title: 40

description: Gene expression data from MPM tumors.


title: Yeast_nhp6_mutant_replicate3

status: Public on May 19 2011

type: RNA

city: Oxford

first: Jiannis

last: Ragoussis

address: Roosevelt Drive

country: United Kingdom

institute: Wellcome Trust Centre For Human Genetics, University of Oxford

hyb_protocol: Affymetrix Hybridization station, Yeast 2.0 arrays, hybridization conditions according to manufacturer's recommendations

scan_protocol: Arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G

data_processing: Raw data (.CEL files) were processed and summarised using the RMA algorithm (R statistical software using the 'affy' package). Statistical analysis was performed in GeneSpring GX 11.0.1 to find significant differences between nhp6 and wildtype groups (adjusted p<0.05 and fold change>1.5)

label: Biotin

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Yeast nhp6 mutant

label_protocol: 3'IVT labelling kit from Affymetrix, according to manufacturer's recommendations

growth_protocol: YPD medium, 30oC

extract_protocol: Total RNA was extracted from yeast cells using the RNeasy tissue kit (Qiagen). RNA quality was assessed using the 2100 Bioanalyzer (Agilent) and all samples had an RNA Integrity Number greater than 8.

tag: genotype/variation

value: nhp6 mutant


title: 37

city: New York

first: Yupu

last: Liang

state: NY

address: 1230 York Avenue

country: USA

institute: The Rockefeller University

description: Gene expression data from MPM tumors.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the GeneChip Human U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data is normalized through the RMA method with default parameters using Bioconductor.

label: biotin

organism: Homo sapiens

source_name: Mesothelioma tumor, epi

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

extract_protocol: RNA was extracted using the Qiagen RNeasy plus mini kit according to the manufacturer's instructions.

tag: tissue

value: malignant pleural mesothelioma (MPM)

tag: subtype

value: epi


title: 43

description: Gene expression data from MPM tumors.


title: 52

description: Gene expression data from MPM tumors.


title: 3bis

description: Gene expression data from MPM tumors.

source_name: Mesothelioma tumor, biphasic

value: biphasic


title: 33

description: Gene expression data from MPM tumors.


title: 50

description: Gene expression data from MPM tumors.


title: 41

description: Gene expression data from MPM tumors.


title: 75bis

description: Gene expression data from MPM tumors.


title: Yeast_wildtype_replicate1

source_name: Yeast wildtype

value: wildtype


title: Yeast_wildtype_replicate2


title: Yeast_wildtype_replicate3


title: Yeast_nhp6_mutant_replicate2


title: 42

description: Gene expression data from MPM tumors.


title: 32

description: Gene expression data from MPM tumors.


title: MN1 leukemic_rep1

city: Gothenburg

first: Lars

last: Palmqvist

address: Sahlgrenska University Hospital

department: Institute of Biomedicine

country: Sweden

institute: University of Gothenburg

description: All arrays were performed at British Columbia Genome Sciences Centre, Vancouver, BC, Canada.

hyb_protocol: Hybridization was done on the Affymetrix GeneChip Mouse430 2.0 microarray according to manufacturer’s instructions. Protocol EukGE-WS2v5 Wash A1 Recovery Mixes 0 Wash A1 Temperature (C) 30 Number of Wash A1 Cycles 10 Mixes per Wash A1 Cycle 2 Wash B Recovery Mixes 0 Wash B Temperature (C) 50 Number of Wash B Cycles 6 Mixes per Wash B Cycle 15 Stain Temperature (C) 35 First Stain Time (seconds) 300 Wash A2 Recovery Mixes 0 Wash A2 Temperature (C) 30 Number of Wash A2 Cycles 10 Mixes per Wash A2 Cycle 4 Second Stain Time (seconds) 300 Third Stain Time (seconds) 300 Wash A3 Recovery Mixes 0 Wash A3 Temperature (C) 35 Number of Wash A3 Cycles 15 Mixes per Wash A3 Cycle 4 Holding Temperature (C) 25

scan_protocol: Pixel Size 1.56 Filter 570 Scan Temperature Scanner ID 50206370 Number of Scans 1 Scanner Type M10

data_processing: Data were processed using MAS5 with default setting with GCOS 1.3.0.

organism: Mus musculus

source_name: Bone marrow

label_protocol: The labeling was done according to the manufacturer instructions.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen), and RNA quality was assessed using the Bioanalyzer 2100 (Agilent Technologies, Mississauga, ON).

treatment_protocol: Bone marrow cells were harvested from mice treated with 150 mg of 5-fluorouracil/kg 4 days before harvest  and stimulated for 48 hours in Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/mL of human interleukin-6 (hIL-6), 6 ng/mL of murine interleukin-3 (mIL-3), and 20 ng/mL of murine stem cell factor (mSCF; all from StemCell Technologies Inc., Vancouver, Canada). MN1 was introduced into bone marrow cells by cocultivation with irradiated (4,000 cGy) GP+ E86 viral producer cells in the presence of 5 µg/mL protamine sulfate (Sigma-Aldrich, Oakville, Canada). Cells were then sorted for GFP expression and maintained in 6 ng/ml mIL-3, 10 ng/ml hIL-6, and 20 ng/ml mSCF. The transduced bone marrow cells from C57BL/6J mice were then injected into the tail vein of lethally irradiated syngeneic recipient mice that were exposed to a single dose of 750 cGy total-body irradiation accompanied by a life-sparing dose of 1 x 105 freshly isolated bone marrow cells from syngeneic mice. Donor chimerism was monitored by tail vein bleeds and FACS analysis of GFP expressing cells every four weeks. We have showed at the single cell level that CMPs, but not GMPs, are susceptible to MN1-induced transformation. To identify transcriptional differences between CMPs and GMPs that may explain this difference in susceptibilities to MN1 transformation we produced gene expression profiles of bone marrow cells from MN1 leukemic mice and mature myeloid bone marrow cells (Gr1+/CD11b+) from healthy mice and compared those to already published gene expression profiles of CMPs and GMPs (Krivtsov, A.V., et al. (2006). Transformation from committed progenitor to leukaemia stem cell initiated by MLL-AF9. Nature 442, 818-822).

tag: cell type

value: MN1 leukemic

value: Bone marrow

tag: strain

tag: location

value: bred and maintained in the animal research center of the British Columbia Cancer Agency, Vancouver, BC, Canada


title: Yeast_nhp6_mutant_replicate1


title: 30

description: Gene expression data from MPM tumors.


title: 36

description: Gene expression data from MPM tumors.


title: 27

description: Gene expression data from MPM tumors.


title: 28

description: Gene expression data from MPM tumors.


title: 20

description: Gene expression data from MPM tumors.


title: O24B

type: genomic

description: Hybridized to 250K_Nsp

hyb_protocol: Labeled cDNA were hybridized, according to the Afymetrix protocol, for 16-18 hr, at 60 rpm, at 50C on a GeneChip Genome-Wide Human SNP Array 500K. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with GTYPE using Affymetrix default analysis settings and the BRLMM algorithm.

molecule: genomic DNA

source_name: Mesothelioma cell line

label_protocol: 500ng of DNA starting material was digested, ligated with adaptors, PCR amplified, cleaned-up, fragmented, and labeled according to the Affymetrix protocol.

growth_protocol: All cells were grown in RPMI with 10% FCS, penicillin/streptomycin at 37 degrees C and 5% CO2.

extract_protocol: Genomic DNA was extracted using the Qiagen Dneasy Blood & Tissue Kit according to the manufacturerss instructions.

treatment_protocol: No treatment.

tag: cell line

value: mesothelioma cells


title: Pt_winter_1

city: Yongin

first: Jae-Heung

last: Ko

state: Gyeonggi

address: 1 Seocheon-dong, Giheung-gu

department: Plant & Environmental Resources

country: South Korea

institute: Kyung Hee University

description: Gene expression data from stem tissue of Poplar harvested in winter (December 2005)

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Populus trichocarpa

source_name: Poplar stem harvested in winter

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Poplar (Populus trichocarpa) were grown on field (nursery bed).

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

treatment_protocol: no treatment; harvested in summer and winter.

value: Poplar stem (20 cm sections of 10 cm above ground) harvested in winter (December)

tag: age

value: one-year-old field grown poplar


title: Pt_winter_2


title: MSTO211H

description: Hybridized to 250K_Nsp


title: OLD1612

description: Hybridized to 250K_Nsp


title: VGE

description: Hybridized to 250K_Nsp

value: VGE


title: 18

description: Gene expression data from MPM tumors.


title: PTEN KO Prostate Castrate Rep3

first: Yu

last: Chen

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: The  amplified, biotin-labeled antisense RNA (aRNA) was purified and quality  was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano  kit. 750 ng of aRNA in 5 ul was mixed with 10 ul of hybridization  reagents and heated at 65C for 10min. After cooled to room temperature,  total 15 ul of the hyb solution was applied to Illumina MouseRef-8 v2  chip. The chip was incubated for about 18 hours at 58C.

scan_protocol: After washing  and staining with streptavidin-Cy3, the chip was scanned using Illumina  BeadArray Reader. The scanning was done using standard DirectHyb Gene  Expression protocol with the following settings: Factor=1, PMT=587,  Filter=100%.

data_processing: The raw data was extracted using Illumina BeadStudio  software without normalization. Raw data was imported into Partek genomic suite.

source_name: Mouse Prostate

label_protocol: ~500 ng of^ total RNA was used to prepare biotin-labeled RNA using Ambion Illumina TotalPrep RNA Amplification Kit (Cat# AMIL1791,  Applied Biosystems, Foster City, CA).  Briefly, 500 ng of total RNA was used to synthesize the first strand of  cDNA using ArrayScript reverse transcriptase and an oligo(dT) primer  bearing a T7 promoter. The single-stranded cDNA was then converted into  a double-stranded DNA (dsDNA) by DNA polymerase^ I in the presence of  /E. coli/ RNase H and DNA ligase. After column purification, the dsDNA  was served as a template for in vitro transcription in a reaction  containing biotin-labeled UTP, unlabeled NTPs and T7 RNA Polymerase.

extract_protocol: RNA is extracted using Rneasy per protocol. RNA quality was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano kit (Agilent Technologies Inc., Palo Alto, CA).

treatment_protocol: Mice were either castrated or left intact and RNA was isolated 3 days after castration.

tag: organ

value: Prostate

tag: genotype

value: PbCre x PTEN f/f

tag: androgen

value: Castrate


title: SU511

description: Hybridized to 250K_Nsp


title: VAMT

description: Hybridized to 250K_Nsp

value: VAMT


title: 17

description: Gene expression data from MPM tumors.


title: Pt_summer_2

description: Gene expression data from stem tissue of Poplar harvested in summer (August 2005)

source_name: Poplar stem harvested in summer

value: Poplar stem (20 cm sections of 10 cm above ground) harvested in summer (August)


title: PTEN KO Prostate Castrate Rep1


title: PTEN KO Prostate Castrate Rep2


title: MESO56

description: Hybridized to 250K_Nsp


title: Sty51

description: Hybridized to 250K_Nsp


title: Pt_summer_1


title: 11

description: Gene expression data from MPM tumors.


title: ONE58

description: Hybridized to 250K_Nsp


title: PTEN KO Prostate Intact Rep4

value: Intact


title: PTEN KO Prostate Intact Rep3


title: 111

description: Gene expression data from MPM tumors.

