient labelled with AlexFluor647

tag: Female, 14 years, left femur


title: MDS tumor cells patient 5

description:
Agilent Feature Extraction file: sample_5.txt
MDS tumor cells

source_name: MDS tumor cells, patient 5

tag: gender

source_name: control DNA


title: Non-malignant bone_NB08_replicate 4

tag: Male, 56 years


title: Biopsy_non-metastatic_NM06_rep 1

tag: Male, 17 years, left tibia


title: Biopsy_non-metastatic_NM07_dye-swap_rep 2

source_name: Total RNA from osteosarcoma biopsy of metastatic patient labelled with AlexaFluor555


title: MDS tumor cells patient 51

description:
Agilent Feature Extraction file: sample_51.txt
MDS tumor cells

source_name: MDS tumor cells, patient 51


title: MDS tumor cells patient 43

description:
Agilent Feature Extraction file: sample_43.txt
MDS tumor cells

source_name: MDS tumor cells, patient 43


title: Biopsy_non-metastatic_NM05_rep 1

tag: Male, 18 years, right femur


title: Biopsy_non-metastatic_NM02_dye-swap_rep 2

source_name: Total RNA from osteosarcoma biopsy of metastatic patient labelled with AlexFluor555

tag: Female, 15 years, right femur


title: Biopsy_non-metastatic_NM02_rep 1


title: Biopsy_non-metastatic_NM03_dye-swap_rep 2

tag: Male, 18 years, left tibia


title: Biopsy_non-metastatic_NM05_dye-swap_rep 2


title: Biopsy_non-metastatic_NM01_dye-swap_rep 2

tag: Male, 15 years, right tibia


title: Biopsy_non-metastatic_NM04_rep 1

tag: Male, 19 years, right femur


title: Biopsy_metastatic_M10_dye-swap_rep 2

tag: Female, 7 years, tibia


title: Biopsy_non-metastatic_NM03_rep 1


title: Biopsy_metastatic_M08_dye-swap_rep 2

tag: Female, 37 years, right tibia


title: Biopsy_non-metastatic_NM01_rep 1


title: Biopsy_metastatic_M10_rep 1

source_name: Total RNA from osteosarcoma biopsy of metastatic patient labelled with AlexFluor647


title: Biopsy_metastatic_M11_rep 1

tag: Female, 29 years, sacrum


title: Biopsy_metastatic_M08_rep 1


title: Biopsy_metastatic_M03_dye-swap_rep 2

tag: Female, 19 years, right femur


title: Biopsy_metastatic_M09_rep 1

tag: Female, 13 years, right femur

tag: HDF, COLO-16, LNCap, DU145, SK-BR3, U2OS, HT29, DG75


title: Biopsy_metastatic_M05_dye-swap_rep 2

tag: Male, 12 years, left femur


title: Biopsy_metastatic_M06_dye-swap_rep 2

tag: Female, 15 years, right humerus


title: Biopsy_metastatic_M11_dye-swap_rep 2


title: Biopsy_metastatic_M04_dye-swap_rep 2

tag: Male, 14 years, right femur


title: Biopsy_metastatic_M05_rep 1


title: Biopsy_metastatic_M09_dye-swap_rep 2


title: Biopsy_metastatic_M07_rep 1

tag: Female, 27 years, right humerus


title: Biopsy_non-metastatic_NM04_dye-swap_rep 2


title: Biopsy_metastatic_M03_rep 1

source_name: Total RNA from osteosarcoma biopsy of metastatic patient labelled with AlexaFluor647


title: Biopsy_metastatic_M01_dye-swap_rep 2

tag: Female, 76 years, left tibia


title: Biopsy_metastatic_M06_rep 1


title: Biopsy_metastatic_M04_rep 1


title: Hybridization of TFT-resistant H630-4TFT cell line versus parental cell line

status: Public on Jun 15 2010

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

country: Netherlands

institute: Vrije Universiteit Medical Center

description: The log2 ratios were calculated between the H630 cell line variant resistant to TFT (H630-4TFT) and the parental H630 cell line, labeled with the same dyes and hybridized on different arrays within the same 4 × 44 K slide according to Buffart et al.(Genes Chromosomes Cancer. 2008 Nov;47(11):994-1004), PMID: 18663753.

hyb_protocol: Hybridization protocol available via www.agilent.com.

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.

data_processing:
The log2 resistant cell line to parental cell line ratio was calculated for each spot and normalized against the median of the ratios.

Raw data is available in the supplementary files linked to the Series GSE18137 record. H630-4TFT raw data is in channel 1 of MAF_251495016981_S01_CGH-v4_95_Feb07_1_3.txt; parental H630 raw data is in channel 1 of MAF_251495016981_S01_CGH-v4_95_Feb07_1_1.txt.

label_protocol: Labeling of genomic DNA was performed using the Enzo Genomic DNA Labeling kit according to the manufacturer’s instructions (Enzo Life Sciences, Farmingdale, NY, USA).

growth_protocol: Resistance to TFT(5-chloro-6-[1-(2-iminopyrrolidinyl)methyl]-uracil hydrochloride) was induced by 4 hr exposure every 7 days (starting at 5 μM) over a period of 12 months. This resulted in the H630 variant H630-4TFT resistant to 250 μM.

extract_protocol: The genomic DNA of the cell lines was isolated using the Wizard Genomic DNA Purification Kit (Promega, A1120).

tag: cell line

tag: cell line description

value: H630 variant resistant to TFT

value: derived from a human colorectal carcinoma


title: Adult_Remec_4

status: Public on Jul 16 2010

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12332

hyb_protocol: Affymetrix standard protocol. Amount labeled target hybridized to array: 2.5µg The arrays were washed and stained using a Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0007.

scan_protocol: Probe arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G and Affymetrix scanning software Genechip Operating Software Version 1.4.

data_processing: Analysis method: Affymetrix Expression Console and GeneSpring 10.

label: Biotin

organism: Mus musculus

source_name: juxtaglomerular complex

label_protocol: The FL-Ovation cDNA Biotin Module V2 (NuGEN) is used to chemically modify fragments and label target sense cDNA.

extract_protocol: Potter protocol: 'RNA purification'

treatment_protocol:
pool size: approx 2 Adult Kidneys
Pooled sample: Yes
Dissection Method: Juxtaglomerular cells from Ren1c-YFP transgenic mice kidneys were isolated using a combination of  Collagenase A digestion and sieving followed by FACS.
Renin expressing cells were isolated by FACS from kidneys of our Ren1c-YFP mice (Pentz et al., 2008) in which renin expression is marked by YFP. The kidneys were dissected out in ice-cold PBS and the kidney and isolated cells were kept cold at all times. The medulla was removed and the cortex was digested with collagenase A, washed and then digested with trypsin. After stopping the trypsin digestion, the cells were washed and filtered through a 100µm filter. Red blood cells were lysed, the cells were washed and then filtered through a 70µm filter. Cells were pelleted, resuspended in 2%FBS/PBS and sorted immediately using a high-speed digital BD FACS Aria II Cell Sorter. As a control, cells were isolated in parallel from wild type kidneys to provide the baseline for excluding unlabeled cells.

