title: larvae_MANFdelta96_66

description:
Ldelta96_66
gene expression of zygotic MANF mutant D96


title: larvae_69B>MANF_3

status: Public on Apr 20 2012

type: RNA

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description:
LOVER_3
gene expression of MANF ectopic overexpression

hyb_protocol: 5µg of each differentially labelled aaRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent's fruit fly Microarray Kit 4x44k, P/N G2519F(Agilent Microarray Design ID 018972) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing and drying on theAxon 4200AL Scanner using three color scan setting for 4x44k array slides.

data_processing: The microarrays images were segmented and the median intensity of each spot was estimated by the software GenePixPro® 6.0 (Axon). The data were then imported into R software and preprocessed by the BioConductor package Limma.

molecule: total RNA

organism: Drosophila melanogaster

source_name: larvae 29-44 hrs AEL

label_protocol: Diluted spike controls (Agilent) were added to 1µg total RNA and labelled aaRNA was prepared using either cyanine 3 (Cy3) or Cy5 or Alexa 488 dye with Amino Allyl MessageAmp II aRNA kit (Ambion) according to the manufacturer's instructions.  Dye incorporation and received aaRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Drosophila melanogaster adults, embryos and larvae were growing at 25 degrees C, adults were laying eggs on apple juice agar plates with yeast paste

extract_protocol: total RNA was extracted with Qiagene RNAeasy extraction Kit (Qiagene) according to manufacturer's recommendations, treated with DNase (Promega) and purified by RNA purification kit (Qiagene). RNA was quantified using a NanoDrop-1000 spectrophotometer,  quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: embryos were collected from apple juice plates, washed with embryowash and dechorionated by routine chlorine treatment and washed carefully, embryos and larvae were picked according to genotypes under microscope into fresh applejuice plates, collected into Eppendorf tubes and snap freezed in liquid nitrogen.

tag: tissue

value: whole animal

tag: developmental stage

value: larval

tag: gene expression

value: MANF ectopic overexpression


title: larvae_MANFdelta96_2

description:
Ldelta96_2
gene expression of zygotic MANF mutant D96

source_name: larvae 29-50 hrsAEL

value: zygotic MANF mutant D96


title: larvae_Wmix_65

description:
WL65
wild type gene expression

source_name: larvae 30-45 hrs AEL

value: wild type


title: larvae_69B>MANF_2

description:
LOVER_2
gene expression of MANF ectopic overexpression


title: larvae_Wmix_1

description:
WL1
wild type gene expression


title: Wildtype mRNA, technical rep 1

city: Chicago

first: Jim

last: Holaska

state: IL

address: 5841 S. Maryland Ave, MC 6088

department: Medicine, Section of Cardiology

country: USA

institute: University of Chicago

hyb_protocol: 1 ug of tailed RNA were hybridized for 16 hr at 48C on GeneChip miRNA Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

label: biotin

organism: Mus musculus

source_name: Proliferative wildtype H2K myogenic precursor cells

label_protocol: Biotinylated cRNA was preparedfrom 1ug total RNA according to the FlashTag protocol (Genisphere).

growth_protocol: Cultured in DMEM containing 10% HI-FBS, 2% L-glutamine, 2% Chick embryo extract and 1% Pen/Strep.

extract_protocol: Qiagen miRNeasy kit according to manufacterer's instructions.

treatment_protocol: Cells were collected according to miRNeasy kit protocol.

tag: cell line

value: H2K Myoblasts

tag: genotype


title: embryos_paternalrescue_84

description:
EPRES_84
gene expression of maternal MANF mutant D96  paternal rescue

source_name: embryos late st 17, tracheas filling with air

value: embryo


title: embryos_paternalrescue_2

description:
EPRES_2
gene expression of maternal MANF mutant D96 paternal rescue


title: embryos_paternalrescue_66

description:
EPRES_66
gene expression of maternal MANF mutant D96  paternal rescue


title: larvae_Wmix_63

description:
WL63
wild type gene expression


title: larvae_Wmix_2

description:
WL2
wild type gene expression


title: control wild-type strain vs ΔphaA1 strain replicate 3

city: Beijing

first: Jing

last: Han

address: NO.1 West Beichen Road, Chaoyang District

country: China

institute: Institute of Microbiology, Chinese Academy of Sciences

description: compare gene expression profiles of wild-type strain with ΔphaA1 strain

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, lowess normalized log2 ratio (test/control) was calculated. SAM (significance Analysis of Microarrays, version 2.23b) software was used to normalize data.

organism: Haloferax mediterranei

source_name: wild-type strain

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: The wild-type strain and ΔphaA1 strain were were cultivated at 37°C to late exponential growth phase in MG medium containing 10 g/L glucose as carbon source.

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

treatment_protocol: The wild-type strain and ΔphaA1 strain were harvested at the late exponential stage.

tag: Stage

value: late exponential

tag: strain

value: wild-type

source_name: ΔphaA1 strain


title: embryos_MANFmzdelta96_88

description:
EMZdelta96_88
gene expression of maternal and zygotic MANF mutant  D96

source_name: embryos late st 17, 21-24 hrs AEL

value: maternal and zygotic MANF mutant  D96


title: embryos_paternalrescue_1

description:
EPRES_1
gene expression of maternal MANF mutant D96 paternal rescue


title: control wild-type strain vs ΔphaA1 strain replicate 4


title: embryos_MANFmzdelta96_4

description:
EMZdelta96_4
gene expression of maternal and zygotic MANF mutant  D96


title: control wild-type strain vs ΔphaA1 strain replicate 1


title: control wild-type strain vs ΔphaA1 strain replicate 2


title: control wild-type strain vs ΔphaEC strain replicate 2

description: compare gene expression profiles of wild-type strain with ΔphaEC strain

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy,the geometric mean of lowess normalized log2 ratio (test/control) of two dye-swap slides was calculated. SAM (significance Analysis of Microarrays, version 2.23b) software was used to normalize data.

growth_protocol: The wild-type strain and ΔphaEC strain were were cultivated at 37°C to late exponential growth phase in MG medium containing 10 g/L glucose as carbon source.

treatment_protocol: The wild-type strain and ΔphaEC strain were harvested at the late exponential stage.

source_name: ΔphaEC strain

value: ΔphaEC


title: embryos_Wmix_83

description:
WE83
wild type gene expression


title: control wild-type strain vs ΔphaEC strain replicate 1

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, hybridizations were performed by using a reversal fluorescent strategy,the geometric mean of lowess normalized log2 ratio (test/control) of dye-swap slides was calculated. SAM (significance Analysis of Microarrays, version 2.23b) software was used to normalize data.