value: malignant pleural mesothelioma (MPM)


title: PTEN KO Prostate Intact Rep2


title: MESO10

description: Hybridized to 250K_Nsp


title: MESO37

description: Hybridized to 250K_Nsp


title: 109

description: Gene expression data from MPM tumors.

value: epi


title: Meso09

description: Hybridized to 250K_Nsp


title: 108

description: Gene expression data from MPM tumors.


title: 107

description: Gene expression data from MPM tumors.


title: JU77

description: Hybridized to 250K_Nsp


title: WT Prostate Castrate Rep3

value: WT


title: LO68

description: Hybridized to 250K_Nsp


title: PTEN KO Prostate Intact Rep1


title: JMN

description: Hybridized to 250K_Nsp

value: JMN


title: 105

description: Gene expression data from MPM tumors.

source_name: Mesothelioma tumor, sarc

value: sarc


title: WT Prostate Castrate Rep1


title: 104bis

description: Gene expression data from MPM tumors.

value: biphasic


title: 102

description: Gene expression data from MPM tumors.


title: WT Prostate Intact Rep4


title: HO275

description: Hybridized to 250K_Nsp


title: 100

description: Gene expression data from MPM tumors.


title: MH

description: Hybridized to 250K_Nsp

value: MH


title: 101

description: Gene expression data from MPM tumors.


title: WT Prostate Intact Rep1


title: HMESO

description: Hybridized to 250K_Nsp

value: HMESO

value: mesothelioma cells


title: 112

description: Gene expression data from MPM tumors.


title: WT Prostate Castrate Rep2


title: WT Prostate Intact Rep2


title: H2052

description: Hybridized to 250K_Nsp


title: H28

description: Hybridized to 250K_Nsp


title: HMESO1A

description: Hybridized to 250K_Nsp


title: H2452

description: Hybridized to 250K_Nsp


title: GAY2911

description: Hybridized to 250K_Nsp


title: WT Prostate Intact Rep3


title: H2373

description: Hybridized to 250K_Nsp


title: Whole embryo 43

status: Public on May 18 2011

city: Morristown

first: Nathan

last: Treff

address: 111 Madison Ave

institute: RMA of New Jersey

description:
EM43
Hybridized to 250K_Nsp

hyb_protocol: DNA was digested with the NspI restriction enzyme, ligated to an adapter molecule, PCR amplified, fragmented with DNase I, labeled and hybridized to each array according to the manufacturer's instructions (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930).

scan_protocol: Each array was washed using Affymetrix fluidics station 640, and scanned using the Gene Chip Scanner 7G as recommended (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930).

data_processing: CEL files were processed using GTYPE version 4 (Affymetrix Inc., Genotyping Console 4.0 Manual) using the DM algorithm for genotype calls.  Copy number was calculated from CHP files using CNAT version 4.1 (Affymetrix Inc., Genotyping Console 4.0 Manual) analysis against a reference set of 30 normal females (published in GEO submission GSE24690) at a 5Mb Gaussian smoothing for aneuploid screening and 1Mb Gaussian smoothing for microdeletion detection. Both sets of CN and LOH files have been included.

source_name: whole embryo

label_protocol: Fragmented DNA was biotinylated using the manufacturers recommendations (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930)

extract_protocol: Biopsied trophectoderm and whole embryo samples underwent alkaline lysis for genomic DNA extraction as described previously (Cui et al., 1989; PNAS 86, 9389-93).  Whole genome amplification was performed as previously described (Treff et al., 2010, Fertil. Steril., In Press).

tag: blastocyst snp microarray result

tag: blastocyst fish result

value: not applicable


title: Paternal, gDNA

description:
Paternal
Hybridized to 250K_Nsp

source_name: gDNA, blood


title: Whole embryo 42

description:
EM42
Hybridized to 250K_Nsp


title: Newborn, gDNA

description:
Newborn
Hybridized to 250K_Nsp

source_name: gDNA, buccal swab


title: Whole embryo 40

description:
EM40
Hybridized to 250K_Nsp


title: Whole embryo 47

description:
EM47
Hybridized to 250K_Nsp


title: Whole embryo 36

description:
EM36
Hybridized to 250K_Nsp


title: Whole embryo 39

description:
EM39
Hybridized to 250K_Nsp


title: Maternal, gDNA

description:
Maternal
Hybridized to 250K_Nsp


title: Whole embryo 48

description:
EM48
Hybridized to 250K_Nsp


title: Whole embryo 37

description:
EM37
Hybridized to 250K_Nsp

value: 46,XX (euploid unaffected)


title: Whole embryo 44

description:
EM44
Hybridized to 250K_Nsp

value: 46, XX (euploid unaffected)


title: Whole embryo 32

description:
EM32
Hybridized to 250K_Nsp


title: Whole embryo 34

description:
EM34
Hybridized to 250K_Nsp


title: Whole embryo 38

description:
EM38
Hybridized to 250K_Nsp


title: Whole embryo 26

description:
EM26
Hybridized to 250K_Nsp


title: Whole embryo 28

description:
EM28
Hybridized to 250K_Nsp


title: Whole embryo 35

description:
EM35
Hybridized to 250K_Nsp


title: Whole embryo 31

description:
EM31
Hybridized to 250K_Nsp


title: Whole embryo 41

description:
EM41
Hybridized to 250K_Nsp


title: Whole embryo 30

description:
EM30
Hybridized to 250K_Nsp


title: Whole embryo 29

description:
EM29
Hybridized to 250K_Nsp


title: Whole embryo 27

description:
EM27
Hybridized to 250K_Nsp


title: Whole embryo 25

description:
EM25
Hybridized to 250K_Nsp


title: Whole embryo 45

description:
EM45
Hybridized to 250K_Nsp

value: nonconcurrent


title: Whole embryo 33

description:
EM33
Hybridized to 250K_Nsp


title: Whole embryo 46

description:
EM46
Hybridized to 250K_Nsp

value: 46,XY (euploid unaffected)


title: Whole embryo 23

description:
EM23
Hybridized to 250K_Nsp


title: Whole embryo 24

description:
EM24
Hybridized to 250K_Nsp


title: Whole embryo 22

description:
EM22
Hybridized to 250K_Nsp


title: htz1Δswc5Δ replicate2

city: SEVILLE

first: ELOISA

last: ANDUJAR

state: SEVILLE

address: AVDA. AMERICO VESPUCIO S/N

department: GENOMICS

country: Spain

institute: CABIMER-CSIC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Yeast Genome 2.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G and the images were acquired by Affymetrix default GeneChip® Operating System 1.4.0.036 (GCOS), and converted in .DAT files.

data_processing: The .DAT image files for each array were converted into .CEL files using Affymetrix GCOS software. These .CEL files were further processed into expression values using Robust Multiarray Average (RMA) method by Irrizarry et al. The following statistical data analysis were performed using the limma package (affylmGUI interface) of R/Bioconductor project.

source_name: htz1-swc5 mutant

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA One-Cycle Target Labeling Assays (GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004).

growth_protocol: The yeast cells were grown on SMM at 30ºC to mid-log phase for further totalRNA isolation

extract_protocol: Rneasy® midi kit (Qiagen) of total RNA was performed according to the manufacturer's instructions.


title: htz1Δswc5Δ replicate1


title: htz1Δswc5Δ replicate3


title: swc5Δ replicate2

source_name: swc5 mutant


title: swc5Δ replicate1


title: htz1Δswc2Δ replicate3

source_name: htz1-swc2 mutant


title: swc5Δ replicate3


title: htz1Δswc2Δ replicate2


title: htz1Δswc2Δ replicate1


title: Whole embryo 21

description:
EM21
Hybridized to 250K_Nsp


title: htz1Δswr1Δ replicate3

source_name: htz1-swr1 mutant


title: 2,4-D-induced callus replicate 3

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

description: Biological replicate (different callus) 3 of 3.

hyb_protocol: Fragmented 1.65 micro g labeled cRNAs with hybridization buffer (Agilent GE hybridization buffer HI-PRM) were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).

data_processing:
Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction.
Ln value of background-subtracted signal intensity (gProcessedSignal) divided by median value of filter-passed spots.

organism: Arabidopsis thaliana

source_name: 2,4-D induced callus cultured with MS medium containing 500 micro g/L 2,4-D

label_protocol: 1 µg of total RNA were used for reverse transcription at 40°C for 2 h, and labeled cRNA were prepared using T7 RNA polymerase with Cy3-labeled CTP at 40°C for 2 h following manufacture's instructions (Agilent Quick Amp Labeling kit).

growth_protocol: Grown or cultured on solid MS medium with or without 500 nM NAA or 500 micro g/L 2,4-D.

extract_protocol: Total RNA was extracted using Trizol.

treatment_protocol: Mediums for T87 callus and 2,4-D-induced callus contain 500 nM NAA or 500 micro g/L 2,4-D to keep them callus state.

value: wt

tag: treatment group

value: 500 micro g/L 2,4-D

tag: morphology

value: callus


title: swc2Δ replicate1

source_name: swc2 mutant


title: htz1Δswr1Δ replicate1


title: swc2Δ replicate2


title: htz1Δswr1Δ replicate2


title: 2,4-D-induced callus replicate 2

description: Biological replicate (different callus) 2 of 3.


title: 2,4-D-induced callus replicate 1

description: Biological replicate (different callus) 1 of 3.


title: Whole embryo 18

description:
EM18
Hybridized to 250K_Nsp


title: swr1Δ replicate3

source_name: swr1 mutant


title: T87 callus replicate 3

source_name: Callus of T87 cell cultured with MS medium containing 500 nM NAA

value: 500 nM NAA


title: Whole embryo 20

description:
EM20
Hybridized to 250K_Nsp


title: T87 callus replicate 2


title: swr1Δ replicate2


title: Embryo 15, trophectoderm

description:
EM15
Hybridized to 250K_Nsp

source_name: trophectoderm, biopsied blastocyst


title: swr1Δ replicate1


title: htz1Δ replicate2

source_name: htz1 mutant


title: Whole embryo 19

description:
EM19
Hybridized to 250K_Nsp


title: htz1Δ replicate3


title: T87 callus replicate 1


title: wt replicate3

source_name: wild type


title: swc2Δ replicate3


title: Embryo 5, trophectoderm

description:
EM5
Hybridized to 250K_Nsp

value: Alagille


title: 35S:WIND1 callus replicate 1

source_name: Callus-like Arabidospsis thaliana expressing 35S:WIND1 with no treatment


title: 35S:WIND1 callus replicate 2


title: 14d control seedling replicate 3

description: Biological replicate (different plant) 3 of 3.

source_name: 14d Arabidopsis thaliana Col-0 control seedling with no treatment

value: intact plant

value: seedling


title: Embryo 3, trophectoderm

description:
EM3
Hybridized to 250K_Nsp

value: Unbalanced Female


title: Embryo 1, trophectoderm

description:
EM1
Hybridized to 250K_Nsp

value: Normal Female


title: Embryo 7, trophectoderm

description:
EM7
Hybridized to 250K_Nsp


title: Embryo 10, trophectoderm

description:
EM10
Hybridized to 250K_Nsp


title: Embryo 11, trophectoderm

description:
EM11
Hybridized to 250K_Nsp


title: Embryo 8, trophectoderm

description:
EM8
Hybridized to 250K_Nsp

value: 46,XY (indeterminate -q6)


title: Embryo 16, trophectoderm

description:
EM16
Hybridized to 250K_Nsp


title: Embryo 4, trophectoderm

description:
EM4
Hybridized to 250K_Nsp

value: Indeterminate Female


title: wt replicate2


title: wt replicate1


title: 14d control seedling replicate 2

description: Biological replicate (different plant) 2 of 3.


