title: blood-aCGH-sample 46-exp 2

status: Public on Feb 28 2011

type: genomic

city: Spokane

first: Blake

middle: C.

last: Ballif

state: WA

address: 2820 North Astor Street

department: Research & Development

country: USA

institute: Signature Genomic Laboratories

hyb_protocol: The subject and reference DNA were co-hybridized to one microarray and then oppositely labeled and hybridized to a second microarray. Prior to hybridization, 500 ng of subject DNA was combined with an equal amount of reverse-sex reference DNA, co-precipitated with 50 ug of Cot1-DNA (Invitrogen), and hydrated with 15.5 uL ULTRAhyb (Ambion). Hybridization was performed in an incubation chamber at 37 degrees C with shaking for 14-16 hours. Slides were washed using 50% formamide, 2x SSC, 0.1% SDS at 45 degrees C for 20 min and 1x PBS for 20 min at room temperature.

scan_protocol: Images were acquired using a GenePix 400B dual-laser scanner and individual spots were analyzed with GenePix Pro 5.0 imaging software. Two simultaneous scans of each array were obtained at wavelengths of 635 nm and 532 nm.

data_processing:
After subtraction of background noise, the ratio of fluorescence intensities derived from hybridized test and reference DNA was calculated and normalized by the ratios measured from the reference spots on the same slide. Average ratios of the four spots were then converted to log2 scale and plotted using custom array CGH analysis software Genoglyphix (Signature Genomics).
A block normalization procedure was used for this platform. The array is configured so that the probes are arranged in multiple blocks. It is assumed that the average log ratio of each block is representative of normal. The log ratio of each probe in each block is normalized with the average log ratio of that block. This serves a dual purpose: it normalizes the data for experiment-dependent inequalities and it spatially corrects position-dependent fluorescence.

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral blood

label_protocol: 500 ng of sonicated DNA was labeled with Cy5 or Cy3 using BioPrime Total labeling kit (Invitrogen) per manufacturer's instructions.

extract_protocol: Genomic DNA was extracted from lymphoblastoid cell lines, peripheral blood, or cultured tissues of the subjects and phenotypically normal male and female references using an M48 or the Puregene DNA isolation kit according to the manufacturer's instructions.

tag: gender

value: Female

tag: test

value: patient 46

value: Male

tag: reference

value: control


title: blood-aCGH-sample 25-exp 2

value: patient 25


title: blood-aCGH-sample 14-exp 2

value: patient 14


title: blood-aCGH-sample 32-exp 2

value: patient 32


title: blood-aCGH-sample 15-exp 2

value: patient 15


title: blood-aCGH-sample 49-exp 1

value: patient 49


title: blood-aCGH-sample 13-exp 2

value: patient 13


title: blood-aCGH-sample 14-exp 1


title: blood-aCGH-sample 37-exp 2

value: patient 37


title: blood-aCGH-sample 28-exp 2

value: patient 28


title: blood-aCGH-sample 13-exp 1


title: blood-aCGH-sample 46-exp 1


title: blood-aCGH-sample 15-exp 1


title: blood-aCGH-sample 12-exp 1

value: patient 12


title: blood-aCGH-sample 5-exp 1

value: patient 5


title: blood-aCGH-sample 37-exp 1


title: blood-aCGH-sample 49-exp 2


title: blood-aCGH-sample 32-exp 1


title: blood-aCGH-sample 25-exp 1


title: blood-aCGH-sample 2-exp 2

value: patient 2


title: blood-aCGH-sample 28-exp 1


title: blood-aCGH-sample 5-exp 2


title: blood-aCGH-sample 12-exp 2


title: blood-aCGH-sample 2-exp 1


title: SRF silenced R1881 rep 2

type: RNA

city: Rochester

first: Keith

last: Anderson

state: MN

address: 200 First Street SW

institute: Mayo Clinic

description: Gene expression data from SRF silenced cells treated with R1881

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The software R was used along with bioconductor.  The GC corrections steps were used from GCRMA, then the PM probes were normalized using fastlo, and then the median-polish portion of rma was used to summarize the expression values into probesets.

label: biotin

molecule: total RNA

source_name: SRF silenced, treated with R1881, biological rep 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 1-Cycle protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: LNCaP cells were cultured under androgen deprived conditions for 48 hours, and transfected with control siRNA or siRNA directed against SRF

extract_protocol: Trizol extraction followed by Rneasy column purification

treatment_protocol: 42 hours post-transfection, cells were treated for 48 hours with 5nM R1881 or ethanol vehicle

tag: cell line

value: LNCaP androgen-sensitive human prostate  adenocarcinoma cell line

tag: sirna transfection protocol

value: SRF Silencing

tag: agent (treatment)


title: SRF silenced R1881 rep 3

source_name: SRF silenced, treated with R1881, biological rep 3


title: 10^-6M BPA treatment replicate2

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse320_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: RMA normalization

source_name: normal breast epithelium

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

growth_protocol: standard conditions (37°C and 5% CO2 until confluent)

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

treatment_protocol: 10^-6M BPA continuously for two weeks

tag: treatment


title: SRF silenced R1881 rep 1

source_name: SRF silenced, treated with R1881, biological rep 1


title: SRF silenced EtOH rep 2

description: Gene expression data from SRF silenced cells treated with EtOH

source_name: SRF silenced, treated with EtOH, biological rep 2

value: EtOH vehicle


title: MSI-3

city: Granada

first: Francisco

last: Ruiz-Cabello

address: Avenida Fuerzas Armadas 2

country: Spain

institute: Hospital Universitario Virgen de las Nieves

description: MSI/HLA-

hyb_protocol: Samples were hybridized to Affymetrix HT HG-133+PM 24 Array Plate GeneChips using the Affymetrix standard hybridization protocol.

scan_protocol: Gene Titan System.

data_processing: Data were normalized using the RMA method included in the R Bioconductor package limma.

label: Biotin

source_name: Colorectal, MSI

label_protocol: GeneChip 3’ IVT Express kit.

extract_protocol: RNeasy mini kit (Qiagen) + QIAshredder.

tag: tissue

value: colorectal cancer

tag: microsatellite phenotype

value: high-level microsatellite instability

tag: hla expression

value: HLA-


title: MSI-1

description: MSI/HLA-


title: MSI-2

description: MSI/HLA-


title: MSI-7

description: MSI/HLA-


title: MSS-5

description: MSS/HLA-

source_name: Colorectal, MSS/HLA-

value: microsatellite stability


title: MSS-3

description: MSS/HLA-


title: MSI-8

description: MSI/HLA-


title: MSI-5

description: MSI/HLA-


title: MSI-4

description: MSI/HLA-


title: Control-7

description: MSS/HLA+

source_name: Colorectal, control

value: HLA+


title: SRF silenced EtOH rep 3

source_name: SRF silenced, treated with EtOH, biological rep 3


title: SRF silenced EtOH rep 1

source_name: SRF silenced, treated with EtOH, biological rep 1


title: MSS-1

description: MSS/HLA-


title: Control-8

description: MSS/HLA+


title: MSS-4

description: MSS/HLA-


title: 10^-5M BPA treatment replicate1

treatment_protocol: 10^-5M BPA continuously for two weeks


title: MSS-6

description: MSS/HLA-


title: DMSO replicate1

treatment_protocol: DMSO

value: DMSO


title: DMSO replicate2


title: 10^-5M BPA treatment replicate2


title: MSS-2

description: MSS/HLA-


title: LNCaP R1881 rep 3

description: Gene expression data from LNCaP cells treated with R1881

source_name: LNCaP cells, treated with R1881, biological rep 3

value: control siRNA


title: 10^-6M BPA treatment replicate1


title: MSI-6

description: MSI/HLA-


title: Gliosarcoma

city: Oslo

first: Hanne-Sofie

middle: S

last: Dahlback

address: Montebello

department: Section for Cancer Cytogenetics

country: Norway

institute: The Norwegian Radium Hospital

hyb_protocol: The protocol used for hybridization and labeling of the samples was the “Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Enzymatic labeling for Blood Cells or Tissues (with a High Throughput option) Version 6.1, August 2009”.

scan_protocol: All slides were scanned with the Agilent DNA Microarray Scanner with Surescan High-Resolution technology and data extracted using the Agilent Feature Extraction Software v. 10.5.1.1 as described in the Agilent Oligo aCGH protocol.

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) and Genomic Workbench software (Agilent Technologies Inc., Palo Alto, California, USA). Aberrant DNA copy number intervals identified using the Aberration Detection Method 2 (ADM-2), default threshold setting 6.0, and Fuzzy Zero correction algorithm applied. To ensure the exclusion of very low or very small aberrations, we added a custom-made aberration filter defining a region with a copy number aberration as a region with minimum five probes gained/lost and with minimum absolute average log2 ratio of 0.2 (gain) or -0.2 (loss). A loss defined as homozygous when the log2 ratio was lower than -1, and a gain was regarded as high level amplification when the log2 ratio was higher than 1.

source_name: Human brain

growth_protocol: Fresh-frozen

extract_protocol: Mag-Attract DNA Mini M48 kit (QIAGEN, Hilden, Germany)

value: Gliosarcoma tumor

tag: disease state

value: Gliosarcoma with Osseous Metaplasia

value: Male

tag: sample type

value: control DNA


title: LNCaP R1881 rep 2

source_name: LNCaP cells, treated with R1881, biological rep 2


title: Control-5

description: MSS/HLA+


title: blood-aCGH-sample 27-exp 2

value: Female

value: patient 27

value: control


title: Control-6

description: MSS/HLA+


title: Control-2

description: MSS/HLA+


title: LNCaP EtOH rep 3

description: Gene expression data from LNCaP cells treated with EtOH

source_name: LNCaP cells, treated with EtOH, biological rep 3

value: LNCaP androgen-sensitive human prostate  adenocarcinoma cell line


title: Control-1

description: MSS/HLA+


title: Control-3

description: MSS/HLA+


title: LNCaP R1881 rep 1

source_name: LNCaP cells, treated with R1881, biological rep 1


title: Control-4

description: MSS/HLA+


title: LNCaP EtOH rep 2

source_name: LNCaP cells, treated with EtOH, biological rep 2


title: LNCaP EtOH rep 1

source_name: LNCaP cells, treated with EtOH, biological rep 1


title: blood-aCGH-sample 27-exp 1

source_name: Peripheral blood


title: blood-aCGH-sample 21-exp 2

value: patient 21


title: blood-aCGH-sample 11-exp 2

value: patient 11


title: patient 047, cancer, homogenized [OPG study]

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

description:
Gene expression profile of surgically resected material
CH047

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

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.

