title: Colorectal Carcinoma derived from Hong Kong, Case no. 28, Chr18

city: Cambridge

first: George

last: Poulogiannis

address: Tennis Court Road

department: Pathology

country: United Kingdom

institute: University of Cambridge

description: Log2 tumour/reference intensity ratios for analysis of copy number variations

hyb_protocol: The purified DNA from test and reference were pooled and mixed with 45µg of Cot1 DNA and ethanol precipitated. The precipitated DNA was dissolved in 30µl of hybridisation buffer, incubated at 37˚C for 2 hours and applied to the prehybridised microarray. Hybridisation was performed in a humidified Micro Array Hybridisation Chamber (Camlab, Cambridge, UK) at 37˚C for 48 hours under a coverslip. The arrays were then washed successively in 1x PBS/0.05% Tween20 at room temperature for 15 min twice, 50% formamide/2xSSC at 42˚C for 30 min once, 1x PBS/0.05% Tween20 at room temperature for 15min and 1x PBS for 5min twice.

scan_protocol: Scanned on an Axon GenePix 4100A personal scanner. Images were quantified using GenePix Pro version 5.1.

data_processing: The median of the ratio of test/reference spot intensity, after subtraction of local background, of the 5Mb-clones in each subarray was used as the normalization factor. The chromosomal arm on which most microsatellite markers showed allelic balance was chosen for normalization. The test/reference ratio of each clone was divided by the normalization factor for each subarray, an average of the duplicate calculated and log2-transformed.

source_name: Primary tumour sample

label_protocol: 400ng of genomic DNA was labelled with a Bioprime labelling kit (Invitrogen)

extract_protocol: Proteinase K digestion followed by phenol:chloroform extraction

tag: gender

value: Male

tag: location

value: Hepatic flexure

tag: msi

tag: stage

value: Dukes' C

tag: recurrence

value: Yes

tag: survival

tag: alive/dead at the end of recorded survival

value: Dead

source_name: Mixed normal blood from 20 individuals

label_protocol: 400ng of tumour and reference genomic DNA were labelled with Cy5-dCTP and Cy3-dCTP (GE Healthcare), respectively, using BioPrime kit (Invitrogen) according to the manufacturer’s instruction, except that custom-prepared dNTP (dCTP 1mM, dATP 2mM, dGTP 2mM and dTTP 2mM) was used. After overnight incubation at 37°C, the labelled DNA were purified using a G-50 spin column (GE Healthcare).

value: Female


title: Colorectal Carcinoma derived from Hong Kong, Case no. 33, Chr18

status: Public on Feb 11 2010

type: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: age

value: Rectum

value: Dukes' B

value: No

value: Alive


title: Colorectal Carcinoma derived from Hong Kong, Case no. 27, Chr18

value: Transverse


title: Colorectal Carcinoma derived from Hong Kong, Case no. 25, Chr18

value: Sigmoid


title: Colorectal Carcinoma derived from Hong Kong, Case no. 38, Chr18


title: Colorectal Carcinoma derived from Hong Kong, Case no. 16, Chr18


title: Colorectal Carcinoma derived from Hong Kong, Case no. 24, Chr18


title: MC58_Iron-replete_3

type: RNA

city: Boston

first: Ryan

middle: S

last: McClure

state: MA

address: 650 Albany St.

department: Microbiology

country: USA

institute: Boston University

description: One of three biological replicates of RNA isolated from wild-type MC58 under iron-replete conditions

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Nimblegen 4-plexTM microarrays are single-channel arrays meaning cDNA samples were labeled with only a single dye.  Intensity of bound sample for each probe was quantified using the NimbleScan2.3 software suite to determine an absolute probe intensity value.  Individual probe intensities were then background adjusted within each individual array and normalized between differing arrays using the method of quantile normalization as described by Bolstad et al.  Expression values for a given open reading frame were derived from a given set of corresponding probes using the method of robust multiarray average as described by Irizarry et al.  Subsequent to quantile normalization and RMA analysis, gene expression characteristics were further analyzed using the Arraystar 2.0 software suite (DNAStar Inc., Madison, WI).  Arraystar analysis enabled visualization of gene expression data using scatterplots and agglomerative hierarchical clustering as well as statistical analyses of expression data by the analysis of variance (ANOVA) method.  For each strain and condition three biological replicates were analyzed for a total of 18 arrays.

molecule: total RNA

organism: Neisseria meningitidis MC58

source_name: Neisseria meningitidis MC58 wild-type

label_protocol: Total RNA (30 μg) for each sample was converted to double-stranded cDNA using the SuperScriptTM double-stranded cDNA conversion kit (Invitrogen, Carlsbad, CA).  Samples were labeled, hybridized according to Nimblegen’s protocols.

growth_protocol: For all growth experiments bacteria were plated from glycerol stocks onto GCB agar plates and grown overnight.  Cells were then inoculated into chemically defined media (CDM) or GCK media (GC broth supplemented 1:100 with Kellogg’s I supplement) to an OD600 of .06-.08 using a Genesys 20 spectrophotometer and cuvettes with a pathlength of 10mm.

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.  RNA was DNaseI treated and removal of DNA contamination was verified by PCR.

treatment_protocol: For experiments in which RNA was to be isolated, cells were grown to an OD600 of 0.4-0.5 before being divided and inoculated with either 100 μg/ml Ferric nitrate or 100 μg/ml of the iron chelator desferal to constitute iron-replete or iron-deplete conditions, respectively.  Cultures were grown an additional 30 min before RNA was harvested.

tag: genotype/variation

value: Wild-type

tag: treatment protocol

value: iron-replete


title: Colorectal Carcinoma derived from Hong Kong, Case no. 17, Chr18

value: Ascending Colon


title: UTX chip_Lung_1of2

status: Public on Feb 12 2010

city: Stanford

first: Jordon

middle: K

last: Wang

state: CA

address: 269 Campus Dr.

department: Dermatology

institute: Stanford University

hyb_protocol: Standard Nimblegen hybridization kits and protocols were used

scan_protocol: Arrays were scanned with Axon scanner at 5 um resolution according to standard Nimblegen protocols

data_processing: Arrays were processed using Nimblegens standard protocol for Nimblescan 2.4 ChIP data extraction

source_name: ChIP

label_protocol: Standard Nimblegen ChIP labeling protocol (1 ug of Amplified ChIP DNA, direct incorporation of cy labeled primers with klenow extension

growth_protocol: Fibroblasts were grown in DMEM with 10% Fetal Bovine Serum until ~70% confluent

extract_protocol: ChIP was performed on 4x10^6 fibroblast cells and Farnham ChIP protocol was used to derive ChIP DNA and was amplified by sigma WGA2 kit for 1 round of amplification

tag: cell type

value: lung primary human fibroblasts


title: C-peptide_18hrs_rep3

city: Leicester

first: Nigel

middle: John

last: Brunskill

state: Leics

address: University Road

department: Infection Immunity and Inflammation

institute: University of Leicester

description: HK-2 cells cultured 18h with 5nM C-peptide

hyb_protocol: Standard Illumina hybridization protocol performed by Geneservice (Cambridge, UK)

scan_protocol: Standard Illumina scanning protocol performed by Geneservice (Cambridge, UK)

data_processing: The array intensity data were analysed using Illumina GenomeStudio Gene Expression Module (v1.1.1) (Illumina Cambridge, UK) for visualisation and normalisation.  The quantile normalisation method was used for all analyses and average background correction performed within the Beadstudio software.

label: biotin

source_name: HK-2 cells

growth_protocol: HK-2 cells (passages 18-30) were maintained in DMEM/Hams F12 (DMEM/F12) (17.5mM glucose), supplemented with 10% fetal calf serum (FCS), glutamine (2mM), penicillin (100 IU/ml) and streptomycin (100ng/ml).  Cells were cultured at 37oC in a humidified atmosphere of 5% CO2 in air.  Prior to treatment, cells were cultured in DMEM/F12 low glucose (5mM) (5mM-DMEM/F12) for 48h.

extract_protocol: RNA was prepared by acid-guanidinium extraction using a Genelute mammalian total RNA miniprep kit (Sigma-Aldrich, Poole, UK) following the manufacturer’s instructions.

treatment_protocol: For microarray analyses, cells were cultured in 5mM-DMEM/F12 without supplements (control) or with 5nM C-peptide for either 18h or 48h.  Alternatively, cells were treated with 2ng/ml TGF-b1 either alone or in combination with C-peptide for 48h.  All treatments were performed in triplicate to yield 18 flasks, and RNA from each flask hybridized to a separate chip to give an n of 3 for each of 6 treatments.  Flasks were subjected to identical media changes and cells cultured for identical periods in media without supplements.  In all experiments, cells were serum-starved overnight before agonist addition.  Treatments were initiated such that 18h and 48h incubation periods ended coincidentally and all RNA was prepared at this point.

tag: cell line


title: C-peptide_18hrs_rep1

label_protocol: Standard Illumina hybridization protocol performed by Geneservice (Cambridge, UK)


title: Colorectal Carcinoma derived from Hong Kong, Case no. 8, Chr18

value: Dukes' D


title: TGF-beta_C-peptide_48hrs_rep3

description: HK-2 cells cultured 48h with 2ng/ml TGF-b1 and 5nM C-peptide


title: TGF-beta_C-peptide_48hrs_rep1


title: TGF-beta_C-peptide_48hrs_rep2


title: UTX input_Lung_1of2

source_name: Input


title: UTX input_Foot_2of2

value: foot primary human fibroblasts


title: UTX chip_Lung_2of2


title: Colorectal Carcinoma derived from Hong Kong, Case no. 7, Chr18

value: Male


title: C-peptide_48hrs_rep2

description: HK-2 cells cultured 48h with 5nM C-peptide


title: Colorectal Carcinoma derived from Hong Kong, Case no. 2, Chr18


title: Colorectal Carcinoma derived from Hong Kong, Case no. 3, Chr18

value: Rectosigmoid


title: Colorectal Carcinoma derived from Hong Kong, Case no. 1, Chr18

value: Yes


title: Colorectal Carcinoma derived from Edinburgh, Case no. 68, Chr18

value: Dead


title: C-peptide_48hrs_rep3


title: C-peptide_48hrs_rep1


title: Colorectal Carcinoma derived from Edinburgh, Case no. 62, Chr18

value: Dukes' C

value: Female


title: TGF-beta_48hrs_rep1

description: HK-2 cells cultured 48h with 2ng/ml TGF-b1


title: Colorectal Carcinoma derived from Edinburgh, Case no. 61, Chr18

value: Ascending colon

value: Dukes' B


title: TGF-beta_48hrs_rep3

description: HK-2 cells cultured 48h with 2ng/ml TGF-b3


title: Acute Myeloid Leukemia Kasumi-1 CD34- cell line CGH

city: Buffalo

first: Jeffrey

last: Conroy

state: NY

address: Elm & Carlton Sts

institute: Roswell Park Cancer Institute

description: Image analysis was performed using the Feature Extraction version 9.5.1.1 (Agilent Technologies) and the Agilent's CGH-v4_95_Feb07 protocol.

hyb_protocol: 1ug of reference and test sample genomic DNA were individually fluorescently labeled using the Agilent Genomic DNA Labeling kit, Direct Method, as described by the manufacturer (Agilent Technologies).  Initially, the DNA is denatured in the presence of the random primer at 95C for 3 minutes in a thermalcycler, and then quickly cooled to 4C.  The tubes are transferred to ice and labeling occurs with the addition of dUTP-cyanine 3 mix (or dUTP-cyanine 5) and Exo-Klenow fragment.  Incubation takes place for two hours at 37C in a thermalcycler.  After purification, the labeled DNA is combined and resuspended in 50ug Cot-1 DNA, and 1x Agilent blocking agent and hybridization buffer.  The entire sample is heated to 95C for 3 minutes followed by a 37C incubation for 30 minutes.  Hybridization to the Agilent human 244K CGH array was performed for 40 hours at 65C using a rotating hybridization oven.  Arrays were washed according to the manufacturer's recommendations; air dried, and scanned using an Agilent DNA microarray scanner (Agilent Technologies, Inc), and processed using Agilent's Feature Extraction software.

scan_protocol: Arrays were scanned using an Agilent  DNA microarray scanner (Agilent Technologies, Inc) to generate high-resolution (5 um) images for both Cy3 (control) and Cy5 (test) channels.

data_processing: Data was processed from Agilent's Feature Extraction output by CGH Analytics version 3.4.27 (Agilent Technologies).  Aberration calls were made using Agilent's ADM-1 algorithm with a threshold of 10, comparing the Kasumi-1 CD34- DNA sample versus the control DNA sample.

source_name: Kasumi-1, CD34-

label_protocol: Agilent Genomic DNA Labelling kit, Direct Method, as described by the manufacturer (Agilent Technologies, Palo Alto, CA).  1ug template

growth_protocol: The human AML Kasumi-1 cell line (AML M2, AML1-ETO) was obtained from DMSZ (Braunschweig GERMANY) and maintained in RPMI 1640 (PBI International, Milan, Italy) with 10% fetal bovine serum (FBS; HyClone Laboratories, Logan, UT, USA).