title: control wild-type strain vs ΔphaEC strain replicate 4


title: embryos_MANFmzdelta96_1

description:
EMZdelta96_1
gene expression of maternal and zygotic MANF mutant  D96


title: control wild-type strain vs ΔphaEC strain replicate 3


title: control wild-type strain vs ΔphaEC strain replicate 5


title: control wild-type strain vs ΔphaEC strain replicate 6


title: ulcerative colitis with neoplasia_UCD12

first: Yong

last: Huang

address: 900 East 57th Street

department: Medicine

description:
S51
Gene expression data from human colon biopsy

hyb_protocol: Following fragmentation,  cRNA were hybridized for 16 hr at 45C on Affymetrix human gut microbiota community GeneChip, then washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Quality check and Robust Multichip Normalization using R/Bioconductor affy package

organism: Homo sapiens

source_name: ulcerative colitis with neoplasia

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

extract_protocol: Rneasy kit (Qiagen, Hilden, Germany)

value: colon biopsie


title: embryos_MANFmzdelta96_87

description:
EMZdelta96_87
gene expression of maternal and zygotic MANF mutant D96

value: maternal and zygotic MANF mutant D96


title: ulcerative colitis with neoplasia_UCD10

description:
S48
Gene expression data from human colon biopsy


title: embryos_Wmix_2

description:
WE2
wild type gene expression


title: ulcerative colitis with neoplasia_UCD11

description:
S49
Gene expression data from human colon biopsy


title: embryos_Wmix_82

description:
WE82
wild type gene expression


title: ulcerative colitis with neoplasia_UCD13

description:
S32
Gene expression data from human colon biopsy


title: ulcerative colitis with neoplasia_UCD4

description:
S34
Gene expression data from human colon biopsy


title: ulcerative colitis with neoplasia_UCD7

description:
S45
Gene expression data from human colon biopsy


title: ulcerative colitis with neoplasia_UCD9

description:
S47
Gene expression data from human colon biopsy


title: embryos_Wmix_1

description:
WE1
wild type gene expression


title: ulcerative colitis with neoplasia_UCD1

description:
S8
Gene expression data from human colon biopsy


title: ulcerative colitis with neoplasia_UCD6

description:
S43
Gene expression data from human colon biopsy


title: ulcerative colitis with neoplasia_UCD8

description:
S46
Gene expression data from human colon biopsy


title: ulcerative colitis with neoplasia_UCD3

description:
S33
Gene expression data from human colon biopsy


title: normal control_CTL5

description:
S28
Gene expression data from human colon biopsy

source_name: normal control


title: E9.5_WT_rep3

city: Edinburgh

first: Rachel

middle: Elizabeth

last: Rigby

address: IGMM, Western General Hospital, Crewe Road

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

description: E9.5wt 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Prior to normalization probes not detected (Illumina detection p-value <0.01) on any sample within the experiment were removed from the analysis. The remaining data was quantile normalized in R with the LIMMA package (version 3.10.2 (R version 2.14.0)).

source_name: whole E9.5 embryo_WT

label_protocol: Amplified, biotinylated cRNA was synthesized using Illumina® TotalPrep Amplification Kit (Ambion, Austin, Texas)

extract_protocol: Total RNA was extracted from whole E9.5 embryos using Trizol (Invitrogen) followed by an on-column DNase I treatment and cleanup using an RNeasy Mini Kit (Qiagen)

tag: strain background

tag: genotype/variation

value: whole embryo


title: Ptc MB veh 3w rep2

city: Seattle

first: Michelle

last: Lee

state: WA

address: 1100 Fairview Avenue, D4-100

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

description: replicate 2

data_processing: The data was quantile normalized using the Bioconductor package, “lumi,” and transformed to log2 scale

source_name: Ptc MB veh 3w

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems) for Illumina arrays.

extract_protocol: RNA was extracted with Qiagen RNeasy kit according to manufacturer's instruction. Quality control was performed with Agilent Bioanalyzer.

value: Mouse cerebellum

tag: gender

value: Female

tag: treatment length

value: 3 weeks


title: normal control_CTL4

description:
S26
Gene expression data from human colon biopsy


title: Ptc MB saridegib 6w rep3

description: replicate 3

source_name: Ptc MB saridegib 6w

value: 6 weeks


title: E9.5_WT_rep2

description: E9.5wt 2


title: Ptc MB saridegib 6w rep2

description: replicate 2


title: E9.5_WT_rep1

description: E9.5wt 1


title: Ptc MB saridegib 6w rep1

description: replicate 1

value: Male


title: normal control_CTL2

description:
S11
Gene expression data from human colon biopsy


title: E9.5_mut_rep2

description: E9.5mut 2

source_name: whole E9.5 embryo_mutant

value: lacking functional RNase H2


title: normal control_CTL1

description:
S10
Gene expression data from human colon biopsy


title: E9.5_mut_rep3

description: E9.5mut 3


title: Norwegian patient 23

status: Public on Apr 19 2012

city: Namur

first: jean-pierre

last: gillet

address: 61 Rue de Bruxelles

department: URPhyM

country: Belgium

institute: University of Namur

description:
NPT23
Norwegian Radium Hospital

scan_protocol: ABI Prism 7900 HT Sequence Detection System (Applied Biosystems, Foster City, CA, USA).

data_processing: SDS files were processed in RQ manager software and raw data were then exported in XLS file.

label: FAM

source_name: Primary tumor

label_protocol: cDNA was prepared using the High Capacity cDNA kit with RNAse inhibitor (Applied Biosystems, Foster City, CA, USA) as per the manufacturer’s instructions, but no labelling was performed as TaqMan-based qRT-PCR was performed subsequently.

growth_protocol: The tumor was fresh-frozen at -80°C.

extract_protocol: Total RNA was prepared using the Trizol method (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: Untreated tumors.

tag: age

value: ovarian carcinoma

tag: histology

value: serous

tag: figo stage

tag: tumor grade

tag: preop. ca125

tag: preop. ca125 defined as high or low

value: HIGH

tag: response

value: CR

tag: chemotherapy

value: carbo

tag: surgical debulking or residual disease (cm)

tag: progression-free survival (pfs; months)

tag: overall survival (os; months)

tag: status

value: dead of disease (DOD)

tag: platinum sensitivity

value: unknown

tag: diagnostic date


title: Norwegian patient 21

description:
NPT21
Norwegian Radium Hospital

tag: tissue

value: carbo+taxol


title: Norwegian patient 20

description:
NPT20
Norwegian Radium Hospital


title: normal control_CTL3

description:
S12
Gene expression data from human colon biopsy

value: colon biopsie


title: quiescent ulcerative colitis_UCN4

description:
S29
Gene expression data from human colon biopsy

source_name: quiescent ulcerative colitis


title: Norwegian patient 15

description:
NPT15
Norwegian Radium Hospital

value: alive with disease (AWD)

value: sensitive


title: Norwegian patient 14

description:
NPT14
Norwegian Radium Hospital

value: PR

value: resistant


title: A204_SAHA_sample2

city: Muenster

first: Kornelius

last: Kerl

address: Robert-Koch-Strasse 43

country: Germany

institute: Institute of molecular tumorbiology

description: rhabdoid tumor cell line A204 treated for 12h with 10 m SAHA

hyb_protocol: Hybridisation of the cartridge arrays was performed following the GeneChip WT Terminal Labeling and Hybridisation User Manual for use with Ambion WT Expression Kit

scan_protocol: Arrays were scanned with an Affymetrix GCS3000 7G using the AGCC Scan Control 1.1.0.845

data_processing: To calculate exprssion values, we used the Genepattern ExpressionFileCreator. Normalization was done by applying RMA with quantile normalization

label_protocol: The samples were processed using the Ambion WT Expression Kit for Affymetrix GeneChip Whole Transcript Expression Arrays. Labeling was performed following the GeneChip WT Terminal Labeling and Hybridisation User Manual for use with Ambion WT Expression Kit.