source_name: surgically resected material

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

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

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

tag: metastasis

tag: stage

value: cancer, homogenized


title: patient 032, cancer, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
CH032


title: patient 035, cancer, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
CH035

value: metastasis


title: patient 044, cancer, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
CH044


title: patient 036, cancer, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
CH036


title: blood-aCGH-sample 10-exp 2

value: patient 10


title: patient 045, cancer, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
CH045

value: metastatic recurrence


title: patient 041, cancer, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
CH041


title: blood-aCGH-sample 10-exp 1


title: patient 033, cancer, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
CH033


title: patient 030, cancer, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
CH030


title: L13915642_EC12Cy3-EK14Cy5

city: LOGROÑO

first: Vanessa

last: Penacho

state: LA RIOJA

address: c/ Madre de Dios, 51

department: Oenology & Viticulture

institute: ICVV/CSIC

hyb_protocol: Hybridization was carried out in a hybridization chamber (Corning) and using Pronto Universal Hybridization Kit Quick.

scan_protocol: The hybridization signal was detected with a GenePix 4000B laser Scanner (Axon Instruments), and the signal was transformed to numerical values using the integrated GenePix software version 3.0.

data_processing: Initial filtering: mean red signal must be greater than 3 times the mean red background signal, print-tip-loess within-array normalization (included in this sample table), quantile between-array normalization. All normalized ratios reflect recombinant/ WT. R 2.9.2 software and limma bioconductor package used.

organism: Saccharomyces cerevisiae

label_protocol: Fluorescent-labelled cDNA was synthesized from 5µg of total RNA using the CleanUP System (Pronto). Labelled cDNA was purified using the Pronto Purification kit (Pronto)

growth_protocol: Fermentation experiments and precultures were carried out at 28°C on a 1L synthetic medium MS300 (Bely et al. 1990). Extraction time at stationary-growth phase of fermentation advancement (70 g of released CO2).

extract_protocol: Total RNA was extracted using Trizol reagent (Gibco BRL, Life Technologies) (Chomczynski et Sacchi, 1987) and purified using a “RNA Cleanup kit” from Qiagen

tag: genotype/variation

value: EKD-13 [recombinant]

tag: genetic background

tag: deletion

value: both copies of gene KNR4

tag: sampling

value: fermentation set 1_rep.4 at 70 g of released CO2

tag: strain

value: wildtype

value: fermentation set 1_rep.2 at 70 g of released CO2


title: L13915231_EC21Cy3-EK24Cy5

growth_protocol: Fermentation experiments and precultures were carried out at 28°C on a 1L synthetic medium MS300 (Bely et al. 1990). Extraction time at mid-exponential growth phase of fermentation advancement (10 g of released CO2).

value: fermentation set 2_rep.4 at 10 g of released CO2

value: fermentation set 2_rep.1 at 10 g of released CO2


title: patient 028, cancer, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
CH028


title: L13915646_EC21Cy3_EK24Cy5

value: fermentation set 2_rep.4 at 70 g of released CO2

value: fermentation set 2_rep.1 at 70 g of released CO2


title: blood-aCGH-sample 9-exp 2

tag: gender

value: Male

tag: test

value: patient 9

tag: reference

value: control

value: Female


title: patient 038, cancer, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
CH038

value: cancer, homogenized


title: patient 027, cancer, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
CH027


title: blood-aCGH-sample 11-exp 1

value: patient 11


title: blood-aCGH-sample 21-exp 1

value: patient 21


title: patient 042, cancer, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
CH042


title: blood-aCGH-sample 9-exp 1


title: L13915645_EC22Cy5-EK13Cy3

value: fermentation set 2_rep.2 at 70 g of released CO2

value: fermentation set 1_rep.3 at 70 g of released CO2


title: patient 025, cancer, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
CH025

value: metastatic recurrence


title: patient 031, cancer, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
CH031


title: blood-aCGH-sample 4-exp 2

value: patient 4


title: L13915188_EC11Cy3-EK14Cy5

value: EKD-13 [recombinant]

value: both copies of gene KNR4

value: fermentation set 1_rep.4 at 10 g of released CO2

value: wildtype

value: fermentation set 1_rep.1 at 10 g of released CO2


title: L13915190_EC22Cy5-EK23Cy3

value: fermentation set 2_rep.2 at 10 g of released CO2

value: fermentation set 2_rep.3 at 10 g of released CO2


title: blood-aCGH-sample 4-exp 1

value: Male


title: patient 024, cancer, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
CH024

value: metastasis


title: patient 011, cancer, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
CH011


title: blood-aCGH-Sample 7-Exp 1

data_processing:
After subtraction of background noise, the ratio of fluorescence intensities derived from hybridized test and reference DNA was calculated and normalized by the ratios measured from the reference spots on the same slide. Average ratios of the four spots were then converted to log2 scale and plotted using custom array CGH analysis software Genoglyphix (Signature Genomics).
Each probe on the array was normalized over a set of normal control probes on chromosome 11.

value: control

value: Female

value: patient 7


title: blood-aCGH-Sample 7-Exp 2


title: patient 015, cancer, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
CH015

value: cancer, homogenized


title: patient 006, cancer, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
CH006


title: patient 080, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH080

value: normal, homogenized


title: patient 082, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH082


title: patient 078, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH078


title: patient 077, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH077


title: patient 088, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH088


title: patient 074, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH074


title: patient 063, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH063


title: patient 072, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH072


title: patient 073, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH073


title: blood-aCGH-sample 71

hyb_protocol: Hybridization and washing were perfomed with Nimblegen reagents per manufacturer's instructions

scan_protocol: Scanned on Axon 4000B scanner (Molecular Devices)

data_processing:
Data processing was performed using Nimblescan 2.5 and data was displayed using custom oligonucleotide array CGH software Genoglyphix (Signature Genomics).
Both spatial correction and normalization algorithms are applied to Nimblegen arrays. Spatial correction accounts for position-dependent non-uniformity of signals across the array. Specifically, locally-weighted polynomial regression is used to adjust signal intensities based on feature position. The qspline algorithm is used to apply normalization to the data.

label_protocol: 500 ng of sonicated DNA was labeled with Cy5 or Cy3 using Nimblegen dual-color labeling kit according to the manufacturer's instructions.

value: patient 71


title: patient 057, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH057


title: patient 048, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH048


title: blood-aCGH-sample 69

value: patient 69


title: patient 046, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH046


title: blood-aCGH-sample 70

value: patient 70


title: patient 047, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH047


title: patient 068, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH068


title: blood-aCGH-sample 66

value: patient 66


title: patient 138, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH138


title: patient 139, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH139


title: blood-aCGH-sample 67

value: patient 67


title: blood-aCGH-sample 53

value: patient 53


title: blood-aCGH-sample 68

value: patient 68


title: blood-aCGH-sample 36

value: patient 36


title: blood-aCGH-sample 55

value: patient 55


title: blood-aCGH-sample 64

value: patient 64


title: blood-aCGH-sample 56

value: Male

value: patient 56


title: blood-aCGH-sample 63

value: patient 63

value: control


title: blood-aCGH-sample 65

value: Female

value: patient 65


title: blood-aCGH-sample 54

value: patient 54


title: patient 128, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH128

value: metastasis

value: normal, homogenized


title: patient 135, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH135


title: patient 119, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH119


title: blood-aCGH-sample 24

value: patient 24


title: patient 117, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH117

value: metastatic recurrence


title: blood-aCGH-sample 33

value: patient 33


title: blood-aCGH-sample 23

value: patient 23


title: patient 115, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH115


title: blood-aCGH-patient 62

hyb_protocol: Hybridization and washing were perfomed with Agilent reagents per manufacturer's instructions

data_processing:
Agilent Feature Extraction software v9.5.3.1 and Agilent CGH Analytics software v3.5.14 and displayed using oligonucleotide aCGH analysis software Genoglyphix (Signature Genomics).
The standard Agilent protocol CGH-v4_95_Feb07 was used to normalize the data obtained on this platform.

label_protocol: 500 ng of sonicated DNA was labeled with Cy5 or Cy3 using BioPrime Total labeling kit (Invitrogen) per manufacturer's instructions

value: patient 62


title: blood-aCGH-sample 19

value: patient 19


title: patient 111, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH111


title: patient 097, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C097

data_processing: The data was normalized by robust multichip analysis (RMA) using R/Bioconductor (affy package).

value: cancer, LCM


title: blood-aCGH-patient 59

value: patient 59


title: blood-aCGH-patient 61

value: Male

value: patient 61


title: blood-aCGH-patient 45

value: patient 45


title: blood-aCGH-patient 57

value: patient 57

value: control


title: blood-aCGH-patient 60

value: Female

value: patient 60


title: patient 096, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C096


title: patient 110, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH110


title: patient 084, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C084


title: patient 086, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C086


title: patient 098, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C098


title: blood-aCGH-patient 50

value: patient 50


title: blood-aCGH-patient 34

value: patient 34


title: blood-aCGH-patient 44

value: patient 44


title: patient 089, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C089

value: metastatic recurrence


title: patient 107, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH107

value: normal, homogenized


title: blood-aCGH-patient 35

value: patient 35


title: blood-aCGH-patient 22

value: patient 22


title: patient 079, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C079

value: metastasis


title: patient 090, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C090

value: cancer, LCM


title: blood-aCGH-patient 51

value: patient 51


title: blood-aCGH-patient 16

value: patient 16


title: patient 064, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C064


title: blood-aCGH-patient 26

value: Male

value: patient 26


title: patient 065, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C065


title: patient 070, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C070


title: blood-aCGH-patient 58

value: patient 58


title: patient 052, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C052


title: TP_1d_1 vs Xa21-TP_1d_1

city: Yongin

first: Ki-hong

last: Jung

address: 1 Seocheon-dong

department: Plant Molecular Systems Biotechnology

country: South Korea

institute: Kyung Hee University

description: Biological replicate 1 of 2. Comparison of Xa21 vs TP309 1 day after Xoo inoculation using 6 weeks old leaf

hyb_protocol: NSF45K oligo array and hybridization buffer (GeneFrames hybridization solution, MWG Biotech) were added, and dyes labeled control and target cDNAs were applied to microarrays enclosed in HS4800 Automated Slide Hybridization Station. After hybridization, slides were washed sequentially.

scan_protocol: Images were quantified using Genepix4000B and Genepix pro 4.0 software were used to do spot finding and generate gene pix result (gpr) data.