title: Embryo 17, trophectoderm

description:
EM17
Hybridized to 250K_Nsp


title: Embryo 13, trophectoderm

description:
EM13
Hybridized to 250K_Nsp


title: Embryo 6, trophectoderm

description:
EM6
Hybridized to 250K_Nsp

value: Unbalanced


title: htz1Δ replicate1


title: Embryo 14, trophectoderm

description:
EM14
Hybridized to 250K_Nsp

value: not applicable


title: 14d control seedling replicate 1

description: Biological replicate (different plant) 1 of 3.


title: rtTA-Dmrt5_d9_+Dox_rep_2

city: London

first: Xinsheng

state: England

address: Hammersmith Hospital

institute: MRC Clinical Science Centre

hyb_protocol: 7 ug of biotin-labeled cell extract was hybridized to Affymetrix Mouse Genome 430_2 GeneChips (representing approximately 39,000 transcripts) for a period of 20 hours. The relative level of hybridization to the GeneChip was assessed using the Affymetrix hybridization controls.

scan_protocol: The hybridized arrays were washed, stained and scanned in accordance with the appropriate Nugen and Affymetrix guide lines.

data_processing: Microarray data in CEL format were analysed using GeneSpring GX11 program. Robust Multi-Array Analysis (RMA) Summarization Algorithm was used for normalisation. Baseline was transformed to Median of all samples. Both 'Raw signal values' and 'Normalized signal values' were exported as text files.

source_name: rtTA-Dmrt5 day 9 +Dox

label_protocol: 5ng of total RNA in conjunction with the Nugen Ovation V2 amplification system (www.nugeninc.com) was used for preparation of the biotin-labeled cell extract. The efficacy of conversion of total RNA to labeled cDNA was monitored by the inclusion of Affymetrix polyA controls (www.affymetrix.com).

extract_protocol: Total RNA was prepared using the Stratagene MicroRNA kit as per manufacturer’s instructions with the exception that DNase treatment was extended to 30 minutes and RNAs were resuspended in RNase-free water.

tag: differentiation

value: 9 days

tag: treatment

value: +Dox


title: rtTA-Dmrt5_d9_-Dox_rep_2

source_name: rtTA-Dmrt5 day 9 -Dox

value: -Dox


title: Embryo 9, trophectoderm

description:
EM9
Hybridized to 250K_Nsp


title: Embryo 2, trophectoderm

description:
EM2
Hybridized to 250K_Nsp

value: Alagille Male


title: MCF-7_Si-Wu-Tang_0.256mg/ml_rep3

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

description: Gene expression profiling data from human breast cancer cell line MCF-7

hyb_protocol: For each sample, 10 µg of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to a Human Genome U133 Plus 2.0 microarray for 16 hours at 45ºC.

scan_protocol: GeneChips were scanned with an Affymetrix GeneChip® Scanner 3000.

data_processing: The probeset-level expression data were summarized from probe-level data with Robust Multiarray Averaging method (RMA) by taking all 24 microarrays together.

source_name: Human breast cancer cell line MCF-7

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

growth_protocol: The MCF-7 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1% non-essential amino acids, 100 unit/mL penicillin, 100 μg/mL streptomycin, 1 mM sodium pyruvate, and 2 mM L-glutamine in an atmosphere of 5% CO2 at 37 °C.

extract_protocol: RNA was extracted using QIAGEN RNeasy Mini Kit, following the manufacturer’s protocol.

treatment_protocol: The MCF-7 cells were incubated with hormone free medium and treated by 0.001% DMSO (control group), 0.1 µM 17 β-estradiol, 0.1, 1 or 10 µM of ferulic acid (equivalent to 0.0194, 0.194, and 1.94 mg/ml), 0.0256, 0.256, and 2.56 mg/ml SWT for 6 hours.

value: breast cancer cell line MCF-7

value: Si-Wu-Tang treated


title: MCF-7_Si-Wu-Tang_0.0256mg/ml_rep3


title: MCF-7_Si-Wu-Tang_0.256mg/ml_rep1


title: rtTA-Dmrt5_d9_+Dox_rep_1


title: 35S:WIND1 callus replicate 3

tag: genotype/variation

value: callus


title: rtTA-Dmrt5_d9_-Dox_rep_1


title: rtTA-Dmrt5_d7_+Dox_rep_1

source_name: rtTA-Dmrt5 day 7 +Dox

value: 7 days


title: rtTA-Dmrt5_d7_+Dox_rep_2


title: rtTA-Dmrt5_d7_-Dox_rep_2

source_name: rtTA-Dmrt5 day 7 -Dox


title: GFP-JTV-Alt Transfection - repeat 1 - mAdbID:75971

city: Bethesda

first: David

last: Levens

state: MD

address: 10 Center Drive

department: NCI/CCR

institute: NIH

description: mAdb experiment ID: 75971

hyb_protocol: NCI Oligo Microarray Hybridization Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42°C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 ul COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100°C for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42°C just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42°C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), and spin for 3 minutes at 650 rpm to dry. (Refer to "NCI Microarray Manual")

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000A [55478] ScanPower: 100;; 100 LaserPower: 1.89;; 2.41 Temperature: 35.57

data_processing:
mAdb Data Processing Protocol (v. 1)
Calculation Method: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

source_name: GFP-tranfected HeLa

label_protocol:
Cy3 Sample Labeling Protocol - generic
Other: Labeled using amino allyl conjugation method.

extract_protocol:
Sample Extraction Protocol
Extraction method: Trizol
Other: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA) following manufacturer's protocol. Isopropanol precipitated RNA was further clarified by another ethanol precipitation.

value: HeLa tranfected with pEGFP-C1

source_name: GFP-JTV-Alt-tranfected HeLa

label_protocol:
Cy5 Sample Labeling Protocol - generic
Other: Labeled using amino allyl conjugation method.

value: HeLa tranfected with pEGFP-JTV-Alt


title: GFP-JTV-Alt Transfection - repeat 2 - mAdbID:77133

description: mAdb experiment ID: 77133

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000A [55478] ScanPower: 100;; 100 LaserPower: 1.91;; 2.56 Temperature: 40.49


title: GFP-JTV Transfection - repeat 2 - mAdbID:77132

description: mAdb experiment ID: 77132

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000A [55478] ScanPower: 100;; 100 LaserPower: 1.9;; 2.2 Temperature: 40.17

source_name: GFP-JTV-tranfected HeLa

value: HeLa tranfected with pEGFP-JTV


title: MCF-7_Si-Wu-Tang_0.0256mg/ml_rep2


title: PARP1_siRNA1

city: Ann Arbor

first: Christopher

last: Maher

state: MI

address: 1500 E. Medical Center Drive

institute: Michigan Center for Translational Pathology

hyb_protocol: Standard Agilent protocol

scan_protocol: Scanned on Agilent Technologies Scanner G2505B Images were quantified using Agilent Feature Extraction Software

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

source_name: Control siRNA

label_protocol: Standard Agilent protocol

extract_protocol: Standard Agilent protocol

value: VCaP

value: Control non-targetting siRNA

value: PARP1 siRNA


title: PARP1_siRNA2


title: GFP-JTV Transfection - repeat 1 - mAdbID:75970

description: mAdb experiment ID: 75970

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000A [55478] ScanPower: 100;; 100 LaserPower: 1.92;; 2.72 Temperature: 34.84


title: rtTA-Dmrt5_d7_-Dox_rep_1


title: MCF-7_Si-Wu-Tang_2.56mg/ml_rep3


title: MCF-7_Si-Wu-Tang_0.0256mg/ml_rep1


title: MCF-7_Si-Wu-Tang_2.56mg/ml_rep2


title: DNA-PKcs_siRNA2_1

value: DNAPKcs siRNA


title: DNA-PKcs_siRNA1_2


title: DNA-PKcs_siRNA2_2


title: DNA-PKcs_siRNA1_1


title: rtTA_d7_+Dox_rep_2

source_name: rtTA day 7 +Dox

value: rtTA


title: T cells_NiCl2-treatment_2

city: Sendai

first: Rumiko

last: SAITO

address: 1-1 Seiryo-machi, Aoba-ku

department: Department of Dermatology

institute: Tohoku University Graduate School of Medicine

hyb_protocol: Cy3-labeled cRNA (Cy3 incorporation >9.0 pmol/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containig 10 X Blocking Agent, Nuclease-free water, and 25 X Fragmentation Buffer following the manufature's instructions. On completion of the fragmentation reaction, 55 ul of 2 X GE Hybridization Buffer (HI-RPM) was added to the fragmentation mixture and hybridized to 44K Agilent Whole Human Genome Oligo Microarays (G4112F) containing 45015 features representing 41000 biological probes for 17 hours at 65ºC in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minutes at room temparature with GE Wash Buffer 1 and 1 minute with 37°C GE Wash Buffer 2 (Agilent Technologies).

scan_protocol: After washing according to manufacture's instructions, slides were scanned immediately on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4 X 44K array slides (Scan Area 61 X 21.6 mm, Scan resolution 5 um, Dye channel is set to Green, and eXtended Dynamic Range Scan Mode (Hi; 100%, Low;10%)).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent Technologies) using default parameters (protocol GE1-v1_95 and Grid: 014850_D_F_20060807). The data from all microarrays were analyzed using GeneSpringGX 7.3.1 (Agilent Technologies). After data transformation (to convert any negative value to 0.01), Intensity value of green Processedsignal from the Feature Extraction was normalized per chip to the 75th percentile. 39371 probes were used for analysis after quality control.

source_name: T cells from whole blood, 6hr, NiCl2-treatment, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick-Amp Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA, USA).  Dye incorporation and cRNA yield were checked with the Nanodrop spectrophotometer.

extract_protocol: Total RNA was extracted from T cells using RNeasy Mini Kits accoriding to the manufacture's instructions (Qiagen, Valecia, CA, USA). The concentration of the obtained total RNA was measured using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA). RNA quality was determined using the RNA 6000 Nano Kit (Agilent Technologies, Palo Alto, CA, USA) and an Agilent 2100 bioanalyzer (Agilent Technologies), and RNA was stored in RNase-free water at -80ºC. RNA with an RNA Integrity Number (RIN) of nine or more was used for experiments.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were obtained from healthy donors. PBMCs were isolated from the venous whole blood by density gradient centrifugation using Lymphoprep (Axis-Shield Pos As, Oslo, Norway). After centrifugation and several washes with Dulbecco's PBS, 1×107 PBMCs were purified using Pan T cell isolation kit II (Miltenyi Biothech, Bergisch Gladbach, Germany) by negative selection according to manufacturer's instructions. Obtained 2×106 /ml  T cells were cultured in RPMI-164(Sigma-Aldrich, St.Louis, MO, USA) including 25 mM HEPES, suplemented with 2 mM L-glutamine, 1 mM sodium pyruvate (all from Sigma-Aldrich), Antibiotic-Antimycotic (Invitrogen corp., Carlsbad, CA, USA) and 10% HyCloneTM fetal calf serum (Thermo Fisher Scientiic, Wilmington, USA) at 37ºC, 5% CO2.