growth_protocol: A204 cell were grown in DMEM with 10% FBS

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

treatment_protocol: A204 cells were treated with SAHA 10 m for 12h, A204 control cells were treated with DMSO

tag: cell line

tag: treatment

value: treated for 12h with 10 m SAHA


title: Norwegian patient 10

description:
NPT10
Norwegian Radium Hospital

tag: age


title: Norwegian patient 8

description:
NPT8
Norwegian Radium Hospital

tag: histology

value: PD


title: Norwegian patient 22

description:
NPT22
Norwegian Radium Hospital

tag: figo stage

value: no evidence of disease (NED)


title: A204_control_sample1

description: rhabdoid tumor cell line A204 control

source_name: rhabdoid tumor cell line A204 control


title: Norwegian patient 7

description:
NPT7
Norwegian Radium Hospital

tag: tumor grade


title: Norwegian patient 5

description:
NPT5
Norwegian Radium Hospital

tag: preop. ca125


title: Norwegian patient 19

description:
NPT19
Norwegian Radium Hospital

tag: preop. ca125 defined as high or low


title: Norwegian patient 4

description:
NPT4
Norwegian Radium Hospital

tag: response


title: quiescent ulcerative colitis_UCN2

description:
S3
Gene expression data from human colon biopsy


title: Norwegian patient 18

description:
NPT18
Norwegian Radium Hospital

tag: chemotherapy


title: Norwegian patient 17

description:
NPT17
Norwegian Radium Hospital

value: Unknown

tag: surgical debulking or residual disease (cm)


title: A204_SAHA_sample3

source_name: rhabdoid tumor cell line A204 treated for 12h with 10 m SAHA


title: Norwegian patient 16

description:
NPT16
Norwegian Radium Hospital

value: ovarian carcinoma

tag: progression-free survival (pfs; months)


title: Norwegian patient 13

description:
NPT13
Norwegian Radium Hospital

value: serous

tag: overall survival (os; months)


title: Norwegian patient 1

description:
NPT1
Norwegian Radium Hospital

value: HIGH

tag: status


title: A204_control_sample3

description: rhabdoid tumor cell line A204 control


title: quiescent ulcerative colitis_UCN3

description:
S4
Gene expression data from human colon biopsy


title: Ptc MB veh 3w rep1

description: replicate 1

value: Mouse cerebellum

tag: gender

value: Female

tag: strain

tag: treatment length

value: 3 weeks


title: US Patient 78

description:
PT78
MDA (Houston)

tag: tissue

value: LOW

value: taxol/carboplatin (6X) given prior to surgery, then 3 more cycle of taxol/carbo

value: dead of disease (DOD)

tag: platinum sensitivity

value: unknown

tag: diagnostic date


title: Norwegian patient 11

description:
NPT11
Norwegian Radium Hospital

tag: age

tag: histology

value: CR

value: carbo+taxol

value: sensitive


title: Norwegian patient 9

description:
NPT9
Norwegian Radium Hospital

tag: figo stage

tag: tumor grade

value: carbo


title: A204_control_sample2

description: rhabdoid tumor cell line A204 control

tag: cell line

tag: treatment


title: Norwegian patient 12

description:
NPT12
Norwegian Radium Hospital

tag: preop. ca125

tag: preop. ca125 defined as high or low

tag: response

tag: chemotherapy


title: Norwegian patient 6

description:
NPT6
Norwegian Radium Hospital

tag: surgical debulking or residual disease (cm)

tag: progression-free survival (pfs; months)

tag: overall survival (os; months)

tag: status


title: US Patient 74

description:
PT74
MDA (Houston)

tag: tissue

value: PD

value: taxol/carboplatin & doxil (6X), taxol/ carboplatin (6X), carboplatin

value: alive with disease (AWD)


title: US Patient 73

description:
PT73
MDA (Houston)

value: ovarian carcinoma

value: taxol/carboplatin (8X), carboplatin (3X)

tag: platinum sensitivity


title: US Patient 75

description:
PT75
MDA (Houston)

value: serous

value: HIGH

value: Unknown

value: patient decided to have chemo elsewhere (standard treatment recommendation is carbo/taxol 6X)

tag: diagnostic date


title: Norwegian patient 2

description:
NPT2
Norwegian Radium Hospital

tag: age


title: Norwegian patient 3

description:
NPT3
Norwegian Radium Hospital

tag: histology

value: no evidence of disease (NED)


title: US Patient 80

description:
PT80
MDA (Houston)

tag: figo stage

value: topotecan/carboplatin (4X), then taxol/carboplatin (4X), another carbo/taxol (6X)


title: US Patient 70

description:
PT70
MDA (Houston)

tag: tumor grade

value: taxol (5X)/carboplatin (6X), taxol (9x), carboplatin (4x), doxil (4x), topotecan (3x), navelbine (2x), gemcitabine (2x)

value: dead of disease (DOD)


title: US Patient 79

description:
PT79
MDA (Houston)

value: taxol/carboplatin (6X) given prior to surgery, then 3 more cycle of taxol/carbo

value: unknown


title: US Patient 77

description:
PT77
MDA (Houston)

value: taxol (9X), then taxol/carboplatin (one dose only due to severe neuropathy)


title: US Patient 71

description:
PT71
MDA (Houston)

value: PR

value: taxol/carboplatin (6X), tamoxifen, femara


title: US Patient 72

description:
PT72
MDA (Houston)

value: LOW

value: PD

value: taxol/carboplatin (6X), taxol (6X), carboplatin (2X)


title: US Patient 65

description:
PT65
MDA (Houston)

value: ovarian carcinoma

value: taxol/carboplatin (6X), caboplatin (11X), taxotere (6X), doxil (24X)

value: alive with disease (AWD)


title: quiescent ulcerative colitis_UCN1

description:
S2
Gene expression data from human colon biopsy

value: colon biopsie


title: US Patient 69

description:
PT69
MDA (Houston)

value: serous

value: HIGH

value: Unknown

value: taxol/carboplatin (6X), carboplatin (6x), tamoxifen


title: US Patient 76

description:
PT76
MDA (Houston)

value: taxol/ carboplatin (6X), topotecan (4X), carboplatin (4X)

value: dead of disease (DOD)


title: US Patient 67

description:
PT67
MDA (Houston)

value: unknown


title: US Patient 63

description:
PT63
MDA (Houston)