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Green signal (Cy3)/processed Red signal (Cy5). We used LMGene Package. To account for dye-swaps, ratios are reported as LG(NH1ox)/LG or LG(NRRox)/LG or Xa21/TP309.

organism: Oryza sativa

source_name: TP309 plant 1 day after Xoo inoculation (1d) biological replicate 1

label_protocol: We isolated 50ug-100 ug total RNA using TRIZOL reagent and the total RNA was DNaseI-treated for 15 minutes then purified using the RNeasy Midi Kit (Qiagen, Germantown, MD). The total RNA was then enriched for poly-A RNA (50-100 ng) by using the Oligotex mRNA Kit (Qiagen). 50-100 ng of mRNAs were amplified with SuperScript indirect RNA amplification system (Invitrogen) and then resulting antisense (a) RNAs were labeled with Cy3 or Cy5. For more detail protocol of above amplification method, please go to the following website, http://www.interactivebioscience.cz/admin/_docs/protokol%20Invitrogen%20%20Indirect%20Labelling%20+%20Amplifikace.pdf

growth_protocol: The seeds of rice (Oryza sativa) cv LG, NH1 overexpressed line NH1ox (LG) and NRR overexpressed line NRRox (LG), TP309 and TP309 line carrying Xa21 gene were sterilized in 1%(v/v) sodium hypochlorite for 1 h and rinsed thoroughly with deionized water. Seeds were placed on wet filter paper for 3 d at 25.8C in the dark, and pregerminated seeds were transplanted into soil containing pots and grown for 6 weeks in a greenhouse (30°C day, 20°C night) under natural light conditions. And then we moved these plants to growth chamber and adapted them for 2 days before Xoo inoculation.

extract_protocol: 500ug total RNA extracted using Trizol following manufacturer's instructions. And then, 4-5ug mRNAs were isolated using Qiagen oligotex mRNA isolation midi kit. We used 0.5-1ug mRNAs for each hybridization.

treatment_protocol: Four biological replicates of NH1ox vs LG and NRRox vs LG were prepared at two time points (0 d and 1 d Xoo inoculation) and two biological replicates of Xa21vs TP309 were prepared at three time points (0d, 1d, and 2d Xoo inoculation).

tag: background

value: wild type

tag: age

value: 6 weeks old

value: leaf

source_name: Xa21 plant on TP309 background 1 day after Xoo inoculation (1d) biological replicate 1

value: carrying Xa21 gene


title: patient 059, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C059

tag: tissue


title: patient 134, normal, homogenized [OPG study]

description:
Gene expression profile of surgically resected material
NH134


title: blood-aCGH-patient 6

value: Female

value: patient 6

value: control


title: patient 055, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C055


title: Xa21-TP_0d_1 vs TP_0d_1

description: Biological replicate 1 of 2. Comparison of Xa21 vs TP309 before Xoo inoculation using 6 weeks old leaf

source_name: Xa21 plant on TP309 background before Xoo inoculation (0d) biological replicate 1

source_name: TP309 plant before Xoo inoculation (0d) biological replicate 1


title: Xa21-TP_1d_2 vs TP_1d_2

description: Biological replicate 2 of 2. Comparison of Xa21 vs TP309 1 day after Xoo inoculation using 6 weeks old leaf

source_name: Xa21 plant on TP309 background 1 day after Xoo inoculation (1d) biological replicate 2

source_name: TP309 plant 1 day after Xoo inoculation (1d) biological replicate 2


title: patient 045, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C045

value: metastatic recurrence


title: NRRox_1d_4 vs LG_1d_4_dye-swap

description: Dye-swap_biological replicate 4 of 4. Comparison of NRRox vs LG 1 day after Xoo inoculation using 6 weeks old leaf

source_name: LG plant 1 day after Xoo inoculation (1d) biological replicate 4

tag: cultivar

value: LG

source_name: NRR overexpressed plant 1 day after Xoo inoculation (1d) biological replicate 4

value: NH1 overexpressed line NRRox


title: Xa21-TP_0d_2 vs TP_0d_2

description: Biological replicate 2 of 2. Comparison of Xa21 vs TP309 before Xoo inoculation using 6 weeks old leaf

source_name: Xa21 plant on TP309 background before Xoo inoculation (0d) biological replicate 2

source_name: TP309 plant before Xoo inoculation (0d) biological replicate 2


title: TP_2d_1 vs Xa21-TP_2d_1

description: Biological replicate 1 of 2. Comparison of Xa21 vs TP309 2 day after Xoo inoculation using 6 weeks old leaf

source_name: TP309 plant 2 day after Xoo inoculation (2d) biological replicate 1

source_name: Xa21 plant on TP309 background 2 day after Xoo inoculation (2d) biological replicate 1


title: patient 035, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C035

value: metastasis


title: patient 044, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C044

value: cancer, LCM


title: patient 042, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C042


title: patient 027, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C027


title: TP_2d_2 vs Xa21-TP_2d_2

description: Biological replicate 2 of 2. Comparison of Xa21 vs TP309 2 day after Xoo inoculation using 6 weeks old leaf

source_name: TP309 plant 2 day after Xoo inoculation (2d) biological replicate 2

source_name: Xa21 plant on TP309 background 2 day after Xoo inoculation (2d) biological replicate 2


title: NRRox_1d_3 vs LG_1d_3

description: Biological replicate 3 of 4. Comparison of NRRox vs LG 1 day after Xoo inoculation using 6 weeks old leaf

source_name: NRR overexpressed plant 1 day after Xoo inoculation (1d) biological replicate 3

source_name: LG plant 1 day after Xoo inoculation (1d) biological replicate 3


title: NRRox_1d_2 vs LG_1d_2

description: Biological replicate 2 of 4. Comparison of NRRox vs LG 1 day after Xoo inoculation using 6 weeks old leaf

source_name: NRR overexpressed plant 1 day after Xoo inoculation (1d) biological replicate 2

source_name: LG plant 1 day after Xoo inoculation (1d) biological replicate 2


title: patient 028, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C028

source_name: surgically resected material


title: E12.5 control culture

city: Dallas

first: Michelle

last: Tallquist

state: TX

address: 5323 Harry Hines BLVD MC9148

department: Molecular Biology

institute: University of Texas Southwestern Medical Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization with BeadStudio Software v3.3 and exported to Excel for analysis

organism: Mus musculus

source_name: Control embryonic heart without conotruncal region

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA amplification kit for Illumina arrays

growth_protocol: E12.5 hearts were isolated and epicardial cells were allowed grow from the heart for 3 days.  Hearts were removed and epicardial cells were cultured for 2 additional days.

extract_protocol: RNA was extracted from a minimum of 3 cultures for each sample using the Trizol reagent and QIAGEN RNeasy micro kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: After heart removal, 12h and 24h prior to isolation, GSM671879 and GSM671880 were treated with 20ng/ml PDGFBB, respectively.  GSM671881 and GSM671882 were treated with vehicle or 20ng/ml PDGFBB, 10ng/ml hTGFb1, 25ng/ml bFGF during the 2 day additional culture.

tag: background/strain

value: mixed C57

value: wildtype

tag: treatment

value: Vehicle


title: E12.5 wild type PDGFBB, bFGF, TGFb1 treated culture

source_name: Wild type epicardial culture

value: 20ng/ml PDGFBB, 10ng/ml hTGFb1, 25ng/ml bFGF


title: E12.5 control heart

data_processing: The data were normalised using quantile normalization with BeadStudio Software v3.3 and exported to Excel for analysis.

extract_protocol: E12.5 hearts were isolated and conotruncal regions were removed.  Samples were stored in RNA Later until genotyping was completed.  Three hearts of each genotype were pooled and RNA was extracted with Trizol reagent and QIAGEN RNeasy micro kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.


title: E12.5 wild type PDGFBB treated culture - 24h

value: 20ng/ml PDGFBB


title: patient 032, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C032


title: E12.5 wild type Vehicle treated culture


title: NRRox_1d_1 vs LG_1d_1

description: Biological replicate 1 of 4. Comparison of NRRox vs LG 1 day after Xoo inoculation using 6 weeks old leaf

source_name: NRR overexpressed plant 1 day after Xoo inoculation (1d) biological replicate 1

source_name: LG plant 1 day after Xoo inoculation (1d) biological replicate 1

value: wild type


title: E12.5 PDGFR (a and b) epicardial tissue specific knockout

source_name: PDGFR epicardial tissue specific knockout embryonic heart without conotruncal region

value: PDGF receptor epicardial knockout


title: E12.5 wild type PDGFBB treated culture - 12h


title: E12.5 PDGFR (a and b) epicardial tissue specific knockout culture

value: PDGFR epicardial tissue specific knockout


title: NRRox_0d_4 vs LG_0d_4_dye-swap

description: Dye-swap_ biological replicate 4 of 4. Comparison of NRRox vs LG before Xoo inoculation using 6 weeks old leaf

source_name: LG plant before Xoo inoculation (0d) biological replicate 4

value: 6 weeks old

value: leaf

source_name: NRR overexpressed plant before Xoo inoculation (0d) biological replicate 4


title: patient 019, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C019


title: patient 146, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C146


title: NRRox_0d_3 vs LG_0d_3

description: Biological replicate 3 of 4. Comparison of NRRox vs LG before Xoo inoculation using 6 weeks old leaf

source_name: NRR overexpressed plant before Xoo inoculation (0d) biological replicate 3

source_name: LG plant before Xoo inoculation (0d) biological replicate 3


title: NH1ox_1d_4 vs LG_1d_4_dye-swap

description: Dye-swap_biological replicate 4 of 4. Comparison of NH1ox vs LG 1 day after Xoo inoculation using 6 weeks old leaf

source_name: LG plant 1 day after Xoo inoculation (1d) biological replicate 4

source_name: NH1 overexpressed plant 1 day after Xoo inoculation (1d) biological replicate 4

value: NH1 overexpressed line NH1ox


title: patient 141, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C141


title: patient 130, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C130


title: NRRox_0d_2 vs LG_0d_2

description: Biological replicate 2 of 4. Comparison of NRRox vs LG before Xoo inoculation using 6 weeks old leaf

source_name: NRR overexpressed plant before Xoo inoculation (0d) biological replicate 2

source_name: LG plant before Xoo inoculation (0d) biological replicate 2


title: NH1ox_1d_2 vs LG_1d_2

description: Biological replicate 2 of 4. Comparison of NH1ox vs LG 1 day after Xoo inoculation using 6 weeks old leaf

source_name: NH1 overexpressed plant 1 day after Xoo inoculation (1d) biological replicate 2


title: patient 149, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C149


title: NH1ox_1d_3 vs LG_1d_3

description: Biological replicate 3 of 4. Comparison of NH1ox vs LG 1 day after Xoo inoculation using 6 weeks old leaf

source_name: NH1 overexpressed plant 1 day after Xoo inoculation (1d) biological replicate 3

source_name: LG plant 1 day after Xoo inoculation (1d) biological replicate 3


title: NRRox_0d_1 vs LG_0d_1

description: Biological replicate 1 of 4. Comparison of NRRox vs LG before Xoo inoculation using 6 weeks old leaf

source_name: NRR overexpressed plant before Xoo inoculation (0d) biological replicate 1

source_name: LG plant before Xoo inoculation (0d) biological replicate 1


title: NH1ox_0d_3 vs LG_0d_3

description: Biological replicate 3 of 4. Comparison of NH1ox vs LG before Xoo inoculation using 6 weeks old leaf

source_name: NH1 overexpressed plant before Xoo inoculation (0d) biological replicate 3


title: patient 133, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C133

source_name: surgically resected material


title: patient 140, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C140


title: NH1ox_0d_2 vs LG_0d_2

description: Biological replicate 2 of 4. Comparison of NH1ox vs LG before Xoo inoculation using 6 weeks old leaf

source_name: NH1 overexpressed plant before Xoo inoculation (0d) biological replicate 2


title: patient 121, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C121


title: patient 131, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C131


title: NH1ox_0d_1 vs LG_0d_1

description: Biological replicate 1 of 4. Comparison of NH1ox vs LG before Xoo inoculation using 6 weeks old leaf

source_name: NH1 overexpressed plant before Xoo inoculation (0d) biological replicate 1


title: TP_2d_1 vs Xa21-TP_2d_1

description: Biological replicate 1 of 2. Comparison of Xa21 vs TP309 2 day after Xoo inoculation using 6 weeks old leaf

hyb_protocol: NSF45K oligo array and hybridization buffer (GeneFrames hybridization solution, MWG Biotech) were added, and dyes labeled control and target cDNAs were applied to microarrays enclosed in HS4800 Automated Slide Hybridization Station . After hybridization, slides were washed sequentially.