tag: tissue

value: whole blood

tag: agent

value: 1000 μM nickel chloride


title: T cells_NiCl2-treatment_3

source_name: T cells from whole blood, 6hr, NiCl2-treatment, replicate 3


title: T cells_Control_2

source_name: T cells from whole blood, 6hr, Control, replicate 2


title: T cells_Control_1

source_name: T cells from whole blood, 6hr, Control, replicate 1


title: MCF-7_Ferulic acid_1μM_rep2

value: Ferulic acid treated


title: rtTA_d7_+Dox_rep_1

value: +Dox


title: T cells_NiCl2-treatment_1

source_name: T cells from whole blood, 6hr, NiCl2-treatment, replicate 1


title: midbrain ventral lateral_3

source_name: E10.5 embryo midbrain ventral lateral region

tag: gender

value: mix

value: embryonic 10.5 days

tag: region

value: ventral lateral region


title: MCF-7_Si-Wu-Tang_2.56mg/ml_rep1

value: breast cancer cell line MCF-7

value: Si-Wu-Tang treated


title: MCF-7_Ferulic acid_1μM_rep1


title: T cells_Control_3

source_name: T cells from whole blood, 6hr, Control, replicate 3


title: MCF-7_Ferulic acid_1μM_rep3


title: MCF-7_Ferulic acid_0.1μM_rep3


title: rtTA_d7_-Dox_rep_2

source_name: rtTA day 7 -Dox

value: 7 days

value: -Dox


title: rtTA_d7_-Dox_rep_1


title: midbrain ventral lateral_2

tag: strain


title: MCF-7_Ferulic acid_0.1μM_rep2

tag: cell line


title: Embryo 12, trophectoderm

description:
EM12
Hybridized to 250K_Nsp

source_name: trophectoderm, biopsied blastocyst

value: not applicable


title: stage 4 transplanted on June 27_20080813_07_st4_n1

first: Takeshi

last: Izawa

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences

hyb_protocol: 825ng of labeled cRNA were used for hybridization according to manufacturer's protocol. Open-lab in rgrc in NIAS was used.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.9.5.3.1). LOWESS normalization.

organism: Oryza sativa

source_name: rice, leaf, Norin 8

label_protocol: 400 ng of total RNA were primed with 0.6 µl of 100 µM T7 promoter primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of 0.5ul of MMLV-RT, and 500 µM dNTP, then labelled by T7 RNA polymerase using  NTP and 400 µM Cy3 CTP at 40 40°C for 2h. Labelled cRNA were purifed by columns in the Quiagen RNeasy mini kit.

growth_protocol: Rice plants were grown in a paddy field in Tsukuba, Japan on 2008 using a typical cultivation method. Transplanting dates were June 6, June 13, June 20, June 27 to obtain RNA from plants at different developmental stages on the sampling date.

extract_protocol: Total RNA extracted using QIAGEN RNeasy Plant Mini Kit following manufacturer's instructions

treatment_protocol: Rice leaves were sampled at the paddy field. Cut leaves were frozen using liquid N imeditately after sampling. 2h interval. From 7:00am on Aug.12th to 7:00 a.m. on Aug.13th.

value: Norin 8

tag: developmental stage

value: stage 4 transplanted on June 27

tag: sampling time

source_name: rice, leaf, osgi

label_protocol: 400 ng of total RNA were primed with 0.6 µl of 100 µM T7 promoter primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of 0.5ul of MMLV-RT, and 500 µM dNTP, then labelled by T7 RNA polymerase using  NTP and 400 µM Cy5 CTP at 40 40°C for 2h. Labelled cRNA were purifed by columns in the Quiagen RNeasy mini kit.

value: osgi


title: stage 4 transplanted on June 27_20080813_07_st4_n2

tag: genotype


title: stage 3 transplanted on June 20_20080813_07_st3_n2

value: stage 3 transplanted on June 20


title: stage 3 transplanted on June 20_20080813_07_st3_n1


title: stage 2 transplanted on June 13_20080813_07_st2_n1

value: stage 2 transplanted on June 13


title: stage 2 transplanted on June 13_20080813_07_st2_n2


title: stage 1 transplanted on June6 _20080813_07_st1_n2

value: stage 1 transplanted on June6


title: MCF-7_Ferulic acid_0.1μM_rep1

source_name: Human breast cancer cell line MCF-7


title: midbrain floor plate_3

source_name: E10.5 embryo midbrain floor plate

tag: age

value: floor plate


title: midbrain floor plate_2

hyb_protocol: 7 ug of biotin-labeled cell extract was hybridized to Affymetrix Mouse Genome 430_2 GeneChips (representing approximately 39,000 transcripts) for a period of 20 hours. The relative level of hybridization to the GeneChip was assessed using the Affymetrix hybridization controls. The hybridized arrays were washed, stained and scanned in accordance with the appropriate Nugen and Affymetrix guide lines.

extract_protocol: Total RNA from the aforementioned replicate groups was prepared using the Stratagene MicroRNA kit as per manufacturer’s instructions with the exception that DNase treatment was extended to 30 minutes and RNAs were resuspended in RNase-free water.


title: MCF-7_Ferulic acid_10μM_rep3

value: Ferulic acid treated


title: midbrain ventral lateral_1


title: stage 4 transplanted on June 27_20080813_05_st4_n2


title: MCF-7_Estradiol_0.1μM_rep3

value: Estradiol treated


title: stage 3 transplanted on June 20_20080813_05_st3_n1


title: MCF-7_Ferulic acid_10μM_rep1


title: MCF-7_Ferulic acid_10μM_rep2


title: stage 2 transplanted on June 13_20080813_05_st2_n1


title: P12-Otx2-CKO-ex2

city: Suita

first: Takahisa

last: Furukawa

state: Osaka

address: 6-2-4 Furuedai

department: Developmental Biology

institute: Osaka Bioscience Institute

description: Gene expression data from the control retina at P12

hyb_protocol: cRNA was hybridized to GeneChip mouse genome 430 2.0 arrayin Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: Signal intensity was determined using GeneChip Operating Software 1.4.

source_name: P12 retinas of Otx2 CKO mice

label_protocol: Biotin-labeled cRNA was prepared using IVT labeling kit.

growth_protocol: Mice were housed in a temperature-controlled room with a 12 h light/dark cycle.  Fresh water and rodent diet were available at all times.

extract_protocol:
The mouse retinas were dissected using forceps.
Total RNA (5 ug) of the retina was isolated using TRIzol reagent (Invitrogen) and converted to cDNA using One-Cycle cDNA synthesis kit (Affymetrix) according to the manufacture’s instruction.

value: retina

value: otx2 flox/flox; Crx-Cre+

tag: time


title: stage 3 transplanted on June 20_20080813_05_st3_n2


title: MCF-7_Si-Wu-Tang_0.256mg/ml_rep2


title: stage 1 transplanted on June6 _20080813_07_st1_n1


title: P12-Otx2-CKO-ex3


title: stage 2 transplanted on June 13_20080813_05_st2_n2


title: stage 1 transplanted on June6 _20080813_05_st1_n2


title: midbrain floor plate_1

value: mix

value: embryonic 10.5 days


title: stage 4 transplanted on June 27_20080813_05_st4_n1


title: stage 4 transplanted on June 27_20080813_03_st4_n2


title: stage 1 transplanted on June6 _20080813_05_st1_n1


title: stage 4 transplanted on June 27_20080813_03_st4_n1


title: stage 3 transplanted on June 20_20080813_03_st3_n2


title: MCF-7_0.001%DMSO_rep3

value: breast cancer cell line MCF-7

value: DMSO treated


title: MCF-7_Estradiol_0.1μM_rep1


title: stage 2 transplanted on June 13_20080813_03_st2_n1


title: stage 2 transplanted on June 13_20080813_03_st2_n2


title: stage 3 transplanted on June 20_20080813_03_st3_n1


title: HS04-2999   (Pancreatic cancer_Adenocarcinoma)

first: Adam

middle: Enver

last: Frampton

institute: Imperial College

hyb_protocol: according to manufacturers instruction (febit biomed)

scan_protocol: Wizard software on standard Microsoft Windows Workstation PC

data_processing: summarizing of technical replica by median and VSN normalization. Following BG correction, negative values were corrected to 1

source_name: Pancreatic cancer_Adenocarcinoma

label_protocol: MPEA, microfluidic primer extension assay Biotin labeling

extract_protocol: Total RNA was isolated from the FFPE slides (1-2μM thick, 1-2 cm2 ) according to the instructions of the QiaGen RNeasy FFPEKit.  (Qiagen GmbH, Hilden).

treatment_protocol: stored at -20 degree

value: male


title: HS06-828   (Pancreatic cancer_Adenocarcinoma)

value: female


title: P12-Otx2-CKO-ex1


title: P12-control-ex3

description: Gene expression data from the Otx2 CKO retina at P12

source_name: P12 retinas of control mice

value: otx2 flox/flox; Crx-Cre- (control)


title: MCF-7_Estradiol_0.1μM_rep2


title: stage 1 transplanted on June6 _20080813_03_st1_n1

value: Norin 8


title: MCF-7_0.001%DMSO_rep2


title: stage 1 transplanted on June6 _20080813_03_st1_n2

value: osgi


title: 41HS06-5146 (Pancreatic cancer_Adenocarcinoma)


title: MCF-7_0.001%DMSO_rep1


title: P1-Otx2-CKO-ex3

description: Gene expression data from the control retina at P1

source_name: P1 retinas of Otx2 CKO mice


title: P12-control-ex2


title: stage 4 transplanted on June 27_20080813_01_st4_n1

value: stage 4 transplanted on June 27


title: stage 3 transplanted on June 20_20080813_01_st3_n2

value: stage 3 transplanted on June 20


title: HS06-9721  (Pancreatic cancer_Adenocarcinoma)


title: P12-control-ex1


title: stage 3 transplanted on June 20_20080813_01_st3_n1


title: HS06-9894  (Pancreatic cancer_Adenocarcinoma)


title: HS09-166 (Pancreatic cancer_Adenocarcinoma)


title: HS08-12448 (Pancreatic cancer_Adenocarcinoma)


title: stage 2 transplanted on June 13_20080813_01_st2_n1

value: stage 2 transplanted on June 13


title: stage 1 transplanted on June6 _20080813_01_st1_n2

value: stage 1 transplanted on June6


title: stage 2 transplanted on June 13_20080813_01_st2_n2


title: P1-control-ex3

description: Gene expression data from the Otx2 CKO retina at P1

source_name: P1 retinas of control mice


title: HS08-12190 (Pancreatic cancer_Adenocarcinoma)


title: stage 3 transplanted on June 20_20080812_23_st3_n2


title: P1-control-ex2


title: HS07-3070 (Pancreatic cancer_Adenocarcinoma)


title: stage 4 transplanted on June 27_20080813_01_st4_n2


title: P1-control-ex1


title: stage 4 transplanted on June 27_20080812_23_st4_n1


title: stage 3 transplanted on June 20_20080812_23_st3_n1


title: stage 4 transplanted on June 27_20080812_23_st4_n2


title: P1-Otx2-CKO-ex1


title: stage 1 transplanted on June6 _20080812_23_st1_n1


title: stage 2 transplanted on June 13_20080812_23_st2_n2


title: HS07-3024 (Pancreatic cancer_Adenocarcinoma)


title: HS07-1771 (Pancreatic cancer_Adenocarcinoma)


title: stage 3 transplanted on June 20_20080812_21_st3_n2


title: stage 4 transplanted on June 27_20080812_21_st4_n2


title: HS07-545 (Pancreatic cancer_Adenocarcinoma)


title: stage 1 transplanted on June6 _20080812_23_st1_n2


title: HS08-12130 (Pancreatic cancer_Adenocarcinoma)


