title: primary_lung_cancer_B350

status: Public on Nov 19 2013

first: Ming

last: Tsao

address: 610 University Avenue

department: Ontario Cancer Institute

institute: University of Toronto

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133A 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 preprocessed using RMA v0.5.

source_name: primary lung cancer

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

value: primary lung cancer

tag: Post Surgical Treatment

value: OBS

tag: Stage

tag: Sex

value: Male

tag: Cause of death

value: Alive

tag: Histology type

value: ADC

tag: OS time

tag: OS status

tag: dss survival time

tag: DSS status

tag: dcc sample

value: Yes

tag: predominant subtype

value: solid


title: Diffuse Intrinsic Pontine Glioma 29 - Tumour-6.0

status: Public on Mar 31 2014

type: genomic

city: Toronto

first: Pawel

last: Buczkowicz

state: Ontario

address: 686 Bay Street

department: Paediatric Laboratory Medicine

country: Canada

institute: Hospital for Sick Children

description:
Dx: diagnosis, OS: overral survival
Hybridized to 6.0

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

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

data_processing:
CEL files  were processed using Partek Genome Suite V6.6 and Genotyping Console V4.1 using Segmentation and Hidden-Markov Model Analysis. Tumour samples were normalized to their matched normal. Tumour samples with no corresponding matched normal were normalized using HapMap.
CHP files for samples analyzed on the 6.0 platform were normalized using Birdseed V2 algorithm.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

label_protocol: As per manufacturer (Affymetrix)

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

tag: tissue

value: Diffuse Intrinsic Pontine Glioma

tag: cell type

value: DIPG

tag: gender

value: F

tag: age at dx (years)

tag: os (years)


title: placenta mnr female rep2

status: Public on Dec 06 2013

type: RNA

city: San Antonio

first: Laura

middle: L

last: Cox

state: Texas

department: Genetics

country: USA

institute: Texas Biomedical Research Institute

description: 27365 MNR Female

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were all median normalised and log2 transformed in Genesifter Analysis Edition (http://www.geospiza.com/Products/AnalysisEdition.shtml)

label: biotin

molecule: total RNA

organism: Papio hamadryas

source_name: placenta mnr

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Tissue samples were flash frozen immediately at collection and stored at -80 degrees C.

value: female

tag: nutrient availability

value: nutrient restricted

tag: developmental stage (days of gestation)

value: 165 dGa

value: placenta


title: Diffuse Intrinsic Pontine Glioma 37 - Tumour-6.0

value: M


title: primary_lung_cancer_B334

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

tag: Post Surgical Treatment

tag: Stage

tag: age

value: Solid


title: Diffuse Intrinsic Pontine Glioma 27 - Tumour-6.0


title: placenta control male rep3

description: 27188 Con Male

source_name: placenta control

value: male

value: normal (control)


title: placenta control female rep1

description: 26246 Con Female


title: primary_lung_cancer_B299

value: primary lung cancer

value: OBS

tag: Sex

value: Female

tag: Cause of death

tag: Histology type


title: placenta control male rep1

description: 26201 Con Male


title: placenta mnr female rep3

description: 27648 MNR Female


title: placenta control male rep2

description: 26991 Con Male


title: primary_lung_cancer_B298

value: Male

value: Lung cancer

value: ADC

tag: OS time

tag: OS status

value: Dead

tag: dss survival time

value: Lepidic


title: primary_lung_cancer_B259

value: Alive

tag: DSS status

tag: dcc sample

value: Yes

tag: predominant subtype

value: Papillary


title: primary_lung_cancer_B252

tag: tissue

value: Unknown


title: Diffuse Intrinsic Pontine Glioma 30 - Tumour-6.0

value: Diffuse Intrinsic Pontine Glioma

tag: cell type

value: DIPG

tag: gender

tag: age at dx (years)


title: primary_lung_cancer_B192

value: ACT

value: Acinar


title: primary_lung_cancer_B250


title: primary_lung_cancer_B188

value: Other conditions


title: primary_lung_cancer_B107

value: primary lung cancer


title: primary_lung_cancer_B094

value: OBS

value: Solid


title: primary_lung_cancer_B176

value: Male


title: Diffuse Intrinsic Pontine Glioma 6 - Tumour-6.0

source_name: Diffuse Intrinsic Pontine Glioma 5 - Tumour

value: M

tag: os (years)