source_name: TP309 plant 2 day after Xoo inoculation (2d) biological replicate 1

source_name: Xa21 plant on TP309 background 2 day after Xoo inoculation (2d) biological replicate 1

value: carrying Xa21 gene


title: NH1ox_1d_1 vs LG_1d_1

description: Biological replicate 1 of 4. Comparison of NH1ox vs LG 1 day after Xoo inoculation using 6 weeks old leaf

source_name: NH1 overexpressed plant 1 day after Xoo inoculation (1d) biological replicate 1

source_name: LG plant 1 day after Xoo inoculation (1d) biological replicate 1


title: Xa21-TP_1d_2 vs TP_1d_2

description: Biological replicate 2 of 2. Comparison of Xa21 vs TP309 1 day after Xoo inoculation using 6 weeks old leaf

source_name: Xa21 plant on TP309 background 1 day after Xoo inoculation (1d) biological replicate 2

source_name: TP309 plant 1 day after Xoo inoculation (1d) biological replicate 2


title: patient 109, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C109


title: patient 129, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C129


title: patient 106, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C106

value: metastatic recurrence


title: TP_2d_2 vs Xa21-TP_2d_2

description: Biological replicate 2 of 2. Comparison of Xa21 vs TP309 2 day after Xoo inoculation using 6 weeks old leaf

source_name: TP309 plant 2 day after Xoo inoculation (2d) biological replicate 2

source_name: Xa21 plant on TP309 background 2 day after Xoo inoculation (2d) biological replicate 2


title: patient 094, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C094


title: NH1ox_0d_4 vs LG_0d_4_dye-swap

description: Dye-swap_biological replicate 4 of 4. Comparison of NH1ox vs LG before Xoo inoculation using 6 weeks old leaf

source_name: LG plant before Xoo inoculation (0d) biological replicate 4

value: LG

source_name: NH1 overexpressed plant before Xoo inoculation (0d) biological replicate 4


title: Xa21-TP_0d_2 vs TP_0d_2

description: Biological replicate 2 of 2. Comparison of Xa21 vs TP309 before Xoo inoculation using 6 weeks old leaf

source_name: Xa21 plant on TP309 background before Xoo inoculation (0d) biological replicate 2

source_name: TP309 plant before Xoo inoculation (0d) biological replicate 2


title: patient 099, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C099


title: patient 095, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C095


title: TP_1d_1 vs Xa21-TP_1d_1

description: Biological replicate 1 of 2. Comparison of Xa21 vs TP309 1 day after Xoo inoculation using 6 weeks old leaf

source_name: TP309 plant 1 day after Xoo inoculation (1d) biological replicate 1

source_name: Xa21 plant on TP309 background 1 day after Xoo inoculation (1d) biological replicate 1


title: Ft84C_vs_Ft16A_14146909_MDS.mev.refIsIA.out

city: Rockville

first: Chun-Hua

last: Wan

state: MD

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

institute: The J. Craig Venter Institute

hyb_protocol: Aminosilane-coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42 C degree for 60 min.  The slides then were washed at room temperature with distilled water, dipped in isopropanol, and allowed to dry.  Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were heated to 95 C degree  prior to hybridization.  The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 C degree.   Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature, then dried in air.

scan_protocol: Hybridized slides were scanned with an Axon GenePix 4000 scanner

data_processing: Individual TIFF images from each channel were analyzed with TIGR Spotfinder (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html). Microarray data were normalized by using TM4 software MIDAS (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html).  Data were read into MIDAS using the default settings except that the 'Generous' one bad channel policy was set to preserve data where one of the two channel intensities falls below background.  In these cases Midas replaces this zero intensity value with the 10th-percentile value for that channel on that array to permit log ratio computation in later analysis.  This policy selection is critical since some query strains may have a gene deletion that results in no signal in the query channel and yet these occurrences are biologically important to note and retain by this policy.  LOWESS normalization was performed in MIDAS using the default parameters.  In-Slide replicates analysis was performed by MIDAS to take the geometric mean of spot replicates (spots having the same oligo sequence and target gene) within each slide.

organism: Francisella tularensis

source_name: FRAN016 Schu S4

label_protocol: DNA probes for microarray experiments were generated by adding 2 ug of total RNA in a mixture containing 6 ug of random hexamers (Invitrogen), 0.01 M dithiothreitol, an aminoallyl-deoxynucleoside triphosphate mixture containing 25 mM each dATP, dCTP, and dGTP, 15 mM dTTP, and 10 mM amino-allyl-dUTP (aa-dUTP) (Sigma), reaction buffer, and 400 units of SuperScript III reverse transcriptase (Invitrogen) at 42 C degree overnight. The RNA template then was hydrolyzed by adding NaOH and EDTA to a final concentration of 0.2 and 0.1 M, respectively, and incubating at 70 C degree for 15 min. Unincorporated aa-dUTP was removed with a Minelute column (Qiagen). The probe was eluted with a phosphate elution buffer (4 mM KPO4, pH 8.5, in ultrapure water), dried, and resuspended in 0.1 M sodium carbonate buffer (pH 9.0). To couple the amino-allyl cDNA with fluorescent labels, normal human serum-Cy3 or normal human serum-Cy5 (Amersham) was added at room temperature for 1h. Uncoupled label was removed using the Qiagen Minelute column (Valencia, CA).

growth_protocol: Cells were grown in Cahamberlain’s medium to midlog phase before the RNA was harvested.

extract_protocol: Per Qiagen RNeasy Total RNA extraction kit.

value: Clade A1

value: Clade A2


title: patient 088, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C088

source_name: surgically resected material

value: cancer, LCM


title: NRRox_1d_3 vs LG_1d_3

description: Biological replicate 3 of 4. Comparison of NRRox vs LG 1 day after Xoo inoculation using 6 weeks old leaf

source_name: NRR overexpressed plant 1 day after Xoo inoculation (1d) biological replicate 3

value: NH1 overexpressed line NRRox

source_name: LG plant 1 day after Xoo inoculation (1d) biological replicate 3


title: Ft84B_vs_Ft16A_14181848_MDS.mev.refIsIA.out


title: Ft84BvsFt16A_14146952_MDS.mev.refIsIA.out


title: patient 082, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C082


title: Ft83C_vs_Ft16A_14146910_MDS.mev.refIsIA.out

value: Clade B


title: Ft82CvsFt16A_14147005_MDS.mev.refIsIA.out


title: patient 083, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C083


title: patient 078, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C078


title: Xa21-TP_0d_1 vs TP_0d_1

description: Biological replicate 1 of 2. Comparison of Xa21 vs TP309 before Xoo inoculation using 6 weeks old leaf

source_name: Xa21 plant on TP309 background before Xoo inoculation (0d) biological replicate 1

source_name: TP309 plant before Xoo inoculation (0d) biological replicate 1


title: NRRox_1d_4 vs LG_1d_4_dye-swap

description: Dye-swap_biological replicate 4 of 4. Comparison of NRRox vs LG 1 day after Xoo inoculation using 6 weeks old leaf

source_name: LG plant 1 day after Xoo inoculation (1d) biological replicate 4

source_name: NRR overexpressed plant 1 day after Xoo inoculation (1d) biological replicate 4


title: patient 081, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C081

value: metastasis


title: Ft83B_vs_Ft16A_14146911_MDS.mev.refIsIA.out


title: patient 077, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C077


title: Ft82BvsFt16A_14147003_MDS.mev.refIsIA.out


title: Ft83A_vs_Ft16A_14181803_MDS.mev.refIsIA.out


title: Ft53C_vs_Ft16A_14146906_MDS.mev.refIsIA.out

source_name: FRAN053 HOLT

value: Clade C


title: NRRox_1d_2 vs LG_1d_2

description: Biological replicate 2 of 4. Comparison of NRRox vs LG 1 day after Xoo inoculation using 6 weeks old leaf

source_name: NRR overexpressed plant 1 day after Xoo inoculation (1d) biological replicate 2

source_name: LG plant 1 day after Xoo inoculation (1d) biological replicate 2


title: Ft81B_vs_Ft16A_14146918_MDS.mev.refIsIA.out


title: Ft51BvsFt16A_14146955_MDS.mev.refIsIA.out

source_name: FRAN051 Pennington


title: Ft53B_vs_Ft16A_14181850_MDS.mev.refIsIA.out


title: Ft50B_vs_Ft16A_14146919_MDS.mev.refIsIA.out

source_name: FRAN050 RUSS


title: Ft51AvsFt16A_14146956_MDS.mev.refIsIA.out


title: Ft80C_vs_Ft16A_14146923_MDS.mev.refIsIA.out


title: Ft81A_vs_Ft16A_14181858_MDS.mev.refIsIA.out


title: Ft51A_vs_Ft16A_14146932_MDS.mev.refIsIA.out


title: NRRox_1d_1 vs LG_1d_1

description: Biological replicate 1 of 4. Comparison of NRRox vs LG 1 day after Xoo inoculation using 6 weeks old leaf

source_name: NRR overexpressed plant 1 day after Xoo inoculation (1d) biological replicate 1

source_name: LG plant 1 day after Xoo inoculation (1d) biological replicate 1


title: NRRox_0d_4 vs LG_0d_4_dye-swap

description: Dye-swap_biological replicate 4 of 4. Comparison of NRRox vs LG before Xoo inoculation using 6 weeks old leaf