extract_protocol: DNA was isolated from Kasumi-1 CD34- subpopulation cells using the NucleoSpin Tissue kit (Macherey-Nagel, Gmbh & Co. KG) according to the manufacturer's instructions. DNA quality and concentration were evaluated using spectrophotometer NANODROP 1000 ( Thermo Fischer Scientific Inc.).

treatment_protocol: Kasumi-1 cells, after washing and blocking, were stained with Cy7-phycoerythrine (PE) conjugated anti-CD34 antibody,  (Becton Dickinson, BD Biosciences). Cell sorting of CD34- subpopulation was performed using a Facs Vantage SE Laser 488nm Interprise Coherent flow cytometer (Becton Dickinson, BD Biosciences), and gates were set up to exclude not viable cells and debris. The purity of sorted fractions was assessed to ensure sort quality.

value: male

tag: facs-sorted

value: CD34- Kasumi-1 subpopulation

source_name: reference control

extract_protocol: Qiagen FlexiGene DNA kit protocol (Cat# 51206).

value: female

tag: phenotype

value: normal pooled

tag: tissue

value: peripheral blood


title: Colorectal Carcinoma derived from Edinburgh, Case no. 66, Chr18

value: Rectum

value: Dukes' A

value: No


title: Colorectal Carcinoma derived from Edinburgh, Case no. 67, Chr18

value: Transverse

value: Alive


title: Control_18hrs_rep1

description: HK-2 cells cultured 18h without supplements


title: C-peptide_18hrs_rep2


title: Control_18hrs_rep2


title: Control_48hrs_rep3

description: HK-2 cells cultured 48h without supplements


title: Colorectal Carcinoma derived from Edinburgh, Case no. 31, Chr18

value: Male


title: Control_18hrs_rep3


title: Colorectal Carcinoma derived from Hong Kong, Case no. 38

value: MSS

value: Yes


title: Colorectal Carcinoma derived from Edinburgh, Case no. 28, Chr18

value: Sigmoid

value: Dead


title: Colorectal Carcinoma derived from Edinburgh, Case no. 25, Chr18

value: Dukes' C

value: Female


title: Colorectal Carcinoma derived from Edinburgh, Case no. 30, Chr18


title: Colorectal Carcinoma derived from Hong Kong, Case no. 37


title: TGF-beta_48hrs_rep2

description: HK-2 cells cultured 48h with 2ng/ml TGF-b2


title: Colorectal Carcinoma derived from Edinburgh, Case no. 21, Chr18

value: Dukes' D


title: Control_48hrs_rep2


title: Colorectal Carcinoma derived from Hong Kong, Case no. 35


title: Colorectal Carcinoma derived from Hong Kong, Case no. 34

value: MSI-H

value: Dukes' B


title: Colorectal Carcinoma derived from Edinburgh, Case no. 16, Chr18

value: Caecum


title: Colorectal Carcinoma derived from Edinburgh, Case no. 20, Chr18

value: Sensored


title: Colorectal Carcinoma derived from Edinburgh, Case no. 12, Chr18

value: Ascending Colon


title: Acute Myeloid Leukemia Kasumi-1 CD34+CD38- cell line CGH

scan_protocol: Arrays were scanned using an Agilent DNA microarray scanner (Agilent Technologies, Inc) to generate high-resolution (5 um) images for both Cy3 (control) and Cy5 (test) channels.

data_processing: Data was processed from Agilent's Feature Extraction output by CGH Analytics version 3.4.27 (Agilent Technologies).  Aberration calls were made using Agilent's ADM-1 algorithm with a threshold of 10, comparing the Kasumi-1 CD34+CD38- DNA sample versus the control DNA sample.

source_name: Kasumi-1, CD34+CD38-

extract_protocol: DNA was isolated from Kasumi-1 CD34+CD38- subpopulation cells using the NucleoSpin Tissue kit (Macherey-Nagel, Gmbh & Co. KG) according to the manufacturer's instructions. DNA quality and concentration were evaluated using spectrophotometer NANODROP 1000 ( Thermo Fischer Scientific Inc.).

treatment_protocol: Kasumi-1 cells, after washing and blocking, were stained with Cy7-phycoerythrine (PE) conjugated anti-CD34 antibody and PE conjugated anti-CD38,  (Becton Dickinson, BD Biosciences). Cell sorting of CD34+CD38- subpopulation was performed using a Facs Vantage SE Laser 488nm Interprise Coherent flow cytometer (Becton Dickinson, BD Biosciences), and gates were set up to exclude not viable cells and debris. The purity of sorted fractions was assessed to ensure sort quality.

value: male

value: CD34+CD38- Kasumi-1 subpopulation

value: female

value: normal pooled

value: peripheral blood


title: Control_48hrs_rep1


title: Colorectal Carcinoma derived from Hong Kong, Case no. 33

value: Male

value: Rectum

value: MSS

value: No

value: Alive


title: MC58_Iron-replete_2

value: Wild-type

value: iron-replete


title: Colorectal Carcinoma derived from Hong Kong, Case no. 32

value: Dukes' C

value: Female


title: Colorectal Carcinoma derived from Hong Kong, Case no. 36

value: Hepatic flexure

value: MSI-H

value: Dukes' B


title: Colorectal Carcinoma derived from Hong Kong, Case no. 30

value: Yes


title: Colorectal Carcinoma derived from Edinburgh, Case no. 10, Chr18

value: Dead


title: Colorectal Carcinoma derived from Edinburgh, Case no. 8, Chr18


title: Colorectal Carcinoma derived from Hong Kong, Case no. 29


title: Colorectal Carcinoma derived from Edinburgh, Case no. 3, Chr18


title: Colorectal Carcinoma derived from Hong Kong, Case no. 28


title: Colorectal Carcinoma derived from Edinburgh, Case no. 2, Chr18

value: Dukes' D


title: Colorectal Carcinoma derived from Hong Kong, Case no. 27

value: Transverse


title: Colorectal Carcinoma derived from Hong Kong, Case no. 26


title: Colorectal Carcinoma derived from Hong Kong, Case no. 25

value: Sigmoid


title: Colorectal Carcinoma derived from Hong Kong, Case no. 24

value: Male


title: Colorectal Carcinoma derived from Hong Kong, Case no. 23

value: Descending Colon


title: Acute Myeloid Leukemia Kasumi-1 cell line CGH

description: Image analysis was performed using the Feature Extraction version 9.5.1.1 (Agilent Technologies) and the Agilent’s CGH-v4_95_Feb07 protocol.

hyb_protocol: 1μg of reference and test sample genomic DNA were individually fluorescently labeled using the Agilent Genomic DNA Labeling kit, Direct Method, as described by the manufacturer (Agilent Technologies).  Initially, the DNA is denatured in the presence of the random primer at 95˚C for 3 minutes in a thermalcycler, and then quickly cooled to 4˚C.  The tubes are transferred to ice and labeling occurs with the addition of dUTP-cyanine 3 mix (or dUTP-cyanine 5) and Exo-Klenow fragment.  Incubation takes place for two hours at 37˚C in a thermalcycler.  After purification, the labeled DNA is combined and resuspended in 50μg Cot-1 DNA, and 1x Agilent blocking agent and hybridization buffer.  The entire sample is heated to 95˚C for 3 minutes followed by a 37˚C incubation for 30 minutes.  Hybridization to the Agilent human 244K CGH array was performed for 40 hours at 65˚C using a rotating hybridization oven.  Arrays were washed according to the manufacturer’s recommendations; air dried, and scanned using an Agilent DNA microarray scanner (Agilent Technologies, Inc), and processed using Agilent’s Feature Extraction software.

scan_protocol: Arrays were scanned using an Agilent 2565AA DNA microarray scanner (Agilent Technologies, Inc) to generate high-resolution (5 μm) images for both Cy3 (control) and Cy5 (test) channels.

data_processing: Data was processed from Agilent’s Feature Extraction output by CGH Analytics version 3.4.27 (Agilent Technologies).  Aberration calls were made using Agilent’s ADM-1 algorithm with a threshold of 10, comparing the Kasumi-1 DNA sample versus the control DNA sample.

extract_protocol: DNA was isolated from Kasumi-1 total cell line using the NucleoSpin Tissue kit (Macherey-Nagel, Gmbh & Co. KG) according to the manufacturer’s instructions. DNA quality and concentration were evaluated using spectrophotometer NANODROP 1000 ( Thermo Fischer Scientific Inc.).

value: male

value: female

value: normal pooled

value: peripheral blood


title: C2TA knock-out_7

city: Munich

first: Maria

last: Hinterberger

address: Goethestr. 31

department: Institut für Immunologie

country: Germany

institute: LMU

description: 3 biological replicates.

hyb_protocol: hybridization, washing, staining: WT Expression Kit

scan_protocol: hardware: Genechip Scanner 3000 7G: Software: Genechip Command Console Fluidics Console

data_processing: RMA normalization

organism: Mus musculus

source_name: CD80+ medullary thymic epithelial cells from C2TA knock-out, 3 biological replicates

label_protocol: WT Expression Kit

extract_protocol: Total RNA was isolated from thymic medullary epithelial cells using the miRNAeasy kit (Qiagen) according to the manufacturer´s recommendations.

tag: strain

value: Balb/c

value: thymus

value: CD80+ medullary thymic epithelial cells

value: 4-6 weeks

value: C2TA knockout


title: C2TA knock-out_8

description: 3 biological replicates.


title: C2TA knock-out_9

description: 3 biological replicates.


title: C2TA knockdown_6

description: 3 biological replicates.

source_name: CD80+ medullary thymic epithelial cells from C2TA knockdown, 3 biological replicates

value: C2TA knockdown


title: Colorectal Carcinoma derived from Hong Kong, Case no. 10

value: Female

value: MSS

value: Dukes' B

value: No

value: Alive


title: Colorectal Carcinoma derived from Hong Kong, Case no. 21

value: Hepatic flexure

value: MSI-H

value: Dukes' C

value: Dead

value: Male


title: Colorectal Carcinoma derived from Hong Kong, Case no. 13

value: Rectum


title: Colorectal Carcinoma derived from Hong Kong, Case no. 20

value: Rectosigmoid


title: Colorectal Carcinoma derived from Hong Kong, Case no. 22

value: Sigmoid


title: Colorectal Carcinoma derived from Hong Kong, Case no. 14

value: Dukes' D


title: Colorectal Carcinoma derived from Hong Kong, Case no. 18

value: Transverse


title: Colorectal Carcinoma derived from Hong Kong, Case no. 17

value: Ascending Colon


title: Colorectal Carcinoma derived from Hong Kong, Case no. 16

value: Yes


title: C2TA knockdown_4

description: 3 biological replicates.

value: female

value: Balb/c

value: thymus

value: CD80+ medullary thymic epithelial cells

value: 4-6 weeks

value: C2TA knockdown


title: C2TA wild-type_2

description: 3 biological replicates.

source_name: CD80+ medullary thymic epithelial cells from WT, 3 biological replicates

value: C2TA wild type


title: Colorectal Carcinoma derived from Hong Kong, Case no. 12

value: Caecum

value: MSS

value: Dukes' B

value: No

value: Alive

value: Female


title: C2TA wild-type_3

description: 3 biological replicates.


title: Colorectal Carcinoma derived from Hong Kong, Case no. 9

value: Male

value: Hepatic flexure

value: Dukes' C


title: Colorectal Carcinoma derived from Hong Kong, Case no. 7

value: Sigmoid

value: MSI-L

value: Yes

value: Dead


title: Colorectal Carcinoma derived from Hong Kong, Case no. 8

value: Dukes' D


title: Colorectal Carcinoma derived from Hong Kong, Case no. 6

value: Rectum

value: Dukes' A


title: Colorectal Carcinoma derived from Hong Kong, Case no. 2


title: Colorectal Carcinoma derived from Hong Kong, Case no. 4


title: Colorectal Carcinoma derived from Hong Kong, Case no. 5


title: C2TA wild-type_1

description: 3 biological replicates.

value: female

value: Balb/c

value: thymus

value: CD80+ medullary thymic epithelial cells

value: 4-6 weeks

value: C2TA wild type


title: C2TA knockdown_5

description: 3 biological replicates.