tag: gene reported

tag: strain

tag: Sex

value: Male

tag: developmental stage

value: Adult

tag: theiler stage

tag: somite count

tag: developmental landmark


title: Remec_PO1

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12327

treatment_protocol:
pool size: approx 4 E18.5 kidneys
Pooled sample: Yes
Dissection Method: Juxtaglomerular cells from Ren1c-YFP transgenic mice kidneys were isolated using a combination of  Collagenase A digestion and sieving followed by FACS.
Renin expressing cells were isolated by FACS from kidneys of our Ren1c-YFP mice (Pentz et al., 2008) in which renin expression is marked by YFP. The kidneys were dissected out in ice-cold PBS and the kidney and isolated cells were kept cold at all times. The medulla was removed and the cortex was digested with collagenase A, washed and then digested with trypsin. After stopping the trypsin digestion, the cells were washed and filtered through a 100µm filter. Red blood cells were lysed, the cells were washed and then filtered through a 70µm filter. Cells were pelleted, resuspended in 2%FBS/PBS and sorted immediately using a high-speed digital BD FACS Aria II Cell Sorter. As a control, cells were isolated in parallel from wild type kidneys to provide the baseline for excluding unlabeled cells.

value: unknown


title: Remec_PO3

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12329


title: Adult_Remec_2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12330


title: Adult_Remec_3

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12331

treatment_protocol:
pool size: approx 2 Adult Kidneys
Pooled sample: Yes
Dissection Method: Juxtaglomerular cells from Ren1c-YFP transgenic mice kidneys were isolated using a combination of  Collagenase A digestion and sieving followed by FACS.
Adult Renin-GFP male mice were euthanized by standard carbon dioxide Renin expressing cells were isolated by FACS from kidneys of our Ren1c-YFP mice (Pentz et al., 2008) in which renin expression is marked by YFP. The kidneys were dissected out in ice-cold PBS and the kidney and isolated cells were kept cold at all times. The medulla was removed and the cortex was digested with collagenase A, washed and then digested with trypsin. After stopping the trypsin digestion, the cells were washed and filtered through a 100µm filter. Red blood cells were lysed, the cells were washed and then filtered through a 70µm filter. Cells were pelleted, resuspended in 2%FBS/PBS and sorted immediately using a high-speed digital BD FACS Aria II Cell Sorter. As a control, cells were isolated in parallel from wild type kidneys to provide the baseline for excluding unlabeled cells.


title: Biopsy_metastatic_M02_dye-swap_rep 2

tag: Male, 39 years, left pelvis


title: Biopsy_metastatic_M02_rep 1


title: Remec_PO2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12328


title: Hybridization of the H630 cell line versus XX reference pool

description: Reference consists of pooled DNA from the blood of 18 healthy individuals.

data_processing:
The log2 H630 cell line to reference ratio was calculated for each spot and normalized against the median of the ratios.

Raw data is available in the supplementary files linked to the Series GSE18137 record. H630 raw data is in channel 1 of MAF_251495016981_S01_CGH-v4_95_Feb07_1_1.txt; normal reference raw data is in channel 2 of MAF_251495016981_S01_CGH-v4_95_Feb07_1_1.txt.

source_name: Normal reference (XX)

extract_protocol: DNAzol (Invitrogen) according to manufacturer's protocol.

tag: tissue

value: blood

tag: reference

value: pooled DNA from 18 healthy individuals


title: Biopsy_metastatic_M01_rep 1

tag: HDF, COLO-16, LNCap, DU145, SK-BR3, U2OS, HT29, DG75


title: 13R2778Rpt

status: Public on Jul 19 2010

city: Chapel Hill

first: Jen Jen

last: Yeh

state: NC

address: LCCC, 450 West Drive

department: Surgical Oncology

institute: University of North Carolina at Chapel Hill

hyb_protocol: As described in Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp labeling) v 5.7 [Manual G4140-90050]

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent G2505C fluorescent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction (v10.5) software.

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken using Agilent Feature Extraction (v10.5) software.

source_name: Human Reference

extract_protocol: Total RNA isolated by Qiagen

value: Stratagene Human reference RNA

source_name: Pancreas Tissue

extract_protocol: Qiagen Rneasy Kit

value: Patient Primary Pancreatic Tumor

tag: tumor type


title: Proximal stomach adenocarcinoma 61

status: Public on May 29 2010

city: Lund

first: Anna

middle: Isinger

last: Ekstrand

address: Barngatan 2b

department: Oncology

country: Sweden

institute: Clinical Sciences

description: Gastroesophageal cancer

hyb_protocol: Hybridizations were performed in 4 x SSC, 0.1% SDS, 0,5 NOTE human 0,8-1,0 µg/µl Cot-1 DNA at 42degC overnight. Arrays were washed three times 4xSSC RT, twice 2xSSC / 0.1% SDS at 42degC, one time 0.2xSSC, and  one time 0.1xSSC RT.

scan_protocol: Arrays were scanned in Agilent scanner (Agilent Technologies)

data_processing: Image analysis was performed using Genepix v4.0. Result files were uploaded into BASE where they were filtered and normalized.

source_name: Gastric adenocarcinoma, fresh frozen tissue

label_protocol: Direct labeled by random priming (Promega, Pronto)

extract_protocol: Total RNA extracted using Trizol (Invitrogen) according to the manufacures recommendations. RNA integrity was checked on a Bioanalyzer (Agilent).

tag: biomaterial

value: Fresh frozen tissue

tag: gender

tag: tumor stage

value: II

source_name: Human Reference RNA (Stratagene), pool of ten cell lines

value: Pool of 10 different cellines


title: Junctional adenocarcinoma 98

description: Gastroesophageal cancer

source_name: Gastroesophageal adenocarcinoma (type II), fresh frozen

value: Female


title: Junctional adenocarcinoma 98_replicate_2

description: Gastroesophageal cancer


title: Proximal stomach adenocarcinoma 46

description: Gastroesophageal cancer


title: Proximal stomach adenocarcinoma 57

description: Gastroesophageal cancer

value: IV


title: Hybridization of TFT-resistant H630-cTFT cell line versus parental cell line

description: The log2 ratios were calculated between the H630 cell line variant resistant to TFT (H630-cTFT) and the parental H630 cell line, labeled with different dyes and hybridized on different arrays within the same 4 × 44 K slide according to Buffart et al. (Genes Chromosomes Cancer. 2008 Nov;47(11):994-1004), PMID: 18663753.

data_processing:
The log2 resistant cell line to parental cell line ratio was calculated for each spot and normalized against the median of the ratios.