source_name: LG plant before Xoo inoculation (0d) biological replicate 4

source_name: NRR overexpressed plant before Xoo inoculation (0d) biological replicate 4


title: Ft80B_vs_Ft16A_14181861_MDS.mev.refIsIA.out

source_name: FRAN016 Schu S4


title: patient 073, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C073

source_name: surgically resected material


title: patient 068, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C068


title: NRRox_0d_1 vs LG_0d_1

description: Biological replicate 1 of 4. Comparison of NRRox vs LG before Xoo inoculation using 6 weeks old leaf

source_name: NRR overexpressed plant before Xoo inoculation (0d) biological replicate 1

source_name: LG plant before Xoo inoculation (0d) biological replicate 1


title: Ft50C_vs_Ft16A_14146915_MDS.mev.refIsIA.out


title: NRRox_0d_3 vs LG_0d_3

description: Biological replicate 3 of 4. Comparison of NRRox vs LG before Xoo inoculation using 6 weeks old leaf

source_name: NRR overexpressed plant before Xoo inoculation (0d) biological replicate 3

source_name: LG plant before Xoo inoculation (0d) biological replicate 3


title: NRRox_0d_2 vs LG_0d_2

description: Biological replicate 2 of 4. Comparison of NRRox vs LG before Xoo inoculation using 6 weeks old leaf

source_name: NRR overexpressed plant before Xoo inoculation (0d) biological replicate 2

source_name: LG plant before Xoo inoculation (0d) biological replicate 2


title: patient 057, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C057


title: patient 072, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C072


title: NH1ox_1d_4 vs LG_1d_4_dye-swap

description: Dye-swap_biological replicate 4 of 4. Comparison of NH1ox vs LG 1 day after Xoo inoculation using 6 weeks old leaf

source_name: LG plant 1 day after Xoo inoculation (1d) biological replicate 4

source_name: NH1 overexpressed plant 1 day after Xoo inoculation (1d) biological replicate 4


title: patient 063, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C063


title: Ft50A_vs_Ft16A_14181799_MDS.mev.refIsIA.out


title: Ft49BvsFt16A_14146958_MDS.mev.refIsIA.out

source_name: FRAN049 Carery


title: patient 061, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C061


title: Ft49AvsFt16A_14146959_MDS.mev.refIsIA.out


title: Ft74A_vs_Ft16A_14181862_MDS.mev.refIsIA.out


title: Ft74C_vs_Ft16A_14146924_MDS.mev.refIsIA.out


title: Ft47C_vs_Ft16A_14146928_MDS.mev.refIsIA.out

source_name: FRAN047 SCHU-S5


title: NH1ox_1d_3 vs LG_1d_3

description: Biological replicate 3 of 4. Comparison of NH1ox vs LG 1 day after Xoo inoculation using 6 weeks old leaf

source_name: NH1 overexpressed plant 1 day after Xoo inoculation (1d) biological replicate 3

source_name: LG plant 1 day after Xoo inoculation (1d) biological replicate 3


title: Ft49A_vs_Ft16A_14146933_MDS.mev.refIsIA.out


title: patient 053, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C053


title: Ft47A_vs_Ft16A_14181854_MDS.mev.refIsIA.out


title: Ft73C_vs_Ft16A_14146926_MDS.mev.refIsIA.out


title: patient 046, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C046


title: NH1ox_0d_4 vs LG_0d_4_dye-swap

description: Dye-swap_biological replicate 4 of 4. Comparison of NH1ox vs LG before Xoo inoculation using 6 weeks old leaf

source_name: NH1 overexpressed plant before Xoo inoculation (0d) biological replicate 4


title: Ft60A_vs_Ft16A_14181802_MDS.mev.refIsIA.out

source_name: FRAN060 BISH M1 (R)


title: Ft73A_vs_Ft16A_14181852_MDS.mev.refIsIA.out


title: Ft60B_vs_Ft16A_14146912_MDS.mev.refIsIA.out


title: NH1ox_0d_3 vs LG_0d_3

description: Biological replicate 3 of 4. Comparison of NH1ox vs LG before Xoo inoculation using 6 weeks old leaf

source_name: NH1 overexpressed plant before Xoo inoculation (0d) biological replicate 3


title: NH1ox_1d_1 vs LG_1d_1

description: Biological replicate 1 of 4. Comparison of NH1ox vs LG 1 day after Xoo inoculation using 6 weeks old leaf

source_name: NH1 overexpressed plant 1 day after Xoo inoculation (1d) biological replicate 1

source_name: LG plant 1 day after Xoo inoculation (1d) biological replicate 1


title: NH1ox_1d_2 vs LG_1d_2

description: Biological replicate 2 of 4. Comparison of NH1ox vs LG 1 day after Xoo inoculation using 6 weeks old leaf

source_name: NH1 overexpressed plant 1 day after Xoo inoculation (1d) biological replicate 2

source_name: LG plant 1 day after Xoo inoculation (1d) biological replicate 2


title: patient 038, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C038

source_name: surgically resected material


title: patient 041, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C041


title: Drosophila melanogaster preimmune ChIP-chip array rep2

city: Los Altos

first: Manoj

last: Samanta

state: CA

address: 2240 Homestead Court #309

institute: Systemix Institute

description: High-Resolution ChIP-chip map of pre-immune binding.

hyb_protocol: Hybridization was performed by Nimblegen at their Iceland core facility using Nimblegen protocol. Hybridization was performed by Nimblegen at their Iceland core facility using Nimblegen protocol.

scan_protocol: Features were scanned using Nimblescan software.

data_processing: Custom software tools were used for data processing. Quantile normalization was performed with data on all arrays.

organism: Drosophila melanogaster

source_name: pre-immunoprecipitated DNA from Drosophila

label_protocol: Standard Nimblegen protocol was used to generate labeled DNA.

extract_protocol:
Chromatin was prepared from 2 grams of yw embryos of 1-3 hours in
age. No antibody was used. The resulting DNA library
was labeled and hybridized.

tag: sample type

value: Chromatin pre-immunoprecipated sample

value: yw

value: embryo

source_name: Genomic DNA from Drosophila melanogaster

extract_protocol:
It was processed equivalent to ch1 except that the sample
was genomic DNA and not immunoprecipated chromatin.

value: input DNA


title: Ft58C_vs_Ft16A_14146913_MDS.mev.refIsIA.out

source_name: FRAN016 Schu S4

source_name: FRAN058  CARR


title: Ft45C_vs_Ft16A_14146920_MDS.mev.refIsIA.out


title: Ft45B_vs_Ft16A_14181859_MDS.mev.refIsIA.out


title: patient 037, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C037

tag: metastasis


title: NH1ox_0d_2 vs LG_0d_2

description: Biological replicate 2 of 4. Comparison of NH1ox vs LG before Xoo inoculation using 6 weeks old leaf

source_name: NH1 overexpressed plant before Xoo inoculation (0d) biological replicate 2

value: 6 weeks old

source_name: LG plant before Xoo inoculation (0d) biological replicate 2

value: wild type


title: Drosophila melanogaster weckle ChIP-chip array rep1

description: High-Resolution ChIP-chip map of weckle binding.

source_name: immunoprecipitated DNA from Drosophila

extract_protocol:
Chromatin was prepared from 2 grams of yw embryos of 1-3 hours in
age. Anti-weckle antibody was used. The resulting DNA library
was labeled and hybridized.

value: Chromatin immunoprecipated sample with weckle

tag: antibody

value: in-house produced anti-weckle


title: Ft58B_vs_Ft16A_14181801_MDS.mev.refIsIA.out


title: NH1ox_0d_1 vs LG_0d_1

description: Biological replicate 1 of 4. Comparison of NH1ox vs LG before Xoo inoculation using 6 weeks old leaf

source_name: NH1 overexpressed plant before Xoo inoculation (0d) biological replicate 1

tag: genotype/variation

value: NH1 overexpressed line NH1ox

value: leaf

source_name: LG plant before Xoo inoculation (0d) biological replicate 1


title: Ft44D_vs_Ft16A_14146922_MDS.mev.refIsIA.out

value: Clade A1

source_name: FRAN044 LI

value: Clade D


title: Drosophila melanogaster twist ChIP-chip array rep1

description: High-Resolution ChIP-chip map of twist binding.

extract_protocol:
Chromatin was prepared from 2 grams of yw embryos of 1-3 hours in
age. Rat anti-twist antibody was used. The resulting DNA library
was labeled and hybridized.

value: Chromatin immunoprecipated sample with twist

value: in-house produced anti-twist


title: Ft57B_vs_Ft16A_14181851_MDS.mev.refIsIA.out

source_name: FRAN057 STOLL


title: Ft57C_vs_Ft16A_14146962_MDS.mev.refIsIA.out


title: Ft40CvsFt16A_14146954_MDS.mev.refIsIA.out

source_name: FRAN040 MAX


title: Ft44A_vs_Ft16A_14181860_MDS.mev.refIsIA.out


title: patient 048, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C048

tag: stage

value: cancer, LCM


title: patient 036, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C036


title: Ft40C_vs_Ft16A_14146936_MDS.mev.refIsIA.out


title: Ft40B_vs_Ft16A_14181849_MDS.mev.refIsIA.out

value: Clade B


title: patient 033, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C033


title: patient 034, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C034


title: patient 031, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C031


title: Drosophila melanogaster dorsal ChIP-chip array rep3

description: High-Resolution ChIP-chip map of dorsal binding.

extract_protocol:
Chromatin was prepared from 2 grams of yw embryos of 1-3 hours in
age. Anti-dorsal antibody was used. The resulting DNA library
was labeled and hybridized.

value: Chromatin immunoprecipated sample with dorsal

value: in-house produced anti-dorsal


title: Drosophila melanogaster snail ChIP-chip array rep1

description: High-Resolution ChIP-chip map of snail binding.

extract_protocol:
Chromatin was prepared from 2 grams of yw embryos of 1-3 hours in
age. Anti-snail antibody was used. The resulting DNA library
was labeled and hybridized.

value: Chromatin immunoprecipated sample with snail

value: in-house produced anti-snail

value: yw


title: Ft37BvsFt16A_14146960_MDS.mev.refIsIA.out

source_name: FRAN037 COLL


title: Ft39B_vs_Ft16A_14146907_MDS.mev.refIsIA.out

source_name: FRAN039 GIB


title: Ft39A_vs_Ft16A_14181826_MDS.mev.refIsIA.out


title: ubb_d28_ko_1

city: Pullman

first: Ryan

last: Evanoff

department: School of Molecular Biosciences

institute: Washington State University

description: Gene expression data from 28dpp Ubb knockout testis.