value: C2TA knockdown


title: Colorectal Carcinoma derived from Hong Kong, Case no. 3

value: Male

value: Rectosigmoid

value: MSS

value: Dukes' B

value: No

value: Alive

value: Female


title: Colorectal Carcinoma derived from Hong Kong, Case no. 11

value: MSI-H


title: Colorectal Carcinoma derived from Hong Kong, Case no. 1

value: Rectum

value: Yes

value: Dead


title: Colorectal Carcinoma derived from Edinburgh, Case no. 81

value: Transverse

value: Dukes' C


title: Colorectal Carcinoma derived from Edinburgh, Case no. 79

value: Sigmoid


title: Colorectal Carcinoma derived from Edinburgh, Case no. 80


title: Colorectal Carcinoma derived from Edinburgh, Case no. 74


title: Colorectal Carcinoma derived from Edinburgh, Case no. 77

value: Caecum


title: Colorectal Carcinoma derived from Edinburgh, Case no. 73


title: Colorectal Carcinoma derived from Edinburgh, Case no. 69


title: Colorectal Carcinoma derived from Edinburgh, Case no. 58

value: Ascending Colon


title: Colorectal Carcinoma derived from Edinburgh, Case no. 68

value: Dukes' D


title: Colorectal Carcinoma derived from Edinburgh, Case no. 66

value: Male

value: Dukes' A


title: Colorectal Carcinoma derived from Edinburgh, Case no. 65

value: MSS


title: Colorectal Carcinoma derived from Edinburgh, Case no. 59


title: Colorectal Carcinoma derived from Edinburgh, Case no. 70


title: Colorectal Carcinoma derived from Edinburgh, Case no. 60

value: Dukes' B


title: Colorectal Carcinoma derived from Edinburgh, Case no. 64

value: Ascending colon


title: Colorectal Carcinoma derived from Edinburgh, Case no. 62

value: No


title: Colorectal Carcinoma derived from Edinburgh, Case no. 57

value: Female


title: Colorectal Carcinoma derived from Edinburgh, Case no. 67

value: Alive


title: Colorectal Carcinoma derived from Edinburgh, Case no. 55

value: Rectum


title: Colorectal Carcinoma derived from Edinburgh, Case no. 54


title: Colorectal Carcinoma derived from Edinburgh, Case no. 56


title: Colorectal Carcinoma derived from Edinburgh, Case no. 78


title: Colorectal Carcinoma derived from Edinburgh, Case no. 61


title: Colorectal Carcinoma derived from Edinburgh, Case no. 52

value: MSI-L

value: Yes


title: Colorectal Carcinoma derived from Edinburgh, Case no. 53

value: Dead


title: Colorectal Carcinoma derived from Edinburgh, Case no. 51

value: Dukes' C


title: Colorectal Carcinoma derived from Edinburgh, Case no. 48

value: Sigmoid


title: Colorectal Carcinoma derived from Edinburgh, Case no. 50


title: Colorectal Carcinoma derived from Edinburgh, Case no. 49


title: Colorectal Carcinoma derived from Edinburgh, Case no. 47


title: Colorectal Carcinoma derived from Edinburgh, Case no. 46


title: Colorectal Carcinoma derived from Edinburgh, Case no. 44


title: Colorectal Carcinoma derived from Edinburgh, Case no. 45


title: Colorectal Carcinoma derived from Edinburgh, Case no. 34


title: Colorectal Carcinoma derived from Edinburgh, Case no. 40


title: Colorectal Carcinoma derived from Edinburgh, Case no. 32


title: Colorectal Carcinoma derived from Edinburgh, Case no. 31


title: Colorectal Carcinoma derived from Edinburgh, Case no. 38


title: Colorectal Carcinoma derived from Edinburgh, Case no. 42

value: MSI-H


title: Colorectal Carcinoma derived from Edinburgh, Case no. 39


title: Colorectal Carcinoma derived from Edinburgh, Case no. 41


title: Colorectal Carcinoma derived from Edinburgh, Case no. 43


title: circle willis 3

city: Durham

first: Heather

middle: A

last: Himburg

state: NC

address: PO BOX 91013

department: Medicine/Cellular Therapy

institute: Duke University Medical Center

hyb_protocol: see www.genome.duke.edu for standard hybridization protocol

scan_protocol: scan according to Axon GenePix 4000B recommendations

data_processing: Data were normalized in GeneSpring to the Stratagene Universal Human reference control (Cy3 channel)

source_name: endothelial cell

label_protocol: Ambion MessageAmpII Protocol - 1 round Amplification

growth_protocol: Endothelial cells were cultured in gelatin-coated 24 well culture plates in an endothelial cell growth medium containing 10%FBS, 1% Pen/Strep, 1% l-glutamine, 1X heparin and 60 mg/L endothelial cell grwoth supplement  in M199.

extract_protocol: Total RNA was extracted using the Qiagen Rneasy kit

treatment_protocol: Cells were not treated.

tag: source

value: brain derived

value: RMUCLA

source_name: Stratagene Universal Human reference

value: Stratagene Universal Human reference


title: circle willis 2


title: Colorectal Carcinoma derived from Edinburgh, Case no. 33

tag: gender

value: Descending Colon

value: Male


title: posterior cortical 1

value: Postcort


title: arachnoid plexus 3

value: ARACH


title: basilar artery2 3


title: Colorectal Carcinoma derived from Edinburgh, Case no. 35

tag: location

value: MSS


title: posterior cortical 2


title: posterior cortical 3


title: middle cerebral artery 1

value: MCA


title: circle willis 1


title: Colorectal Carcinoma derived from Edinburgh, Case no. 37

tag: msi

value: Dukes' A

value: Female


title: middle cerebral artery 2


title: basilar artery2 1


title: Colorectal Carcinoma derived from Edinburgh, Case no. 29

tag: stage

value: Dukes' B

value: No

value: Alive


title: basilar artery2 2


title: middle cerebral artery 3


title: Colorectal Carcinoma derived from Edinburgh, Case no. 30

value: Dukes' C

tag: recurrence

value: Yes

value: Dead


title: arachnoid plexus 1

value: brain derived


title: arachnoid plexus 2


title: basilar artery1 5


title: Colorectal Carcinoma derived from Edinburgh, Case no. 28

value: Sigmoid

tag: survival


title: Colorectal Carcinoma derived from Edinburgh, Case no. 27

tag: alive/dead at the end of recorded survival


title: Colorectal Carcinoma derived from Edinburgh, Case no. 26

tag: age

value: Rectum


title: Colorectal Carcinoma derived from Edinburgh, Case no. 24


title: Colorectal Carcinoma derived from Edinburgh, Case no. 25


title: Colorectal Carcinoma derived from Edinburgh, Case no. 22

value: Descending Colon


title: Colorectal Carcinoma derived from Edinburgh, Case no. 23

value: Male


title: dermal microvessel 3

value: non-brain derived

value: HDMEC

value: Stratagene Universal Human reference


title: Colorectal Carcinoma derived from Edinburgh, Case no. 20

value: MSS

value: Sensored


title: Colorectal Carcinoma derived from Edinburgh, Case no. 17

value: Dukes' A

value: Female


title: Colorectal Carcinoma derived from Edinburgh, Case no. 18

value: Dukes' B

value: No


title: dermal microvessel 1


title: dermal microvessel 2


title: Colorectal Carcinoma derived from Edinburgh, Case no. 21

value: Dukes' D


title: iliac artery 2

value: HIAEC


title: umbilical artery 1

value: HUAEC


title: lung microvessel 2

value: HLMEC


title: lung microvessel 1


title: Colorectal Carcinoma derived from Edinburgh, Case no. 16

value: Caecum

value: Alive


title: Colorectal Carcinoma derived from Edinburgh, Case no. 15

value: Rectum

value: MSI-H

value: Dukes' C


title: Colorectal Carcinoma derived from Edinburgh, Case no. 13

value: Male


title: Colorectal Carcinoma derived from Edinburgh, Case no. 14


title: basilar artery1 4

value: brain derived

value: Stratagene Universal Human reference


title: Colorectal Carcinoma derived from Edinburgh, Case no. 11


title: iliac artery 1

value: non-brain derived


title: umbilical artery 3


title: coronary artery 3

value: HCAEC


title: umbilical artery 2


title: Colorectal Carcinoma derived from Edinburgh, Case no. 12

value: Female

value: Ascending Colon

value: MSS

value: Yes

value: Dead


title: basilar artery1 3


title: coronary artery 1


title: Colorectal Carcinoma derived from Edinburgh, Case no. 10


title: Colorectal Carcinoma derived from Edinburgh, Case no. 9

value: Dukes' A

value: No


title: pulmonary artery 3

value: HPAEC


title: Colorectal Carcinoma derived from Edinburgh, Case no. 7

value: Dukes' B

value: Alive


title: pulmonary artery 1


title: pulmonary artery 2


title: Colorectal Carcinoma derived from Edinburgh, Case no. 6

value: Sigmoid


title: Colorectal Carcinoma derived from Edinburgh, Case no. 5

value: Caecum

value: MSI-H

value: Dukes' C

value: Sensored


title: Colorectal Carcinoma derived from Edinburgh, Case no. 4

value: Male

value: Rectum


title: Colorectal Carcinoma derived from Edinburgh, Case no. 8

value: MSI-L

value: Female


title: coronary artery 2

value: non-brain derived

value: HCAEC

value: Stratagene Universal Human reference


title: Colorectal Carcinoma derived from Edinburgh, Case no. 3

value: MSS

value: Dead


title: aorta 2

value: HAEC


title: uterus microvessel 3

value: HUMEC


title: uterus microvessel 2


title: aorta 3


title: basilar artery1 2

value: brain derived


title: Colorectal Carcinoma derived from Edinburgh, Case no. 2

value: Dukes' D

value: Yes


title: Colorectal Carcinoma derived from Edinburgh, Case no. 1

value: Caecum

value: MSI-H

value: Dukes' B

value: No

value: Alive


title: aorta 1


title: 4635311088_L

status: Public on Feb 10 2010

first: Thomas

last: Down

department: WT/CRUK Gurdon Institute

hyb_protocol: Standard Illumina protocol for Human Methylation27 DNA Analysis bead chip

data_processing: Standard processing using Illumina BeadStudio 3.2.3 with methylation module.

source_name: CD4+ T-cells

extract_protocol: DNA was extracted from cells using standard protocols

tag: sex


title: 4635311088_G

scan_protocol: Standard Illumina protocol for Human Methylation27 DNA Analysis bead chip


title: Sertoli cell_cAMP_biological rep1

city: Pullman

first: Michael

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: Gene expression data from 20-day old rat Sertoli cell cultured for 72 h with cAMP

hyb_protocol: Following fragmentation, cRNA were hybridized on RAE230A array according to standard Affymetrix protocol. Chips were washed and stained in the  Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix Scanner 3000.

data_processing: The data were analyzed with GCOS using MAS5.0 algorithm with Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 125.

organism: Rattus norvegicus

source_name: P20 rat Sertoli cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from at least 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 20 days old male rats were euthanized and testis were removed according to IACUC-approved animal use protocols.  Sertoli cells (SC) were isolated as previously described (Tung, et al. 1984).

extract_protocol: TRI reagent (Sigma) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: SC were plated under serum-free conditions in 24-well Falcon plates (Oxnard, CA) at 1 x 10^6 cell/well. Cells were maintained in 5% CO2 atmosphere in Ham's F-12 medium (Life Technologies) with 0.01% BSA at 32 oC for 72 h prior to collections.

value: Sertoli cells isolated and cultured for 72 h

value: Sprague-Dawley

value: male

tag: developmental stage

value: 20-days old


title: basilar artery1 1

value: Stratagene Universal Human reference


title: block6_b4

label_protocol: Standard Illumina protocol for Human Methylation27 DNA Analysis bead chip

value: Female


title: uterus microvessel 1

value: non-brain derived


title: block5_a6

value: Male


title: block6_a7


title: 4635311043_D


title: Sertoli cell_cAMP_biological rep2

tag: cell type


title: 4635311072_K


title: 4635311072_C


title: Sertoli cell_control_biological rep2

description: Gene expression data from 20-day old rat Sertoli cell cultured for 72 h as controls with no treatment


title: 4635311065_E


title: batch4_d7


title: block6_a5


title: Sertoli cell_control_biological rep1


title: 4635311065_J


title: 4635311043_B


title: 4635311047_G


title: 4635311047_A


title: 4635311084_H


title: batch4_a8


title: 4635311072_G


title: 4635311088_H


title: 4635311043_E

source_name: CD14+ monocytes


title: block6_b3


title: 4635311084_J


title: 4635311066_C


title: 4635311075_L


title: block6_a1


title: 4635311065_G


title: batch4_d5


title: block5_b10


title: block6_a9


title: 4635311043_F


title: 4635311075_K


title: block5_b1


title: batch4_c7


title: block6_a11


title: batch4_d8


title: block6_b8


title: 4635311065_K


title: block6_a10


title: 4635311065_I


title: 4635311066_E


title: 4635311047_H


title: 4635311088_K


title: 4635311084_I


title: 4635311084_F


title: 4635311043_J


title: 4635311043_C


title: 4635311065_B


title: 4635311043_H


title: Blood - 4770230034_I - 68281

first: Tsun-Po

last: Yang

address: Wellcome Trust Genome Campus

department: Human Genetics

institute: Wellcome Trust Sanger Institute

data_processing: Standard processing using Illumina GenomeStudio V2009.1 with methylation module (1.1.1); quantile normalisation using limma package in R