value: taxol/carboplatin (6X),carboplatin(3X), doxil(12X), taxol/ avastin(5X), topotecan(3X)


title: US Patient 66

description:
PT66
MDA (Houston)

value: carboplatin/topotecan(4X), carbo/taxol(4X), doxil(4X), topotecan(2X), taxotere (3X), Xelado (3X), taxol (4X)


title: US Patient 68

description:
PT68
MDA (Houston)

value: CR

value: taxol/carboplatin (6X), taxol (2x), letrozole

value: sensitive


title: US Patient 59

description:
PT59
MDA (Houston)

value: PD

value: carboplatin (6X), subopt tRS, interferon (2x), carboplatin (12x), tamoxifen, doxorubicin (9x), taxol (3x), topotecan


title: US Patient 58

description:
PT58
MDA (Houston)

value: ovarian carcinoma

value: carboplatin/cytoxan (3x)


title: US Patient 57

description:
PT57
MDA (Houston)

value: taxol/cisplatin (7x), taxol/carboplatin (3x), carbo (6x), whole brain XRt, intra-thecal topotecan and iv topotecan (1x)


title: US Patient 60

description:
PT60
MDA (Houston)

value: serous

value: Elevated

value: carboplatin/cytoxan (8X)

value: no evidence of disease (NED)


title: US Patient 56

description:
PT56
MDA (Houston)

value: HIGH

value: cisplatin/taxol (6X)


title: US Patient 55

description:
PT55
MDA (Houston)

value: Unknown

value: taxol/carboplatin (6x), carboplatin (4x), tamoxifen

value: dead of disease (DOD)

value: unknown


title: US Patient 54

description:
PT54
MDA (Houston)

value: LOW

value: CR

value: carboplatin (9x), taxol (12x), tamoxifen, XRt, xeloda (4x), doxil (9x), carboplatin (7x), arimidex


title: A204_SAHA_sample1

tag: cell line

value: treated for 12h with 10 m SAHA


title: US Patient 53

description:
PT53
MDA (Houston)

value: ovarian carcinoma

value: taxol/carbo (1x)


title: US Patient 64

description:
PT64
MDA (Houston)

value: taxol/carboplatin (6X)


title: US Patient 52

description:
PT52
MDA (Houston)

value: serous


title: US Patient 49

description:
PT49
MDA (Houston)

value: PD

value: taxol/ cisplatin (6X), carboplatin (15X), tamoxifen, taxol (2X)


title: US Patient 46

description:
PT46
MGH (Boston)

value: t/c

value: alive with disease (AWD)


title: US Patient 48

description:
PT48
MGH (Boston)

value: HIGH

value: no evidence of disease (NED)

value: sensitive


title: US Patient 47

description:
PT47
MGH (Boston)

value: Carcinoma arising in borderline


title: US Patient 45

description:
PT45
MGH (Boston)

value: IP taxol/carbo

value: dead of disease (DOD)

value: unknown


title: US Patient 44

description:
PT44
MGH (Boston)

value: CR

value: taxol/carboplatin


title: US Patient 42

description:
PT42
MGH (Boston)

value: ovarian carcinoma


title: US Patient 43

description:
PT43
MGH (Boston)

value: LOW


title: US Patient 38

description:
PT38
MGH (Boston)

value: Unknown


title: US Patient 37

description:
PT37
MGH (Boston)

value: serous

value: taxol/carbo


title: US Patient 39

description:
PT39
MGH (Boston)

value: IP taxol/carboplatin


title: US Patient 40

description:
PT40
MGH (Boston)

value: serous, transitional


title: US Patient 50

description:
PT50
MDA (Houston)

value: PD

value: carboplatin (6X) then surgery and then taxol (6X), carboplatin (6x)


title: US Patient 33

description:
PT33
MGH (Boston)

value: HIGH


title: US Patient 34

description:
PT34
MGH (Boston)


title: US Patient 35

description:
PT35
MGH (Boston)

value: no evidence of disease (NED) ?


title: US Patient 29

description:
PT29
MGH (Boston)

value: tcA


title: US Patient 32

description:
PT32
MGH (Boston)


title: US Patient 51

description:
PT51
MDA (Houston)

value: taxol/ cisplatin (6X), carboplatin (6X),carbo (5x), topotecan (23x), gemcitabine (12x), tamoxifen, doxil (18x), xeloda (15x), arimidex


title: US Patient 41

description:
PT41
MGH (Boston)

value: dead of disease (DOD)

value: resistant


title: US Patient 62

description:
PT62
MDA (Houston)

value: carboplatin (2X)

value: unknown


title: US Patient 36

description:
PT36
MGH (Boston)

value: ovarian carcinoma

value: CR

value: taxol/carboplatin

value: alive with disease (AWD)

value: sensitive


title: US Patient 28

description:
PT28
MGH (Boston)

value: serous


title: US Patient 31

description:
PT31
MGH (Boston)


title: US Patient 30

description:
PT30
MGH (Boston)

value: PR

value: t/c, carbo


title: US Patient 25

description:
PT25
MGH (Boston)


title: E9.5_mut_rep1

description: E9.5mut 1

tag: strain background

tag: genotype/variation

value: lacking functional RNase H2

tag: developmental stage

value: whole embryo


title: US Patient 4

description:
PT4
Cleveland Clinic

tag: preop. ca125

tag: preop. ca125 defined as high or low

value: HIGH

tag: response

value: Unknown

value: accrued from Apr-01 to Aug-05


title: US Patient 27

description:
PT27
MGH (Boston)

tag: chemotherapy

value: IP taxol/carbo

tag: surgical debulking or residual disease (cm)

tag: progression-free survival (pfs; months)


title: US Patient 7

description:
PT7
Cleveland Clinic

tag: tissue

value: SD

value: carbo/taxol

tag: overall survival (os; months)

tag: status

value: dead of disease (DOD)

value: resistant


title: US Patient 26

description:
PT26
MGH (Boston)

tag: age

value: ovarian carcinoma

value: serous, transitional

value: CR

value: carbo/taxane

value: alive with disease (AWD) ?