hyb_protocol: Fragmented, biotin labeled cDNA was hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with Microarray Suite 5.0 using a scaling factor of 125 and imported into Genespring 7.0.

source_name: 28dpp Ubb knockout testis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

value: Ubb knockout

value: testis


title: patient 030, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C030


title: Ft55C_vs_Ft16A_14146927_MDS.mev.refIsIA.out

source_name: FRAN055 Memp


title: ubb_d28_wt_2

description: Gene expression data from 28dpp wild type testis.

source_name: 28dpp wild type testis

value: wild type


title: ubb_d28_wt_1


title: ubb_d21_wt_2

description: Gene expression data from 21dpp wild type testis.

source_name: 21dpp wild type testis


title: patient 025, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C025

source_name: surgically resected material

value: metastatic recurrence


title: Ft37AvsFt16A_14146961_MDS.mev.refIsIA.out

source_name: FRAN016 Schu S4


title: Ft36B_vs_Ft16A_14146930_MDS.mev.refIsIA.out

source_name: FRAN036 Canadian Water (NBL)


title: Ft55B_vs_Ft16A_14181853_MDS.mev.refIsIA.out


title: patient 026, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C026


title: ubb_d21_wt_1


title: ubb_d28_ko_2


title: patient 024, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C024

value: metastasis


title: Ft04C_vs_Ft16A_14146931_MDS.mev.refIsIA.out

source_name: FRAN004 LVS

value: Clade C


title: Ft54A_vs_Ft16A_14181800_MDS.mev.refIsIA.out

value: Clade A1

source_name: FRAN054 LR


title: Ft54BvsFt16A_14146953_MDS.mev.refIsIA.out


title: patient 015, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C015


title: Ft36A_vs_Ft16A_14181855_MDS.mev.refIsIA.out


title: patient 023, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C023


title: ubb_d14_wt_1

description: Gene expression data from 14dpp wild type testis.

source_name: 14dpp wild type testis


title: Ft54B_vs_Ft16A_14146914_MDS.mev.refIsIA.out


title: patient 155, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C155


title: ubb_d21_ko_2

description: Gene expression data from 21dpp Ubb knockout testis.

source_name: 21dpp Ubb knockout testis


title: ubb_d14_ko_2

description: Gene expression data from 14dpp Ubb knockout testis.

source_name: 14dpp Ubb knockout testis


title: Ft04B_vs_Ft16A_14181857_MDS.mev.refIsIA.out


title: patient 156, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C156


title: ubb_d7_wt_1

description: Gene expression data from 7dpp wild type testis.

source_name: 7dpp wild type testis


title: patient 022, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C022


title: ubb_d14_wt_2


title: ubb_d21_ko_1


title: patient 154, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C154


title: ubb_d7_wt_2


title: patient 150, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C150


title: ubb_d14_ko_1


title: patient 145, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C145


title: patient 153, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C153


title: YF050524MOT16

city: montreal

first: bing

last: han

state: qc

address: 2099 alexandre deseve

department: medicine

country: Canada

institute: university of montreal

hyb_protocol: The labeled cRNA was hybridized on GeneChip Mouse Genome 430 2.0 Arrays. Hybridized target cRNA was stained with streptavidin phycoerythrin. See http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf

scan_protocol: Arrays were scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the GeneChip array. See http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf

data_processing: RMA data were generated by McGill University Genome Quebec Innovation Centre through software FlexArray. Student t test was used to analyze the difference between groups.

source_name: mouse islet, 48h

label_protocol: Target RNA was reverse transcribed into cDNA, and in-vitro transcription was performed to generate biotin-labeled cRNA for subsequent hybridization.

growth_protocol: Cultured in F12K medium with 10%FBS, 37°C, 5% CO2 incubator.

extract_protocol: Total RNA was extracted from islets with QIAGEN RNeasy Micro Kits.

treatment_protocol: No treatment.

value: islets

tag: time after isolation

value: 48 hr


title: patient 152, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C152


title: patient 144, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C144


title: ubb_d7_ko_2

description: Gene expression data from 7dpp Ubb knockout testis.

source_name: 7dpp Ubb knockout testis


title: patient 148, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C148


title: patient 138, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C138


title: YF050524MOT15


title: YF050524MOT09

source_name: mouse islet, 24h

value: 24 hr


title: YF050524MOT17


title: patient 142, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C142

value: cancer, LCM


title: YF050524MOT18


title: ubb_d7_ko_1


title: patient 135, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C135


title: patient 139, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C139


title: patient 143, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C143


title: patient 147, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C147


title: YF050524MOT11


title: YF050524MOT14


title: YF050524MOT12


title: YF050524MOT10


title: YF050524MOT13


title: patient 134, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C134


title: YF050524MOT08


title: patient 128, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C128


title: YF050524MOT07


title: YF050524MOT06

source_name: mouse islet, 0h

value: 0 hr


title: YF050524MOT04


title: patient 124, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C124


title: YF050524MOT03


title: patient 136, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C136


title: patient 011, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C011


title: patient 123, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C123


title: patient 125, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C125


title: Clostridium acetobutylicum ATCC 824 WT vs. SigG mutant (Hour 36)

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

hyb_protocol: Microarrays were hybridized and washed according to Agilent Technologies' recommended protocols.

scan_protocol: Microarrays were scanned according to Agilent Technologies' recommended protocols.

data_processing: Data was normalized using the LOESS method and implemented using the Bioconductor package in the statistical application R [Dudoit S, et al. Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. The Analysis of Gene Expression Data: Methods and Software. Springer, NY, 2002.][Yang YH, et al. Nucleic Acids Res. 2002;30(4):e15.]. Dye swaps and replicate spots were averaged together to give one expression value per gene. If the spot's intensity was not greater than 50, the spot was assigned a value of NA because it was not above background intensity [Jones SW, et al. Genome Biol. 2008;9(7):R114.].

organism: Clostridium acetobutylicum ATCC 824

source_name: C. acetobutylicum SigG mutant, 36 hrs

label_protocol: cDNA was generated and labeled as described in [Jones SW, et al. Genome Biol. 2008;9(7):R114.].

growth_protocol: Colonies were grown on solid 2xYTG plates at 37°C under anaerobic conditions. Mutants were grown on or in media containing 5 µg/ml thiamphenicol. Individual colonies were picked and put in 10 ml of acetate-buffered CGM. WT colonies more than 5 days old were heat-shocked for 10 min at 70-80°C. Mutant colonies were not heat-shocked and were less than 3 days old. Tubes were grown to an OD600 ~1.0 and then used to inoculate 400 ml of acetate-buffered CGM (2.5% inoculum). Flasks were allowed to grow for 24 hrs before inoculating BioFlo 310 Benchtop Fermentors (10% inoculum). Fermentors were operated as described in [Jones SW, et al. Genome Biol. 2008;9(7):R114.]. Glucose levels were kept above 200 mM by adding 3.5 M glucose as needed.

extract_protocol: Total RNA was extracted as described in [Jones SW, et al. Genome Biol. 2008;9(7):R114.].

tag: genotype

value: SigG mutant

tag: timepoint

value: 36 hrs

source_name: C. acetobutylicum WT, 36 hrs

value: WT


title: YF050524MOT02

tag: strain


title: Clostridium acetobutylicum ATCC 824 WT vs. SigG mutant (Hour 30)

source_name: C. acetobutylicum SigG mutant, 30 hrs

value: 30 hrs

source_name: C. acetobutylicum WT, 30 hrs


title: patient 127, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C127

source_name: surgically resected material


title: Clostridium acetobutylicum ATCC 824 WT vs. SigG mutant (Hour 34)

source_name: C. acetobutylicum SigG mutant, 34 hrs

value: 34 hrs

source_name: C. acetobutylicum WT, 34 hrs


title: YF050524MOT01


title: Clostridium acetobutylicum ATCC 824 WT vs. SigG mutant (Hour 28)

source_name: C. acetobutylicum SigG mutant, 28 hrs

value: 28 hrs

source_name: C. acetobutylicum WT, 28 hrs


title: patient 118, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C118


title: patient 119, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C119


title: Clostridium acetobutylicum ATCC 824 SigG mutant vs. SigE mutant (Hour 32)

source_name: C. acetobutylicum SigE mutant, 32 hrs

value: SigE mutant

value: 32 hrs

source_name: C. acetobutylicum SigG mutant, 32 hrs


title: patient 117, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C117

value: metastatic recurrence


title: Clostridium acetobutylicum ATCC 824 SigG mutant vs. SigE mutant (Hour 30)

source_name: C. acetobutylicum SigE mutant, 30 hrs


title: Clostridium acetobutylicum ATCC 824 SigG mutant vs. SigE mutant (Hour 26)

source_name: C. acetobutylicum SigE mutant, 26 hrs

value: 26 hrs

source_name: C. acetobutylicum SigG mutant, 26 hrs


title: patient 116, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C116


title: patient 115, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C115


title: patient 113, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C113

value: metastasis


title: Clostridium acetobutylicum ATCC 824 SigG mutant vs. SigE mutant (Hour 24)

source_name: C. acetobutylicum SigE mutant, 24 hrs

value: 24 hrs

source_name: C. acetobutylicum SigG mutant, 24 hrs


title: patient 111, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C111


title: Clostridium acetobutylicum ATCC 824 SigG mutant vs. SigF mutant (Hour 26)

source_name: C. acetobutylicum SigF mutant, 26 hrs

value: SigF mutant


title: patient 110, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C110


title: WCE for Scc2 on circular chromosome

first: Katsuhiko

last: Shirahige

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

institute: The University of Tokyo

hyb_protocol: Hybridization, blocking and washing steps were carried out as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998). Each sample was hybridized to the array in 150ul containing 6XSSPE, 0.005% TritonX-100, 15ug fragmented denatured salmon sperm DNA (Gibco-BRL), and 1nmole of a 3’-biotin control oligonucleotide (oligo B2 probes) that hybridized to the border features on the array. Samples were heated to 100°C for 10 min., and then cooled on ice. Samples were hybridized for 16h at 42°C in a hybridization oven (GeneChip hybri oven 320, Affymetrix, CA). Washing and staining protocol (Mini_euk1 ver2) provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 400, Affymetrix, CA).

scan_protocol: Each array was scanned by HP GeneArray Scanner (Affymetrix, CA) at an emission wavelength of 560nm at 7.5uM resolution. Grids were aligned to the scanned images using the know feature of the array. Primary data analyses were carried out using the Affymetrix Microarray Suite Ver.5.0 software to obtain hybridization intensity, fold change value, change p-value, and detection p-value for each locus.