source_name: blood

extract_protocol: DNA was extracted from blood using standard protocols

value: 62.51 years

value: blood


title: Blood - 4770230034_J - 58091

value: 65.53 years


title: Blood - 4770230034_H - 51871

value: 67.89 years


title: Blood - 4770230034_K - 20751

value: 53.84 years


title: Blood - 4770230034_B - 16331

value: 56.12 years


title: 4635311075_B


title: Blood - 4770230034_F - 10561

value: 55.09 years


title: Blood - 4770230034_E - 4152

value: 57.94 years


title: Blood - 4770230034_L - 52791

value: 62.28 years


title: Blood - 4720865032_L - 17772

value: 67.41 years


title: Blood - 4720865032_J - 57471

value: 71.82 years


title: Blood - 4770230034_G - 51601

value: 68.27 years


title: Blood - 4720865032_I - 80971

value: 60.9 years


title: Blood - 4770230034_C - 32062

value: 58.47 years


title: Blood - 4720865032_K - 7221

value: 64.04 years

value: Female


title: 4635311072_A


title: Blood - 4720865032_F - 32272

value: 71.67 years


title: Blood - 4720865032_A - 50902

value: 66.26 years


title: Blood - 4720865031_J - 54092

value: 60.73 years

value: blood


title: Blood - 4720865032_B - 59421


title: Blood - 4720865031_L - 52162

value: 58.83 years


title: Blood - 4720865032_E - 33271

value: 49.3 years


title: Blood - 4720865032_G - 51622

value: 70.45 years


title: Blood - 4720865032_C - 14592

value: 73.19 years


title: Blood - 4720865032_H - 91322

value: 60.83 years


title: Blood - 4720865031_I - 90192

value: 61.96 years


title: Blood - 4720865032_D - 9592

value: 53.15 years


title: Blood - 4720865031_H - 91321


title: Blood - 4720865031_K - 51512

value: 68.9 years


title: Blood - 4720865031_B - 50661

value: 63.15 years


title: Blood - 4720865031_F - 2891

value: 54.09 years


title: Blood - 4720865031_D - 9591


title: Blood - 4720865031_G - 53312

value: 63.55 years


title: Blood - 4720865030_K - 7222

value: 64.05 years


title: Blood - 4720865030_I - 80972

value: 60.9 years

value: Female


title: Blood - 4720865031_A - 5842

value: 64.02 years


title: Blood - 4720865031_C - 14591


title: negative control siRNA.48h.replicate2

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: granulosa cells treated with forskolin and universal siRNA control for 48hrs

hyb_protocol: The Affymetrix Rat 230 2.0 genechip array was hybridized with the labelled probes using the standard protocol in the Affymetrix GeneChip Expression Analysis Manual

scan_protocol: The genechip array was  scanned using  a Affymetrix GCS 3000 7G scanner

data_processing: The signal intensity on each chip is normalized using quantile normalization algorithm of MAS5, following the Affymetrix GeneChip protocol.  The overall intensity for each chip is then scaled to a target intensity of 500

source_name: granulosa cells from PMSG primed rat ovary

label_protocol: The total RNA was transferred to a nitrocellulose membrane and used as a template for cDNA synthesis, and biotinylated antisense cRNA probe was prepared as described by the manufacturers of the SuperScript System Kit (Invitrogen) and the ENZO BioArray HighYield RNA labeling Kit (Enzo Diagnostics, Farmingdale, NY).

growth_protocol: Granulosa cells were isolated from the ovary collected from immature rats primed with PMSG for 48 h. The cells were maintained in Opti-MEM® I Reduced Serum medium supplemented with 0.05 mg/ml of gentamycin, and 1x ITS (insulin, transferin, and selenium).

extract_protocol: Total RNA was isolated from cultured granulosa cells using a RNeasy mini kit.

treatment_protocol: Runx2 siRNA (20 nM) or negative control siRNA (20 nM) were transfected to the cells. Transfected cells were cultured with Forskolin (10 μM) for 48 hours.

value: female

value: Sprague Dawley

value: 27 days


title: Blood - 4720865031_E - 21281

value: 64.92 years

value: blood


title: Blood - 4720865030_J - 57732

value: 64.43 years


title: Blood - 4720865030_H - 53621

value: 68.2 years


title: Blood - 4720865030_E - 15811

value: 50.31 years


title: negative control siRNA.48h.replicate1

value: granulosa cells from PMSG primed rat ovary


title: Blood - 4720865030_G - 15821

value: 52.13 years


title: Blood - 4720865030_D - 71691

value: 60.88 years


title: Runx2 siRNA.48h.replicate2

description: granulosa cells treated with forskolin and Runx2 siRNA for 48hrs


title: Blood - 4720865030_B - 50662

value: 63.15 years


title: Blood - 4720865030_C - 21442

value: 71.02 years


title: Blood - 4720865027_I - 10602

value: 58.5 years


title: Blood - 4720865027_L - 11382

value: 66.82 years


title: Blood - 4720865027_E - 60531

value: 63.24 years

value: Female


title: Blood - 4720865030_A - 1381

value: 71.06 years


title: Blood - 4720865027_J - 7251

value: 55.29 years


title: Runx2 siRNA.48h.replicate1

value: female

value: Sprague Dawley

value: 27 days


title: Blood - 4720865027_H - 53381

value: 67.52 years

value: blood


title: Blood - 4720865027_F - 1531

value: 73.78 years


title: Blood - 4720865027_A - 1971

value: 62.58 years


title: Blood - 4720865030_F - 2892

value: 54.09 years


title: Blood - 4720865027_B - 60461

value: 67.93 years


title: Blood - 4720865026_K - 51511

value: 68.9 years


title: Blood - 4720865027_D - 71692

value: 60.88 years


title: Blood - 4720865026_L - 52161

value: 58.83 years


title: Blood - 4720865026_J - 54091

value: 60.73 years


title: Blood - 4720865027_C - 1571

value: 65.79 years


title: Blood - 4720865026_H - 52212

value: 72.58 years

value: Female


title: Blood - 4720865026_E - 92602

value: 63.09 years


title: Blood - 4720865026_D - 10562

value: 55.09 years


title: Blood - 4720865026_F - 32271

value: 71.67 years


title: ESC_k27m3_rep3

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

description:
Ch1: ChIP
Ch2: input

hyb_protocol: Hybridization done by Nimblegen as per normal service protocol.

scan_protocol: Scanning done by Nimblegen as per normal service protocol.

data_processing: log2 (ChIP/Input) with biweight mean of values subtracted.

source_name: ChIP of H3K27me3 from mouse ES cells

label_protocol: Labeling done by Nimblegen as per normal service protocol.

growth_protocol: ES cells were cultured feeder-free for 6-8 passages

extract_protocol: ChIP was done from a pool of isolated ICMs and TEs. Antibody was coupled to Dynabeads Protein A in RIPA buffer. ICMs and TEs were cross-linked with 1% formaldehyde for 8 min and quenched with 125 mM glycine. Cells were lysed in lysis buffer and sonicated for 3 x 30 sec on ice with 30 sec pauses using a probe sonicator (Labsonic-M) to produce ~400-500 bp chromatin fragments. RIPA buffer was added, samples were centrifuged and supernatants pooled and used for ChIP. Beads were released into chromatin and incubated for 2 h at 4oC. ChIP material was washed, eluted in presence of RNase and proteinase K. ChIP DNA was purified and dissolved in water. ChIP and input DNA were amplified using WGA4 GenomePlex Whole Genome Amplification Kit (Sigma), cleaned up, purified and diluted to in water. Samples were labeled and hybridized onto Nimblegen promoter arrays.

treatment_protocol: ES cells were undifferentiated

value: embryonic stem cells

tag: chip ab

source_name: Input DNA from mouse ES cells

treatment_protocol: Undifferentiated cells


title: Blood - 4720865026_I - 90191

value: 61.96 years


title: Blood - 4720865026_G - 66891

value: 57.68 years

value: blood


title: Blood - 4720865030_L - 23381

value: 68.41 years


title: ESC_k27m3_rep2

description:
Ch1: ChIP
Ch2: input


title: Blood - 4720865027_G - 16971

value: 61.84 years


title: ESC_k4m3_rep2

description:
Ch1: ChIP
Ch2: input

source_name: ChIP of H3K4me3 from mouse ES cells


title: TE_k27m3_rep3

description:
Ch1: ChIP
Ch2: input

source_name: ChIP of H3K27me3 from mouse  TE

growth_protocol: Embryos were at developmental stage E4

treatment_protocol: TEs were isolated by bisection

value: trophectoderm (TE)


title: ESC_k4m3_rep3

description:
Ch1: ChIP
Ch2: input


title: 510 Sto

city: Philadelphia

first: Anil

last: Rustgi

state: PA

address: 415 Curie Blvd, 600 CRB

department: Medicine-Gastroenterology

institute: University of Pennsylvania

description: 9515 510 Sto.CEL

hyb_protocol: hybridization of cRNAs to Affymetrix chips were performed according manufacturer's instructions

scan_protocol: scanning of Affymetrix chips were performed according manufacturer's instructions

data_processing: The Cel files were processed using R/Bioconductor software using GC-RMA algorithm to calculate probeset intensity values.  These intensity values were log2 transformed.

label_protocol: Biotinylated cRNA were prepared according to standard Affymetrix protocols.

extract_protocol: Tissue was aseptically removed from mouse, dispase treated and the epithelium was mechanically removed from the tissue and placed in trizol. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: C57Bl/6 and 129 mixed

value: forestomach mass

tag: genome/variation

value: Cre/p120 flox/flox


title: 426 Sto

description: 9514 426 Sto.CEL


title: Blood - 4720865009_L - 52792

value: 62.28 years


title: Blood - 4720865026_A - 5841

value: 64.02 years


title: TE_k27m3_rep1

description:
Ch1: ChIP
Ch2: input


title: Blood - 4720865026_C - 15852

value: 66.52 years


title: TE_k4m3_rep1

description:
Ch1: ChIP
Ch2: input

source_name: ChIP of H3K4me3 from mouse TE


title: TE_k4m3_rep2

description:
Ch1: ChIP
Ch2: input


title: TE_k27m3_rep2

description:
Ch1: ChIP
Ch2: input


title: ICM_k27m3_rep2

description:
Ch1: ChIP
Ch2: input

source_name: ChIP of H3K27me3 from mouse ICM

treatment_protocol: ICMs were isolated by bisection and immunosurgery

value: inner cell mass (ICM)


title: TE_k4m3_rep3

description:
Ch1: ChIP
Ch2: input


title: Blood - 4720865009_K - 20752

value: 53.84 years

value: Female


title: 412 Sto

description: 9513 412 Sto.CEL


title: 217 Sto

description: 9511 217 Sto.CEL

value: forestomach


title: 216 Sto

description: 9510 216 Sto.CEL


title: ICM_k27m3_rep3

description:
Ch1: ChIP
Ch2: input

value: embryonic stem cells


title: Blood - 4720865009_G - 10322

value: 67.37 years


title: Blood - 4720865026_B - 70821

value: 62.85 years


title: Blood - 4720865009_J - 58092

value: 65.53 years

value: blood


title: 335 Eso

description: 9508 335 Eso.CEL

value: esophagus


title: ICM_k4m3_rep3

description:
Ch1: ChIP
Ch2: input

source_name: ChIP of H3K4me3 from mouse ICM


title: 214 Sto

description: 9509 214 Sto.CEL


title: Blood - 4720865009_H - 52211

value: 72.58 years


title: Blood - 4720865009_F - 21432

value: 52.9 years


title: 313 Eso

description: 9507 313 Eso.CEL

value: C57Bl/6 and 129 mixed


title: 307 Eso

description: 9506 307 Eso.CEL

value: Cre/p120 flox/flox


title: 193 Eso

description: 9505 193 Eso.CEL


title: ICM_k27m3_rep1

description:
Ch1: ChIP
Ch2: input


title: 217 Eso

description: 9503 217 Eso.CEL


title: ICM_k4m3_rep2

description:
Ch1: ChIP
Ch2: input


title: Blood - 4720865009_E - 92601

value: 63.09 years


title: Blood - 4720865009_D - 98832

value: 49.39 years


title: ICM_k4m3_rep1

description:
Ch1: ChIP
Ch2: input


title: 214 Eso

description: 9504 214 Eso.CEL


title: Blood - 4720865009_C - 15851

value: 66.52 years


title: Blood - 4720865007_L - 53291

value: 71.69 years


title: Blood - 4720865007_I - 22992

value: 59.74 years


title: 216 Eso

description: 9502 216 Eso.CEL


title: D10 cell lines,biological rep2

city: Tianjin

first: Yueying

last: Li

address: 288 Nanjing Road

country: China

institute: Institute of Hematology and Blood Diseases Hospital

description: Gene expression data from re-derived D10 cell lines

hyb_protocol: Following fragmentation and labeling, 10 ug of cDNA were hybridized to GeneChip MoGene 1.0 ST Array for 16 hr at 45℃. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000 7G.