Raw data is available in the supplementary files linked to the Series GSE18137 record. H630-cTFT raw data is in channel 2 of MAF_251495016981_S01_CGH-v4_95_Feb07_1_3.txt; parental H630 raw data is in channel 1 of MAF_251495016981_S01_CGH-v4_95_Feb07_1_1.txt.

growth_protocol: Resistance to TFT(5-chloro-6-[1-(2-iminopyrrolidinyl)methyl]-uracil hydrochloride) was induced by continuous exposure (starting at 0.5 μM to stepwise increasing concentrations of TFT (depending on the growth rate observed)) over a period of 12 months. This resulted in the H630 variant H630-cTFT resistant to 20μM.

tag: cell line


title: Proximal stomach adenocarcinoma 20

description: Gastroesophageal cancer

value: I


title: Distal esophageal adenocarcinoma 35

description: Gastroesophageal cancer

source_name: Esophageal adenocarcinoma (type I), fresh frozen tissue

value: III


title: Junctional adenocarcinoma 63

description: Gastroesophageal cancer


title: Distal esophageal adenocarcinoma 70

description: Gastroesophageal cancer


title: Junctional adenocarcinoma 42

description: Gastroesophageal cancer


title: Junctional adenocarcinoma 59

description: Gastroesophageal cancer


title: Distal esophageal adenocarcinoma 202

description: Gastroesophageal cancer


title: Junctional adenocarcinoma 68

description: Gastroesophageal cancer


title: Distal esophageal adenocarcinoma 39

description: Gastroesophageal cancer


title: Junctional adenocarcinoma 21

description: Gastroesophageal cancer


title: Junctional adenocarcinoma 184

description: Gastroesophageal cancer


title: Distal esophageal adenocarcinoma 162

description: Gastroesophageal cancer


title: Proximal stomach adenocarcinoma 1

description: Gastroesophageal cancer


title: Distal esophageal adenocarcinoma 112

description: Gastroesophageal cancer


title: Proximal stomach adenocarcinoma 15

description: Gastroesophageal cancer


title: Proximal stomach adenocarcinoma 110

description: Gastroesophageal cancer


title: Distal esophageal adenocarcinoma 117

description: Gastroesophageal cancer


title: Proximal stomach adenocarcinoma 110_replicate_2

description: Gastroesophageal cancer


title: Distal esophageal adenocarcinoma 137

description: Gastroesophageal cancer


title: Junctional adenocarcinoma 133

description: Gastroesophageal cancer


title: Distal esophageal adenocarcinoma 104

description: Gastroesophageal cancer


title: Distal esophageal adenocarcinoma 191

description: Gastroesophageal cancer


title: Junctional adenocarcinoma 155

description: Gastroesophageal cancer


title: 35 Polypoid lesion

status: Public on May 27 2010

city: Zurich

first: Giancarlo

last: Marra

address: Winterthurerstrasse 190

department: Molecular Cancer Research

country: Switzerland

institute: University of Zurich

description:
endoscopic biopsies
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

hyb_protocol: After ribosomal RNA reduction, the RNA sample was reverse-transcribed to cDNA with random hexamers tagged with a T7 promoter.  The cDNA was amplified with T7 RNA polymerase and subjected to a second cDNA synthesis.  The sense-oriented, single-stranded DNA produced with this step was then fragmented, biotin-labeled, and hybridized to the GeneChip Human Exon 1.0 ST array (Affymetrix).

scan_protocol: Arrays were analyzed in the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Cell intensities (.CEL files) were measured with Affymetrix GeneChip Operating Software (GCOS), and Affymetrix Expression Console Software as well as PartekGenomicSuite ver6.5 Software was used for quality assessment.

source_name: colorectum

label_protocol: Biotin labeling

extract_protocol: Sampling in RNAlater and total RNA extraction with Rneasy Mini Kit Qiagen.

tag: colon segment

value: sigma


title: Proximal stomach adenocarcinoma 107

description: Gastroesophageal cancer


title: 36 Polypoid lesion

value: ascending


title: 33 Normal mucosa

value: descending


title: 32 Polypoid lesion


title: 33 Polypoid lesion


title: 37 Normal mucosa


title: 35 Normal mucosa


title: 34 Normal mucosa


title: 32 Normal mucosa


title: 36 Normal mucosa


title: 34 Polypoid lesion


title: 30 Normal mucosa

value: rectum


title: 37 Polypoid lesion


title: 31 Polypoid lesion


title: 30 Polypoid lesion


title: 29 Normal mucosa


title: 31 Normal mucosa


title: 29 Polypoid lesion


title: 27 Polypoid lesion


title: 26 Normal mucosa


title: 25 Normal mucosa


title: 24 Normal mucosa


title: 27 Normal mucosa


title: 25 Polypoid lesion


title: 23 Normal mucosa


title: 21 Nonpolypoid lesion


title: 22 Normal mucosa


title: 23 Polypoid lesion


title: 22 Polypoid lesion


title: 18 Nonpolypoid lesion


title: 20 Normal mucosa


title: 26 Polypoid lesion


title: 24 Polypoid lesion


title: 28 Polypoid lesion


title: 20 Nonpolypoid lesion


title: 19 Nonpolypoid lesion


title: 17 Normal mucosa

value: cecum


title: 16 Normal mucosa

value: transversum


title: 17 Nonpolypoid lesion


title: 19 Normal mucosa


title: 28 Normal mucosa


title: 21 Normal mucosa


title: 16 Nonpolypoid lesion


title: 12 Normal mucosa


title: 14 Normal mucosa


title: 18 Normal mucosa


title: 15 Normal mucosa


title: 13b Nonpolypoid lesion


title: 11 Normal mucosa


title: 13b Normal mucosa


title: 15 Nonpolypoid lesion


title: 14 Nonpolypoid lesion


title: 11 Nonpolypoid lesion


title: 12 Nonpolypoid lesion


title: 13a Nonpolypoid lesion


title: 13a Normal mucosa


title: 9 Nonpolypoid lesion


title: 8 Normal mucosa

value: hepatic flexure


title: 9 Normal mucosa


title: 10 Normal mucosa


title: 7 Normal mucosa


title: 6 Nonpolypoid lesion


title: 7 Nonpolypoid lesion


title: 3 Nonpolypoid lesion


title: 10 Nonpolypoid lesion


title: 2b Nonpolypoid lesion


title: 8 Nonpolypoid lesion


title: 4 Nonpolypoid lesion


title: 2b Normal mucosa


title: 6 Normal mucosa


title: 5 Normal mucosa


title: 2a Nonpolypoid lesion


title: 5 Nonpolypoid lesion


title: 4 Normal mucosa


title: 2a Normal mucosa


title: 1a Normal mucosa


title: 1b Nonpolypoid lesion


title: 1b Normal mucosa


title: EPN_483, recurrent

status: Public on Oct 01 2009

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

institute: CU Anschutz Medical Campus

description: Gene expression data from surgical tumor sample of ependymoma

hyb_protocol: Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.