title: HS09-1184 (Pancreatic cancer_Adenocarcinoma)


title: stage 2 transplanted on June 13_20080812_21_st2_n1


title: HS05-1028 (Carcinoma EX IPMN)

source_name: Carcinoma EX IPMN


title: stage 3 transplanted on June 20_20080812_21_st3_n1


title: stage 2 transplanted on June 13_20080812_21_st2_n2


title: HS06-6436 (Carcinoma EX IPMN)


title: stage 2 transplanted on June 13_20080812_23_st2_n1


title: HS09-935 (Carcinoma EX IPMN)


title: stage 4 transplanted on June 27_20080812_21_st4_n1


title: stage 1 transplanted on June6 _20080813_01_st1_n1


title: HS07-7887 (Carcinoma EX IPMN)


title: HS07-7038 (Carcinoma EX IPMN)


title: HS04-2594 (Carcinoma EX IPMN)


title: stage 1 transplanted on June6 _20080812_21_st1_n2


title: stage 2 transplanted on June 13_20080812_19_st2_n1


title: stage 3 transplanted on June 20_20080812_19_st3_n2


title: HS06-3072 (Carcinoma EX IPMN)


title: HS07-2682 (Carcinoma EX IPMN)


title: stage 1 transplanted on June6 _20080812_21_st1_n1


title: stage 2 transplanted on June 13_20080812_19_st2_n2


title: stage 4 transplanted on June 27_20080812_19_st4_n1


title: stage 2 transplanted on June 13_20080812_17_st2_n2


title: stage 1 transplanted on June6 _20080812_19_st1_n2


title: stage 4 transplanted on June 27_20080812_17_st4_n2


title: stage 1 transplanted on June6 _20080812_17_st1_n2


title: stage 4 transplanted on June 27_20080812_17_st4_n1


title: stage 3 transplanted on June 20_20080812_17_st3_n2


title: HS05-4503 (Carcinoma EX IPMN)


title: stage 4 transplanted on June 27_20080812_19_st4_n2

description:
20080812_19_st4_n2
We used only Cy3 channel data (gProcessedSignal) in '20080812_19_st4_n2' sample for our data analysis despite two-color experiment. The reason is that Cy5 data has a high variance with the other data.


title: stage 4 transplanted on June 27_20080812_15_st4_n1


title: stage 3 transplanted on June 20_20080812_15_st3_n2


title: stage 4 transplanted on June 27_20080812_15_st4_n2


title: stage 3 transplanted on June 20_20080812_19_st3_n1


title: HS09-1244 (Benign Pancreatic Cystic Tumor_IPMN)

source_name: Benign Pancreatic Cystic Tumor_IPMN


title: stage 1 transplanted on June6 _20080812_19_st1_n1


title: stage 2 transplanted on June 13_20080812_17_st2_n1


title: HS08-8660 (Benign Pancreatic Cystic Tumor_IPMN)


title: stage 3 transplanted on June 20_20080812_17_st3_n1


title: stage 3 transplanted on June 20_20080812_15_st3_n1


title: stage 1 transplanted on June6 _20080812_17_st1_n1


title: stage 1 transplanted on June6 _20080812_15_st1_n1


title: stage 2 transplanted on June 13_20080812_13_st2_n2


title: stage 2 transplanted on June 13_20080812_15_st2_n2


title: stage 3 transplanted on June 20_20080812_13_st3_n2


title: stage 4 transplanted on June 27_20080812_13_st4_n1


title: stage 1 transplanted on June6 _20080812_15_st1_n2


title: HS08-3742 (Benign Pancreatic Cystic Tumor_IPMN)


title: stage 3 transplanted on June 20_20080812_13_st3_n1


title: HS08-3842 (Benign Pancreatic Cystic Tumor_IPMN)


title: HS07-411 (Benign Pancreatic Cystic Tumor_IPMN)


title: HS06-965 (Benign  Pancreatic Cystic Tumor_Mucinous)

source_name: Benign  Pancreatic Cystic Tumor_Mucinous


title: stage 4 transplanted on June 27_20080812_11_st4_n2


title: stage 4 transplanted on June 27_20080812_13_st4_n2


title: 0104583V (Benign  Pancreatic Cystic Tumor_Mucinous)


title: stage 1 transplanted on June6 _20080812_13_st1_n2


title: stage 3 transplanted on June 20_20080812_11_st3_n2


title: stage 2 transplanted on June 13_20080812_11_st2_n1


title: HS07-5431 (Benign  Pancreatic Cystic Tumor_Mucinous)


title: stage 4 transplanted on June 27_20080812_11_st4_n1


title: stage 2 transplanted on June 13_20080812_11_st2_n2


title: stage 1 transplanted on June6 _20080812_11_st1_n2


title: stage 3 transplanted on June 20_20080812_11_st3_n1


title: P1-Otx2-CKO-ex2


title: stage 2 transplanted on June 13_20080812_15_st2_n1


title: stage 4 transplanted on June 27_20080812_09_st4_n1


title: 0302782 (Benign  Pancreatic Cystic Tumor_Mucinous)


title: stage 4 transplanted on June 27_20080812_09_st4_n2


title: stage 3 transplanted on June 20_20080812_09_st3_n2


title: stage 1 transplanted on June6 _20080812_11_st1_n1


title: HS06-8724 (Benign  Pancreatic Cystic Tumor_Mucinous)


title: stage 2 transplanted on June 13_20080812_09_st2_n2


title: stage 2 transplanted on June 13_20080812_09_st2_n1


title: HS06-7174 (Benign  Pancreatic Cystic Tumour_Microcystic)


title: stage 4 transplanted on June 27_20080812_07_st4_n2


title: HS06-5090  (Benign Pancreatic Cystic Tumour_Microcystic)


title: HS06-7019  (Benign Pancreatic Cystic Tumour_Microcystic)


title: HS07-4138  (Benign Pancreatic Cystic Tumour_Microcystic)


title: 0109444 (Benign  Pancreatic Cystic Tumour_Microcystic)


title: 9903668  (Benign  Pancreatic Cystic Tumour_Microcystic)


title: HS05-4483  (Benign Pancreatic Cystic Tumour_Microcystic)


title: stage 3 transplanted on June 20_20080812_09_st3_n1


title: stage 1 transplanted on June6 _20080812_09_st1_n2


title: stage 3 transplanted on June 20_20080812_07_st3_n1


title: stage 1 transplanted on June6 _20080812_07_st1_n2


title: stage 2 transplanted on June 13_20080812_07_st2_n1


title: stage 3 transplanted on June 20_20080812_07_st3_n2


title: stage 2 transplanted on June 13_20080812_07_st2_n2


title: wild_type-ypd_vs_wild_type-ypd_reverse

status: Public on May 17 2011

city: Seattle

first: Jennifer

middle: Joy

last: Smith

state: WA

address: 1441 North 34th Street

institute: Institute for Systems Biology

description: biological replicate 2 of 2 (this experiment was used to emperically determine threshold for lambda (likelihood for differential expression) to result in a false positive rate of 0.001)

hyb_protocol: Equal amounts of differently labeled cDNA samples were mixed and hybridized to S.cerevisiae oligonucleotide arrays (Agilent design number 15984).  Hybridization was performed as described in Agilent's Two-Color Microarray-Based Gene Expression Analysis protocol version 5.5.

scan_protocol: Scanning was performed with an Agilent High-Resolution DNA Microarray Scanner, following Agilent's Two-Color Microarray-Based Gene Expression Analysis protocol version 5.5.

data_processing: Image analysis was performed with Agilent Feature Extraction. Data was normalized and differential expression statistics generated using the VERA/SAM pipeline (see http://db.systemsbiology.net/software/ArrayProcess/index.html).  Significantly differentially expressed genes were those with a lambda value above 20.74, which was determined empirically to correspond to a false positive rate of 0.001.

source_name: wild-type cells grown in YPD to a density of 1 x 10E7 cells/mL.

label_protocol: cDNA was synthesized and labeled using a Superscript indirect cDNA labeling system (Invitrogen).

growth_protocol: Transcription factor deletion strains were compared to an isogenic wild type strain by microarray analysis under conditions used for ChIP-CHIP analysis of the factors (Harbison et al., 2004).  All mutant and wild-type strains were grown in YPD to a density of 1 x 10E7 cells/mL, treated with stimulus, and compared.  For analysis of rox1, xbp1 and phd1 deletion strains, cells were exposed to 4 mM hydrogen peroxide for 30 min, 0.4 mM hydrogen peroxide for 20 min, or 1% butanol for 90 min, respectively.

extract_protocol: Total RNA was isolated by hot acid phenol extraction and then purified on Qiagen RNeasy columns according to the manufacturer’s instructions


title: stage 1 transplanted on June6 _20080812_09_st1_n1


title: DROX1-high_h2o2_vs_wild_type-high_h2o2_forward

description: biological replicate 1 of 2

source_name: deltaROX1 grown in YPD to a density of 1 x 10E7 cells/mL, then hydrogen peroxide was added to 4 mM and the culture was grown for an additional 30 min.

value: ROX1::G418 deletion from BY4742 deletion library (Invitrogen, Carlsbad, CA)

source_name: wild-type cells grown in YPD to a density of 1 x 10E7 cells/mL


title: stage 4 transplanted on June 27_20080812_07_st4_n1


title: DROX1-high_h2o2_vs_wild_type-high_h2o2_reverse

description: biological replicate 2 of 2


title: wild_type-ypd_vs_wild_type-ypd_forward

description: biological replicate 1 of 2 (this experiment was used to emperically determine threshold for lambda (likelihood for differential expression) to result in a false positive rate of 0.001)


title: wild_type-butanol_vs_wild_type-ypd_reverse

description: biological replicate 1 of 2

source_name: wild-type cells grown in YPD to a density of 1 x 10E7 cells/mL, then butanol was added to 1% final concentration and culture was grown for an additional 90 min.


title: wild_type-butanol_vs_wild_type-ypd_forward

description: biological replicate 2 of 2


title: stage 1 transplanted on June6 _20080812_07_st1_n1


title: DPHD1-butanol_vs_wild_type-butanol_reverse

description: biological replicate 2 of 2

source_name: deltaPHD1 grown in YPD to a density of 1 x 10E7 cells/mL, then butanol was added to 1% final concentration and culture was grown for an additional 90 min.

value: PHD1::G418 deletion from BY4742 deletion library (Invitrogen, Carlsbad, CA)


title: DXBP1-low_h2o2_vs_wild_type-low_h2o2_reverse

description: biological replicate 2 of 2

source_name: wild-type cells grown in YPD to a density of 1 x 10E7 cells/mL, then hydrogen peroxide was added to 0.4 mM and culture was grown for an additional 20 min.

source_name: deltaXBP1 grown in YPD to a density of 1 x 10E7 cells/mL, then hydrogen peroxide was added to 0.4 mM and culture was grown for an additional 20 min.

value: XBP1::G418 deletion from BY4742 deletion library (Invitrogen, Carlsbad, CA)


title: 1731

city: Göteborg

first: Kristina

last: Levan

address: Blå Stråket 2

department: Department of Oncology

hyb_protocol: The probes were purified using ChipShot™ labelling cleanup system (Promega). The hybridizations were carried out using Pronto! Micro Array reagent systems (Corning Inc.). For each sample, labelled tumour cDNA and reference cDNA were co-precipitated and hybridised to the oligoarray slide. After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Genepix 6.0.0.45 (Axon Instruments).

data_processing: Data processing Intensities were calculated by median spot - median background. Flagged spots and spots for which background adjusted intensities were <0 or >65 000 were excluded as well as spots with intensities below 20 in both channels. Intensities below 20 in one channel were set to 20 to compensate for extreme quotients. pin-based Lowess normalization were performed with 12 blocks in each group

source_name: fresh frozen tumour from endometrial cancer patients

label_protocol: Probes labelled with Cy3 were synthesized from 5 µg of the total tumour RNA and reference labelled with Cy5 were synthesized from 5 µg of commercial reference RNA by reverse transcription.