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. The data were transformed to log2 scale.

source_name: re-derived D10 cell lines

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Whole Transcript (WT) Sense Target   Labeling Assay Manual, 2007, Affymetrix).

growth_protocol: Cells were cultured on dishes covered with feeder cells in ESC culture medium.

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

treatment_protocol: Single-cell suspension from the BM of transplanted mice was treated with red cell lysis buffer and digested by 0.05% trypsin EDTA. The BM cells were passed through a 70-μm nylon mesh before sorting. The sorted GFP+ cells were cultured on 35mm dishes covered with feeder cells in ESC culture medium. 5-6 days later, GFP+ cell colonies were transferred into 96-well plate and passaged gradually onto larger culture dishes covered with feeder cells to be stable cell lines.

tag: cell line

value: D10 cell line, derived from bone marrow at day 10 post-transplantation

value: C57BL/6×Oct4/EGFP transgenic OG2 mice (B57BL13/CBA strain)


title: Blood - 4720865027_K - 91912

value: 55.65 years

value: Female

tag: tissue


title: Blood - 4720865007_J - 94192

value: 66.74 years


title: Blood - 4720865009_B - 16332

value: 56.12 years


title: Blood - 4720865007_K - 16591

value: 64.45 years

value: blood


title: D5 cell lines,biological rep3

description: Gene expression data from re-derived D5 cell lines

source_name: re-derived D5 cell lines

value: D5 cell line, derived from bone marrow at day 5 post-transplantation

tag: strain

value: C57BL/6×Oct4/EGFP transgenic OG2 mice (B57BL11/CBA strain)


title: Blood - 4720865007_F - 53622

value: 68.2 years


title: ES cell lines, biological rep2

description: Gene expression data from embryonic stem cells (oGFP+ ESCs)

source_name: Embryonic stem cells (oGFP+ ESCs)

value: ES embryonic stem cell line, derived from 3.5-day-old blastocyst stage mouse embryos

value: C57BL/6×Oct4/EGFP transgenic OG2 mice (B57BL7/CBA strain)


title: Blood - 4720865007_B - 60321

value: 69.65 years


title: D10 cell lines,biological rep3

value: C57BL/6×Oct4/EGFP transgenic OG2 mice (B57BL14/CBA strain)


title: D10 cell lines,biological rep1

value: C57BL/6×Oct4/EGFP transgenic OG2 mice (B57BL12/CBA strain)


title: D5 cell lines,biological rep1

value: C57BL/6×Oct4/EGFP transgenic OG2 mice (B57BL9/CBA strain)


title: Blood - 4720865007_C - 1572

value: 65.79 years


title: ES cell lines, biological rep1

value: C57BL/6×Oct4/EGFP transgenic OG2 mice (B57BL6/CBA strain)


title: Blood - 4720865007_D - 98831

value: 49.39 years


title: Blood - 4720865007_A - 1382

value: 71.06 years

value: Female


title: Blood - 4720865007_G - 15822

value: 52.13 years


title: Blood - 4720865007_H - 57472

value: 71.82 years


title: D5 cell lines,biological rep2

value: C57BL/6×Oct4/EGFP transgenic OG2 mice (B57BL10/CBA strain)


title: Blood - 4720865009_I - 68282

value: 62.51 years

value: blood


title: ES cell lines, biological rep3

value: C57BL/6×Oct4/EGFP transgenic OG2 mice (B57BL8/CBA strain)


title: Blood - 4720865007_E - 24191

value: 60.68 years


title: stomach MKN74

city: Bunkyo-ku

first: rie

last: wada

state: Tokyo

address: Yushima 1-5-45

department: Molecular Oncology

country: Japan

institute: Tokyo Medical and Dental University

description: No information.

hyb_protocol: A 3x miRNA Hybridization Buffer (Ambion) was added to the fluorescently labeled miRNAs and the solution was heated at 95ºC for 3 min. Slides were hybridized form 12 h at 42 ºC in sealed cassettes using a water bath. Following hybridization, the slides were washed and dried.

scan_protocol: MicroArray were scanned at 5-micron resolution on a GenePix 4000B (Axon Instruments, CA, USA). Raw data were normalized and analyzed using Array-Pro Analyzer Version 4.5 (Media Cybernetics, Inc.,Silver Spring, MD, USA).

data_processing:
We used Array-Pro Analyzer Ver4.5 (Media Cybernetics, Inc., Silver Spring, MD, USA) to determine the signal intensity of each spot and its local background on microarrays.
We calculated net intensity by subtracting the mean intensity of all pixels within the local background area from the mean intensity of all pixels within the spot areas.
We normalized biases in net intensity between the two fluorescent dye channel in a microarray by locall regression (loess) normalization using its software. Analyzed data were selected by using MicroArray Data Analysis Tool (Filgen, Inc.).

source_name: non-cancerous human stomach tissue

label_protocol: Chemically synthesized oligoribonucleotides (Ambion), or purified miRNAs were labeled with the mirVanaTM miRNA Labeling Kit (Ambion) and amine-reactive dyes as recommended by the manufacturer. Poly(A) polymerase and a mixture of unmodified and amine-modified nucleotides were first used to append a poly-nucleotide tail. The amine-modified miRNAs were then cleaned up and coupled to NHS-ester modified Cy5 dye (GE Healthcare Bio-Science Corp., Piscataway, NJ, USA). Unincorporated dyes were removed with a second glass fiber filter-based cleaning procedure.

extract_protocol: To isolate miRNA fractions from total RNA, 30μｇ total RNA was fractionated and cleaned up with the flashPAGETM fractionator System and reagents (Ambion) per the manufacturer’s recommendation.

value: male

source_name: human gastric cancer

label_protocol: Chemically synthesized oligoribonucleotides (Ambion), or purified miRNAs were labeled with the mirVanaTM miRNA Labeling Kit (Ambion) and amine-reactive dyes as recommended by the manufacturer. Poly(A) polymerase and a mixture of unmodified and amine-modified nucleotides were first used to append a poly-nucleotide tail. The amine-modified miRNAs were then cleaned up and coupled to NHS-ester modified Cy3 dye (GE Healthcare Bio-Science Corp., Piscataway, NJ, USA). Unincorporated dyes were removed with a second glass fiber filter-based cleaning procedure.


title: stomach MKN7

description: No information.

scan_protocol: MicroArray were scanned at 5-micron resolution on a GenePix 4000B (Axon Instruments, CA, USA).  Raw data were normalized and analyzed using Array-Pro Analyzer Version 4.5 (Media Cybernetics, Inc., Silver Spring, MD, USA).

data_processing:
We used Array-Pro Analyzer Ver4.5 (Media Cybernetics, Inc., Silver Spring, MD, USA) to determine the signal intensity of each spot and its local background on microarrays.　We calculated net intensity by subtracting the mean intensity of all pixels within the local background area from the mean intensity of all pixels within the spot areas.
We normalized biases in net intensity between the two fluorescent dye channel in a microarray by locall regression (loess) normalization using its software. Analyzed data were selected by using MicroArray Data Analysis Tool (Filgen, Inc.).

value: man


title: stomach NUGC4

description: No information.


title: 46-R_Mapping250K_Nsp

status: Public on Feb 09 2010

city: Tokyo

first: Motohiro

last: Kato

address: 7-3-1, Hongo, Bunkyo-ku

institute: University of Tokyo

description: We have used anonymous normal references (own-lab-generated) for SNP array analysis.

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: CNAG/AsCNAR 3.0 After appropriate normalization of mean array intensities, signal ratios between tumours and anonymous normal references were calculated in an allele-specific manner, and allele-specific copy numbers were inferred from the observed signal ratios based on the hidden Markov model using CNAG/AsCNAR 3.0 software (http://www.genome.umin.jp).

source_name: chronic myeloid leukemia

label_protocol: Affymetrix standard

extract_protocol: standard DNA extraction

tag: patient identifier

tag: disease state

value: chronic myeloid leukemia (in remission)

tag: tyrosine kinase inhibitor (tki) resistance status

value: resistant


title: 41-R_Mapping250K_Nsp


title: 45-R_Mapping250K_Nsp


title: 44_Mapping250K_Nsp

value: chronic myeloid leukemia


title: 20-R_Mapping250K_Nsp


title: 40-R_Mapping250K_Nsp


title: 28_Mapping250K_Nsp


title: 45_Mapping250K_Nsp


title: 44-R_Mapping250K_Nsp


title: 5_Mapping250K_Nsp


title: 42-R_Mapping250K_Nsp


title: 42_Mapping250K_Nsp


title: 41_Mapping250K_Nsp


title: 7_Mapping250K_Nsp


title: 40_Mapping250K_Nsp


title: 46_Mapping250K_Nsp


title: 43_Mapping250K_Nsp


title: 37-R_Mapping250K_Nsp


title: 36-R_Mapping250K_Nsp


title: 29-R_Mapping250K_Nsp


title: 31_Mapping250K_Nsp


title: 33-R_Mapping250K_Nsp


title: 38-R_Mapping250K_Nsp


title: 32-R_Mapping250K_Nsp


title: 10_Mapping250K_Nsp


title: 39-R_Mapping250K_Nsp


title: 39_Mapping250K_Nsp


title: 19_Mapping250K_Nsp


title: 22-R_Mapping250K_Nsp


title: Lung Squamous Cell Carcinoma (SCC) 35 (Chr 3 BAC/PAC array with 3q26.3 tiling)

city: ILLKIRCH

last: Hussenet

address: 1 rue Laurent Fries

department: Cancer Biology Department

country: France

institute: IGBMC

hyb_protocol: Every step was performed in the HS 4800 hybridization station (Tecan, Mannedorf, Switzerland). Slide pretreatment included (a) stripping: 2.5 mmol/L Na2HPO4, 0.1% SDS at 76°C for 1 min; (b) slide blocking: 3% bovine serum albumin (fraction V; Sigma-Aldrich), 5× SSC, 0.2% SDS at 42°C for 20 min; and (c) prehybridization: 400 μg of salmon testes DNA and 67.5 μg of COT human DNA in 200 μL of hybridization solution incubated 1 h at 37°C.  Hybridization was performed during 18 h at 37°C under low agitation.Four posthybridization washes were performed: 50% formamide, 2× SSC, 0.1% SDS at 45°C for 37 sec, four times; 2× SSC, 0.1% SDS at 45°C for 37 sec, four times; 4× SSC, 0.1 Tween 20 at 45°C for 37 sec, four times; slides were finally nitrogen-dried.

scan_protocol: ScanArray 4000 (Packard Bioscience, Meriden, CT). Images were quantified using the system's Imagene 5.1 software as described previously.

data_processing: Images were quantified using the system's Imagene 5.1 software. Array analyses  were done as detailed in Hussenet et al., 2006 (PMID:  ). Background substraction, clone replicates averaging and normalization of chromosome 3 clones to the median of sub-telomeric clones. For each sample, individual array replicates are averaged (geometric mean)

source_name: Tumor genomic DNA

label_protocol: Bioprime Labelling Kit (Invitrogen)

extract_protocol: Phenol/Choloroform

value: lung SCC

source_name: Normal genomic DNA

value: Normal


title: 34_Mapping250K_Nsp


title: 21-R_Mapping250K_Nsp


title: 38_Mapping250K_Nsp


title: Lung Squamous Cell Carcinoma (SCC) 15 (Chr 3 BAC/PAC array with 3q26.3 tiling)


title: 4-R_Mapping250K_Nsp


title: Lung Squamous Cell Carcinoma (SCC) 8 (Chr 3 BAC/PAC array with 3q26.3 tiling)


title: 18_Mapping250K_Nsp


title: 15_Mapping250K_Nsp


title: 24_Mapping250K_Nsp


title: 3_Mapping250K_Nsp


title: Lung Squamous Cell Carcinoma (SCC) 33 (Chr 3 BAC/PAC array with 3q26.3 tiling)


title: 32_Mapping250K_Nsp


title: Lung Squamous Cell Carcinoma (SCC) 2 (Chr 3 BAC/PAC array with 3q26.3 tiling)


title: Lung Squamous Cell Carcinoma (SCC) 44 (Chr 3 BAC/PAC)

scan_protocol: ScanArray 4000 (Packard Bioscience, Meriden, CT). Images were quantified using the system's Imagene 5.1 software as described previously [18].

data_processing: Images were quantified using the system's Imagene 5.1 software. Background substraction, replicates averaging and normalization to the median of sub-telomeric clones.