tag: platinum sensitivity

value: unknown

tag: diagnostic date


title: US Patient 21

description:
PT21
MGH (Boston)

tag: histology

value: serous

tag: figo stage

tag: tumor grade

value: PD

value: taxotere/carboplatin


title: US Patient 20

description:
PT20
MGH (Boston)

value: HIGH

value: tcA

value: no evidence of disease (NED)

value: sensitive


title: US Patient 22

description:
PT22
MGH (Boston)

value: IP/IV platinum/taxol

value: alive with disease (AWD)


title: US Patient 23

description:
PT23
MGH (Boston)

value: PR

value: taxol/carboplatin/Avastin


title: US Patient 24

description:
PT24
MGH (Boston)

value: ovarian carcinoma


title: US Patient 5

description:
PT5
Cleveland Clinic

value: dead of disease (DOD)

value: accrued from Apr-01 to Aug-05


title: US Patient 6

description:
PT6
Cleveland Clinic

value: CR

value: carbo/taxol


title: US Patient 9

description:
PT9
Cleveland Clinic


title: US Patient 10

description:
PT10
Cleveland Clinic

value: resistant


title: US Patient 11

description:
PT11
Cleveland Clinic

value: serous


title: US Patient 8

description:
PT8
Cleveland Clinic

value: PD

value: carbo/taxol/taxol


title: US Patient 15

description:
PT15
MGH (Boston)

value: HIGH

value: taxol/carboplatin

value: unknown


title: US Patient 18

description:
PT18
MGH (Boston)

value: Unknown

value: sensitive


title: US Patient 16

description:
PT16
MGH (Boston)


title: US Patient 19

description:
PT19
MGH (Boston)

value: serous, transitional


title: US Patient 17

description:
PT17
MGH (Boston)


title: US Patient 12

description:
PT12
MGH (Boston)

value: PR

value: modifed triple doublets

value: alive with disease (AWD)


title: US Patient 14

description:
PT14
MGH (Boston)

value: ovarian carcinoma

value: no evidence of disease (NED)


title: US Patient 13

description:
PT13
MGH (Boston)

value: carboplatin

value: dead of disease (DOD)


title: US Patient 3

description:
PT3
Cleveland Clinic

value: carbo/taxol

value: resistant

value: accrued from Apr-01 to Aug-05


title: US Patient 61

description:
PT61
MDA (Houston)

value: serous, endometrioid

value: taxol/carboplatin (6X)


title: US Patient 1

description:
PT1
Cleveland Clinic

value: serous

value: HIGH

value: CR

value: carbo/taxol/gem/toxo/doxil


title: breast_R-1

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

country: Sweden

institute: Lund University, Sweden

hyb_protocol: Labeled RNA was hybridized overnight to miRCURY LNA™ microRNA arrays discovery version 9.2, 11.0 and 11.5, for the 3 sets, respectively, on a Tecan HS Pro 4800 hybridization station

scan_protocol: After hybridization, the rinsed and dried arrays were scanned in a DNA microarray scanner (Agilent, model G2565BA, California, USA).

data_processing: The data was both treated as one channel data using the Hy3 signal intensities, and as two-channel data using the Hy3/Hy5 ratios. Here, we only present the one-channel data, as the ratio analysis gave comparable results. Initially, background subtraction was performed in R v.2.2.1 using the backgroundCorrectmethod in the LIMMA (Linear Models for Microarary Data) package, which is available as part of the Bioconductor project (http://www.bioconductor.org). The intensity values were then log2-scaled and the median probe signals were quantile normalized. Thus, the statistical analysis is based on the quantile normalized log2-scaled Hy3 signals.

source_name: primary breast cancer

label_protocol: A common reference design, where the common reference contained an equimolar mixture of total RNA from all samples, per set, was applied to enable both one and two-channel analysis of the data. The sample channel was labeled with Hy3™ dye, while the reference channel was labeled with Hy5™ dye according to the manufacturer’s recommendation (Exiqon A/S, Vedbaek, Denmark).

extract_protocol: Five sections of 10 μm were de-paraffinized and total RNA was extracted with Roche high pure kit according to the manufacturer’s protocol (Roche, Basel, Switzerland).

treatment_protocol: All patients had archival formalin-fixed, paraffin-embedded, (FFPE) tumor tissue stored in the dark

tag: slide id

tag: age at op

tag: size (mm)

tag: er-status

tag: pgr-status

tag: nodal-status, positive

tag: nodal-status, total removed

tag: duration of tamoxifen (years)

tag: time.to.recurrence (years)

tag: time.to.death (years)


title: US Patient 2

description:
PT2
Cleveland Clinic

tag: tissue

tag: preop. ca125

tag: preop. ca125 defined as high or low

tag: response

tag: chemotherapy

tag: surgical debulking or residual disease (cm)

tag: progression-free survival (pfs; months)

tag: overall survival (os; months)

tag: status

value: sensitive


title: breast_nonR-40

tag: slide id

tag: age at op

tag: size (mm)


title: mouse primary hepatocytes, KD3010, technical replicate 2

city: La Jolla

first: Ruth

middle: T

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

description: technicall replicate 2

data_processing: The data were normalized using cubic spline in Illumina GenomeStudio and also using the VAMPIRE Bayesian model with a 2-sided Bonferroni-corrected threshold of 0.05.

source_name: mouse primary hepatoctyes

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

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

tag: strain

value: wildtype c57Bl6/J bkg

tag: age

value: 10 week old

tag: cell type

value: hepatocyte

tag: treatment

tag: gender

value: male


title: mouse primary hepatocytes, DMSO, technical replicate 2

description: technicall replicate 2

value: DMSO


title: mouse primary hepatocytes, GW1516, technical replicate 1

description: technical replicate 1


title: mouse primary hepatocytes, DMSO, technical replicate 1

description: technical replicate 1


title: breast_R-2

tag: er-status

tag: pgr-status

tag: nodal-status, positive

tag: nodal-status, total removed

tag: duration of tamoxifen (years)

tag: time.to.recurrence (years)

tag: time.to.death (years)


title: Parenchyma cells at 28mm, biological rep2

city: Pullman

first: Siau Sie

last: Voo

address: 100 Dairy Road

department: Institute of Biological Chemistry

institute: Washington State University

description: Gene expression data from parenchyma cells in albedo tissue of grapefruit at diameter 28 mm.

hyb_protocol: The fragmented, biotin-labeled cDNA were then hybridized for 16 hours at 45°C on GeneChip Citrus Genome Arrays.

scan_protocol: GeneChips were washed and stained following recommended protocol (Nugen Technologies) on an Affymetrix Fluidics Station 450 (FS450_004).

data_processing: The data were analyzed with Partek Genomics Suite using Affymetrix default analysis settings and global scaling as normalization method.

organism: Citrus x paradisi

source_name: Peel of grapefuit at equatorial diameter 28 mm.

label_protocol: Fragmented, biotin-labeled cDNA were prepared according to the protocol of FL-Ovation cDNA Biotin Module V2 kit (Nugen Technologies) using 5 µg amplified cDNA.

growth_protocol: Grapefruit samples were from grapefruit tree that grows under greenhouse condition: 14/10 hours day/night, average humidity 60%, minimal light intensity 200 µm.

extract_protocol: Extraction of total RNA from cells was performed using Qiagen Rneasy Micro Kit according to manufacturer's instructions.

treatment_protocol: Grapefruit peels were fixed in 5:1 ratio of ethanol:acetic acid, embedded in parrafin and sectioned prior to laser microdissection for collecting the epithelial cells and parenchyma cells.

tag: tissue

value: Albedo tissue

value: Parenchyma cell


title: Epithelial cells at 41mm, biological rep3

description: Gene expression data from epithelial cells in secretory glands of grapefruit at diameter 41 mm.

source_name: Peel of grapefuit at equatorial diameter 41 mm.