data_processing: For the discrimination of positive and negative signals for the binding, we compared ChIP fraction with Sup (supernatant) fraction by using three criteria as follows. First, the reliability of strength of signal was judged by detection p-value of each locus (p-value lower than 0.025 was considered as significant). Secondly, reliability of binding ratio was judged by change p-value (p-value lower than 0.025 was considered as significant). Thirdly, clusters consisted of at least three contiguous loci which filled above two criteria were selected as significantly enriched locus, because it is apparent that a single site of protein-DNA interaction will result in immuno-precipitation of DNA fragments that hybridized not only to the locus of the actual binding site but also to its neighbors. This third criterion is very unique, make the data highly reliable and can be only applicable to the chip data obtained by our high-resolution tiling array.

source_name: Scc2 tagged with FLAG

label_protocol: DNA was end-labelled with Biotin-N6ddATP by Terminal Transferase as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998)

extract_protocol: 1.5X10^8 cells were disrupted by MULTI-BEADS SHOCKER (MB400U, YASUI KIKAI, Osaka), which was able to keep cells precisely at lower than 6°C during disruption by glass beads. This enabled us to retrieve more than 60% of tagged proteins to soluble fraction routinely. Chromosomal DNA was shared into the average size of 400-600bp by sonication. Anti-HA monoclonal antibody HA.11 (16B12) (CRP Inc., Denver, PA) and anti-FLAG monoclonal antibody M2 (Sigma-Aldrich Co., St Louis, MO) were used for chromatin immuno-precipitation. Immunoprecipitated chromosomal DNA was subsequently purified following the protocol of Young’s lab (Genome wide location analysis web page, MIT). Purified DNA was random primed and amplified by the protocol of Brown’s lab (Stanford). 2ug of amplified DNA was digested with DNaseI to a mean size of 100bp and used for labeling as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998).

value: WCE for Scc2 on circular chromosome

tag: protein

tag: cell cycle phase


title: Drosophila melanogaster weckle ChIP-chip array rep3

description: High-Resolution ChIP-chip map of weckle binding.

source_name: immunoprecipitated DNA from Drosophila

extract_protocol:
Chromatin was prepared from 2 grams of yw embryos of 1-3 hours in
age. Rat anti-weckle antibody was used. The resulting DNA library
was labeled and hybridized.

value: Chromatin immunoprecipated sample with weckle

value: in-house produced anti-weckle

value: yw

value: embryo

source_name: Genomic DNA from Drosophila melanogaster

value: input DNA


title: Scc2 WT WCE

source_name: WCE fraction for Scc2WT

value: Scc2 WT WCE


title: patient 104, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C104

source_name: surgically resected material

value: cancer, LCM


title: Clostridium acetobutylicum ATCC 824 SigG mutant vs. SigF mutant (Hour 22)

source_name: C. acetobutylicum SigF mutant, 22 hrs

value: 22 hrs

source_name: C. acetobutylicum SigG mutant, 22 hrs

value: SigG mutant


title: patient 108, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C108


title: Clostridium acetobutylicum ATCC 824 SigG mutant vs. SigF mutant (Hour 24)

source_name: C. acetobutylicum SigF mutant, 24 hrs


title: Drosophila melanogaster twist ChIP-chip array rep2

description: High-Resolution ChIP-chip map of twist binding.

value: Chromatin immunoprecipated sample with twist

value: in-house produced anti-twist


title: Clostridium acetobutylicum ATCC 824 SigE mutant vs. SigF mutant (Hour 22)

source_name: C. acetobutylicum SigE mutant, 22 hrs

value: SigE mutant


title: WCE fraction for Smc2 distribution in G2(on circular ChrIII)

source_name: Smc2 tagged with FLAG epitope


title: Drosophila melanogaster snail ChIP-chip array rep3

description: High-Resolution ChIP-chip map of snail binding.

value: Chromatin immunoprecipated sample with snail

value: in-house produced anti-snail


title: WCE fraction for Smc2 distribution in WT


title: patient 102, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C102


title: Drosophila melanogaster dorsal ChIP-chip array rep2

description: High-Resolution ChIP-chip map of dorsal binding.

value: Chromatin immunoprecipated sample with dorsal

value: in-house produced anti-dorsal


title: Scc2 on circular chromosome

value: Scc2 on circular chromosome

value: anti-FLAG monoclonal antibody M2

tag: antibody manufacturer

value: Sigma-Aldrich Co., St Louis, MO


title: Drosophila melanogaster weckle ChIP-chip array rep2

value: Chromatin immunoprecipated sample with weckle

value: in-house produced anti-weckle

value: yw


title: patient 107, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C107


title: Scc2 in Wild type

value: Scc2 in Wild type


title: Clostridium acetobutylicum ATCC 824 SigE mutant vs. SigF mutant (Hour 28)

source_name: C. acetobutylicum SigF mutant, 28 hrs

value: SigF mutant

value: 28 hrs

source_name: C. acetobutylicum SigE mutant, 28 hrs


title: patient 103, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C103

value: cancer, LCM


title: WCE fraction for Smc1 distribution in G2(on circular ChrIII)

source_name: Smc1 tagged with FLAG epitope


title: WCE fraction for Smc6 distribution on circular chrIII

source_name: Smc6 tagged with FLAG epitope


title: patient 101, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C101


title: Clostridium acetobutylicum ATCC 824 SigE mutant vs. SigF mutant (Hour 24)

value: 24 hrs

source_name: C. acetobutylicum SigE mutant, 24 hrs


title: Clostridium acetobutylicum ATCC 824 SigG mutant vs. SigF mutant (Hour 28)

source_name: C. acetobutylicum SigG mutant, 28 hrs

value: SigG mutant


title: patient 100, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C100


title: Drosophila melanogaster snail ChIP-chip array rep2

value: embryo

value: input DNA


title: Drosophila melanogaster dorsal ChIP-chip array rep1


title: Drosophila melanogaster preimmune ChIP-chip array rep3

description: High-Resolution ChIP-chip map of preimmune binding.

source_name: pre-immunoprecipitated DNA from Drosophila

value: Chromatin pre-immunoprecipated sample


title: Clostridium acetobutylicum ATCC 824 SigE mutant vs. Spo0A mutant (Hour 22)

source_name: C. acetobutylicum Spo0A mutant, 22 hrs

value: Spo0A mutant

value: 22 hrs

value: SigE mutant


title: Clostridium acetobutylicum ATCC 824 SigE mutant vs. Spo0A mutant (Hour 14)

source_name: C. acetobutylicum Spo0A mutant, 14 hrs

value: 14 hrs

source_name: C. acetobutylicum SigE mutant, 14 hrs


title: WCE fraction for Nse4 distribution in WT

source_name: Nse4 protein tagged with FLAG


title: Clostridium acetobutylicum ATCC 824 SigE mutant vs. Spo0A mutant (Hour 16)

source_name: C. acetobutylicum Spo0A mutant, 16 hrs

value: 16 hrs

source_name: C. acetobutylicum SigE mutant, 16 hrs


title: WCE fraction for Smc6 in G2 (in mre11 deletion mutant with circular chrIII)


title: patient 006, cancer, LCM [OPG study]

description:
Gene expression profile of surgically resected material
C006

source_name: surgically resected material

value: metastatic recurrence


title: S3.USA300.Cy3_S3.18.Cy5_13944965_MDS.refIsIA

first: Sarah

last: Akkoush

address: 9704 Medical Center Drive

institute: J. Craig Venter Institute

data_processing: Individual TIFF images from each channel were analyzed with TIGR Spotfinder (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html). Microarray data were normalized by LOWESS normalization and with in-slide replicate analysis using TM4 software MIDAS (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html)

organism: Staphylococcus aureus

source_name: Staphylococcus aureus USA300

growth_protocol: Cells were grown in TSA media overnight.  Overnight cultures were diluted to an OD600 of 0.1.  Cells were grown to stationary phase.

extract_protocol: Total RNA was extracted using the Ambion mirVana RNA extraction protocol as described by the manufacturer.

tag: time course

value: stationary phase

source_name: Staphylococcus aureus USA300 Prophage-free mutant lysogenized with both ϕSa2mw and ϕSa3usa


title: Clostridium acetobutylicum ATCC 824 SigF mutant vs. Spo0A mutant (Hour 22)

source_name: C. acetobutylicum SigF mutant, 22 hrs


title: Drosophila melanogaster preimmune ChIP-chip array rep1

description: High-Resolution ChIP-chip map of pre-immune binding.

value: yw

tag: tissue

source_name: Genomic DNA from Drosophila melanogaster


title: Drosophila melanogaster twist ChIP-chip array rep3

source_name: immunoprecipitated DNA from Drosophila

value: Chromatin immunoprecipated sample with twist

value: in-house produced anti-twist


title: Clostridium acetobutylicum ATCC 824 SigF mutant vs. Spo0A mutant (Hour 20)

source_name: C. acetobutylicum Spo0A mutant, 20 hrs

value: 20 hrs

source_name: C. acetobutylicum SigF mutant, 20 hrs

value: SigF mutant


title: Clostridium acetobutylicum ATCC 824 SigE mutant vs. Spo0A mutant (Hour 20)

source_name: C. acetobutylicum SigE mutant, 20 hrs


title: WCE fraction for Smc1 distribution in WT

source_name: Smc1 tagged with FLAG epitope


title: WCE fraction for Smc6 in WT (Control for Smc6 in fragmented ChrIV)

source_name: Smc6 tagged with FLAG epitope


title: S3.USA300.Cy3_S3.16.Cy5_13944962_MDS.refIsIA

source_name: Staphylococcus aureus USA300 Prophage-free mutant lysogenized with ϕSa2mw


title: S2.USA300.Cy3_S2.17.Cy5_13944957_MDS.refIsIA

growth_protocol: Cells were grown in TSA media overnight.  Overnight cultures were diluted to an OD600 of 0.1.  Cells were grown to mid log phase.

value: mid log phase

source_name: Staphylococcus aureus USA300 Prophage-free mutant lysogenized with ϕSa3usa


title: S2.USA300.Cy3_S2.18.Cy5_13944958_MDS.refIsIA

value: USA300 Prophage-free mutant lysogenized with both ϕSa2mw and ϕSa3usa


title: S3.USA300.Cy3_S3.14.Cy5_13944960_MDS.refIsIA

source_name: Staphylococcus aureus USA300 with deletion of ϕSa3usa

value: USA300 with deletion of ϕSa3usa


title: S3.USA300.Cy3_S3.15.Cy5_13944961_MDS.refIsIA

source_name: Staphylococcus aureus USA300 Prophage-free mutant

value: USA300 Prophage-free mutant


title: Placenta_Early_PE_6

city: Uppsala

first: Katja

last: Junus

address: University Hospital

department: Department of Women's and Children's Health

country: Sweden

institute: Uppsala University

description: Sample values are normalized log ratio (reference/test) data that are comparable across rows and Samples

hyb_protocol: Arrays were hybridized using Pronto! Microarray Hybridization kit following manufacturer's instructions