title: Lung Squamous Cell Carcinoma (SCC) 46 (Chr 3 BAC/PAC)


title: Lung Squamous Cell Carcinoma (SCC) 43 (Chr 3 BAC/PAC)


title: Lung Squamous Cell Carcinoma (SCC) 41 (Chr 3 BAC/PAC)


title: Lung Squamous Cell Carcinoma (SCC) 40 (Chr 3 BAC/PAC)


title: Lung Squamous Cell Carcinoma (SCC) 39 (Chr 3 BAC/PAC)


title: Lung Squamous Cell Carcinoma (SCC) 38 (Chr 3 BAC/PAC)


title: 13_Mapping250K_Nsp


title: 35_Mapping250K_Nsp


title: 21_Mapping250K_Nsp


title: 16_Mapping250K_Nsp


title: 1_Mapping250K_Nsp


title: 23_Mapping250K_Nsp


title: 22_Mapping250K_Nsp


title: TS cell, day 14, rep2

city: Rockland

first: Benjamin

middle: L

last: Kidder

address: 1 Technology Place

department: Reproductive Health

institute: EMD Serono Research Institute

description: Gene expression data from differentiated TS cells at T=day 14, biological rep-2

hyb_protocol: 14 µg of aRNA were hybridized for 16 hr at 45 deg C on Affymetrix mouse 430 v2.0 microarrays. GeneChips were washed and stained using an Affymetrix Fluidics Station.

scan_protocol: Arrays were scanned using an Affymetrix Scanner 3000 7G

source_name: RNA from TS cells

label_protocol: 14 µg biotinylated aRNA were prepared using a MessageAmpTM Premier RNA Amplification kit (Ambion) protocol from 100 ng total RNA.

growth_protocol: TS cells were grown on feeder-free dishes for 2 passages to remove iMEFs

extract_protocol: Total RNA was isolated at several time points from TS cells cultured without Fgf4 for two weeks using an RNeasy Mini Kit (Qiagen, Valencia, CA).  For each duplicate biological replicate, 100 ng of RNA was amplified using a MessageAmpTM Premier RNA Amplification kit (Ambion), and 14 µg of fragmented aRNA was hybridized to Affymetrix mouse 430 v2.0 microarrays.  Analysis was performed as previously described with some modifications (Kidder, Palmer and Knott 2008).  Briefly, CEL files were loaded into ArrayAssist (Stratagene, La Jolla, CA) and probes were normalized using the GC-RMA algorithm.  ANOVA was performed on all groups using a Benjamini and Hochberg FDR correction.  Genes whose expression differed by at least 2-fold between any two groups with a P-value less than 5 % were considered differentially expressed.  Validation of microarrays was performed using Q-RT-PCR with Taqman probes as described above.

treatment_protocol: TS cells were cultured without Fgf4 for two weeks.

value: Trophoblast stem cells

tag: source

value: E3.5 blastocyst

tag: time point

value: day 14


title: 14_Mapping250K_Nsp


title: TS cell, day 14, rep1

description: Gene expression data from differentiated TS cells at T=day 14, biological rep-1

data_processing: CEL files were loaded into ArrayAssist (Stratagene, La Jolla, CA) and probes were normalized using the GC-RMA algorithm.  ANOVA was performed on all groups using a Benjamini and Hochberg FDR correction.  Genes whose expression differed by at least 2-fold between any two groups with a P-value less than 5 % were considered differentially expressed.


title: 30_Mapping250K_Nsp


title: 29_Mapping250K_Nsp


title: 6-R_Mapping250K_Nsp


title: 33_Mapping250K_Nsp


title: 27_Mapping250K_Nsp


title: 43-R_Mapping250K_Nsp


title: Lung Squamous Cell Carcinoma (SCC) 31 (Chr 3 BAC/PAC)


title: 2_Mapping250K_Nsp


title: 26_Mapping250K_Nsp


title: 37_Mapping250K_Nsp


title: Lung Squamous Cell Carcinoma (SCC) 30 (Chr 3 BAC/PAC)


title: Lung Squamous Cell Carcinoma (SCC) 35 (Chr 3 BAC/PAC)


title: Lung Squamous Cell Carcinoma (SCC) 23 (Chr 3 BAC/PAC)


title: TS cell, day 10, rep1

description: Gene expression data from differentiated TS cells at T=day 10, biological rep-1

value: day 10


title: FIZ1_Mouse_Retina_P25

city: Rochester

first: Kenneth

middle: P

last: Mitton

state: MI

address: 4th Floor - Dodge Hall

department: Eye Research Institute

institute: Oakland University

description: FIZ1 ChIP P25 retina

hyb_protocol: Probe DNA (1µg) was hybridized to GeneChip Mouse Promoter 1.0R arrays (Affymetrix) overnight at 45°C. One array was used for each time point with Pol-II and a third array hybridized with non-ChIP total genomic DNA for normalization. A forth array was used for FIZ1 ChIP DNA at P-25. Arrays were hybridized and washed simultaneously in a GeneChip Fluidics Station (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip scanner (Affymetrix).

data_processing:
Array data files (CEL files) were analyzed using Affymetrix Tiling Array Software (TAS).
Each sample was processed using the TAS pairwise analysis mode, using the total genomic (non-ChIP) chromatin sample as the control. Array raw input data were normalized using linear scaling to a target intensity (median intensity) of 500 using all PM probes (perfect match). Two sample analysis was used, with each time point ChIP sample (treatment) compared to the whole genomic chromatin (control).  Tail type was one-sided upper with a bandwidth of 400 base pairs.  Wilcoxon signed rank test was applied to log-transformed intensities of the ChIP treatment sample versus the control values for all probes within the analysis window for each feature in the array. Fold enrichment was calculated using the Hodges-Lehmann Estimator (Pseudo Median) applied to the signal log ratio (log2) between the treatment and control signal. Using these ratios, Walsh averages were calculated for each feature in the array, and a final probe signal value (S) calculated as the median Walsh average. The parameters for track interval determination were: minimum length 300, gap 180, and intermediate thresholds of 2.5 for FIZ1 and 4.0 for Pol-II.
Results file descriptions: Bed Files are generated with TAS software (Tiling Array Software) from Affymetrix, using pairwise analysis for each Pol-II or FIZ1 ChIP against mouse retina genomic DNA control.

label_protocol: DNAs were amplified using random priming amplification. A fixed sequence of 17 bases containing 9 random bases at the 3’ end was used in four linear amplification reactions using Sequenase (USB, Cleveland, Ohio). Following purification, the randomly primed ChIP DNA was amplified for 30 cycles using a fixed primer sequence. The resulting amplified DNA was purified, quantified, and tested by Q-PCR again to test for conservation of enrichment. Amplified DNA was fragmented and fluorolabeled using the DNA Terminal Labeling Kit (Affymetrix, Santa Clara, CA).

extract_protocol: Lysates were then sonicated and the DNA sheared to an average length of 300-500 base pairs. Genomic DNA (input) was prepared by treating aliquots of chromatin with Rnase, proteinase K and heat (65°C) to reverse cross linking, followed by phenol and chloroform extractions and ethanol precipitation. Pellets were resuspended in TE and the resulting DNA was quantified on a Nanodrop spectrophotometer. Immunoprecipitation for ChIP-on-Chip. For ChIP, an aliquot of chromatin (20µg) was precleared with protein-A agarose beads . FIZ1 binding was detected using a polyclonal antibody specific for the FIZ1 protein, Anti-GST-bFIZ1, previously qualified for quantitative ChIP analysis . RNA Polymerase-II binding was detected using an antibody qualified for ChIP. After incubation at 4°C overnight, protein-A beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS wash buffer, and subjected to Rnase and proteinase-K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.

treatment_protocol: Retinas are dissected from eyes in PBS, drained of excess PBS and fast frozen. For both P-2 and P-25 ages, the retinas were dissected to be free from optic nerve, retinal pigment epithelium and ciliary body. To obtain sufficient chromatin for ChiP-on-Chip, 46 retinas were pooled for P-2 and 60 retinas were pooled for P-25. More tissue was required with P-25 retinas that yield less chromatin than P-2 retina. Frozen neural retina tissue were kept at -80°C until protein/chromatin cross-linking with freshly prepared formaldehyde (1%) for 15 minutes at room temperature, with agitation. Cross linking was stopped by 0.125 M glycine (final concentration), and tissue disrupted with a Dounce homogenizer.

value: Postnatal Day 2

value: neural retina

tag: antibody

source_name: retinal chromatin not ChIP'd (input DNA control)


title: 20_Mapping250K_Nsp


title: Lung Squamous Cell Carcinoma (SCC) 33 (Chr 3 BAC/PAC)


title: PolII_Mouse_Retina_P25

description: PolII ChIP P25 retina

value: Postnatal Day 5

value: anti-RNA Polymerase-II


title: 36_Mapping250K_Nsp


title: TS cell, day 6, rep2

description: Gene expression data from differentiated TS cells at T=day 6, biological rep-2

value: day 6


title: PolII_Mouse_Retina_P2

description: PolII ChIP P2 retina


title: TS cell, day 10, rep2

description: Gene expression data from differentiated TS cells at T=day 10, biological rep-2


title: Gata3_Genome_mm8_1

description: Gata3 ChIP biological replicates 1-7

hyb_protocol: 5 μg of DNA was hybridzed to Affymetrix mouse 1.0R tiling arrays array using the Affymetrix hybridization kit.  Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven.

data_processing:
Data was quantile normalized and analyzed using TileMap. Log2 (IP/Input) fold change values (fc) and TileMap moving average (ma) statistics were reported in BAR files.
fc.bar and ma.bar files were generated using CisGenome software. fc.bar files contain log2 (IP/Input) fold change values for each probe. ma.bar files contain a moving average statistic for each probe.

source_name: ChIP DNA from TS cells

label_protocol: Samples were enzymatically fragmented using Dnase and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments

extract_protocol: ChIP-chip experiments were performed as previously described with minor modifications (Kidder, Palmer and Knott 2008).  Mouse TS cells (TSC-BK12) were grown on feeder-free dishes for 2 passages to remove iMEFs, and chemically crosslinked with 1% formaldehyde (Sigma) for 20 hours at 4 deg C and subsequently sonicated.  Sonicated cell extracts equivalent to 2 X 10^6 cells were used for immunoprecipitation assays.  5 micrograms purified ChIP-enriched DNA (Tcfap2c-chip, Smarca4-chip, Eomes-chip, Ets2-chip, Gata3-chip, and Input) was amplified, DNase treated, labeled, and hybridized to Affymetrix mouse promoter 1.0R tiling arrays.  At least three biological replicates were used for each ChIP-chip analysis.  Peak detection and gene annotation were performed as previously described (Kidder, Palmer and Knott 2008; Kidder, Yang and Palmer 2008).  Briefly, peak detection was performed using the TileMap (Ji and Wong 2005) application in CisGenome (Ji, Jiang, Ma, Johnson, Myers and Wong 2008).  Enrichment peaks were annotated with the closest gene using build 36 of the mouse genome.

source_name: Input DNA from TS cells


title: Lung Squamous Cell Carcinoma (SCC) 19 (Chr 3 BAC/PAC)


title: Lung Squamous Cell Carcinoma (SCC) 22 (Chr 3 BAC/PAC)


title: Lung Squamous Cell Carcinoma (SCC) 20 (Chr 3 BAC/PAC)


title: Lung Squamous Cell Carcinoma (SCC) 36 (Chr 3 BAC/PAC)


title: Ets2_Genome_mm8_1

description: Ets2 ChIP biological replicates 1-6


title: Lung Squamous Cell Carcinoma (SCC) 15 (Chr 3 BAC/PAC)


title: Lung Squamous Cell Carcinoma (SCC) 14 (Chr 3 BAC/PAC)


title: Lung Squamous Cell Carcinoma (SCC) 13 (Chr 3 BAC/PAC)


title: TS cell, 48hr, rep2

description: Gene expression data from differentiated TS cells at T=48hr, biological rep-2


title: Smarca4_Genome_mm8_1

description: Smarca4 ChIP biological replicates 1-4


title: TS cell, 72hr, rep1

description: Gene expression data from differentiated TS cells at T=72hr, biological rep-1


title: TS cell, day 6, rep1

description: Gene expression data from differentiated TS cells at T=day 6, biological rep-1


title: 11_Mapping250K_Nsp


title: Lung Squamous Cell Carcinoma (SCC) 10 (Chr 3 BAC/PAC)


title: 25_Mapping250K_Nsp


title: TS cell, 72hr, rep2

description: Gene expression data from differentiated TS cells at T=72hr, biological rep-2


title: 9_Mapping250K_Nsp


title: Lung Squamous Cell Carcinoma (SCC) 8 (Chr 3 BAC/PAC)


title: Lung Squamous Cell Carcinoma (SCC) 7 (Chr 3 BAC/PAC)


title: Tcfap2c_Genome_mm8_1

description: Ap-2g ChIP biological replicates 1-3


title: Eomes_Genome_mm8_1

description: Eomes ChIP biological replicates 1-5

value: Eomes


title: Lung Squamous Cell Carcinoma (SCC) 3 (Chr 3 BAC/PAC)


title: Lung Squamous Cell Carcinoma (SCC) 4 (Chr 3 BAC/PAC)


title: Lung Squamous Cell Carcinoma (SCC) 21 (Chr 3 BAC/PAC)


title: Lung Squamous Cell Carcinoma (SCC) 2 (Chr 3 BAC/PAC)


title: TS cell, 48hr, rep1

description: Gene expression data from differentiated TS cells at T=48hr, biological rep-1


title: 9-R_Mapping250K_Nsp


title: 8_Mapping250K_Nsp


title: 4_Mapping250K_Nsp


title: 12_Mapping250K_Nsp


title: 6_Mapping250K_Nsp


title: TS cell, 0hr, rep2

description: Gene expression data from undifferentiated TS cells at T=0hr, biological rep-2


title: TS cell, 24hr, rep1

description: Gene expression data from differentiated TS cells at T=24hr, biological rep-1


title: TS cell, 24hr, rep2

description: Gene expression data from differentiated TS cells at T=24hr, biological rep-2


title: Lymphoid standard RNA

status: Public on Feb 08 2010

city: omaha

first: Javeed

last: Iqbal

state: NE

address: 40th street

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

description:
Gene expression data from lymphoid standard  RNA.
CLN-Std

hyb_protocol: Following fragmentation, 20 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix Scanning Protocol.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further analysis (e.g., clustering, classification) was carried using BRB-ArrayTools version (3.7.0).