title: Diffuse Intrinsic Pontine Glioma 5 - Tumour-6.0

source_name: Diffuse Intrinsic Pontine Glioma 4 - Tumour

value: F


title: primary_lung_cancer_B134

tag: Post Surgical Treatment

value: Female

value: ADC


title: primary_lung_cancer_B158

tag: Stage

value: Lung cancer

value: Dead


title: primary_lung_cancer_B136

tag: age

value: Yes

value: Papillary


title: Diffuse Intrinsic Pontine Glioma 25 - Tumour-6.0

value: Diffuse Intrinsic Pontine Glioma


title: primary_lung_cancer_B160

tag: Sex

value: Unknown


title: primary_lung_cancer_B257

value: ACT

tag: Cause of death

value: Alive

value: Lepidic


title: Diffuse Intrinsic Pontine Glioma 28 - Tumour-6.0

value: DIPG


title: primary_lung_cancer_B114

value: primary lung cancer

value: OBS

tag: Histology type


title: primary_lung_cancer_B139

tag: OS time


title: primary_lung_cancer_B057

value: Male

tag: OS status

value: Solid


title: Diffuse Intrinsic Pontine Glioma 26 - Tumour-6.0

value: F


title: primary_lung_cancer_B120

tag: dss survival time

value: invasive mucinous


title: primary_lung_cancer_B111

value: ADC

tag: DSS status


title: primary_lung_cancer_B115

value: Lung cancer

tag: dcc sample

value: Acinar


title: primary_lung_cancer_B092

value: Female

value: Yes

tag: predominant subtype


title: primary_lung_cancer_B090

tag: tissue

value: Dead


title: primary_lung_cancer_B103


title: primary_lung_cancer_B142


title: primary_lung_cancer_B099

value: Unknown


title: primary_lung_cancer_B028

value: Micropapillary


title: primary_lung_cancer_B034

value: ACT


title: primary_lung_cancer_B047

value: Papillary


title: primary_lung_cancer_B035

value: Alive


title: primary_lung_cancer_B008

value: primary lung cancer


title: primary_lung_cancer_B068


title: Diffuse Intrinsic Pontine Glioma 24 - Tumour-6.0

value: Diffuse Intrinsic Pontine Glioma

tag: cell type

value: DIPG


title: primary_lung_cancer_B086

value: Male


title: primary_lung_cancer_B088

value: OBS


title: Diffuse Intrinsic Pontine Glioma 4 - Tumour-6.0

source_name: Diffuse Intrinsic Pontine Glioma 3 - Tumour

tag: gender

value: M


title: primary_lung_cancer_B024

value: ADC

value: Solid


title: primary_lung_cancer_B023


title: primary_lung_cancer_B009


title: normal breast, sample n12

status: Public on Sep 05 2013

city: Gliwice

first: Katarzyna

middle: Marta

last: Lisowska

address: ul. Wybrzeże Armii Krajowej 15

department: Center for Translational Research  and Molecular Biology of Cancer

country: Poland

institute: MSC Memorial Cancer Center and Institute of Oncology, Gliwice Branch

description: Gene expression data from pathologically unchanged breast tissue from patient with BRCA1 mutation-linked breast cancer

hyb_protocol: Following fragmentation, 16 ug of cRNA were hybridized for 16 hr at 45C on HG U133 Plus 2.0 Gene Chip oligonucleotide arrays (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)

data_processing: Data was acquired using GCOS 1.2 software (Affymetrix). The preprocessing was performed by Robust Multiarray Analysis (RMA, Bioconductor).

source_name: frozen surgical sample of pathologically unchanged breast tissue

label_protocol: Total RNA (8 ug) was used for synthesis of double stranded cDNA according to manufacturer's instructions. Half of the cDNA volume was used for synthesis of biotynylated cRNA with the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics).

extract_protocol: Total RNA was isolated using Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.

tag: clinical sample

value: surgical sample of pathologically unchanged breast tissue, adjacent to the tumor

tag: histopathology

value: normal breast

tag: estrogen receptor status (by immunohistochemistry)

value: not analyzed

tag: brca1/2 mutation

value: No mutation

tag: brca1 promoter methylation


title: normal breast, sample n11

tag: age


title: 16-cell_A5.2

status: Public on Oct 29 2013

city: Kyoto

first: Yutaka

last: Satou

state: Kyoto

address: Kitashirakawa Oiwake-tyo, Sakyo-ku

department: Department of zoology, Graduate School of Science

country: Japan

institute: Kyoto University

hyb_protocol: Hybridization and washing were performed using GE Hybridization kit (Agilent) and GE Washing Buffer (Agilent), according to the manufacture’s instructions.

scan_protocol: The slides after washing were scanned on an Agilent G2505C Microarray Scanner (Agilent Technologies) using default settings. The scanned file option, TIFF file dynamic range was set to 20-bit.

data_processing: The scanned images were quantified by Feature Extraction Software ver.10.7( Agilent Technologies) using default parameters.

organism: Ciona intestinalis

source_name: blastomere, A5.2

label_protocol: 50ng total RNA was labeled using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacture’s instructions (www.agilent.com/).

growth_protocol: Wild Ciona intestinalis adults were used.

extract_protocol: The total RNA was extracted using RNeasy Mini Kit (QIAGEN). The quality of extracted RNA was analyzed on the Agilent 2100 Bioanalyzer (Agilent Technologies) using Agilent RNA 6000 Pico Kit (Agilent). The RNA yield was measured with Quant-iT RNA Assay Kit (Invitrogen).

treatment_protocol: Unfertilized eggs and sperm of C.intestinalis were obtained by dissection. After insemination, eggs were dechorionized and developed in Millipore-filtered seawater at 18℃.Each blastomere was isolated by a fine glass needle under a stereomicroscope and transferred into RNAlater (Ambion), immediately.

tag: developmental stage


title: Diffuse Intrinsic Pontine Glioma 1 - Tumour-6.0

value: F

tag: age at dx (years)

tag: os (years)


title: normal breast, sample n03

description: Gene expression data from pathologically unchanged breast tissue from patient with sporadic breast cancer


title: normal breast, sample 07


title: normal breast, sample n02

description: Gene expression data from pathologically unchanged breast tissue from patient with hereditary, BRCA1 mutation-linked breast cancer


title: normal breast, sample n21


title: primary_lung_cancer_B384

tag: Post Surgical Treatment

tag: Stage

tag: Sex

value: Female

tag: Cause of death

tag: Histology type

tag: OS time

tag: OS status

value: Yes


title: primary_lung_cancer_B140

tag: tissue

value: ACT

tag: dss survival time

tag: DSS status

tag: dcc sample

tag: predominant subtype


title: sporadic, sample 05

description: Gene expression data from sporadic breast cancer

source_name: frozen surgical sample of breast cancer, sporadic

tag: clinical sample

value: surgical tumor sample

tag: histopathology

value: ductal breast ca.