data_processing: Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 18,624 genes.

source_name: EPN_483, recurrent

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol and ENZO biotin-labelling kit protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol:
Tumor samples were snap frozen in liquid nitrogen immediated after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500)
RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

value: brain tumor (ependymoma)

tag: genotype


title: EPN_459, non-recurrent

source_name: EPN_459, non-recurrent


title: 1a Nonpolypoid lesion


title: 3 Normal mucosa


title: EPN_507, recurrent

source_name: EPN_507, recurrent


title: EPN_388, non-recurrent

source_name: EPN_388, non-recurrent


title: EPN_306, non-recurrent

source_name: EPN_306, non-recurrent


title: EPN_419, non-recurrent

source_name: EPN_419, non-recurrent


title: EPN_393, recurrent

source_name: EPN_393, recurrent


title: EPN_319, recurrent

source_name: EPN_319, recurrent


title: EPN_242, recurrent

source_name: EPN_242, recurrent


title: EPN_285, non-recurrent

source_name: EPN_285, non-recurrent


title: EPN_392, non-recurrent

source_name: EPN_392, non-recurrent


title: EPN_246, recurrent

source_name: EPN_246, recurrent


title: EPN_364, recurrent

source_name: EPN_364, recurrent


title: EPN_135, recurrent

source_name: EPN_135, recurrent


title: EPN_80, non-recurrent

source_name: EPN_80, non-recurrent


title: EPN_110, recurrent

source_name: EPN_110, recurrent


title: MF patient 38

status: Public on Sep 15 2009

first: Rocio

last: Salgado

address: Passeig Marítim, 25-29

institute: IMIM-Hospital del Mar

description: MFt 38

hyb_protocol: Human cot-1 DNA, Agilent 10x blocking agent and Agilent 2x hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version 8.1).

data_processing: Linear normalized background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: Skin tumor, tumor-stage mycosis fungoides

label_protocol: 0.5µg-1.5 µg of total DNA previously digested were primed with 5 µl Random primers at 95ºC for 3 min. Then the primed DNA was mixed with the Labeling Master Mix (containing 2 µl Nuclease free water, 10 µl 5X Buffer, 10X dNTP, 3 µl Cy3 or Cy5 depending on sample or control DNA labeling and 1µl Exo-Klenow fragment) and incubating at 37ºC for 2 hours.

extract_protocol: Total DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany) following the protocol supplied by the manufacturer.

treatment_protocol: Skin biopsies were snap frozen.

tag: age

value: skin tumor

tag: disease

value: tumor-stage mycosis fungoides

source_name: Commercial pools of healthy DNA (Promega, Madison, WI, USA)

value: Peripheral blood


title: MF patient 40

description: MFt 40


title: MF patient 33

description: MFt 33

value: Male


title: MF patient 36

description: MFt 36


title: MF patient 41

description: MFt 41


title: MF patient 32

description: MFt 32


title: MF patient 24

description: MFt 24


title: MF patient 25

description: MFt 25


title: MF patient 35

description: MFt 35


title: MF patient 20

description: MFt 20


title: MF patient 29

description: MFt 29


title: MF patient 26

description: MFt 26


title: MF patient 34

description: MFt 34


title: MF patient 37

description: MFt 37


title: MF patient 30

description: MFt 30


title: MF patient 21

description: MFt 21


title: MF patient 28

description: MFt 28


title: MF patient 31

description: MFt 31


title: MF patient 22

description: MFt 22


title: MF patient 18

description: MFt 18


title: MF patient 39

description: MFt 39


title: MF patient 23

description: MFt 23


title: MF patient 27

description: MFt 27


title: MF patient 16

description: MFt 16


title: MF patient 17

description: MFt 17


title: EPN_416, non-recurrent

source_name: EPN_416, non-recurrent


title: EPN_318, non-recurrent

source_name: EPN_318, non-recurrent


title: MF patient 14

description: MFt 14


title: MF patient 19

description: MFt 19


title: MF patient 15

description: MFt 15


title: breast cancer cell line_CAL-148

status: Public on Jan 12 2009

city: South San Francisco

first: Mark

last: Lackner

state: CA

address: 1 DNA Way

institute: Genentech

description: breast cancer cell line_CAL-148

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133P 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Breast cancer

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

growth_protocol: Cell maintained in RPMI1640 or DMEM supplemented with 10% fetal bovine serum, non-essential amino acids and 2mmol/L L-glutamine

extract_protocol: Qiagen Rneasy kit used for the extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells untreated