source_name: Standardised lymphoid RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from at least 3 micrograms of total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: All the tissues used in the study were fresh frozen and stored below -70 degree C.

extract_protocol: Total RNA was extracted with Trizol and further purified with RNeasy Mini Columns (Qiagen, Valencia, CA) before aliquots were run in agarose gel electrophoresis and measured by spectrophotometer at 260 and 280 nm to assess the quality of the RNA.

treatment_protocol: The cryopreserved tissues from pre-treated biopsies obtained at the time of diagnosis had been stored in liquid nitrogen or -80 degree C before total RNA extraction.

value: lymphoid


title: SL1344_LB_1

city: Hamilton

first: Brian

last: Coombes

state: Ontario

address: 1200 Main St. West

department: Biochemistry & Biomedical Sciences

country: Canada

institute: McMaster University

description: 0181__251939910001_S01_CGH-v4_95_Feb07_1_4

hyb_protocol: Purified, labeled ChIP DNA was hybridized by OGT per OGT protocol in 500uL buffer containing 42uL 12x MES, 100uL 5M NaCl, 100uL formamide, 20uL 0.5M EDTA, 50uL 10% Triton, 78uL H2O, 50uL Cy3 target, 50uL Cy5 target, 10uL RAND105 oligo control.  Labeled target DNA was added to the hybridization reaction after denaturation at 94C for 3 minutes.  Total 500uL hybridization reaction was added to the OGT array and hybridized at 55C for 48-72hrs in a rotisserie hybridization oven (4pm).  Arrays were washed in 50mL washing buffer 1 (for 1L: 300mL 20X SSPE, 0.25mL 20% N-Lauoylsarcosine, 700mL H2O) for 5 minutes then 50mL washing buffer 2 (for 1L: 3mL 20X SSPE, 1.8mL PEG200, 995mL H2O) for 5 minutes.  Slides blow dried with dry nitrogen.

scan_protocol: Arrays were scanned by Oxford Gene Technology (OGT) on an Agilent scanner according to in-house protocol

data_processing: Probe signals normalized to channel medians

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: SL1344 ChIP DNA isolated from LB condition

label_protocol: 0.4 µg ChIP or control DNA was directly labeled by Klenow (BioPrime) random priming with Cy3- or Cy5-dCTP by OGT per OGT protocol.  Labeled samples silica column purified (Qiagen).

growth_protocol: LB overnight cultures subcultured 1:50 into LB, grown to OD600 ~0.5

extract_protocol: Bacterial cultures were grown in either LB or LPM (pH 5.8) to OD600 ~0.6. Formaldehyde was added (final concentration of 1%) and incubated at room temperature for 5 min on an orbital shaker set at 35 rpm. Cross-linking was quenched by the addition of glycine to 125 mM followed by incubation for 5 min, swirling briefly every minute. Cells were harvested by centrifugation, washed twice with cold phosphate-buffered saline (pH 7.4), and resuspended in a 1:1 mix of ChIP lysis buffer consisting of 10 mM Tris (pH 8.0), 50 mM NaCl, 10 mM EDTA (pH 8.0), 20% sucrose, 10 mg/mL lysozyme and 2X RIPA solution containing 100 mM Tris (pH 8.0), 300 mM NaCl, 20% Tergitol (type NP-40), 10% sodium deoxycholate, 10% SDS, 1X EDTA-free protease inhibitor cocktail (Roche), in a volume 1/10 the original culture  volume. The cell suspension was incubated at 37oC for 30 min to lyse bacteria. 0.5 ml of cell lysate was sonicated (5 x 15 second pulses) using a Fisher 500 Dismembrator (Fisher Scientific) set at 20% intensity. DNA was verified for proper shearing within 200-1000 bp by running the input DNA on an agarose gel after RNase treatment. Cell debris was removed by centrifugation, and the supernatant was retained for use as the input sample in immunoprecipitation experiments. For immunoprecipitation of SsrBFLAG cross-linked DNA, 800 μL of input DNA was incubated with 50 μL pre-washed α-FLAG-M2 agarose resin (Sigma) at 4oC overnight on a rolling shaker. After overnight incubation, IP resin was washed twice with cold 1X RIPA solution, twice with LiCl wash buffer (10 mM Tris [pH 8.0], 250 mM LiCl, 1 mM EDTA [pH 8.0], 0.5% Tergitol [type NP-40], 0.5% sodium deoxycholate), and once with TE buffer (10 mM Tris [pH 8.0], 1 mM EDTA [pH 8.0]). Fifty microliters of input DNA was reserved as input control. Resin-bound IP DNA and input DNA were treated with RNase A (20 μg/mL) for 30 min at 37oC to remove RNA. IP resin was washed once more with TE buffer and resuspended in 200 μL ChIP elution buffer (50 mM Tris [pH8.0], 10 mM EDTA [pH 8.0], 1% SDS). 150 μL of ChIP elution buffer was also added to input DNA for a final volume of 200 μL. Samples were incubated for 10 min at 65oC, followed by the addition of Proteinase K (final concentration 0.8 mg/mL) and samples were incubated for 2 h at 42oC, following with overnight incubation at 65oC.  The eluted IP DNA and input DNA were purified using phenol/chloroform extraction, precipitated with ethanol, and resuspended in nuclease-free water (Invitrogen). Three IP samples were pooled together for each ChIP replicate, then brought to the appropriate concentration for hybridization to the array.

tag: genotype

source_name: SL1344 sheared genomic DNA isolated from LB condition (input control)


title: WT-smoke-med-5 month+13d-R1

status: Public on Feb 06 2010

city: Koeln

first: Stephan

last: Gebel

address: Fuggerstr. 3

institute: Philip Morris Research Laboratories

description:
RNA isolated from lung tissue of CD-1 wildtype mouse, smoke treated
gene expression data

hyb_protocol: Ten µg of biotinylated fragmented cRNA was hybridized to GeneChip® Mouse Genome 430 2.0 for 16 hours at 60 rpm in a 45°C GeneChip® Hybridization Oven 640 (Affymetrix)

scan_protocol: Affymetrix.com:Protocol:Scan-M10, Agilent GeneArray® Scanner 3000 7G

data_processing: .CEL files were processed using R/Biocondcutor packages affy and gcrma.

source_name: Lung tissue of CD-1 wildtype mouse, smoke treated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: RNA was extracted from left lung lobes, which were deep-frozen in liquid N2 immediately after dissection and stored at -70°C, by using RNeasy Midi Kit (Qiagen, Hilden, Germany). RNA integrity was determined using Agilent 2100 Bioanalyzer

treatment_protocol: Mice were exposed in whole body exposure chambers to diluted mainstream cigarette smoke (CS) at a target concentration of 750 µg TPM/l for 2, 3, or 4 h/day or to conditioned fresh air (control) for 4 h/day. The CS exposure started with a dose adaptation period, i.e. 125 µg TPM/l on day 1 and gradually reached the target concentration on day 17.

value: lung tissue

value: 13 weeks + 5 month + 13 days

tag: treatment

value: 2R4F whole mainstream smoke 750 µg/ml, treatment over 5 month + 15 days recovery, 3x1h exposure per day


title: SL1344_LPM_2

description: 0181__251939910001_S01_CGH-v4_95_Feb07_1_2

source_name: SL1344 ChIP DNA isolated from LPM condition

growth_protocol: LB overnight cultures subcultured 1:50 into LPM pH=5.8, grown to OD600 ~0.5

source_name: SL1344 sheared genomic DNA isolated from LPM condition (input control)


title: WT-sham-5 month+13d-R1

description:
RNA isolated from lung tissue of CD-1 wildtype mouse, control group
gene expression data

source_name: Lung tissue of CD-1 wildtype mouse, control group

tag: age

value: fresh air, treatment over 5 month + 15 days recovery, 4x1h exposure per day


title: WT-sham-5 month+13d-R2


title: KN-smoke-med-5 month+13d-R4

description:
RNA isolated from lung tissue of Nrf2 knock-out mouse, smoke treated
gene expression data

source_name: Lung tissue of Nrf2 knock-out mouse, smoke treated


title: WT-smoke-med-5 month+13d-R2


title: TS cell, 0hr, rep1

description: Gene expression data from undifferentiated TS cells at T=0hr, biological rep-1


title: SL1344_LPM_1

description: 0181__251939910001_S01_CGH-v4_95_Feb07_1_1


title: WT-sham-5 month+13d-R4


title: KN-smoke-med-5 month+13d-R2


title: KN-smoke-med-5 month+13d-R1


title: 17_Mapping250K_Nsp

description: We have used anonymous normal references (own-lab-generated) for SNP array analysis.

value: chronic myeloid leukemia

value: resistant


title: WT-smoke-med-5 month+13d-R4


title: WT-smoke-med-5 month+13d-R3


title: WT-sham-5 month+13d-R3


title: KN-sham-5 month+13d-R4

description:
RNA isolated from lung tissue of Nrf2 knock-out mouse, control group
gene expression data

source_name: Lung tissue of Nrf2 knock-out mouse, control group


title: SL1344_LPM_3

description: 0181__251939910001_S01_CGH-v4_95_Feb07_1_3


title: KN-smoke-med-5 month+13d-R3


title: KN-smoke-high-5 month+1d-R4

value: 13 weeks + 5 month + 1 day

value: 2R4F whole mainstream smoke 750 µg/ml, treatment over 5 month + 1 day recovery, 4x1h exposure per day


title: KN-smoke-high-5 month+1d-R3


title: KN-sham-5 month+13d-R2


title: KN-sham-5 month+13d-R3


title: KN-sham-5 month+13d-R1


title: KN-smoke-high-5 month+1d-R1


title: KN-smoke-med-5 month+1d-R3

value: 2R4F whole mainstream smoke 750 µg/ml, treatment over 5 month + 1 day recovery, 3x1h exposure per day


title: KN-smoke-high-5 month+1d-R2


title: KN-smoke-low-5 month+1d-R4

value: 2R4F whole mainstream smoke 750 µg/ml, treatment over 5 month + 1 day recovery, 2x1h exposure per day


title: KN-smoke-med-5 month+1d-R4


title: KN-sham-5 month+1d-R2

value: fresh air, treatment over 5 month + 1 day recovery, 4x1h exposure per day


title: KN-smoke-med-5 month+1d-R1


title: KN-smoke-low-5 month+1d-R1


title: KN-smoke-med-5 month+1d-R2


title: KN-sham-5 month+1d-R4


title: KN-sham-5 month+1d-R3


title: KN-smoke-low-5 month+1d-R3


title: KN-smoke-low-5 month+1d-R2


title: WT-smoke-high-5 month+1d-R4


title: WT-smoke-high-5 month+1d-R3


title: WT-smoke-med-5 month+1d-R3


title: WT-smoke-high-5 month+1d-R1


title: WT-smoke-low-5 month+1d-R2


title: WT-smoke-med-5 month+1d-R4


title: WT-smoke-low-5 month+1d-R1


title: WT-smoke-high-5 month+1d-R2


title: WT-smoke-low-5 month+1d-R4


title: KN-smoke-high-5 month-R3

value: 13 weeks + 5 month

value: 2R4F whole mainstream smoke 750 µg/ml, treatment over 5 month, 4x1h exposure per day


title: KN-sham-5 month+1d-R1


title: WT-smoke-low-5 month+1d-R3


title: KN-smoke-high-5 month-R2


title: KN-smoke-med-5 month-R4

value: 2R4F whole mainstream smoke 750 µg/ml, treatment over 5 month, 3x1h exposure per day


title: WT-smoke-med-5 month+1d-R1


title: WT-sham-5 month+1d-R2


title: WT-sham-5 month+1d-R4


title: KN-smoke-low-5 month-R4

value: 2R4F whole mainstream smoke 750 µg/ml, treatment over 5 month, 2x1h exposure per day