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Gene Pix Pro 4.1 software

data_processing: Data was analayzed using the Bio Array Software Environment (BASE). Spots with intensities below 100 in both of the two channels were excluded. The intensity of the spot also had to be two times as high as the background to be included in further analysis. Using Lowess and global median centering, data was normalized for labelling and reference bias respectively. Fluorescence ratios were calculated as Cy3/Cy5 and log2 transformed.

source_name: Placenta Early-onset PE

label_protocol: 5 µg of total RNA were labelled using Corning ChipShot labelling system following manufacturer's instructions. Before hybridization, 50pmol Cy3 labelled cDNA from each experimental sample was pooled with 50pmol of reference Cy-5 labelled cDNA

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

tag: gestational age (w+d)

source_name: Total RNA from pooled human term healthy placenta

tag: gestational age

value: term


title: WCE fraction for Smc6 distribution on Fragmented Chromosome IV


title: Clostridium acetobutylicum ATCC 824 SigF mutant vs. Spo0A mutant (Hour 16)

source_name: C. acetobutylicum Spo0A mutant, 16 hrs

value: Spo0A mutant

source_name: C. acetobutylicum SigF mutant, 16 hrs


title: Placenta_Early_PE_8


title: Clostridium acetobutylicum ATCC 824 SigF mutant vs. Spo0A mutant (Hour 14)

source_name: C. acetobutylicum Spo0A mutant, 14 hrs

source_name: C. acetobutylicum SigF mutant, 14 hrs


title: Placenta_Early_PE_7


title: S3.USA300.Cy3_S3.17.Cy5_13944964_MDS.refIsIA

source_name: Staphylococcus aureus USA300

value: USA300 Prophage-free mutant lysogenized with ϕSa3usa


title: Clostridium acetobutylicum ATCC 824 SigE mutant vs. SigF mutant (Hour 26)

source_name: C. acetobutylicum SigF mutant, 26 hrs

value: 26 hrs

source_name: C. acetobutylicum SigE mutant, 26 hrs

value: SigE mutant


title: Placenta_Early_PE_5


title: S2.USA300.Cy3_S2.15.Cy5_13944955_MDS.refIsIA


title: Placenta_Early_PE_3


title: Placenta_Early_PE_4


title: S2.USA300.Cy3_S2.14.Cy5_13944954_MDS.refIsIA


title: Placenta_Early_PE_1


title: Smc2 distribution in WT (with Cirular Chr III)

source_name: Smc2 tagged with FLAG epitope

value: anti-FLAG monoclonal antibody M2

value: Sigma-Aldrich Co., St Louis, MO


title: Placenta_Early_PE_2


title: S2.USA300.Cy3_S2.13.Cy5_13944953_MDS.refIsIA

source_name: Staphylococcus aureus USA300 with deletion of ϕSa2usa

value: USA300 with deletion of ϕSa2usa


title: Placenta_Late_PE_7

source_name: Placenta Late-onset PE


title: S3.USA300.Cy5_S3.17.Cy3_13944940_MDS.refIsIB

data_processing: Individual TIFF images from each channel were analyzed with TIGR Spotfinder (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html). Microarray data were normalized by LOWESS normalization and with in-slide replicate analysis using TM4 software MIDAS (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html).

value: stationary phase


title: S3.USA300.Cy5_S3.16.Cy3_13944939_MDS.refIsIB

value: USA300 Prophage-free mutant lysogenized with ϕSa2mw


title: S2.USA300.Cy3_S2.16.Cy5_13944956_MDS.refIsIA


title: Smc1 distribution in G2(on circular ChrIII)

source_name: Smc1 tagged with FLAG epitope


title: Placenta_Late_PE_5


title: Placenta_Late_PE_6


title: Smc1 distribution in G2

value: Smc1 distribution in G2


title: Placenta_Late_PE_4


title: S3.USA300.Cy5_S3.18.Cy3_13944941_MDS.refIsIB

source_name: Staphylococcus aureus USA300 Prophage-free mutant lysogenized with both ϕSa2mw and ϕSa3usa


title: S3.USA300.Cy5_S3.14.Cy3_13944937_MDS.refIsIB


title: S3.USA300.Cy5_S3.15.Cy3_13944938_MDS.refIsIB


title: S3.USA300.Cy3_S3.TB_13.Cy5_13944959_MDS.refIsIA


title: S3.USA300.Cy5_S3.13.Cy3_13944936_MDS.refIsIB


title: WCE fraction for Smc6 in top2-4

source_name: Smc6 tagged with FLAG epitope

value: WCE fraction for Smc6 in top2-4


title: Smc6 distribution on Fragmented Chromosome IV


title: WCE fraction for Smc6 with Cdc6

value: WCE fraction for Smc6 with Cdc6

tag: carbon source

value: Gal


title: WCE fraction for Smc6 without Cdc6

tag: sample type

value: WCE fraction for Smc6 without Cdc6

value: without Gal


title: WCE fraction for Smc6 in G2(-CPT)

value: WCE fraction for Smc6 in G2(-CPT)


title: S2.USA300.Cy5_S2.18.Cy3_13944935_MDS.refIsIB

value: USA300 Prophage-free mutant lysogenized with both ϕSa2mw and ϕSa3usa

value: mid log phase


title: S2.USA300.Cy5_S2.17.Cy3_13944932_MDS.refIsIB

source_name: Staphylococcus aureus USA300 Prophage-free mutant lysogenized with ϕSa3usa


title: Smc6 in G2 (in mre11 deletion mutant with circular chrIII)


title: Smc6 in WT (Control for Smc6 in fragmented ChrIV)


title: Placenta_Late_PE_3

value: term


title: WCE fraction for Smc6 in G2(+CPT)

value: WCE fraction for Smc6 in G2(+CPT)


title: Placenta_Late_PE_1


title: Placenta_Late_PE_2


title: Nse4 distribution in WT

source_name: Nse4 protein tagged with FLAG

value: Nse4 distribution in WT


title: Smc2 distribution in WT

value: Smc2 distribution in WT

value: anti-FLAG monoclonal antibody M2


title: S1.USA300.Cy3_S1.18.Cy5_13944996_MDS.refIsIA

growth_protocol: Cells were grown in TSA media overnight.  Overnight cultures were diluted to an OD600 of 0.1.  Cells were grown to early log phase.

value: early log phase


title: S2.USA300.Cy5_S2.16.Cy3_13944931_MDS.refIsIB

source_name: Staphylococcus aureus USA300 Prophage-free mutant lysogenized with ϕSa2mw


title: S1.USA300.Cy3_S1.17.Cy5_13944994_MDS.refIsIA

value: USA300 Prophage-free mutant lysogenized with ϕSa3usa


title: S1.USA300.Cy3_S1.16.Cy5_13944993_MDS.refIsIA

value: USA300 Prophage-free mutant lysogenized with ϕSa2mw


title: Smc6 distribution on circular chrIII

value: Smc6 distribution on circular chrIII

value: Sigma-Aldrich Co., St Louis, MO


title: S2.USA300.Cy5_S2.15.Cy3_13944930_MDS.refIsIB

source_name: Staphylococcus aureus USA300 Prophage-free mutant

value: USA300 Prophage-free mutant


title: S1.USA300.Cy3_S1.15.Cy5_13945039_MDS.refIsIA


title: S2.USA300.Cy5_S2.13.Cy3_13944928_MDS.refIsIB

value: USA300 with deletion of ϕSa2usa


title: S2.USA300.Cy5_S2.14.Cy3_13944929_MDS.refIsIB

source_name: Staphylococcus aureus USA300 with deletion of ϕSa3usa

value: USA300 with deletion of ϕSa3usa


title: Smc6 in G2 (without CPT)

value: Smc6 in G2 (without CPT)


title: S1.USA300.Cy3_S1.14.Cy5_13945038_MDS.refIsIA


title: Smc6 tagged with FLAG epitope

source_name: Smc6 w/o Cdc6

value: Smc6 tagged with FLAG epitope

value: Galactose


title: blood-aCGH-patient 30

first: Blake

last: Ballif

institute: Signature Genomic Laboratories

source_name: Peripheral blood

extract_protocol: Genomic DNA was extracted from lymphoblastoid cell lines, peripheral blood, or cultured tissues of the subjects and phenotypically normal male and female references using an M48 or the Puregene DNA isolation kit according to the manufacturer's instructions.

tag: gender

value: Male

tag: test

value: patient 30

tag: reference

value: control


title: blood-aCGH-patient 38

value: patient 38


title: blood-aCGH-patient 41

value: patient 41


title: blood-aCGH-patient 40

value: patient 40


title: S1.USA300.Cy5_S1.18.Cy3_13945003_MDS.refIsIB

value: USA300 Prophage-free mutant lysogenized with both ϕSa2mw and ϕSa3usa

value: early log phase


title: blood-aCGH-patient 39

value: Female

value: patient 39


title: Smc6 in the presence of Cdc6

value: Smc6 in the presence of Cdc6

tag: antibody

value: anti-FLAG monoclonal antibody M2

value: Sigma-Aldrich Co., St Louis, MO


title: blood-aCGH-patient 48

value: patient 48


title: blood-aCGH-patient 43

value: patient 43


title: blood-aCGH-patient 47

value: patient 47


title: blood-aCGH-patient 31

value: patient 31


title: S1.USA300.Cy5_S1.16.Cy3_13945001_MDS.refIsIB

value: USA300 Prophage-free mutant lysogenized with ϕSa2mw


title: S1.USA300.Cy5_S1.17.Cy3_13945002_MDS.refIsIB

value: USA300 Prophage-free mutant lysogenized with ϕSa3usa


title: blood-aCGH-patient 29

value: Male

value: patient 29

value: control


title: Smc6 in top2-4

value: Smc6 in top2-4


title: blood-aCGH-patient 42

value: patient 42


title: blood-aCGH-patient 18

value: patient 18


title: blood-aCGH-patient 17

value: patient 17


title: WCE fraction for Smc6 in G2

source_name: WCE fraction for Smc6 ChIP in G2

value: WCE fraction for Smc6 in G2


title: blood-aCGH-patient 8

value: Female

value: patient 8


title: Smc6 in G2

value: Smc6 in G2

value: anti-FLAG monoclonal antibody M2

value: Sigma-Aldrich Co., St Louis, MO


title: S1.USA300.Cy5_S1.15.Cy3_13945000_MDS.refIsIB

value: USA300 Prophage-free mutant

value: early log phase

source_name: Staphylococcus aureus USA300


title: S1.USA300.Cy3_S1.13.Cy5_13945037_MDS.refIsIA

value: USA300 with deletion of ϕSa2usa


title: Smc6 Distribution under the presence of CPT