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

tag: status

value: Dead

tag: surgical stage

value: IIIa

tag: differentation grade

value: poor

tag: age at diagnosis

value: fresh frozen tumour

source_name: Universal Human Reference RNA purchased from Stratagene

value: reference


title: DPHD1-butanol_vs_wild_type-butanol_forward

description: biological replicate 1 of 2


title: DXBP1-low_h2o2_vs_wild_type-low_h2o2_forward

description: biological replicate 1 of 2


title: 1624


title: 1599

value: Ib


title: 1242

value: IIa

value: moderate


title: 1246


title: 1235

value: Alive


title: 1593

value: IIb


title: 1157

value: IVb

value: well


title: 1218


title: 1349

value: Ia


title: 1190


title: 1277


title: 1055


title: 1029


title: 992


title: 1035


title: 971


title: 979

value: IIIc


title: 955


title: HS06-965 (Benign Pancreatic Cystic Tumor_IPMN)

value: female


title: 1155


title: HS08-6898 (Benign Pancreatic Cystic Tumor_IPMN)

value: male


title: 664


title: 818


title: 619


title: 943


title: 945

value: Well


title: 1299

value: Dead

value: Ic


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 203

city: San Francisco

first: Brian

middle: M

last: Green

state: CA

address: 600 16th Street, S376 Genentech Hall

department: Department of Biochemistry

institute: University of California, San Francisco

description: Supp Table 6

hyb_protocol: Hybridization was performed in 3X SSC, 25mM HEPES pH7.0, 0.25% SDS at 63oC for 16 to 24 hours

scan_protocol: Arrays were scanned with an Axon 3000B scanner using GenePix4.0.

data_processing:
Data were filtered in GenePix to flag as bad features that had (1) obvious defects, (2) saturated pixels, (3) regression r^2 values less than 0.5 or (4) fewer than 55% of their pixels with flourescence intensity greater than 2 standard deviations above background. BLAST analysis was used to generate a filter that would flag as bad elements whose PCR product were excessively repetitive. Raw Cy5/Cy3 median of ratios values were normalized such that the average ratio was equal to 1.
Value is the log2 of the normalized ratio of Cy5 to Cy3 – note that to convert to usable replication profiles, raise two to the indicated value.

source_name: negative control MC2A strain in G2/M

label_protocol: amino-allyl-dUTP incorporation with Klenow. Chemical coupling of dye to aa-dUTP labelled DNA.

extract_protocol: see BM Green et al. 2006

tag: sector induction

tag: sample type

value: negative control MC2A strain in G2/M

source_name: red sector arising after re-replication at ChrIV567 in rad52 background


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 202

description: Supp Table 6

source_name: negative control M strain in G2/M

value: negative control M strain in G2/M

value: red sector arising after re-replication at ChrIV567 in rad52 background


title: stage 2 transplanted on June 13_20080812_13_st2_n1

source_name: rice, leaf, Norin 8

value: Norin 8

value: stage 2 transplanted on June 13

source_name: rice, leaf, osgi

value: osgi


title: B Cell 4 (U133)

city: Durham

first: Luftig

last: Laboratory

state: NC

address: 220 CARL Bldg Duke U Med Center

department: MGM

institute: Duke University

description: See Affy Hyb, wash, stain kit #900720

hyb_protocol: Hybridization targets were prepared  from totalRNA and hybridized to GeneChip HuEx 1.0 ST and U133 2.0 Plus arrays according to standard Affymetrix (Santa Clara,CA) protocols

scan_protocol: GeneChip Scanner 3000 7G with GeneChip Fluidics Station 450

data_processing:
Raw .CEL data was normailized and consolidated into a probeset level expression file via Affymetrix Power Tools RMA (rma sketch) normalization of the 8 .CEL files.  Power tools settings were as follows for the HuEX analysis: rma-sketch, dabg, HuEx-1_0-st-v2.r2.pgf, HuEx-1_0-st-v2.r2.clf, HuEx-1_0-st-v2.r2.clf, background probes file HuEx-1_0-st-v2.r2.antigenomic.bgp, filter - HuEx_PSID_filer.txt (only exons overlapping known transcripts): FOR U133 ANALYIS: rma-sketch, dabg, HG-U133_Plus_2.cdf, U133_UCSC_PSID_filter.txt (only probesets that overlap known UCSC transcripts)
HuEx-1_0-st-v2.r2.pgf, HuEx-1_0-st-v2.r2.clf for Exon Array and HG-U133_Plus_2.cdf for U133

source_name: Purified B Cells from PBMCs

label_protocol: cDNA preparation, labeling, fragmentation performed with Gene Chip cDNA synthesis/amplification kit (Affymetrix # 900673) and Exon Array Labeling kit (Affymetrix #900671) for HuEx samples and by 1-cycle IVT GeneChip labeling (Affymetrix#900449) and Affy Hyb, Wash, Stain kit (#900720) for labeling of cRNA for U133

growth_protocol: Infected cells (PBMCs) were maintained in RPMI 1640 + 15% FCS + cyclosporin A + Pen/Strep

extract_protocol: CD19+ B cells were purified from PBMC using the BD iMag Negative Isolation Kit (BD #558007).  Total RNA from CD19+ B cells or monocloncal LCLs was isolated via miRvana organic extraction (Ambion Inc) according to manufacturer's protocol

treatment_protocol: Infected cells were incubated with EBV for 1h at 37 C.  CFSE treatment was performed as described (Quah et al, Nature Protocols 2007).

tag: infection

value: uninfected

tag: cell type

value: Purified B Cells, from negative selection of PBMCs

tag: day post infection of extraction


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 200

description: Supp Table 6

value: re-replication at ChrIV567 in rad52 background


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 201

description: Supp Table 6


title: stage 1 transplanted on June6 _20080812_13_st1_n1

value: stage 1 transplanted on June6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 197

description: Supp Table 6


title: B Cell 3 (U133)

description: See Affy Hyb, wash, stain kit #900720


title: LCL 2 (U133)

description: See Affy Hyb, wash, stain kit #900720

source_name: Monoclonal LCL derived by limited EBV dilution on PBMCs

value: Epstein-Barr virus infected, immortalized

value: Lymphoblastoid Cell Line, EBV-infected, monoclonal


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 198

description: Supp Table 6


title: LCL 1 (U133)

description: See Affy Hyb, wash, stain kit #900720


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 199

description: Supp Table 6


title: B Cell 1 (U133)

description: See Affy Hyb, wash, stain kit #900720


title: LCL 4 (U133)

description: See Affy Hyb, wash, stain kit #900720


title: LCL 3 (U133)

description: See Affy Hyb, wash, stain kit #900720


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 193

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 194

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 191

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 192

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 188

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 195

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 196

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 187

description: Supp Table 6


title: B Cell 2 (U133)

description: See Affy Hyb, wash, stain kit #900720


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 186

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 190

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 189

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 185

description: Supp Table 6


title: HS06-9964 (Benign  Pancreatic Cystic Tumor_Mucinous)

source_name: Benign  Pancreatic Cystic Tumor_Mucinous

tag: gender

value: female


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 183

description: Supp Table 6

tag: strain


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 180

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 179

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 178

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 184

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 182

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 175

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 173

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 164

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 172

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 171

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 181

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 169

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 176

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 167

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 166

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 168

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 165

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 177

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 163

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 174

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 170

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 160

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 159

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 162

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 161

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_dnl4_background sample 155

description: Supp Table 6

source_name: red sector arising after re-replication at ChrIV567 in dnl4 background


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 156

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 157

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_rad52_background sample 158

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_dnl4_background sample 146

description: Supp Table 6

value: red sector arising after re-replication at ChrIV567 in dnl4 background


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_dnl4_background sample 150

description: Supp Table 6

value: re-replication at ChrIV567 in dnl4 background


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_dnl4_background sample 154

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_dnl4_background sample 151

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_dnl4_background sample 139

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_dnl4_background sample 153

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_dnl4_background sample 140

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_dnl4_background sample 143

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_dnl4_background sample 147

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_dnl4_background sample 148

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_dnl4_background sample 145

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_dnl4_background sample 144

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_dnl4_background sample 133

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_dnl4_background sample 149

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_dnl4_background sample 135

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_dnl4_background sample 138

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_dnl4_background sample 136

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_dnl4_background sample 132

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_dnl4_background sample 134

description: Supp Table 6


title: genomic_changes_due_to_phleomycin_treatment sample 129

description: Supp Table 5

source_name: red sector arising after phleomycin treatment

value: phleomycin treatment


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_dnl4_background sample 141

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_dnl4_background sample 142

description: Supp Table 6


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_dnl4_background sample 137

description: Supp Table 6


title: genomic_changes_due_to_phleomycin_treatment sample 131

description: Supp Table 5

value: red sector arising after phleomycin treatment


title: genomic_changes_due_to_phleomycin_treatment sample 128

description: Supp Table 5

value: negative control MC2A strain in G2/M


title: genomic_changes_due_to_phleomycin_treatment sample 130

description: Supp Table 5


title: genomic_changes_due_to_phleomycin_treatment sample 126

description: Supp Table 5


title: genomic_changes_due_to_phleomycin_treatment sample 123

description: Supp Table 5


title: genomic_changes_due_to_phleomycin_treatment sample 116

description: Supp Table 5


title: genomic_changes_due_to_phleomycin_treatment sample 120

description: Supp Table 5


title: genomic_changes_due_to_phleomycin_treatment sample 119

description: Supp Table 5


title: genomic_changes_due_to_phleomycin_treatment sample 118

description: Supp Table 5


title: genomic_changes_due_to_phleomycin_treatment sample 122

description: Supp Table 5


title: genomic_changes_due_to_phleomycin_treatment sample 127

description: Supp Table 5


title: genomic_changes_due_to_phleomycin_treatment sample 124

description: Supp Table 5


title: genomic_changes_due_to_phleomycin_treatment sample 125

description: Supp Table 5


title: genomic_changes_due_to_phleomycin_treatment sample 115

description: Supp Table 5


title: genomic_changes_due_to_phleomycin_treatment sample 121

description: Supp Table 5


title: genomic_changes_due_to_phleomycin_treatment sample 111

description: Supp Table 5


title: genomic_changes_due_to_phleomycin_treatment sample 112

description: Supp Table 5


title: genomic_changes_due_to_phleomycin_treatment sample 109

description: Supp Table 5


title: genomic_changes_due_to_phleomycin_treatment sample 114

description: Supp Table 5


title: genomic_changes_due_to_phleomycin_treatment sample 110

description: Supp Table 5


title: genomic_changes_due_to_phleomycin_treatment sample 108

description: Supp Table 5


title: genomic_changes_due_to_phleomycin_treatment sample 113

description: Supp Table 5


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 107

description: Supp Table 4

source_name: red sector arising after negative control non-re-replication at ChrIV567