value: Basal

value: Nonamplified


title: breast cancer cell line_SW527

description: breast cancer cell line_SW527


title: breast cancer cell line_HCC70

description: breast cancer cell line_HCC70


title: breast cancer cell line_KPL1

description: breast cancer cell line_KPL1

value: Luminal


title: breast cancer cell line_EVSA-T

description: breast cancer cell line_EVSA-T


title: breast cancer cell line_HCC1419

description: breast cancer cell line_HCC1419

value: Her2 amplified


title: breast cancer cell line_HCC2218

description: breast cancer cell line_HCC2218


title: breast cancer cell line_ZR75-30

description: breast cancer cell line_ZR75-30


title: breast cancer cell line_JIMT-1

description: breast cancer cell line_JIMT-1


title: breast cancer cell line_CAL-120

description: breast cancer cell line_CAL-120


title: breast cancer cell line_CAL-51

description: breast cancer cell line_CAL-51


title: breast cancer cell line_HCC38

description: breast cancer cell line_HCC38


title: breast cancer cell line_HCC1954

description: breast cancer cell line_HCC1954


title: breast cancer cell line_HDQ-P1

description: breast cancer cell line_HDQ-P1


title: breast cancer cell line_HCC1569

description: breast cancer cell line_HCC1569


title: breast cancer cell line_HCC1395

description: breast cancer cell line_HCC1395


title: breast cancer cell line_EFM19

description: breast cancer cell line_EFM19


title: breast cancer cell line_UACC-893

description: breast cancer cell line_UACC-893


title: breast cancer cell line_HCC1937

description: breast cancer cell line_HCC1937


title: breast cancer cell line_HCC1428

description: breast cancer cell line_HCC1428


title: breast cancer cell line_HCC1143

description: breast cancer cell line_HCC1143


title: breast cancer cell line_HCC1500

description: breast cancer cell line_HCC1500


title: breast cancer cell line_EFM-192A

description: breast cancer cell line_EFM-192A


title: breast cancer cell line_MFM-223

description: breast cancer cell line_MFM-223


title: breast cancer cell line_CAL85-1

description: breast cancer cell line_CAL85-1


title: breast cancer cell line_UACC-812

description: breast cancer cell line_UACC-812


title: breast cancer cell line_MDA-MB-453

description: breast cancer cell line_MDA-MB-453


title: breast cancer cell line_MDA-MB-415

description: breast cancer cell line_MDA-MB-415


title: breast cancer cell line_MDA-MB-231

description: breast cancer cell line_MDA-MB-231


title: breast cancer cell line_SKBR3

description: breast cancer cell line_SKBR3


title: breast cancer cell line_CAMA-1

description: breast cancer cell line_CAMA-1


title: breast cancer cell line_ZR75-1

description: breast cancer cell line_ZR75-1


title: breast cancer cell line_T47D

description: breast cancer cell line_T47D


title: breast cancer cell line_MDA-MB-436

description: breast cancer cell line_MDA-MB-436


title: breast cancer cell line_MDA-MB-361

description: breast cancer cell line_MDA-MB-361


title: breast cancer cell line_MCF7

description: breast cancer cell line_MCF7


title: breast cancer cell line_BT-549

description: breast cancer cell line_BT-549


title: breast cancer cell line_MDA-MB-435s

description: breast cancer cell line_MDA-MB-435s


title: breast cancer cell line_Hs578T

description: breast cancer cell line_Hs578T


title: breast cancer cell line_MDA-MB-468

description: breast cancer cell line_MDA-MB-468


title: breast cancer cell line_DU4475

description: breast cancer cell line_DU4475


title: breast cancer cell line_MDA-MB-175VII

description: breast cancer cell line_MDA-MB-175VII


title: breast cancer cell line_HCC1806

description: breast cancer cell line_HCC1806


title: breast cancer cell line_BT474

description: breast cancer cell line_BT474


title: breast cancer cell line_BT483

description: breast cancer cell line_BT483


title: breast cancer cell line_AU565

description: breast cancer cell line_AU565


title: NB tumor_2704

status: Public on Dec 31 2008

city: Genova

first: PAOLA

last: SCARUFFI

state: GE

address: LARGO R. BENZI, 10

country: Italy

institute: "San Martino" Hospital

description: Microarray images were processed by Feature Extraction software (version 9.5.3.1, Agilent Technologies).

hyb_protocol: Dye incorporations of post-labelling products were measured by ND-1000 spectrophotometer (NanoDrop Technologies) and the parameters that predicted successful hybridization were a minimum Cy3 incorporation of 0.5 pmol/ul and Cy5 incorporation of 0.3 pmol/ul. Fluorescent-labelled reference and tumour DNAs (1 ug each) were mixed with 50 ug of human Cot-1 DNA (Invitrogen Life Technologies) and control targets (Agilent Technologies) and were hybridized to Human Genome CGH Microarray 4x44K (Agilent Technologies). Slides were hybridized in SureHyb gasket (Agilent Technologies) placed in rotisserie (20 RPM rotation speed) in hybridization oven at 65° C for 24 hrs. After hybridization the slides were washed with Agilent washing solutions (including Stabilization and Drying solutions), according to Agilent Oligonucleotide array-based CGH for genomic DNA analysis protocol (version 5.0).

scan_protocol: Slides were scanned at 10 µm resolution by using the Agilent G2565BA Scanner. Scan Settings: • Scan region was set to Scan Area (61 × 21.6 mm). • Green PMT was set to 100%. • Red PMT was set to 100%.

data_processing:
Array CGH analysis was performed by using the aCGH Analytics Software (version 3.5.14, Agilent Technologies). A statistical analysis based on hypergeometric Z-scores was used to identify all aberrant regions in each sample. The scoring method has two steps. First, it identifies the total number of probes with log ratios significantly different from zero in a normal sample. These probes are referred to as aberrant probes and the normal sample is referred to as calibration sample. These statistics can be calculated using a sample with no genetic abnormalities or they can be calculated from the test array itself, which is the recommended procedure and the method used in this study. The log ratios from each sample are converted to normalized log ratios. In the normalization step, the expected mean log ratio is subtracted from all log ratios, and these modified log ratios are divided by the estimated variance of the log ratios. In this case, the expected mean is set to 0 and variance is computed as the Derivative Log Ratio Spread (DLRSpread) of the array. Chromosomes X and Y are not included in the estimation of mean and variance as differences between arrays in these probes may offset the statistics. The number of probes for which normalized log ratios are above and below the user specified thresholds (2.0, in this case) are counted and reported as the calibration statistics. In the second step, aberrant regions are identified by comparing the proportion of aberrant probes identified in a given region of the genome in the test sample as compared to that calculated in the first step. If significantly more probes are detected as aberrant in a given genomic region in the test sample then this region gets a higher score and is called as an aberrant region. In this step the over or under abundance of aberrant log ratios is analyzed for each sample using the user specified window size. In this case, a moving window of size 2 Mb is used. For each position of this window, the number of probes with log ratios above and below the user specified cut off of 2.0 is calculated. Then, a z-score is computed that measures the over or under abundance of aberrant positive log ratios in that particular position of 2 Mb window using an equation that reflects a hypergeometric distribution. The score is assigned to the probe in the middle of that window. This score identifies statistically significant groups of probes that appear to deviate from the typical distribution of log ratios around the mean for the given microarray and provides predictive power to make calls of gain/amplification or deletion events. Probes with a log ratio value > 2 were considered as amplified.

Z-score data is not available for GEO submission.

source_name: Human primary neuroblastoma tumor sample (frozen) from male patient

label_protocol: 1.5 ug of test genomic DNAs were digested with AluI/RsaI restriction enzyme mix (Promega, Madison, WI). Fragmented DNA was labelled by direct enzymatic incorporation of fluorescent tags. Genomic DNA was labelled with Cy5-dUTP (Perkin Elmer, Wellesley, MA) using the Random-Primed Bioprime DNA Labeling kit (Invitrogen Life Technologies, Carlsbad, CA). Briefly, 50 ul reaction mix containing dATP, dGTP and dTTP (120 uM each), dUTP (60 uM) and Cy5-dUTP (60 uM) was incubated with Klenow Fragment (40 units) at 37°C for 2 hrs. Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore, Billerica, MA) according to the manufacturer protocol.