title: KN-smoke-low-5 month-R3


title: KN-smoke-med-5 month-R3


title: KN-smoke-high-5 month-R1


title: KN-sham-5 month-R2

value: fresh air, treatment over 5 month, 4x1h exposure per day


title: KN-smoke-low-5 month-R2


title: WT-sham-5 month+1d-R3


title: WT-smoke-med-5 month+1d-R2


title: WT-sham-5 month+1d-R1


title: KN-smoke-med-5 month-R1


title: KN-smoke-med-5 month-R2


title: WT-smoke-high-5 month-R2


title: KN-sham-5 month-R3


title: WT-smoke-high-5 month-R3


title: KN-smoke-low-5 month-R1


title: KN-sham-5 month-R1


title: WT-smoke-high-5 month-R1


title: WT-smoke-med-5 month-R3


title: WT-smoke-med-5 month-R2


title: WT-smoke-low-5 month-R4


title: WT-sham-5 month-R4


title: WT-smoke-low-5 month-R3


title: WT-smoke-high-5 month-R4


title: KN-smoke-med-2 month-R4

value: 13 weeks + 2 month

value: 2R4F whole mainstream smoke 750 µg/ml, treatment over 2 month, 3x1h exposure per day


title: WT-smoke-med-2 month-R4

value: lung tissue


title: KN-smoke-med-2 month-R1


title: KN-sham-2 month-R2

value: fresh air, treatment over 2 month, 4x1h exposure per day


title: WT-smoke-med-2 month-R1


title: WT-sham-5 month-R2


title: WT-smoke-med-5 month-R4


title: WT-sham-2 month-R4


title: KN-smoke-med-2 month-R2


title: WT-smoke-med-5 month-R1


title: KN-sham-2 month-R1


title: KN-sham-2 month-R4


title: WT-smoke-low-5 month-R2


title: WT-sham-5 month-R3


title: KN-sham-2 month-R3


title: KN-smoke-med-2 month-R3


title: WT-sham-5 month-R1


title: WT-smoke-med-1 day-R2

value: 13 weeks + 1 day

value: 2R4F whole mainstream smoke 125 µg/ml, treatment over 1 day, 3x1h exposure per day


title: WT-smoke-med-2 month-R2


title: WT-sham-2 month-R1


title: WT-smoke-med-1 day-R3


title: WT-smoke-med-1 day-R1


title: WT-sham-2 month-R3


title: WT-sham-2 month-R2


title: J2315 vs. LB400 Replicate 2

city: Boston

first: Deborah

middle: R.

last: Yoder-Himes

address: 77 Louis Pasteur Ave, 1038 NRB

department: Microbiology and Molecular Genetics

institute: Harvard Medical School

description: Biological replicate 2 of 2.

hyb_protocol: Samples were mixed with 45 uL of SlideHyb buffer #1 (Ambion, Austin, TX) by pipetting. Hybridization mixes, loading procedures, and slide washing was performed according to Agilent’s recommended protocols (Agilent Technologies 2007) with a 16 h hybridization time at 65C with agitation and the optional Stabilization and Drying Solution final wash.

scan_protocol: Microarrays were scanned using an Axon GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA) and probe intensities extracted using GenePix Pro 5.0 software.

data_processing: The median background signal was subtracted from the mean probe signal and the ratio of background-subtracted signals of a tester to the reference strain were calculated for each probe and transformed to a logarithm base 10 ratio.

organism: Burkholderia cenocepacia J2315

source_name: Burkholderia cenocepacia J2315

label_protocol: Two micrograms of genomic DNA from each strain was sonicated using a Heat Systems Ultrasonics W-225 20 kHz, 200 watt cup sonicator (Misonix, Farmingdale, NY) to generate sheared genomic DNAs from 0.5 to 5 kb. For each sample, 300 ug of sheared DNA was labeled using the methods described in (Wick et al. 2005). Equal amounts of tester and reference (J2315) samples with similar specific activities were mixed in 4 uL 10 mM EDTA pH8.0 and heated to 95C for 5 min.

growth_protocol: Strains were grown at 37°C in 10 ml Luria Bertani broth (Lennox formulation)

extract_protocol: Genomic DNA from all strains was purified from 5 mL cultures grown in LB medium overnight at 37°C by the Wizard Genomic DNA Purification Kit (Promega, Madison, WI) according to the manufacturer’s instructions.

value: Burkholderia cenocepacia J2315

organism: Paraburkholderia xenovorans LB400

source_name: Burkholderia xenovorans LB400

value: Burkholderia xenovorans LB400


title: WT-smoke-med-1 day-R4


title: WT-sham-1 day-R4

value: fresh air, treatment over 1 day, 3x1h exposure per day


title: WT-smoke-low-5 month-R1


title: J2315 vs. LB400 Replicate 1

description: Biological replicate 1 of 2.


title: WT-sham-1 day-R1


title: J2315 vs. G4 Replicate 4

description: Biological replicate 4 of 4.

organism: Burkholderia vietnamiensis G4

source_name: Burkholderia vietnamiensis G4

value: Burkholderia vietnamiensis G4


title: J2315 vs. G4 Replicate 2

description: Biological replicate 2 of 4.


title: J2315 vs. G4 Replicate 3

description: Biological replicate 3 of 4.


title: J2315 vs. AMMD Replicate 2

description: Biological replicate 2 of 2.

organism: Burkholderia ambifaria AMMD

source_name: Burkholderia ambifaria AMMD

value: Burkholderia ambifaria AMMD


title: WT-sham-1 day-R3


title: J2315 vs. HI2424 Replicate 1

description: Biological replicate 1 of 2.

organism: Burkholderia cenocepacia HI2424

source_name: Burkholderia cenocepacia HI2424

value: Burkholderia cenocepacia HI2424


title: J2315 vs. AU1054 Replicate 2

description: Biological replicate 2 of 2.

organism: Burkholderia orbicola

source_name: Burkholderia cenocepacia AU 1054

value: Burkholderia cenocepacia AU 1054


title: KN-smoke-med-1 day-R3


title: J2315 vs. HI2424 Replicate 2

description: Biological replicate 2 of 2.


title: KN-smoke-med-1 day-R1


title: KN-sham-1 day-R3


title: KN-smoke-med-1 day-R4


title: J2315 vs. G4 Replicate 1

description: Biological replicate 1 of 4.


title: WT-sham-1 day-R2


title: KN-smoke-med-1 day-R2


title: KN-sham-1 day-R4


title: J2315 vs. AU1054 Replicate 1

description: Biological replicate 1 of 2.


title: Zinc_EC50_rep1

status: Public on Feb 05 2010

city: Amsterdam

last: Nota

state: Noord Holland

address: Plesmanlaan 125

department: Research Facilities

country: Netherlands

institute: Sanquin

description: Gene expression after 2 d exposure to zinc (EC50;476.2 mg/kg)

hyb_protocol: 300 ng of Cy3-labeled or Cy5-labeled cRNA (specific activity >8.0 pmol dye/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Custom Gene Expression Microarrays with 8 × 15 k format (GPL7150) for 17 hours at 65°C in a rotating Agilent hybridization oven (10 rpm)  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), washed in acetonitril for 10 seconds, then dried immediately by air.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Red&Green and PMT is set to 100%, XDR Hi 100%, XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE2-v5_95 and Grid: 016342_D_F_20070323) to obtain mean Red or Green intensities and median Red or Green background intesities. In limma, edwards method for background correction was used (offset = 30), and quantile normalizion was done between all arrays.

organism: Folsomia candida

source_name: Zinc, 2d, EC50 (476.2 mg/kg), replicate 1

label_protocol: Cyanine-3 (Cy3) or Cyanine-5 (Cy5) labeled cRNA was prepared from 500 ng total RNA using the Quick Amp Labeling Kit, two-color (Agilent Technologies) according to the manufacturer’s guidelines with a slight modification where the transcription (labeling) reactions were done in half the volume, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cultures were first age synchronized before exposure to soil as follows, 10-20 adult animals were incubated per plastic rings; containing plaster of Paris mixed with charcoal, to lay eggs and were removed after 2 days. The incubation conditions were 20°C with a 12 hour light/dark regime. It took approximately 10 days before the eggs hatched.

extract_protocol: Total RNA was extracted from all animals (~30) per jar, using SV Total RNA isolation System (Promega).

treatment_protocol: Approximately 30 animals, 23 d old, were exposed for two days in glass jars containing ~30 g of: soil spiked with (EC10 or EC50 of) a metal (Ba, Cd, Co, Cr, Pb, or Zn), non-spiked soil, or field soil samples. Exposure was done at 20°C, a 12 h light/dark regime, and 75% humidity. After exposure the animals were extracted from soil with tap water via floatation, put in 1.5 mL tubes and frozen in liquid N2.

tag: sample type

value: pool of ~30 animals

tag: series

tag: classification set

value: training set


title: Zinc_EC50_rep2

source_name: Zinc, 2d, EC50 (476.2 mg/kg), replicate 2


title: J2315 vs. AMMD Replicate 1

description: Biological replicate 1 of 2.


title: KN-sham-1 day-R2


title: KN-sham-1 day-R1


title: Zinc_EC50_rep3

source_name: Zinc, 2d, EC50 (476.2 mg/kg), replicate 3


title: 40 days pf vs control reference rep 2

city: Pacific Grove

first: Luke

last: Gardner

state: California

address: 120 Ocean View Blvd, Hopkins Marine Station

institute: Stanford University

hyb_protocol: cDNA was labelled and hybridised to the array using the 3DNA Array 900 MPX expression array detection kit (Genisphere Inc., Hatfield, PA, USA) according to the manufacturer's protocol.

scan_protocol: Microarray chips were scanned using a Genepix 4000B scanner (Axon Instruments, Union City, CA, USA) at 10 µm pixel resolution. ImaGene (BioDiscovery Inc., El Segundo, CA, USA) was used to process raw scanner images and create spot intensity reports, while CloneTracker (Biodiscovery Inc.) generated gene ID mapping files and assigned gene identification. Final intensity reports were retrieved as raw spot intensities in tab-delimited files.

data_processing: Data was pre-processed and normalized in the following sequence, applying background correction, omitting multiple flagged spots, applying floor correction, omitting low expression spots, calculating ratio values, log-transformation of intensity ratios (base 2), and global LOESS normalization. GeneSight 3.0 was used.

organism: Pinctada maxima

source_name: larvae 40 days

label_protocol: 2 ug of total RNA from pooled temporal larval samples and reference samples (unfertilized eggs) was converted to cDNA then labelled and hybridised to the array using the 3DNA Array 900 MPX expression array detection kit (Genisphere Inc., Hatfield, PA, USA) according to the manufacturer's protocol.

extract_protocol:
Pearl oyster Pinctada maxima animals were collected during a commercial spawning run, courtesy of the Paspaley Pearling Company (Broome, Australia). Samples were taken at a series of time points post fertilization (pf) to accurately represent transitions between larval stages and metamorphosis to juveniles ranging from 24 hrs to 40 days pf. Unfertilized eggs were also collected to serve as an experimental control.
Total RNA was isolated from pools of P. maxima larvae at each stage using Trizol reagent as recommended by the manufacturer (Invitrogen Life Technologies, Carlsbad, CA, USA). RNA was DNase treated using RQ1 RNase free DNase (Promega, Madison, WI, USA) and purified using RNeasy Mini Kit (Qiagen, Valencia, CA, USA) as recommended by the manufacturer.

tag: whole larvae pooled

tag: Age

value: 40 Days

source_name: control reference

tag: unfertilized eggs pooled


title: 40 days pf vs control reference rep 3


title: Zinc_EC50_rep4

source_name: Zinc, 2d, EC50 (476.2 mg/kg), replicate 4

value: validation set


title: 35 days pf vs control reference rep 3

source_name: larvae 35 days

value: 35 Days


title: Zinc_EC10_rep3

description: Gene expression after 2 d exposure to zinc (EC10;285.0 mg/kg)

source_name: Zinc, 2d, EC10 (285.0 mg/kg), replicate 3


title: Zinc_EC10_rep5

source_name: Zinc, 2d, EC10 (285.0 mg/kg), replicate 5


title: 35 days pf vs control reference rep 4


title: Zinc_EC10_rep2

source_name: Zinc, 2d, EC10 (285.0 mg/kg), replicate 2


title: PLO_Field_Soil_rep4

description: Gene expression after 2 d exposure to PLO field soil

source_name: PLO, 2d, field soil, replicate 4


title: 40 days pf vs control reference rep 1


title: PLO_Field_Soil_rep2

source_name: PLO, 2d, field soil, replicate 2

value: field soil set


title: 30 days pf vs control reference rep 2

source_name: larvae 30 days

value: 30 Days


title: PLO_Field_Soil_rep1

source_name: PLO, 2d, field soil, replicate 1


title: 30 days pf vs control reference rep 5


title: 30 days pf vs control reference rep 6


title: 35 days pf vs control reference rep 1


title: 30 days pf vs control reference rep 1