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 105

description: Supp Table 4

value: red sector arising after negative control non-re-replication at ChrIV567


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 106

description: Supp Table 4

value: negative control non-re-replication at ChrIV567


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 102

description: Supp Table 4


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 99

description: Supp Table 4


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 103

description: Supp Table 4


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 101

description: Supp Table 4


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 104

description: Supp Table 4


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 100

description: Supp Table 4


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 98

description: Supp Table 4


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 97

description: Supp Table 4


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 96

description: Supp Table 4


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 95

description: Supp Table 4


title: genomic_changes_due_to_phleomycin_treatment sample 117

description: Supp Table 5


title: Ovarian cancer cell line TO14

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

description: Genomic DNA extracted fromTO14 was genotyped using Illumina Infinium Human1M-Duo Genotyping BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Data was processed in BeadStudio using the standard Illumina protocol. Log R Ratio and B Allele Frequency values were produced by tQN (Staaf et al 2008)

label: C-Bio and A-DNP

source_name: Ovarian cancer cell line TO14

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.

tag: patient number

tag: disease stage

value: Pre-treatment


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 94

description: Supp Table 4


title: genomic_changes_due_to_re-replication_at_ChrIV567_in_dnl4_background sample 152

description: Supp Table 6


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 93

description: Supp Table 4


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 90

description: Supp Table 4


title: 14984302Col - H3K27me3_Col_I_INPUT vs H3K27me3_Col_I_IP

city: Lyon

first: François

last: ROUDIER

address: 46 Allée d'Italie

department: Biologie

country: France

institute: Ecole Normale Supérieure de Lyon

description:
arabidopsis thaliana (col-0)  - age: 10day dev.stage (Boyes et al. Plant Cell 2001):seedling
Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between

hyb_protocol: H3K27me3_Col_I_IP Cy5 / H3K27me3_Col_I_INPUT Cy3 : 80pmol.

scan_protocol: NimbleGen, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 700V,laser power 100%

data_processing: For the ChIP-chip data we performed a normalization step by an ANOVA model (Kerr et.al,2002) to remove technical biases.Let Yplfts be the log2 intensity of the probe s on the chip p and the array l, with treatment t and fluorochrome f.The considered model is: Yplfts=mu+ap+bl+abpl+cf+acpf+Eplfts, where ap+bl+abpl is the support effect (chip, array and interactions), cf is the fluorochrome effect, acpf  is the chip*fluorochrome interaction and the errors Eplfts are centered Gaussian variables.We estimated the parameters of the model and we removed quantified biases from the raw data.The IP and INPUT intensities for each biological replicate were then averaged on the dye-swap to remove gene-specific dye biases.To analyze data, we use ChIPmix, a method proposed by Martin-Magniette et al.(2008) that we have adapted to study several biological replicates simultaneously. The method investigates the relationship between IP and Input by a mixture model of regressions. For a probe, available observation are the two measurements IP and INPUT for the two biological replicates. These latter are assumed to be independent by definition. The (unknown) status of a probe is characterized through a label Z which is 1 if the probe is enriched and 0 if it is normal (not enriched).

label_protocol: labelling Cy3 and Cy5 indirect, amplification=yes, DNA  .

growth_protocol: seedling - 10 days in liquid MS 0.5X at 22 degrees C. Cool white light at 100 uEm-2s-1, 16 hour photoperiod.

extract_protocol: Col_I:50ug.  antibody: H3K27me3 (Upstate 07-449);

treatment_protocol: no treatment

value: 10 day

tag: tissue

value: seedling

tag: antibody

tag: antibody manufacturer

value: Upstate

tag: antibody catalog #

value: input DNA


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 89

description: Supp Table 4


title: 6301302C24 - H3K27me3_C24_I_IP vs H3K27me3_C24_I_INPUT

description:
arabidopsis thaliana (c24)  - age: 15day dev.stage (Boyes et al. Plant Cell 2001):seedling
Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between

hyb_protocol: H3K27me3_C24_I_INPUT Cy5 / H3K27me3_C24_I_IP Cy3 : 80pmol.

tag: age

value: 15 day

extract_protocol: C24_I:50ug.  antibody: H3K27me3 (Upstate 07-449);


title: 14986002ColC24 - H3K27me3_ColxC24_II_IP vs H3K27me3_ColxC24_II_INPUT

hyb_protocol: H3K27me3_ColxC24_II_INPUT Cy5 / H3K27me3_ColxC24_II_IP Cy3 : 80pmol.

extract_protocol: ColxC24_II:50ug.  antibody: H3K27me3 (Upstate 07-449);


title: 6301102C24 - H3K27me3_C24_I_INPUT vs H3K27me3_C24_I_IP

hyb_protocol: H3K27me3_C24_I_IP Cy5 / H3K27me3_C24_I_INPUT Cy3 : 80pmol.


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 92

description: Supp Table 4


title: 6301202Col - H3K27me3_Col_II_IP vs H3K27me3_Col_II_INPUT

hyb_protocol: H3K27me3_Col_II_INPUT Cy5 / H3K27me3_Col_II_IP Cy3 : 80pmol.

extract_protocol: Col_II:50ug.  antibody: H3K27me3 (Upstate 07-449);


title: 14986402COL - H3K4me2_Col_I_INPUT vs H3K4me2_Col_I_IP

description:
arabidopsis thaliana (col-0)  - age: 15day dev.stage (Boyes et al. Plant Cell 2001):seedling
Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between

hyb_protocol: H3K4me2_Col_I_IP Cy5 / H3K4me2_Col_I_INPUT Cy3 : 80pmol.

growth_protocol: seedling - 15 days in liquid MS 0.5X at 22 degrees C. Cool white light at 100 uEm-2s-1, 16 hour photoperiod.

extract_protocol: Col_I:50ug.  antibody: H3K4me2 (upstate_07-030);

value: upstate


title: 14984302C24 - H3K27me3_C24_II_IP vs H3K27me3_C24_II_INPUT

hyb_protocol: H3K27me3_C24_II_INPUT Cy5 / H3K27me3_C24_II_IP Cy3 : 80pmol.

extract_protocol: C24_II:50ug.  antibody: H3K27me3 (Upstate 07-449);


title: 6301302ColC24 - H3K27me3_ColxC24_II_INPUT vs H3K27me3_ColxC24_II_IP

hyb_protocol: H3K27me3_ColxC24_II_IP Cy5 / H3K27me3_ColxC24_II_INPUT Cy3 : 80pmol.


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 88

description: Supp Table 4


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 91

description: Supp Table 4


title: 6302202Cvi - H3K4me2_Cvi_I_IP vs H3K4me2_Cvi_I_INPUT

description:
arabidopsis thaliana (cvi)  - age: 15day dev.stage (Boyes et al. Plant Cell 2001):seedling
Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between

hyb_protocol: H3K4me2_Cvi_I_INPUT Cy5 / H3K4me2_Cvi_I_IP Cy3 : 80pmol.

value: cvi

extract_protocol: Cvi_WT_I:50ug.  antibody: H3K4me2 (upstate_07-030);


title: 14986002C24 - H3K27me3_C24_II_INPUT vs H3K27me3_C24_II_IP

hyb_protocol: H3K27me3_C24_II_IP Cy5 / H3K27me3_C24_II_INPUT Cy3 : 80pmol.


title: 14984402ColC24 - H3K27me3_ColxC24_I_IP vs H3K27me3_ColxC24_I_INPUT

hyb_protocol: H3K27me3_ColxC24_I_INPUT Cy5 / H3K27me3_ColxC24_I_IP Cy3 : 80pmol.

extract_protocol: ColxC24_I:50ug.  antibody: H3K27me3 (Upstate 07-449);


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 87

description: Supp Table 4


title: 14986402Cvi - H3K4me2_Cvi_II_IP vs H3K4me2_Cvi_II_INPUT

hyb_protocol: H3K4me2_Cvi_II_INPUT Cy5 / H3K4me2_Cvi_II_IP Cy3 : 80pmol.

extract_protocol: Cvi_WT_II:50ug.  antibody: H3K4me2 (upstate_07-030);


title: 6302402COL - H3K4me2_Col_II_IP vs H3K4me2_Col_II_INPUT

hyb_protocol: H3K4me2_Col_II_INPUT Cy5 / H3K4me2_Col_II_IP Cy3 : 80pmol.

extract_protocol: Col_II:50ug.  antibody: H3K4me2 (upstate_07-030);


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 85

description: Supp Table 4


title: 6302302Col - H3K27me3_Col_II_IP vs H3K27me3_Col_II_INPUT


title: 6301202ColC24 - H3K27me3_ColxC24_I_INPUT vs H3K27me3_ColxC24_I_IP

hyb_protocol: H3K27me3_ColxC24_I_IP Cy5 / H3K27me3_ColxC24_I_INPUT Cy3 : 80pmol.


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 84

description: Supp Table 4

hyb_protocol: Hybridization was performed in 3X SSC, 25mM HEPES pH7.0, 0.25% SDS at 63oC for 16 to 24 hours


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 86

description: Supp Table 4


title: 16408402COL - H3K4me2_Col_II_INPUT vs H3K4me2_Col_II_IP

hyb_protocol: H3K4me2_Col_II_IP Cy5 / H3K4me2_Col_II_INPUT Cy3 : 80pmol.


title: 6302002Col - H3K27me3_Col_I_IP vs H3K27me3_Col_I_INPUT

hyb_protocol: H3K27me3_Col_I_INPUT Cy5 / H3K27me3_Col_I_IP Cy3 : 80pmol.


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 82

description: Supp Table 4


title: 14984402Col - H3K27me3_Col_II_INPUT vs H3K27me3_Col_II_IP

hyb_protocol: H3K27me3_Col_II_IP Cy5 / H3K27me3_Col_II_INPUT Cy3 : 80pmol.


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 81

description: Supp Table 4


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 83

description: Supp Table 4


title: 16410302Cvi - H3K4me2_Cvi_II_INPUT vs H3K4me2_Cvi_II_IP

hyb_protocol: H3K4me2_Cvi_II_IP Cy5 / H3K4me2_Cvi_II_INPUT Cy3 : 80pmol.


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 78

description: Supp Table 4


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 80

description: Supp Table 4


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 79

description: Supp Table 4


title: 6301102Col - H3K27me3_Col_I_IP vs H3K27me3_Col_I_INPUT


title: 11994602Cvi - H3K4me2_Cvi_I_INPUT vs H3K4me2_Cvi_I_IP

hyb_protocol: H3K4me2_Cvi_I_IP Cy5 / H3K4me2_Cvi_I_INPUT Cy3 : 80pmol.


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 77

description: Supp Table 4


title: 16408502Col - H3K27me3_Col_II_INPUT vs H3K27me3_Col_II_IP


title: genomic_changes_due_to_negative_control_non_re-replication_at_ChrIV567 sample 76

description: Supp Table 4


title: 14986502C24 - H3K27me3_C24_II_IP vs H3K27me3_C24_II_INPUT


title: 6302002C24 - H3K27me3_C24_I_INPUT vs H3K27me3_C24_I_IP

hyb_protocol: H3K27me3_C24_I_IP Cy5 / H3K27me3_C24_I_INPUT Cy3 : 80pmol.


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 75

description: Supp Table 3

source_name: red sector arising after re-replication at ChrIV1089

value: re-replication at ChrIV1089


title: 11994602COL - H3K4me2_Col_I_IP vs H3K4me2_Col_I_INPUT

hyb_protocol: H3K4me2_Col_I_INPUT Cy5 / H3K4me2_Col_I_IP Cy3 : 80pmol.