extract_protocol: Total genomic DNA was extracted from the tumor sample according to Sambrook et al. (Sambrook J, Fritsch EF and Maniatis T: Molecular Cloning. A Laboratory Manual. Second edition. Cold Spring Harbor Laboratory Press, 1989)

tag: The surgically resected tumor was handled according to guidelines by the International Neuroblastoma Pathology Committee (Shimada H, Umehara S, Monobe Y, Hachitanda Y, Nakagawa A, Goto S, Gerbing RB, Stram DO, Lukens JN, Matthay KK. International neuroblastoma pathology classification for prognostic evaluation of patients with peripheral neuroblastic tumors

value: a report from the Children's Cancer Group. Cancer 2001;92:2451-61) and tumor cell content was evaluated. The sample was classified as "Neuroblastoma Schwannian stroma poor tumor" containing more than 80% malignant neuroblasts. According to the criteria of the International Neuroblastoma Staging System, the tumor was classified as stage 4 neuroblastoma.

source_name: normal male DNA

label_protocol: 1.5 ug of reference genomic DNAs were digested with AluI/RsaI restriction enzyme mix (Promega, Madison, WI). Fragmented DNA was labelled by direct enzymatic incorporation of fluorescent tags. Genomic DNA was labelled with Cy3-dUTP (Perkin Elmer, Wellesley, MA) using the Random-Primed Bioprime DNA Labeling kit (Invitrogen Life Technologies, Carlsbad, CA). Briefly, 50 ul reaction mix containing dATP, dGTP and dTTP (120 uM each), dUTP (60 uM) and Cy3-dUTP (60 uM) was incubated with Klenow Fragment (40 units) at 37°C for 2 hrs. Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore, Billerica, MA) according to the manufacturer protocol.

extract_protocol: Commercial DNA

tag: Male genomic DNA


title: NB tumor_2035


title: NB tumor_2056

tag: normal male DNA


title: NB tumor_2425


title: NB tumor_1900


title: NB tumor_1995


title: NB tumor_2362

source_name: Human primary neuroblastoma tumor sample (frozen) from female patient

source_name: normal female DNA

tag: Female genomic DNA


title: NB tumor_1905

label_protocol: 1.5 ug of test genomic DNAs were digested with AluI/RsaI restriction enzyme mix (Promega, Madison, WI). Fragmented DNA was labelled by direct enzymatic incorporation of fluorescent tags. Genomic DNA was labelled with Cy3-dUTP (Perkin Elmer, Wellesley, MA) using the Random-Primed Bioprime DNA Labeling kit (Invitrogen Life Technologies, Carlsbad, CA). Briefly, 50 ul reaction mix containing dATP, dGTP and dTTP (120 uM each), dUTP (60 uM) and Cy3-dUTP (60 uM) was incubated with Klenow Fragment (40 units) at 37°C for 2 hrs. Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore, Billerica, MA) according to the manufacturer protocol.

label_protocol: 1.5 ug of reference genomic DNAs were digested with AluI/RsaI restriction enzyme mix (Promega, Madison, WI). Fragmented DNA was labelled by direct enzymatic incorporation of fluorescent tags. Genomic DNA was labelled with Cy5-dUTP (Perkin Elmer, Wellesley, MA) using the Random-Primed Bioprime DNA Labeling kit (Invitrogen Life Technologies, Carlsbad, CA). Briefly, 50 ul reaction mix containing dATP, dGTP and dTTP (120 uM each), dUTP (60 uM) and Cy5-dUTP (60 uM) was incubated with Klenow Fragment (40 units) at 37°C for 2 hrs. Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore, Billerica, MA) according to the manufacturer protocol.


title: NB tumor_2140


title: NB tumor_2100


title: NB tumor_1965


title: NB tumor_1864


title: NB tumor_1893


title: NB tumor_1768


title: NB tumor_1869


title: NB tumor_1641


title: NB tumor_1699


title: NB tumor_1889


title: NB tumor_1560


title: NB tumor_1439


title: NB tumor_1243


title: NB tumor_1684


title: NB tumor_984


title: NB tumor_1506


title: NB tumor_1401


title: NB tumor_1292


title: NB tumor_1198


title: Peripheral blood cells in patient with poly-articular type juvenile idiopathic arthritis 5

status: Public on Jul 01 2008

city: Ibaraki

first: Norihiro

last: Nishimoto

state: Osaka

address: 7-7-20, Saito-Asagi

country: Japan

institute: Wakayama Medical University

description: Poly-articular type juvenile idiopathic arthritis 5

hyb_protocol: The labeled aRNAs (mixture of Cy3 and Cy5) was hybridized onto microarray slide for 16hours at 42℃. Slides were washed in 2xSSC+0.1%SDS, 2xSSC, 1xSSC, and 0.1xSSC before air pressure drying and scanning.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray Lite (PerkinElmer, Boston, MA) and signal values were calculated using DNASIS Array (Hitachi Software Engineering, Tokyo, Japan).

data_processing: Log2-ratios of median subtracted background intensity levels were analyzed. VALUE is Log2-ratios of Channel 1 (Cy3) to Channel 2 (Cy5).The Cy3/Cy5 ratios of all spots on the DNA microarray were normalized by the method of global ratio median normalization.

label_protocol: Total RNA was amplified, and 5-(3-aminoallyl)-UTP was incorporated to it using AminoAllyl MessageAmp aRNA amplification Kit (Ambion, Austin, Texas). The amino allyl aRNA was furgher labeled by coupling reaction with NHS ester fluorescent dye, Cy3.

extract_protocol: Total RNA was extracted according to the manufacture’s instructions using PAXgene Blood RNA Kit (Qiagen, Valencia, CA, USA) with the optional on-column DNase digestion as described in the manufacture’s protocol.

source_name: Peripheral blood cells from 45 healthy volunteers

label_protocol: Total RNA was amplified, and 5-(3-aminoallyl)-UTP was incorporated to it using AminoAllyl MessageAmp aRNA amplification Kit (Ambion, Austin, Texas). The amino allyl aRNA was furgher labeled by coupling reaction with NHS ester fluorescent dye, Cy5.