tag: molecular subtype (according to sorlie et al., pnas 100, 8418-23 (2003)

value: luminal-like

tag: estrogen receptor status (by immunohistochemistry)

tag: brca1/2 mutation

tag: brca1 promoter methylation

value: unmethylated


title: sporadic /FCA (familial cancer aggregation), sample 15

description: Gene expression data from sporadic /FCA (familial cancer aggregation) breast cancer

source_name: frozen surgical sample of breast cancer, sporadic /FCA (familial cancer aggregation)

tag: age


title: Diffuse Intrinsic Pontine Glioma 3 - Tumour-6.0

source_name: Diffuse Intrinsic Pontine Glioma 2 - Tumour

value: Diffuse Intrinsic Pontine Glioma

tag: cell type

value: DIPG

tag: gender

tag: age at dx (years)

tag: os (years)


title: sporadic, sample 22


title: sporadic, sample 20


title: sporadic /FCA (familial cancer aggregation), sample 18


title: sporadic, sample 31

value: basal-like

value: methylated


title: sporadic, sample 34


title: sporadic /FCA (familial cancer aggregation), sample 25


title: sporadic, sample 27


title: sporadic, sample 29


title: hereditary, BRCAx, sample 36

description: Gene expression data from hereditary BRCAx breast cancer

source_name: frozen surgical sample of breast cancer, hereditary, BRCAx


title: sporadic, sample 06

value: medullary breast ca.


title: sporadic, sample 07


title: hereditary, BRCAx, sample 37


title: sporadic, sample 13


title: hereditary, BRCAx, sample 08


title: hereditary, BRCAx, sample 35


title: hereditary, BRCAx, sample 32


title: hereditary, BRCAx, sample 24


title: hereditary, BRCAx, sample 19


title: hereditary, BRCA2-mutated, sample 10

description: Gene expression data from BRCA1-mutated hereditary breast cancer

source_name: frozen surgical sample of breast cancer, hereditary, BRCA2-mutated

value: BRCA2 9631delC Ex25


title: hereditary, BRCA1-mutated, sample 11

source_name: frozen surgical sample of breast cancer, hereditary, BRCA1-mutated

value: BRCA1 5382insC Ex20


title: primary_lung_cancer_B119

value: primary lung cancer

tag: Post Surgical Treatment

tag: Stage

tag: Sex

tag: Cause of death

value: Alive

tag: Histology type

value: ADC

tag: OS time

tag: OS status

value: Unknown


title: Liver_ISe_animal#48

status: Public on Jun 01 2013

city: Lexington

first: Jennifer

middle: Denyse

last: Patterson

state: KY

address: 215 WP Garrigus

department: Animal and Food Sciences

institute: University of Kentucky

description: daily dietary Se supplementation at 3 mg/ animal of the ISe form

hyb_protocol: Following fragmentation, 10 µg of labeled cRNA was hybridized to Affymetrix Bovine Genome Array for 16 hr at 45°C using the gene chips in the GeneChip Hybridization Oven 640, using 1 chip per RNA sample. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. GeneChips were stained with R-Phycoerythrin Streotavidin, followed by an antibody solution and a second R-Physcoerythrin Streptavidin solution, with all lquid handling performed by a GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 7G GeneChip Scanner (GCS) with AGCC software (Command Console).

data_processing: The raw data were collected with the GeneChip Operating Software (GCOS, version 1.2). The expression intensity values from the software (i.e., the .cel files) were imported into Partek Genomics Suite software (version 6.4; Partek Inc., St. Louis, MO, USA). The algorithm of Robust Multichip Averaging adjusted with the GC oligo content data were further converted into expression values via the algorithms of Quantile normalization of different chips and then Median Polish summarization of multiple probes.

organism: Bos taurus

source_name: ISe Liver

label_protocol: Biotinylated cRNA were prepared from 3 µg of total RNA according to Affymetrix protocol. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA, USA) and oligo(dT)24 primers. Bio-labeled cRNA was prepared by cDNA in vitro transcription biotinylated UTP.

growth_protocol: Thirty-six Angus heifers were randomly assigned (as described in overall design section above) to eight feeding pens of five animals per pen. Heifers were individually fed using 40 Calan gate electronic feeders. A basal mineral-vitamin premix manufactured by Kentucky Nutrition Service (Lawrenceburg, KY, USA) was administered daily by manually mixing into each animal's ration at 85.1 g/ day.

treatment_protocol: The treatment protocol (i.e. dietary Se Supplementation) has been described in the overall design section above.

tag: tissue

value: biopsied liver (right lobe)


title: hereditary, BRCAx, sample 04

tag: clinical sample

tag: histopathology

tag: molecular subtype (according to sorlie et al., pnas 100, 8418-23 (2003)

value: No mutation


title: hereditary, BRCA1-mutated, sample 26

value: surgical tumor sample

tag: estrogen receptor status (by immunohistochemistry)

tag: brca1/2 mutation

tag: brca1 promoter methylation


title: hereditary, BRCA1-mutated, sample 33

value: ductal breast ca.

tag: age


title: hereditary, BRCA1-mutated, sample 9A


title: Liver_Ctrl_animal#41

description: no exogenous dietary Se supplementation

source_name: Control Liver


title: hereditary, BRCA1-mutated, sample 17


title: hereditary, BRCA1-mutated, sample 28


title: Liver_OSe_animal#24

description: daily dietary Se supplementation of 3 mg/ animal of OSe form

source_name: OSe Liver


title: primary_lung_cancer_B126

source_name: primary lung cancer

value: OBS

value: Female

tag: dss survival time

tag: DSS status

tag: dcc sample

value: Yes

tag: predominant subtype

value: Acinar


title: hereditary, BRCA1-mutated, sample 2

value: basal-like

value: unmethylated


title: hereditary, BRCA1-mutated, sample 12

value: BRCA1 4153delA Ex11


title: hereditary, BRCA1-mutated, sample 09B


title: hereditary, BRCA1-mutated, sample 1

value: medullary breast ca.