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 73

description: Supp Table 3

value: red sector arising after re-replication at ChrIV1089


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 74

description: Supp Table 3


title: 6302502C24 - H3K27me3_C24_I_IP vs H3K27me3_C24_I_INPUT

hyb_protocol: H3K27me3_C24_I_INPUT Cy5 / H3K27me3_C24_I_IP Cy3 : 80pmol.


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 71

description: Supp Table 3


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 70

description: Supp Table 3


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 68

description: Supp Table 3


title: 14986502Col - H3K27me3_Col_I_INPUT vs H3K27me3_Col_I_IP

hyb_protocol: H3K27me3_Col_I_IP Cy5 / H3K27me3_Col_I_INPUT Cy3 : 80pmol.


title: 16408502ColC24 - H3K27me3_ColxC24_I_IP vs H3K27me3_ColxC24_I_INPUT


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 66

description: Supp Table 3


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 65

description: Supp Table 3


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 67

description: Supp Table 3


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 72

description: Supp Table 3


title: 6302302ColC24 - H3K27me3_ColxC24_I_INPUT vs H3K27me3_ColxC24_I_IP


title: 6303402COL - H3K4me2_Col_II_IP vs H3K4me2_Col_II_INPUT


title: 14990002ColC24 - H3K27me3_ColxC24_II_IP vs H3K27me3_ColxC24_II_INPUT

hyb_protocol: H3K27me3_ColxC24_II_INPUT Cy5 / H3K27me3_ColxC24_II_IP Cy3 : 80pmol.


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 69

description: Supp Table 3


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 64

description: Supp Table 3


title: 14992002COL - H3K4me2_Col_II_INPUT vs H3K4me2_Col_II_IP


title: 14992802COL - H3K4me2_Col_I_INPUT vs H3K4me2_Col_I_IP

hyb_protocol: H3K4me2_Col_I_IP Cy5 / H3K4me2_Col_I_INPUT Cy3 : 80pmol.


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 61

description: Supp Table 3


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 62

description: Supp Table 3


title: 6302902Cvi - H3K4me2_Cvi_I_IP vs H3K4me2_Cvi_I_INPUT

hyb_protocol: H3K4me2_Cvi_I_INPUT Cy5 / H3K4me2_Cvi_I_IP Cy3 : 80pmol.


title: 11992402COL - H3K4me2_Col_I_IP vs H3K4me2_Col_I_INPUT


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 63

description: Supp Table 3


title: 16412502Cvi - H3K4me2_Cvi_II_INPUT vs H3K4me2_Cvi_II_IP


title: 14992802Cvi - H3K4me2_Cvi_II_IP vs H3K4me2_Cvi_II_INPUT


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 57

description: Supp Table 3


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 56

description: Supp Table 3


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 55

description: Supp Table 3


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 54

description: Supp Table 3


title: 6302502ColC24 - H3K27me3_ColxC24_II_INPUT vs H3K27me3_ColxC24_II_IP

hyb_protocol: H3K27me3_ColxC24_II_IP Cy5 / H3K27me3_ColxC24_II_INPUT Cy3 : 80pmol.


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 60

description: Supp Table 3


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 58

description: Supp Table 3


title: 14992002COLCvi - H3K4me2_ColxCvi_I_IP vs H3K4me2_ColxCvi_I_INPUT

description:
arabidopsis thaliana (colxcvi hybrids)  - age: 15day dev.stage (Boyes et al. Plant Cell 2001):seedling
Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between

hyb_protocol: H3K4me2_ColxCvi_I_INPUT Cy5 / H3K4me2_ColxCvi_I_IP Cy3 : 80pmol.

value: colxcvi hybrids

extract_protocol: ColxCvi_I:50ug.  antibody: H3K4me2 (upstate_07-030);


title: 12001202Col - H3K27me3_Col_I_IP vs H3K27me3_Col_I_INPUT


title: 16412502COLCvi - H3K4me2_ColxCvi_II_IP vs H3K4me2_ColxCvi_II_INPUT

hyb_protocol: H3K4me2_ColxCvi_II_INPUT Cy5 / H3K4me2_ColxCvi_II_IP Cy3 : 80pmol.

extract_protocol: ColxCvi_II:50ug.  antibody: H3K4me2 (upstate_07-030);


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 51

description: Supp Table 2

source_name: red sector arising after re-replication at ChrIV567

value: re-replication at ChrIV567


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 59

description: Supp Table 3


title: 14984102Col - H3K27me3_Col_I_INPUT vs H3K27me3_Col_I_IP


title: 14984202Col - H3K27me3_Col_II_INPUT vs H3K27me3_Col_II_IP


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 52

description: Supp Table 3


title: 6303402COLCvi - H3K4me2_ColxCvi_I_INPUT vs H3K4me2_ColxCvi_I_IP

hyb_protocol: H3K4me2_ColxCvi_I_IP Cy5 / H3K4me2_ColxCvi_I_INPUT Cy3 : 80pmol.


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 49

description: Supp Table 2

hyb_protocol: Hybridization was performed in 3X SSC, 25mM HEPES pH7.0, 0.25% SDS at 63oC for 16 to 24 hours

value: red sector arising after re-replication at ChrIV567


title: 14986302ColCvi - H3K27me3_ColxCvi_II_IP vs H3K27me3_ColxCvi_II_INPUT

hyb_protocol: H3K27me3_ColxCvi_II_INPUT Cy5 / H3K27me3_ColxCvi_II_IP Cy3 : 80pmol.

extract_protocol: ColxCvi_II:20ug.  antibody: H3K27me3 (Upstate 07-449);


title: 6301902ColCvi - H3K27me3_ColxCvi_II_INPUT vs H3K27me3_ColxCvi_II_IP

hyb_protocol: H3K27me3_ColxCvi_II_IP Cy5 / H3K27me3_ColxCvi_II_INPUT Cy3 : 80pmol.


title: 11992402Cvi - H3K4me2_Cvi_I_INPUT vs H3K4me2_Cvi_I_IP


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 48

description: Supp Table 2


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 50

description: Supp Table 2


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 53

description: Supp Table 3


title: 6301902Cvi - H3K27me3_Cvi_I_IP vs H3K27me3_Cvi_I_INPUT

description:
arabidopsis thaliana (cape verde islands)  - age: 15day dev.stage (Boyes et al. Plant Cell 2001):seedling
Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between

hyb_protocol: H3K27me3_Cvi_I_INPUT Cy5 / H3K27me3_Cvi_I_IP Cy3 : 80pmol.

value: cape verde islands

extract_protocol: Cvi_WT_I:50ug.  antibody: H3K27me3 (Upstate 07-449);


title: 6302902COLCvi - H3K4me2_ColxCvi_II_INPUT vs H3K4me2_ColxCvi_II_IP

hyb_protocol: H3K4me2_ColxCvi_II_IP Cy5 / H3K4me2_ColxCvi_II_INPUT Cy3 : 80pmol.


title: 12001202Cvi - H3K27me3_Cvi_I_INPUT vs H3K27me3_Cvi_I_IP

hyb_protocol: H3K27me3_Cvi_I_IP Cy5 / H3K27me3_Cvi_I_INPUT Cy3 : 80pmol.


title: 12001402ColCvi - H3K27me3_ColxCvi_I_INPUT vs H3K27me3_ColxCvi_I_IP

hyb_protocol: H3K27me3_ColxCvi_I_IP Cy5 / H3K27me3_ColxCvi_I_INPUT Cy3 : 80pmol.

extract_protocol: ColxCvi_I:20ug.  antibody: H3K27me3 (Upstate 07-449);


title: 14986302Cvi - H3K27me3_Cvi_II_INPUT vs H3K27me3_Cvi_II_IP

hyb_protocol: H3K27me3_Cvi_II_IP Cy5 / H3K27me3_Cvi_II_INPUT Cy3 : 80pmol.

extract_protocol: Cvi_WT_II:50ug.  antibody: H3K27me3 (Upstate 07-449);


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 45

description: Supp Table 2

extract_protocol: see BM Green et al. 2006

value: negative control MC2A strain in G2/M


title: 14984202ColCvi - H3K27me3_ColxCvi_I_IP vs H3K27me3_ColxCvi_I_INPUT

hyb_protocol: H3K27me3_ColxCvi_I_INPUT Cy5 / H3K27me3_ColxCvi_I_IP Cy3 : 80pmol.


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 46

description: Supp Table 2


title: 16408402COLCvi - H3K4me2_ColxCvi_I_IP vs H3K4me2_ColxCvi_I_INPUT


title: 12051402Col - H3K27me3_Col_II_IP vs H3K27me3_Col_II_INPUT

hyb_protocol: H3K27me3_Col_II_INPUT Cy5 / H3K27me3_Col_II_IP Cy3 : 80pmol.


title: 14981802Col - H3K27me3_Col_II_INPUT vs H3K27me3_Col_II_IP

hyb_protocol: H3K27me3_Col_II_IP Cy5 / H3K27me3_Col_II_INPUT Cy3 : 80pmol.


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 47

description: Supp Table 2


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 42

description: Supp Table 2


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 44

description: Supp Table 2


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 43

description: Supp Table 2


title: 16410302COLCvi - H3K4me2_ColxCvi_II_IP vs H3K4me2_ColxCvi_II_INPUT


title: 6302202COLCvi - H3K4me2_ColxCvi_II_INPUT vs H3K4me2_ColxCvi_II_IP


title: 14984102Cvi - H3K27me3_Cvi_II_IP vs H3K27me3_Cvi_II_INPUT

hyb_protocol: H3K27me3_Cvi_II_INPUT Cy5 / H3K27me3_Cvi_II_IP Cy3 : 80pmol.


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 40

description: Supp Table 2


title: 6302402COLCvi - H3K4me2_ColxCvi_I_INPUT vs H3K4me2_ColxCvi_I_IP


title: 13455893-13455544 - H3K4me2_Col_II_INPUT vs H3K4me2_Col_II_IP

hyb_protocol: H3K4me2_Col_II_IP Cy5 / H3K4me2_Col_II_INPUT Cy3 : 80pmol.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,550V,laser power 100%, Cy5:635nm,pmt voltage 600V,laser power 100%

data_processing: Data were normalized as ChIP-chip data in Turck e al.(2007). This method is based on the properties of dye-swaps to remove technical biases. To be specific, let Yij be the signal of the sample labeled with the dye j on the array i. Given that the second array is a technical replicate of the first one, the distribution of Y21 (respectively Y22) should be close to that of Y12 (respectively Y11). In practice, the relationship between Y21 and Y12 is linear but it is not the identity function. The parameters of the two linear models are estimated by Y21=a+bY12+N(0,sigma2) and Y22=c+dY11+N(0,sigma2),and these estimates are used to define the normalized IP and INPUT values of the second array relative to the first one: Y21=(Y21-a)/b and Y22=(Y22-c)/d.For each sample and for each tile, the values of the two arrays of the dye-swap are then averaged.To analyze data, we use ChIPmix, a method proposed by Martin-Magniette et al.(2008) that we have adapted to study several biological replicates simultaneously. The method investigates the relationship between IP and Input by a mixture model of regressions. For a probe, available observation are the two measurements IP and INPUT for the two biological replicates. These latter are assumed to be independent by definition. The (unknown) status of a probe is characterized through a label Z which is 1 if the probe is enriched and 0 if it is normal (not enriched).

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, DNA  .

extract_protocol: Col_seedlings_II:50ug.  antibody: H3K4me2 (upstate_07-030);