tag: Common reference sample from 45 healthy volunteers


title: NB tumor_806


title: NB tumor_789


title: NB tumor_1558


title: Peripheral blood cells in patient with poly-articular type juvenile idiopathic arthritis 1

description: Poly-articular type juvenile idiopathic arthritis 1


title: NB tumor_1276


title: Peripheral blood cells in patient with poly-articular type juvenile idiopathic arthritis 6

description: Poly-articular type juvenile idiopathic arthritis 6


title: NB tumor_1445


title: Peripheral blood cells in patient with poly-articular type juvenile idiopathic arthritis 3

description: Poly-articular type juvenile idiopathic arthritis 3


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 51

description: Systemic onset juvenile idiopathic arthritis 51


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 49

description: Systemic onset juvenile idiopathic arthritis 49


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 47

description: Systemic onset juvenile idiopathic arthritis 47


title: NB tumor_535


title: Peripheral blood cells in patient with poly-articular type juvenile idiopathic arthritis 2

description: Poly-articular type juvenile idiopathic arthritis 2


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 43

description: Systemic onset juvenile idiopathic arthritis 43


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 39

description: Systemic onset juvenile idiopathic arthritis 39


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 37

description: Systemic onset juvenile idiopathic arthritis 37


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 30

description: Systemic onset juvenile idiopathic arthritis 30


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 48

description: Systemic onset juvenile idiopathic arthritis 48


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 41

description: Systemic onset juvenile idiopathic arthritis 41


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 44

description: Systemic onset juvenile idiopathic arthritis 44


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 32

description: Systemic onset juvenile idiopathic arthritis 32


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 40

description: Systemic onset juvenile idiopathic arthritis 40


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 29

description: Systemic onset juvenile idiopathic arthritis 29


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 34

description: Systemic onset juvenile idiopathic arthritis 34


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 50

description: Systemic onset juvenile idiopathic arthritis 50


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 33

description: Systemic onset juvenile idiopathic arthritis 33


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 38

description: Systemic onset juvenile idiopathic arthritis 38


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 31

description: Systemic onset juvenile idiopathic arthritis 31


title: Peripheral blood cells in patient with poly-articular type juvenile idiopathic arthritis 4

description: Poly-articular type juvenile idiopathic arthritis 4


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 42

description: Systemic onset juvenile idiopathic arthritis 42


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 46

description: Systemic onset juvenile idiopathic arthritis 46


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 45

description: Systemic onset juvenile idiopathic arthritis 45


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 28

description: Systemic onset juvenile idiopathic arthritis 28


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 35

description: Systemic onset juvenile idiopathic arthritis 35


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 27

description: Systemic onset juvenile idiopathic arthritis 27


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 26

description: Systemic onset juvenile idiopathic arthritis 26


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 24

description: Systemic onset juvenile idiopathic arthritis 24


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 17

description: Systemic onset juvenile idiopathic arthritis 17


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 19

description: Systemic onset juvenile idiopathic arthritis 19


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 20

description: Systemic onset juvenile idiopathic arthritis 20


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 21

description: Systemic onset juvenile idiopathic arthritis 21


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 18

description: Systemic onset juvenile idiopathic arthritis 18


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 25

description: Systemic onset juvenile idiopathic arthritis 25


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 23

description: Systemic onset juvenile idiopathic arthritis 23


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 22

description: Systemic onset juvenile idiopathic arthritis 22


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 14

description: Systemic onset juvenile idiopathic arthritis 14


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 15

description: Systemic onset juvenile idiopathic arthritis 15


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 5

description: Systemic onset juvenile idiopathic arthritis 5


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 13

description: Systemic onset juvenile idiopathic arthritis 13


title: Peripheral blood cells - healthy child - 7

description: Healthy child 7

source_name: Peripheral blood cells in healthy child

tag: Healthy child 7


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 8

description: Systemic onset juvenile idiopathic arthritis 8


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 1

description: Systemic onset juvenile idiopathic arthritis 1


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 7

description: Systemic onset juvenile idiopathic arthritis 7


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 6

description: Systemic onset juvenile idiopathic arthritis 6


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 4

description: Systemic onset juvenile idiopathic arthritis 4


title: Peripheral blood cells - healthy child - 8

description: Healthy child 8

tag: Healthy child 8


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 11

description: Systemic onset juvenile idiopathic arthritis 11


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 10

description: Systemic onset juvenile idiopathic arthritis 10


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 16

description: Systemic onset juvenile idiopathic arthritis 16


title: Development of a 37K High-density oligo-nucleotide microarray for rainbow trout

status: Public on Jun 01 2008

city: Morgantown

first: Mohamed

last: Salem

state: WV

address: Division of Animal and Nutritional Sciences, West Virginia University

institute: West Virginia University

hyb_protocol: 100 µl of the mixture was immediately loaded onto the array and microarray hybridizations were manually performed using SureHyb chamber (Agilent provided) for 17 hrs at 65°C in a hybridization oven. The hybridization rotation speed was set to 10 rpm.  The hybridization chamber was disassembled while submerged in Gene Expression Wash Buffer 1 at room temperature.  Arrays were washed for 1 min in Gene Expression Wash Buffer 1 at room temperature, followed by 1 min in Gene Expression Wash Buffer 2 at 37°C (Agilent provided).

scan_protocol: ScanArray Lite (Perkin Elmer, Wellesley, MA) microarray scanner was used to scan arrays at 5 µm resolution. GenePix Pro 6.0 software (Molecular Devices Corporation, Sunnyvale, CA) was used to process and analyze array images: align spots, integrate robot-spotting files with the microarray images, quantify spots, calculate local features’ backgrounds and Log-transform the background-subtracted Cy5/Cy3 ratios.

data_processing: All arrays surpassed the quality control parameters established in GenePix Pro software: median signal-to-background > 10, mean of median background < 500, median signal-to-noise > 10, median % > B+1SD > 90, not found features < 5 %,  bad features < 5 %.  Spots were inspected visually to manually flag low quality spots. In addition, spots with signal-to-noise ratio less than three in both channels or saturated spots, over 65535 signal intensity in any channel, were automatically flagged. Flagged spots were filtered out before analysis. Arrays were then normalized so that the mean of the ratio of medians of all spots is equal to one. The normalized Cy5/Cy3 ratios were subjected to t-tests at a significance level of p < 0.05 and fold-change cut-off (fold change > ± 1.5) using TIGR Multiexperiment Viewer (MeV) analysis software (Saeed et al., 2003).

molecule: polyA RNA

organism: Oncorhynchus mykiss

source_name: Atrophying muscle

label_protocol: 1 µg of mRNA from each trout muscle were used as a template in reverse transcription reactions incorporating amino-allyl dUTP into the cDNA using oligo-d (T) primer and Superscript II reverse transcriptase (Invitrogen). The synthesized cDNAs from atrophying (fertile fish) and nonatrophying muscles (sterile fish) were differentially labeled using N-hydroxysuccinate-derived Cy3 or Cy5 dyes (GE Healthcare, Piscataway, NJ).  Labeled cDNAs were purified using a PCR purification kit (Qiagen) to remove unincorporated dyes. Quality of the labeling reactions were checked by measuring the yield (cDNA concentration) and specific activity (Concentration of Cy3 or Cy5) / (Concentration of cDNA)X1000= pmol Cy3 per μg cDNA using a NanoDrop ND-1000 UV-VIS Spectrophotometer (NanoDrop Technologies, Wilmington, DE).  Labeled cDNAs were used only If the yield is >825 ng and the specific activity is >8.0 pmol Cy3 or Cy5 per μg cDNA (Agilent recommendation).  The Cy3- and Cy5-labeled cDNAs were then combined and concentrated down to 41.8 µl followed by addition of 11 µl of 10X Blocking Agent solution and 2.2 µl  25X fragmentation buffer (Agilent Technologies, Santa Clara, CA) and the mixture was incubated at 60°C for 30 min before 55 µl of 2x GEx Hybridization Buffer HI-RPM (Agilent provided) was added.