title: Liver_OSe_animal#44


title: Liver_Ctrl_animal#40

description: no exogenous dietary Se supplementation


title: Liver_ISe_animal#42


title: hereditary, BRCA1-mutated, sample 21

value: BRCA1 C61G Ex5


title: Liver_OSe_animal#38


title: Liver_Ctrl_animal#46

description: no exogenous dietary Se supplementation


title: Liver_OSe_animal#35


title: Liver_OSe_animal#25


title: Liver_Mix_animal#12

description: daily dietary Se supplementation of 3 mg/ animal of 50:50 mix of ISe and OSe forms

source_name: ISe/OSe Liver


title: Liver_Mix_animal#21


title: Liver_Mix_animal#13


title: Liver_ISe_animal#27


title: Liver_OSe_animal#39


title: Liver_OSe_animal#29


title: Liver_OSe_animal#16


title: Liver_Mix_animal#23


title: Liver_Mix_animal#9


title: Liver_Ctrl_animal#34

description: no exogenous dietary Se supplementation


title: Liver_Ctrl_animal#7

description: no exogenous dietary Se supplementation


title: Liver_Ctrl_animal#17

description: no exogenous dietary Se supplementation


title: Liver_Mix_animal#11


title: Liver_OSe_animal#33


title: Liver_ISe_animal#10


title: Liver_ISe_animal#15


title: Liver_Ctrl_animal#14

description: no exogenous dietary Se supplementation


title: Liver_Ctrl_animal#31

description: no exogenous dietary Se supplementation


title: Liver_Ctrl_animal#18

description: no exogenous dietary Se supplementation


title: Liver_ISe_animal#6


title: Liver_Mix_animal#5


title: Liver_ISe_animal#3


title: Yale_ChipSeq_GM12878_Pol2_std

status: Public on May 22 2012

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

library_source: genomic

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeSydhTfbs

tag: lab

value: Yale

tag: lab description

value: Snyder - Yale University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

tag: cell description

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

tag: cell karyotype

value: normal

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

tag: antibody antibodydescription

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

tag: antibody targetdescription

value: RNA Polymerase II

tag: antibody vendorname

value: Covance

tag: antibody vendorid

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid

tag: labversion

value: remapped from hg18

tag: replicate


title: P. aeruginosa_colonized, worm sorter, replicate 3

status: Public on Jul 20 2012

city: Berkeley

first: Michael

last: Shapira

address: 3060 Valley Life Sciences Bldg room 5163

department: Integrative Biology

institute: UC Berkeley

description:
Sample name:  colonized_WS_04.23
Biological replicate 3 of 3

hyb_protocol: 2 ug of fragmented aRNA in a volume of 13 ul was combined with 13ul of kreablock(Kreatech) and 26 ul of 2X formamide based hybridization buffer (Genisphere). Static hybridizations under M-series Lifterslips from Erie Scientific were done at 43C (16-20hrs). Chambers were humidified with 4X SSC. Arrays were washed according to the Genisphere protocol.

scan_protocol: Scanned on a GenePix 4000B scanner, Images quantified using Genepix Pro 6

data_processing: Median intensity values were used, Signal to Noise (background checking) threshold of 2.5 used, LOWESS normalized, using MIDAS software

organism: Caenorhabditis elegans

source_name: C.elegans fed P. aeruginosa and fully colonized

label_protocol: RNA labeled using the ULS™ aRNA Labeling Kit (Kreatech)

growth_protocol: Animals grown at 25oC

extract_protocol: Total RNA extracted using Trizol (Invitrogen), and polyA RNA amplified using the MessageAmp™ II aRNA Amplification Kit (Ambion)

treatment_protocol: Animals exposed to E.coli or P. aeruginosa at day 2 of adulthood for ~18hrs

tag: strain

tag: age

value: Day 2 old adult

tag: condition

value: P. aeurginosa colonized

source_name: Mixed stage C.elegans fed E.coli strain OP50

tag: sample type

value: reference RNA sample from mixed stage C.elegans cultures


title: P. aeruginosa_colonized, worm sorter, replicate 2

description:
Sample name:  colonized_WS_05.09
Biological replicate 2 of 3


title: P. aeruginosa_colonized, hand picked, replicate 1

description:
Sample name:  colonized_HP_05.09
Biological replicate 1 of 3


title: P. aeruginosa_non-colonized, worm sorter, replicate 2

description:
Sample name:  non-colonized_WS_05.09
Biological replicate 2 of 3

source_name: C.elegans fed P. aeruginosa and not colonized

value: P. aeurginosa non-colonized


title: E.coli, worm sorter, replicate 3

description:
Sample name:  OP50_WS_04.23
Biological replicate 3 of 3

source_name: C.elegans fed E.coli


title: Liver_OSe_animal#2

tag: tissue

value: biopsied liver (right lobe)


title: Liver_ISe_animal#1


title: P. aeruginosa_non-colonized, worm sorter, replicate 3

description:
Sample name:  non-colonized_WS_04.23
Biological replicate 3 of 3


title: P. aeruginosa_non-colonized, hand picked, replicate 1

description:
Sample name:  non-colonized_HP_05.09
Biological replicate 1 of 3


title: E.coli, worm sorter, replicate 2

description:
Sample name:  OP50_WS_05.09
Biological replicate 2 of 3


title: E.coli, hand picked, replicate 1

description:
Sample name:  OP50_ HP_05.09
Biological replicate 1 of 3


title: sporadic /FCA (familial cancer aggregation), sample 30

tag: clinical sample

value: surgical tumor sample

tag: histopathology

value: ductal breast ca.

tag: molecular subtype (according to sorlie et al., pnas 100, 8418-23 (2003)

value: basal-like

tag: estrogen receptor status (by immunohistochemistry)

tag: brca1/2 mutation

value: No mutation

tag: brca1 promoter methylation

value: methylated


title: B16-F10 cells treated with Lipofectamine, biological rep3

status: Public on Jun 04 2011

description: Gene expression data from B16-F10 cells treated with Lipofectamine.