value: secretory gland in flavedo tissue

value: Epithelial cell


title: mouse primary hepatocytes, GW1516, technical replicate 2

description: technicall replicate 2


title: mouse primary hepatocytes, KD3010, technical replicate 1

description: technical replicate 1


title: Parenchyma cells at 41mm, biological rep3

description: Gene expression data from parenchyma cells in albedo tissue of grapefruit at diameter 41 mm.


title: Parenchyma cells at 28mm, biological rep3


title: Parenchyma cells at 41mm, biological rep1


title: Epithelial cells at 28mm, biological rep2

description: Gene expression data from epithelial cells in secretory glands of grapefruit at diameter 28 mm.


title: Epithelial cells at 41mm, biological rep2


title: Parenchyma cells at 28mm, biological rep1


title: RMT1, Pla2g4c, negative control

city: Aomori

first: Naoki

last: Nanashima

state: Aomori

address: 58-1 Mase, Hamadate

department: Department of Nutrition

country: Japan

institute: Aomori University of Health and Welfare

description: Gene expression after negative control-siRNA transfection in RMT-1

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Rat GE 8x60K Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Rattus norvegicus

source_name: RMT1, Pla2g4c, negative control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted by using the RNeasy mini kit (Qiagen, Tokyo, Japan).

treatment_protocol: Rat mammary tumor-1 E4 (RMT-1) cells were purchased from Health Science Research Resources Bank, Osaka, Japan. The cells were routinely cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum at 37ºC in 5% CO2.

tag: cell line

value: RMT-1 clone E4

tag: knockdown

value: control


title: Epithelial cells at 28mm, biological rep3


title: Epithelial cells at 41mm, biological rep1


title: Parenchyma cells at 41mm, biological rep2


title: RMT1, Pla2g4c, siRNA

description: Gene expression after Pla2g4c-siRNA transfection in RMT-1

source_name: RMT1, Pla2g4c, siRNA


title: breast_nonR-34

tag: slide id

tag: age at op


title: Epithelial cells at 28mm, biological rep1


title: breast_nonR-32

tag: size (mm)


title: breast_nonR-39


title: breast_nonR-37


title: breast_nonR-28_rep2


title: Ptc MB veh 3w rep3

description: replicate 3

value: Mouse cerebellum

value: Female

tag: strain

tag: treatment length

value: 3 weeks


title: breast_nonR-28_rep1


title: Positive SCC15

type: genomic

city: London

first: Muy-Teck

last: Teh

state: England

address: Blizard Building, 4, Newark Street,

department: Centre for Clinical & Diagnostic Oral Sciences

institute: Queen Mary University of London

hyb_protocol: Equal amounts (15ug) of labelled MeDIP and Input DNA are loaded onto the arrays and co-hybridized at 42 C for 16-20 hours.

scan_protocol: The arrays are then washed, dryed on the NimbleGen dryer and scanned on the NimbleGen MS200 scanner.

data_processing: Data are extracted and analysed using the NimbleGen NimbleScan software (v2.6 in your case) using the default settings.

molecule: genomic DNA

label_protocol: Briefly the DNA is labelled by klenow extension using Cy3- (Input) or Cy5-(MeDIP) labelled random primers.

extract_protocol: Genomic DNA (gDNA) were extracted from 1 million cells by standard phenol:chloroform method. gDNA were then fragmented by MseI digestion (37°C, 16h) prior to enrichment for CpG-methylated DNA using a MBD2b/MBD3L1-conjugated magnetic bead-based system according to manufacturer’s protocol (MethylCollector Ultra kit, #55005, Active Motif Europe, Belgium).

treatment_protocol: No treatment

value: HNSCC

tag: treatment

value: methylated enriched

value: non-enriched


title: breast_nonR-27


title: Test NOK expressing FOXM1B

treatment_protocol: Retroviral Transduction with FOXM1B

tag: cell type

value: NOK

tag: retrovirus expression

value: FOXM1B (oncogene)


title: breast_nonR-26

tag: er-status

tag: pgr-status


title: breast_nonR-25

tag: nodal-status, positive

tag: nodal-status, total removed


title: MeDIP IPF -12

city: Pittsburgh

first: Einat

middle: Inna

last: Rabinovich

state: PA

address: 3500 Terrace St

institute: University of Pittsburgh

hyb_protocol: Hybridization was performed for 40 hours at 67ºC according the manufacturer's protocol

scan_protocol: Scanned on Agilent G2509C scanner.

data_processing:
CpG_islands_normalized.txt file on Series record represents the CpG islands: We included in the analysis only probes with a hybridization Tm value between 79C and 93C since we assume that anything outside that Tm range is prone to hybridization errors. We subsequently divided the probes according to their Tm into 14 groups/bins differing by 1 C. Probe signals in each bin were standardized to have an average of 0 and a standard deviation of 1. To work in a CpG island oriented manner we scored each island for its likelihood to be methylated. For that purpose, each probe was mapped to the genome and the signals of the probes that were mapped to a single CpG island were averaged to obtain the islands methylation score( reference: Straussman R, Nejman D, Roberts D, Steinfeld I, Blum B, et al. (2009) Developmental programming of CpG island methylation profiles in the human genome. Nat Struct Mol Biol 16: 564-571).
Sample data tables: Agilent feature Extraction Software (ver.9.5.3) was used for background subtraction.

source_name: lung tissue genomic DNA

label_protocol: Methylated DNA was immunoprecipitated (MeDIP) using 5-Methylcytidine monoclonal antibody as instructed in the Agilent protocol. MeDIP and genomic DNA were labeled with Cy3 and Cy5, using Agilent Genomic Labeling kit PLUS.

extract_protocol: Genomic DNA was extracted from 10 mg frozen lung tissue using the DNeasy Blood&Tissue kit, following the manufacturer's protocol.

value: lung

tag: phenotype

value: Idiopathic Pulmonary Fibrosis

source_name: lung tissue MeDIP DNA


title: MeDIP IPF -11


title: MeDIP IPF -9


title: breast_nonR-33

value: IHC-

tag: duration of tamoxifen (years)

tag: time.to.recurrence (years)


title: Control NOK expressing EGFP

treatment_protocol: Retroviral Transduction with EGFP

value: EGFP (control gene)


title: breast_nonR-23


title: MeDIP IPF -5

tag: tissue


title: MeDIP IPF -10


title: MeDIP IPF -3


title: MeDIP IPF -6


title: MeDIP IPF -2


title: MeDIP IPF -8


title: MeDIP cancer 10

source_name: lung adenocarcinoma genomic DNA

value: adenocarcinoma

source_name: lung adenocarcinoma MeDIP DNA


title: MeDIP IPF -1


title: breast_nonR-21


title: breast_nonR-22

value: B+

tag: time.to.death (years)


title: MeDIP cancer 9


title: MeDIP IPF -7


title: MeDIP cancer 7


title: MeDIP IPF -4


title: MeDIP cancer 3


title: breast_nonR-20

tag: slide id


title: MeDIP cancer 6


title: breast_nonR-19

tag: age at op


title: MeDIP cancer 2


title: MeDIP cancer 1


title: 06_Brain

description:
SDU_KG_BC_06_Brain
1_US45103081_13982822_S02_Cropped

hyb_protocol: Approximately 1 μg Hy5TM- and 1 μg Hy3TM-labeled total RNA was co-hybridised on the array for 16 hours at 560C in a Tecan HS 4800 Pro hybridisation station (Tecan, Männedorf, Switzerland). The array was washed and then dried according to the protocol before scanning.