extract_protocol: Total RNA was isolated from each fish (4 fish/group) using the TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instruction. Concentrations of isolated RNA were determined by measuring absorbance at 260 nm. The integrity of RNA was determined by agarose gel electrophoresis. Poly (A) mRNA was purified using Oligotex mRNA Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s instruction.

tag: Atrophying white muscle of  mature fertile (diploid) female, Oncorhynchus mykiss (~500 g) collected during the spawning season.  Fish were cultured in raceways receiving water from spring at 13 ±3°C. Fish were fed ad libitum via demand feeders. Fish had access to feed when sampled. As confirmed by dissection, fertile fish were gravid with a gonado-somatic index (GSI = ovary weight/fish weight x 100) of 15.8 ± 0.3 (n = 4).

source_name: Contol muscle

tag: Normal white muscle of sterile (triploid) female, Oncorhynchus mykiss (~500 g) collected during the spawning season.  Fish were cultured in raceways receiving water from spring at 13 ±3°C. Fish were fed ad libitum via demand feeders. Fish had access to feed when sampled. The GSI of sterile fish was 0.3 ± 0.2 (n = 5).


title: Development of a 37K High-density oligo-nucleotide microarray for rainbow trout 4

department: Division of Animal and Nutritional Sciences

tag: Normal white muscle of sterile (triploid) female, Oncorhynchus mykiss (~500 g) collected during the spawning season. Fish were cultured in raceways receiving water from spring at 13 ±3°C. Fish were fed ad libitum via demand feeders. Fish had access to feed when sampled. The GSI of sterile fish was 0.3 ± 0.2 (n = 5).

tag: Atrophying white muscle of mature fertile (diploid) female, Oncorhynchus mykiss (~500 g) collected during the spawning season. Fish were cultured in raceways receiving water from spring at 13 ±3°C. Fish were fed ad libitum via demand feeders. Fish had access to feed when sampled. As confirmed by dissection, fertile fish were gravid with a gonado-somatic index (GSI = ovary weight/fish weight x 100) of 15.8 ± 0.3 (n = 4).


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 2

description: Systemic onset juvenile idiopathic arthritis 2


title: Peripheral blood cells - healthy child - 2

description: Healthy child 2

tag: Healthy child 2


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 12

description: Systemic onset juvenile idiopathic arthritis 12


title: Peripheral blood cells - healthy child - 6

description: Healthy child 6

tag: Healthy child 6


title: Peripheral blood cells - healthy child - 4

description: Healthy child 4

tag: Healthy child 4


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 36

description: Systemic onset juvenile idiopathic arthritis 36


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 3

description: Systemic onset juvenile idiopathic arthritis 3


title: Development of a 37K High-density oligo-nucleotide microarray for rainbow trout 3


title: Peripheral blood cells - healthy child - 3

description: Healthy child 3

tag: Healthy child 3


title: Development of a 37K High-density oligo-nucleotide microarray for rainbow trout 2

source_name: Control muscle


title: Peripheral blood cells - healthy child - 1

description: Healthy child 1

tag: Healthy child 1


title: Peripheral blood cells - healthy child - 5

description: Healthy child 5

tag: Healthy child 5


title: BONOBO 1 [HSJ (human male) vs. NG05253A (Bonobo cell line)]

status: Public on Jan 06 2006

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37975.gif

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

source_name: Human male genomic DNA

tag: Human male genomic DNA

source_name: Bonobo male cell line genomic DNA

tag: Bonobo male cell line genomic DNA


title: HUMAN 1 [HSR (human female) vs. HSR (human female)]

description:
Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35264.gif

source_name: Human female genomic DNA

tag: Human female genomic DNA


title: BONOBO 3 [HSE (human male) vs. BON5 (Bonobo male)]

description:
Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40312.gif

source_name: Bonobo male genomic DNA

tag: Bonobo male genomic DNA


title: Peripheral blood cells in patient with systemic onset juvenile idiopathic arthritis 9

description: Systemic onset juvenile idiopathic arthritis 9

tag: Common reference sample from 45 healthy volunteers


title: ORANG 3 [HSR (human female) vs. LA27 (Orangutan female)]

description:
Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40423.gif

source_name: Orangutan female genomic DNA

tag: Orangutan female genomic DNA


title: HUMAN 2 [HSR (human female) vs. HSS (human female)]

description:
Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37973.gif


title: GORILLA 2 [HSR (human female) vs. GG2 (Gorilla female)]

description:
Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38709.gif

source_name: Gorilla female genomic DNA

tag: Gorilla female genomic DNA


title: CHIMP 2 [HSR (human female) vs. PTD (Bonobo female)]

description:
Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38128.gif

source_name: Chimpanzee female genomic DNA

tag: Chimpanzee female genomic DNA


title: HUMAN 4 [HSR (human female) vs. HSJ (human male)]

description:
Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38129.gif


title: ORANG 1 [HSR (human female) vs. NG12256 (Orangutan female cell line)]

description:
Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33959.gif

source_name: Orangutan female cell line genomic DNA

tag: Orangutan female cell line genomic DNA


title: CHIMP 1 [HSJ (human male) vs. PTC (Chimp male)]

description:
Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37976.gif

source_name: Chimpanzee male genomic DNA

tag: Chimpanzee male genomic DNA


title: HUMAN 3 [HSJ (human male) vs. HSJ (human male)]

description:
Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37979.gif


title: BONOBO 2 [HSJ (human male) vs. BON4 (Bonobo male)]

description:
Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40311.gif


title: HUMAN 5 [HSJ (human male) vs. HSE (human male)]

description:
Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37980.gif


title: CHIMP 3 [HSR (human female) vs. PTF (Chimp female)]

description:
Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33960.gif


title: CHIMP 4 [HSJ (human male) vs. PTS (Chimp male)]

description:
Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37978.gif


title: ORANG 2 [HSR (human female) vs. NG06209 (Orangutan female cell line)]

description:
Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37968.gif


title: GORILLA 1 [HSR (human female) vs. NG05251 (Gorilla male cell line)]

description:
Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35158.gif

source_name: Gorilla male cell line genomic DNA

tag: Gorilla male cell line genomic DNA


title: GORILLA 3 [HSJ (human male) vs. GG4 (Gorilla male)]

description:
Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40310.gif

source_name: Gorilla male genomic DNA

tag: Gorilla male genomic DNA