hyb_protocol: Following fragmentation, 16 ug of cRNA were hybridized for 16 hr at 45C on Mouse Expression Arrays 430A (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).

organism: Mus musculus

label_protocol: Total RNA (8 ug) was used for synthesis of double-stranded cDNA according to the manufacturer's instructions. Half of the cDNA volume was used for synthesis of biotinylated cRNA with the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics).

growth_protocol: The mouse melanoma B16-F10 cells (ATCC CRL-6475T) were grown in a CO2 incubator at 37°C in RPMI medium (Sigma) supplemented with 10% fetal bovine serum (FBS).

extract_protocol: Total RNA was isolated using the Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Heat shock was performed for 1 h at 42.5°C with 30 min recovery at 37°C. For microarray analysis of LA effect, cells were treated with Lipofectamine 2000 (Invitrogen) for 3 h in Opti-MEM (Gibco BRL) medium, the liposomes-containing medium was replaced with RPMI supplemented with 10% FBS, and the cells were allowed to recover for 30 min at 37°C.  For microarray analysis of BA effect, cells were treated with 40 mM benzyl alcohol for 1h at 37°C, and then allowed to recover in fresh medium for 3h at 37°C.

tag: cell line

tag: cell type

value: melanoma cells

tag: treatment

value: Lipofectamine


title: control B16-F10 cells, biological rep4

description: Gene expression data from control B16-F10 cells.

source_name: control B16-F10 cells


title: heat-shocked B16-F10 cells, biological rep3

description: Gene expression data from B16-F10 cells treated with heat shock.

source_name: heat-shocked B16-F10 cells

value: heat shock


title: B16-F10 cells treated with 40 mM benzyl alcohol, biological rep3

description: Gene expression data from B16-F10 cells treated with benzyl alcohol.

value: benzyl alcohol


title: B16-F10 cells treated with 40 mM benzyl alcohol, biological rep1

source_name: B16-F10 cells treated with benzyl alcohol


title: control B16-F10 cells, biological rep3


title: control B16-F10 cells, biological rep5


title: B16-F10 cells treated with Lipofectamine, biological rep2


title: heat-shocked B16-F10 cells, biological rep2


title: control B16-F10 cells, biological rep1


title: B16-F10 cells treated with Lipofectamine, biological rep1


title: control B16-F10 cells, biological rep2


title: heat-shocked B16-F10 cells, biological rep1


title: B16-F10 cells treated with 40 mM benzyl alcohol, biological rep2


title: Liver_Mix_animal#45


title: patient_sample_CL20041119162AA

status: Public on Sep 09 2010

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Raw data were pre-processed using RMAexpress v0.3 (Bolstad BM, 2003).

label_protocol: As described in Shedden K et al. 2008.

extract_protocol: Total RNA was isolated from frozen tumors by homogenization in guanidium isothiocyanate solution and acid phenol-chloroform extraction

value: primary lung cancer

tag: Post Surgical Treatment

value: OBS

tag: Stage

value: I

tag: Sex

value: Male

tag: Cause of death

value: Lung cancer

tag: Histology type

value: SQCC

tag: OS time

tag: OS status

value: Dead

tag: DSS time

tag: DSS status

value: dead

tag: predominant subtype

value: not applicable


title: patient_sample_CL2004113025AA

tag: tissue

value: II

tag: age

value: Female

value: Alive


title: patient_sample_CL2005060325AA

value: ADC

value: Acinar


title: patient_sample_CL2004113024AA

value: ACT

value: Papillary


title: Breast muscle tissue from feed efficiency (FE) in a single male broiler line Replicate 2

status: Public on Nov 24 2010

city: Fayetteville

first: Walter

middle: G

last: Bottje

state: AR

address: 1260 W. Maple, POSC, O-405

department: Poultry Science

institute: University of Arkansas

description: Biological replicate 2 of 4. Breast muscle tissue from feed efficiency (FE) in a single male broiler line

hyb_protocol: An equal amount (825 ng) of Cy3 and Cy5 labeled cRNA probes were mixed with gene expression hybridization kit (Agilent, part No. 5188-5242) and hybridized on a 4X44K Agilent custom chicken oligo microarray (array ID: 015068). The hybridized slides were washed using a commercial kit package (Agilent).

scan_protocol: Scanned on an Genepix 4000B scanner (Molecular Devices Corporation)

data_processing: Gene Pix Pro (v 6.1) with Accuity software (v 4.0).

organism: Gallus gallus

source_name: Low Efficiency

label_protocol: 2 µg of total RNA were used for this experiment, and all procedures were followed to manufacturer's instructions.

growth_protocol: Broiler males were placed in cages and fed individually.  Body weight gain and feed intake were measured on individual birds to determine feed efficiency (Gain: Feed) or feed conversion ratio (Feed: Gain) from 6 to 7 wk of age.

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

treatment_protocol: There were no treatments in this study.  Birds were provided a corn:soy based diet containing approximately 20.5% protein and 3,280 kcal/kg).