scan_protocol: The arrays were scanned in an Agilent G2565BA Microarray Scanner System (Agilent Technologies, Santa Clara, CA, USA)

data_processing: images were quantified using Imagene v. 8.0 (BioDiscovery, CA). The log2 transformed intensities were normalized as single channel data using quantile normalization in the statistical programming language R with the Bioconductor software package LIMMA (Linear Models for Microarray Data). Poor quality spots were removed and spots were background-corrected using the Normexp method (with an offset of 50) in R with the Bioconductor software package LIMMA.

source_name: breast cancer, brain met

label_protocol: All RNA samples were labeled with Hy3TM and compared on the array to a Hy5TM-labeled common reference sample according to the manufactures protocol (Exiqon).

extract_protocol: Total RNA was isolated from 5x10 μm FFPE tissue using the High Pure miRNA Isolation kit (Roche Applied Science, Indianapolis, IN) according to the manufacturer’s instructions

tag: distant met or lymph node

value: distant

tag: metastasis site

value: brain

tag: patient

tag: prep code

tag: patient nr.

tag: operation date

tag: er status

tag: pgr status


title: MeDIP cancer 4


title: 05_Lymph node

description:
SDU_KG_BC_05_Lymph node
1_US45103081_13982821_S01_Cropped

source_name: breast cancer, lymph node

value: lymph node

value: SDU_KG_BC_05_Lymph node


title: 10_Breast

description:
SDU_KG_BC_10_Breast
1_US45103081_13982834_S02_Cropped

source_name: breast cancer, primary

tag: age at diagnosis

tag: localisation of metastasis

value: Brain

tag: diameter of invasive carcinoma (mm)

tag: malignancygrade

tag: positive lymph nodes

tag: time to recurrence (years)


title: MeDIP control 9

source_name: normal lung tissue genomic DNA

tag: tissue

tag: phenotype

value: normal

source_name: normal lung tissue MeDIP DNA


title: 05_Breast

description:
SDU_KG_BC_05_Breast
1_US45103081_13982820_S02_Cropped


title: MeDIP control 10


title: breast_nonR-18

tag: slide id

tag: age at op

tag: size (mm)

tag: er-status

tag: pgr-status

tag: nodal-status, positive

tag: nodal-status, total removed

tag: duration of tamoxifen (years)

tag: time.to.recurrence (years)


title: MeDIP cancer 8


title: 04_Breast_2

description:
SDU_KG_BC_04_Breast
1_US45103081_13982815_S01_Cropped

tag: distant met or lymph node

tag: metastasis site

tag: patient

tag: prep code

tag: patient nr.


title: 05_Brain1

description:
SDU_KG_BC_05_Brain1
1_US45103081_13982818_S01_Cropped

tag: operation date

tag: er status

value: N/K

tag: pgr status


title: breast_nonR-16

tag: slide id


title: MeDIP cancer 5

tag: tissue

tag: phenotype


title: MeDIP control 8


title: breast_nonR-11

tag: age at op

tag: size (mm)

tag: er-status


title: 19_Brain

description:
SDU_KG_BC_19_Brain
1_US45103081_13982795_S01_Cropped


title: breast_nonR-10

tag: pgr-status

tag: nodal-status, positive

tag: nodal-status, total removed


title: MeDIP control 5


title: 14_Skin

description:
SDU_KG_BC_14_Skin
1_US45103081_13982796_S02_Cropped

source_name: breast cancer, skin met

tag: distant met or lymph node

value: skin


title: 18_Brain

description:
SDU_KG_BC_18_Brain
1_US45103081_13982794_S02_Cropped

tag: metastasis site


title: 18_Breast

description:
SDU_KG_BC_18_Breast
1_US45103081_13982792_S02_Cropped

tag: patient

tag: age at diagnosis

tag: localisation of metastasis

tag: diameter of invasive carcinoma (mm)

tag: malignancygrade

tag: positive lymph nodes

tag: time to recurrence (years)


title: MeDIP control 7

tag: tissue


title: 17_Skin_N

description:
SDU_KG_BC_17_Skin_N
1_US45103081_13982791_S02_Cropped

source_name: skin normal

tag: prep code

tag: patient nr.


title: 18_Lymph node

description:
SDU_KG_BC_18_Lymph node
1_US45103081_13982793_S02_Cropped

value: SDU_KG_BC_18_Lymph node

tag: operation date


title: MeDIP control 6

tag: phenotype


title: breast_nonR-8

source_name: primary breast cancer

tag: slide id

tag: age at op

tag: size (mm)

tag: er-status

value: IHC+

tag: pgr-status

tag: duration of tamoxifen (years)

tag: time.to.recurrence (years)


title: 17_Relapse2_N

description:
SDU_KG_BC_17_Relapse2_N
1_US45103081_13982790_S02_Cropped

source_name: breast normal, relapse

tag: distant met or lymph node

tag: metastasis site

tag: patient


title: MeDIP control 4


title: 03_Breast_N

description:
SDU_KG_BC_03_Breast_N
1_US45103081_13982784_S02_Cropped

source_name: breast normal


title: 17_Relapse2

description:
SDU_KG_BC_17_Relapse2
1_US45103081_13982866_S01_Cropped

source_name: breast cancer, relapse


title: 04_Brain

description:
SDU_KG_BC_04_Brain
1_US45103081_13982786_S01_Cropped

tag: er status

tag: pgr status


title: 04_Breast

description:
SDU_KG_BC_04_Breast
1_US45103081_13982787_S01_Cropped

tag: age at diagnosis

tag: localisation of metastasis

tag: diameter of invasive carcinoma (mm)

tag: malignancygrade

tag: positive lymph nodes

tag: time to recurrence (years)


title: 17_Breast

description:
SDU_KG_BC_17_Breast
1_US45103081_13982788_S02_Cropped

tag: prep code

tag: patient nr.