value: breast muscle

source_name: High Efficiency


title: patient_sample_CL20041119163AA

value: primary lung cancer


title: patient_sample_CL2004113026AA


title: patient_sample_CL20041119166AA

value: Solid


title: patient_sample_CL2005060331AA

value: I


title: patient_sample_CL2005060330AA

value: Male

value: Other conditions


title: patient_sample_CL20041119164AA


title: Breast muscle tissue from feed efficiency (FE) in a single male broiler line Replicate 4

description: Biological replicate 4 of 4. Breast muscle tissue from feed efficiency (FE) in a single male broiler line


title: patient_sample_CL20041119160AA

value: OBS

value: Lung cancer

value: SQCC


title: patient_sample_CL20041119178AA

value: not applicable


title: patient_sample_CL2005060335AA


title: patient_sample_CL20041119168AA

value: II

value: Unknown


title: patient_sample_CL20041119176AA

value: Dead

value: Alive


title: patient_sample_CL20041119172AA


title: patient_sample_CL20041119165AA


title: Breast muscle tissue from feed efficiency (FE) in a single male broiler line Replicate 3

description: Biological replicate 3 of 4. Breast muscle tissue from feed efficiency (FE) in a single male broiler line


title: patient_sample_CL20041119161AA

value: ADC


title: patient_sample_CL20041119174AA

value: dead


title: Breast muscle tissue from feed efficiency (FE) in a single male broiler line Replicate 1

description: Biological replicate 1 of 4. Breast muscle tissue from feed efficiency (FE) in a single male broiler line


title: patient_sample_CL20041119171AA

value: Lepidic


title: patient_sample_CL20041119169AA

value: ACT


title: patient_sample_CL20041116159AA

value: primary lung cancer

value: Micropapillary


title: patient_sample_CL20041119173AA


title: patient_sample_CL20041119170AA

value: I

value: LCUC


title: patient_sample_CL20041116157AA

value: Female

value: Solid


title: patient_sample_CL20041116147AA

value: Male


title: patient_sample_CL20041116158AA

value: SQCC


title: patient_sample_CL20041116143AA

value: OBS

value: Other conditions

value: not applicable


title: hereditary, BRCA1-mutated, sample 14

description: Gene expression data from BRCA1-mutated hereditary breast cancer

tag: clinical sample

value: surgical tumor sample

tag: histopathology

value: medullary breast ca.

tag: molecular subtype (according to sorlie et al., pnas 100, 8418-23 (2003)

value: basal-like

tag: estrogen receptor status (by immunohistochemistry)

tag: brca1/2 mutation

value: BRCA1 5382insC Ex20

value: unmethylated


title: patient_sample_CL20041116144AA

tag: Post Surgical Treatment

value: Alive


title: patient_sample_CL20041116120AA

value: primary lung cancer

tag: Stage


title: patient_sample_CL20041116150AA

value: II

tag: Sex

value: Lung cancer

value: ADC

value: Dead

value: dead

value: Micropapillary


title: patient_sample_CL20041116122AA

value: I

value: Male

tag: Cause of death

value: SQCC


title: patient_sample_CL20041116155AA

value: OBS

value: Female

tag: Histology type

value: LCUC

value: not applicable


title: patient_sample_CL20041116139AA

value: ACT

tag: OS time


title: patient_sample_CL20041116121AA

tag: OS status


title: patient_sample_CL20041116124AA

tag: DSS time


title: patient_sample_CL20041116152AA

tag: DSS status


title: patient_sample_CL20041116140AA

tag: predominant subtype


title: patient_sample_CL20041116141AA

tag: tissue


title: patient_sample_CL20041116154AA

tag: age


title: patient_sample_CL20041116135AA


title: patient_sample_CL20041116130AA

value: Other conditions


title: patient_sample_CL20041116132AA

value: Alive


title: patient_sample_CL20041116137AA

value: primary lung cancer


title: patient_sample_CL20041116151AA


title: patient_sample_CL20041116123AA


title: patient_sample_CL20041116133AA

value: II


title: patient_sample_CL20041116153AA

value: Acinar


title: patient_sample_CL20041116116AA


title: patient_sample_CL20041116149AA

value: ADC

value: Unknown


title: patient_sample_CL20041116119AA


title: patient_sample_CL20041116145AA

value: Lung cancer

value: Dead

value: dead


title: patient_sample_CL20041116142AA

value: Male


title: patient_sample_CL20041116131AA

value: SQCC


title: patient_sample_CL20041116138AA

value: OBS


title: patient_sample_CL20041116115AA

value: I


title: patient_sample_CL20041116118AA


title: patient_sample_CL20041116129AA

value: Solid


title: patient_sample_CL2004111028AA


title: patient_sample_CL2004111035AA

value: Female

value: not applicable


title: patient_sample_CL2004111029AA

value: ACT


title: patient_sample_CL20041116125AA

value: Alive


title: patient_sample_CL2004111011AA

value: primary lung cancer


title: patient_sample_CL2004111023AA

value: II


title: patient_sample_CL2004111036AA


title: patient_sample_CL20041116128AA


title: patient_sample_CL2004111047AA

value: Papillary


title: patient_sample_CL2004111034AA

value: Other conditions

value: ADC


title: patient_sample_CL20041116148AA


title: patient_sample_CL2004111037AA

value: Lung cancer


title: patient_sample_CL2004111027AA


title: patient_sample_CL2004111024AA

value: Dead

value: Lepidic


title: patient_sample_CL2004111030AA


title: patient_sample_CL2004111008AA

value: Male

value: LCUC

value: dead


title: patient_sample_CL2004111039AA

value: Unknown


title: patient_sample_CL2004111019AA

value: I

value: SQCC


title: patient_sample_CL2004111001AA

value: not applicable


title: Liver_ISe_animal#30

description: daily dietary Se supplementation at 3 mg/ animal of the ISe form

value: biopsied liver (right lobe)


title: patient_sample_CL2004111026AA

value: OBS

value: Alive


title: patient_sample_CL2004111012AA

value: primary lung cancer

value: II


title: patient_sample_CL2004111031AA


title: Hepatocellular carcinoma (hcc_128)

status: Public on Oct 15 2008

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Illumina DASL Assay System Manual. Hybridization was performed for 4 DASL assay oligo pool (DAP)s, DAP1~4, including 1536 probes each on 4 separate microarrays.

data_processing: For each probe, Red and Green intensities are computed as average of single bead values. The final signal is the sum of the Red and Green intensities. Data were were then normalized using the cubic spline algorithm for each DAP.

label: Cy3 and Cy5

source_name: hepatocellular carcinoma

extract_protocol: Using 10µm sections taken from formalin-fixed paraffin-embeded tissue blocks, total RNA was extracted using High Pure Paraffin FFPE kit (Roche).

tag: used for prognostic prediction

value: Yes

tag: survival time (days)

tag: survival status (0

value: alive or censored, 1:dead) :0

tag: hepatitis b virus (hbs antigen)

value: negative

tag: hepatitis c virus

value: positive

tag: alcohol (cumulative intake)

tag: microvascular invasion

tag: satellite lesions


title: patient_sample_CL2004111032AA

tag: Post Surgical Treatment

tag: Stage

tag: Sex

tag: Cause of death

value: Lung cancer

value: Dead


title: patient_sample_CL2004111007AA

value: ACT

value: Male

tag: Histology type

value: ADC

tag: OS time

tag: OS status

tag: DSS time

value: Solid


title: patient_sample_CL2004111020AA

tag: tissue

value: I

tag: age

value: LCUC

tag: DSS status

tag: predominant subtype


title: Hepatocellular carcinoma (hcc_133)

scan_protocol: Refer to the Illumina DASL Assay System Manual

tag: used for prognostic prediction

tag: survival time (days)

tag: survival status (0

tag: hepatitis b virus (hbs antigen)


title: patient_sample_CL2004111004AA

value: Other conditions

value: SQCC

value: not applicable


title: patient_sample_CL2004111006AA

value: primary lung cancer

value: OBS

value: Alive


title: Hepatocellular carcinoma (hcc_086)

label_protocol: Refer to the Illumina DASL Assay System Manual

value: Yes

value: alive or censored, 1:dead) :0

tag: hepatitis c virus

tag: alcohol (cumulative intake)

tag: microvascular invasion

tag: satellite lesions


title: patient_sample_CL2004111016AA

tag: Post Surgical Treatment

tag: Stage

tag: Sex

value: Female

tag: Cause of death

value: Acinar


title: Hepatocellular carcinoma (hcc_103)

value: negative

value: positive


title: Hepatocellular carcinoma (hcc_106)

value: alive or censored, 1:dead) :1


title: Hepatocellular carcinoma (hcc_094)


title: Hepatocellular carcinoma (hcc_097)


title: Hepatocellular carcinoma (hcc_101)


title: Hepatocellular carcinoma (hcc_117)


title: Hepatocellular carcinoma (hcc_104)


title: patient_sample_CL2004110925AA

value: II

tag: Histology type

value: ADC

tag: OS time

tag: OS status

tag: DSS time


title: patient_sample_CL2004111021AA

tag: tissue

value: ACT

value: I

tag: age

value: Dead

tag: DSS status

tag: predominant subtype

value: Solid


title: Hepatocellular carcinoma (hcc_084)

tag: used for prognostic prediction

tag: survival time (days)

tag: survival status (0

tag: hepatitis b virus (hbs antigen)


title: Hepatocellular carcinoma (hcc_083)

tag: hepatitis c virus

tag: alcohol (cumulative intake)

tag: microvascular invasion

tag: satellite lesions


title: Hepatocellular carcinoma (hcc_107)


title: Hepatocellular carcinoma (hcc_109)


title: Hepatocellular carcinoma (hcc_082)


title: Hepatocellular carcinoma (hcc_116)


title: Hepatocellular carcinoma (hcc_080)


title: patient_sample_CL2004111014AA

tag: Post Surgical Treatment

tag: Stage

tag: Sex

value: Male

tag: Cause of death

value: Lung cancer

value: SQCC

value: dead

value: not applicable


title: Hepatocellular carcinoma (hcc_126)

value: Yes


title: patient_sample_CL2004111015AA

value: primary lung cancer

value: Alive

tag: Histology type

value: LCUC

tag: OS time

tag: OS status

tag: DSS time


title: Hepatocellular carcinoma (hcc_067)

value: alive or censored, 1:dead) :0

value: negative

value: positive


title: Hepatocellular carcinoma (hcc_066)

value: alive or censored, 1:dead) :1


title: Hepatocellular carcinoma (hcc_075)


title: Hepatocellular carcinoma (hcc_069)


title: Hepatocellular carcinoma (hcc_064)


title: Hepatocellular carcinoma (hcc_056)


title: Hepatocellular carcinoma (hcc_065)


title: Hepatocellular carcinoma (hcc_052)


title: Hepatocellular carcinoma (hcc_062)


title: Hepatocellular carcinoma (hcc_073)


title: Hepatocellular carcinoma (hcc_055)


title: Hepatocellular carcinoma (hcc_079)


title: Hepatocellular carcinoma (hcc_049)


title: Hepatocellular carcinoma (hcc_051)


title: Hepatocellular carcinoma (hcc_053)


title: Hepatocellular carcinoma (hcc_045)


title: Hepatocellular carcinoma (hcc_048)


title: Hepatocellular carcinoma (hcc_043)


title: Hepatocellular carcinoma (hcc_047)


title: Hepatocellular carcinoma (hcc_040)


title: Hepatocellular carcinoma (hcc_039)


title: Hepatocellular carcinoma (hcc_041)


title: Hepatocellular carcinoma (hcc_058)


title: Hepatocellular carcinoma (hcc_031)


title: Hepatocellular carcinoma (hcc_036)


title: Hepatocellular carcinoma (hcc_059)


title: Hepatocellular carcinoma (hcc_032)


title: Hepatocellular carcinoma (hcc_033)


title: Hepatocellular carcinoma (hcc_035)


title: Hepatocellular carcinoma (hcc_029)


title: Hepatocellular carcinoma (hcc_027)


title: Hepatocellular carcinoma (hcc_028)


title: Hepatocellular carcinoma (hcc_025)


title: Hepatocellular carcinoma (hcc_024)


title: Hepatocellular carcinoma (hcc_023)


title: Hepatocellular carcinoma (hcc_038)


title: Hepatocellular carcinoma (hcc_022)


title: Hepatocellular carcinoma (hcc_021)


title: Hepatocellular carcinoma (hcc_015)


title: Hepatocellular carcinoma (hcc_020)


title: Hepatocellular carcinoma (hcc_017)


title: Hepatocellular carcinoma (hcc_002)


title: Hepatocellular carcinoma (hcc_016)


title: Hepatocellular carcinoma (hcc_005)


title: 1476-2

status: Public on Mar 28 2007

city: Inage-ku

first: Hiroshi

last: Watanabe

state: Chiba-shi

address: Anagawa 4-9-1

institute: National institute of radiological sceiences

description: Biopsy sample

data_processing: CodeLink Expression Analysis version 4.1

source_name: biopsy

tag: sample no.

tag: age

value: M

tag: primary site

value: Tongue

tag: pathological diagnosis

value: squamous cell carcinoma

tag: t stage

tag: n status

tag: metastasis-free survival (m)

tag: analytical group

value: Reference


title: 1477-2

description: Biopsy sample

value: F

value: Validation


title: 1479-2

description: Biopsy sample

tag: lymphatic .metastasis


title: 1475-1

description: Biopsy sample


title: 1476-1

description: Biopsy sample


title: 1478-1

description: Biopsy sample


title: 1473-2

description: Biopsy sample


title: 1477-1

description: Biopsy sample


title: hES_ES01_Agilent

status: Public on Jun 27 2007

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

hyb_protocol: according to standard Agilent protocol

scan_protocol: Agilent scanner and software

data_processing: Agilent Feature Extraction software; gProcessedSignal; processed Cy3 Signal

source_name: human ES cell line ES01 - Agilent

label_protocol: Agilent labeling kit

growth_protocol: cultured on irradiated MEFs in DMEM/F12 with 20% KSR, BME, NEAA, L-glutamine, and FGF2

extract_protocol: TRIzol

tag: undifferentiated


title: 1479-1

description: Biopsy sample


title: 1475-2

description: Biopsy sample


title: 1473-1

description: Biopsy sample


title: hES_BG03_Agilent

source_name: human ES cell line BG03 - Agilent


title: hES_H9_Agilent

source_name: human ES cell line H9 - Agilent


title: 1478-2

description: Biopsy sample


title: 1256-2

description: Biopsy sample


title: 1254-1

description: Biopsy sample


title: 1262-2

description: Biopsy sample


title: HDF

status: Public on Nov 22 2007

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

description: Origin of human iPS cells

hyb_protocol: Agilent protocol (one color)

scan_protocol: Agilent scanner

data_processing: Agilent feature extraction

source_name: adult human dermal fibroblasts

label_protocol: Agilent protocol

extract_protocol: Trizol

tag: HDF from facial dermis of 36-year-old Caucasian female were purchased from Cell Applications, Inc. When received, the population doubling was less than 16. We used these cells for the induction of iPS cells within six passages after the receipt.


title: 1256-1

description: Biopsy sample

tag: Sex


title: 1262-1

description: Biopsy sample


title: 1260-1

description: Biopsy sample


title: 1041-1

description: Biopsy sample


title: 1254-2

description: Biopsy sample


title: 1673-1

description: Biopsy sample


title: 1040-2

description: Biopsy sample


title: 1041-2

description: Biopsy sample


title: 1673-2

description: Biopsy sample


title: 1040-1

description: Biopsy sample


title: 1260-2

description: Biopsy sample


title: 1670-2

description: Biopsy sample


title: 1668-2

description: Biopsy sample


title: 1667-1

description: Biopsy sample


title: 1671-2

description: Biopsy sample


title: 1672-1

description: Biopsy sample


title: 1670-1

description: Biopsy sample


title: 1578-2

description: Biopsy sample


title: 1666-2

description: Biopsy sample


title: 1668-1

description: Biopsy sample


title: 1665-1

description: Biopsy sample


title: 1671-1

description: Biopsy sample


title: 1576-2

description: Biopsy sample


title: 1667-2

description: Biopsy sample


title: 1578-1

description: Biopsy sample


title: 1576-1

description: Biopsy sample


title: 1665-2

description: Biopsy sample


title: 1571-2

description: Biopsy sample


title: 1666-1

description: Biopsy sample


title: 1573-2

description: Biopsy sample


title: 1571-1

description: Biopsy sample


title: 1573-1

description: Biopsy sample


title: 1672-2

description: Biopsy sample


title: 1572-2

description: Biopsy sample


title: 0991-2

description: Biopsy sample


title: 1033-1

description: Biopsy sample


title: 1033-2

description: Biopsy sample


title: 1572-1

description: Biopsy sample


title: 1038-2

description: Biopsy sample


title: 1038-1

description: Biopsy sample


title: 1482-2

description: Biopsy sample


title: 1032-1

description: Biopsy sample


title: 0991-1

description: Biopsy sample


title: 0985-1

description: Biopsy sample


title: 1482-1

description: Biopsy sample


title: 0983-2

description: Biopsy sample


title: 0941-2

description: Biopsy sample


title: 1032-2

description: Biopsy sample


title: 0937-2

description: Biopsy sample


title: 0942-1

description: Biopsy sample


title: 0985-2

description: Biopsy sample


title: 0983-1

description: Biopsy sample


title: 0939-2

description: Biopsy sample


title: 0941-1

description: Biopsy sample


title: 0806-2

description: Biopsy sample


title: 0942-2

description: Biopsy sample


title: 0808-2

description: Biopsy sample


title: 0935-2

description: Biopsy sample


title: 0939-1

description: Biopsy sample


title: 0935-1

description: Biopsy sample


title: 0808-1

description: Biopsy sample


title: 0806-1

description: Biopsy sample


title: 0937-1

description: Biopsy sample