tag: operation date

value: Liver


title: 15_Brain2

description:
SDU_KG_BC_15_Brain2
1_US45103081_13982859_S01_Cropped


title: 03_Breast

description:
SDU_KG_BC_03_Breast
1_US45103081_13982762_S02_Cropped


title: breast_nonR-7

tag: slide id

tag: age at op

tag: size (mm)

tag: er-status

tag: pgr-status

tag: nodal-status, positive

tag: nodal-status, total removed


title: breast_nonR-4

tag: duration of tamoxifen (years)

tag: time.to.recurrence (years)

tag: time.to.death (years)


title: breast_nonR-5


title: 06_Breast2

description:
SDU_KG_BC_06_Breast2
1_US45103081_13982825_S02_Cropped

tag: distant met or lymph node

tag: metastasis site

tag: patient

tag: age at diagnosis

tag: localisation of metastasis

tag: diameter of invasive carcinoma (mm)

tag: er status

tag: pgr status


title: breast_nonR-1

tag: slide id

tag: age at op


title: MeDIP control 3

tag: tissue

value: lung

tag: phenotype


title: 11_Breast2

description:
SDU_KG_BC_11_Breast2
1_US45103081_13982839_S02_Cropped

tag: prep code

tag: patient nr.

tag: operation date

tag: malignancygrade

tag: positive lymph nodes

tag: time to recurrence (years)


title: breast_nonR-2

tag: size (mm)

tag: er-status

tag: pgr-status

tag: nodal-status, positive

tag: nodal-status, total removed

tag: duration of tamoxifen (years)

tag: time.to.recurrence (years)

tag: time.to.death (years)


title: MeDIP control 2


title: 05_Brain2

description:
SDU_KG_BC_05_Brain2
1_US45103081_13982819_S01_Cropped

tag: distant met or lymph node

tag: metastasis site

tag: patient

tag: er status

tag: pgr status


title: MeDIP MeDIP control 1

tag: tissue

tag: phenotype


title: 03_Brain2

description:
SDU_KG_BC_03_Brain2
1_US45103081_13982760_S02_Cropped

tag: prep code

tag: patient nr.

tag: operation date


title: 01/12584 R

tag: slide id

value: Slide 40

tag: imagene id

tag: age at op

tag: size (mm)

tag: er-status


title: 01/24040 R

value: Slide 38

tag: pgr-status

tag: nodal-status, positive

tag: nodal-status, total removed

tag: duration of tamoxifen (years)

tag: time.to.recurrence (years)


title: 17_Skin

description:
SDU_KG_BC_17_Skin
1_US45103081_13982867_S01_Cropped

tag: distant met or lymph node

tag: metastasis site

tag: patient


title: 17_Relapse1

description:
SDU_KG_BC_17_Relapse1
1_US45103081_13982865_S01_Cropped


title: 01/17809 R

value: Slide 36


title: 16_Breast

description:
SDU_KG_BC_16_Breast
1_US45103081_13982863_S02_Cropped

tag: age at diagnosis

tag: localisation of metastasis

tag: diameter of invasive carcinoma (mm)

tag: malignancygrade

tag: positive lymph nodes

tag: er status

tag: pgr status

tag: time to recurrence (years)


title: 15_Brain1

description:
SDU_KG_BC_15_Brain1
1_US45103081_13982860_S01_Cropped

tag: prep code

tag: patient nr.

tag: operation date


title: 01/15287 R

tag: slide id

value: Slide 35

tag: imagene id

tag: age at op

tag: size (mm)

tag: er-status

tag: pgr-status

tag: nodal-status, positive

tag: nodal-status, total removed


title: 01/620 R

value: Slide 32

tag: duration of tamoxifen (years)

tag: time.to.recurrence (years)

tag: time.to.death (years)


title: 17_Lymph node

description:
SDU_KG_BC_17_Lymph node
1_US45103081_13982864_S02_Cropped

tag: distant met or lymph node

tag: metastasis site

tag: patient

value: SDU_KG_BC_17_Lymph node


title: 15_Lymph node

description:
SDU_KG_BC_15_Lymph node
1_US45103081_13982858_S01_Cropped

tag: prep code

value: SDU_KG_BC_15_Lymph node


title: 15_Brain2_N

description:
SDU_KG_BC_15_Brain2_N
1_US45103081_13982861_S01_Cropped

source_name: brain normal

tag: patient nr.


title: 03_Brain1

description:
SDU_KG_BC_03_Brain1
1_US45103081_13982761_S02_Cropped

value: distant

value: brain

tag: operation date

tag: er status

tag: pgr status


title: 04_Lymph node

description:
SDU_KG_BC_04_Lymph node
1_US45103081_13982785_S02_Cropped

value: lymph node

value: SDU_KG_BC_04_Lymph node


title: 00/2163 R

tag: slide id

value: Slide 26

tag: imagene id

tag: age at op


title: 00/20755 R

value: Slide 30

tag: size (mm)

tag: er-status

tag: pgr-status


title: 00/6434 R

value: Slide 28

tag: nodal-status, positive

tag: nodal-status, total removed

tag: duration of tamoxifen (years)


title: 97/7748 R

value: Slide 13

tag: time.to.recurrence (years)


title: breast_052_R

tag: data set (out of 3)


title: breast_037_R

value: IHC-

value: IHC+


title: breast_060_R

value: B+

tag: time.to.death (years)


title: breast_043_R


title: breast_064_R


title: breast_092_R


title: breast_247_R


title: breast_256_R


title: 00/23003 R

value: Slide 31


title: 96/19456 R

value: Slide 12


title: 91/24668 R

value: Slide 11


title: breast_022_R


title: breast_233_R


title: 98/22326 R

value: Slide 17


title: breast_221_R


title: breast_218_R


title: 90/979994 R

value: Slide 10

value: B-


title: breast_236_R


title: breast_063_R


title: breast_229_R


title: 97-3565 R

value: Slide 4


title: 98-10714 R

value: Slide 3


title: breast_176_R


title: breast_178_R


title: breast_207_R


title: 99-16903 R

value: Slide 2


title: breast_179_R


title: breast_181_R


title: breast_191_R


title: 99-8799 R

value: Slide 1


title: 01/7441 R

value: Slide 34


title: breast_173_R


title: breast_015_R


title: breast_157_R


title: breast_154_R


title: 01/33102 N

value: Slide 39


title: breast_114_R


title: breast_130_R


title: breast_103_R


title: 01/21828 N

value: Slide 37


title: 01/2862 N

value: Slide 33


title: 00/3452 N

value: Slide 27


title: 00/11487 N

value: Slide 29


title: 99/25641 N

value: Slide 25


title: breast_010_R

value: B+


title: breast_171_R


title: breast_091_nonR


title: breast_045_nonR


title: breast_069_nonR


title: breast_085_nonR

value: IHC+


title: breast_086_nonR


title: breast_042_nonR


title: breast_038_nonR


title: breast_004_nonR


title: breast_026_nonR


title: breast_257_nonR

value: IHC-


title: 99/21933 N

value: Slide 24


title: breast_251_nonR


title: 99/20673 N

value: Slide 23


title: breast_242_nonR


title: 99/19966 N

value: Slide 22


title: breast_243_nonR


title: breast_223_nonR


title: breast_235_nonR


title: 99/14257 N

value: Slide 21


title: breast_216_nonR


title: breast_208_nonR


title: 99/9765 N

value: Slide 20


title: breast_200_nonR


title: breast_174_nonR


title: CamkII-wt, biological replicate 5, technical replicate 2

city: Neuherberg/Munich

first: Benedikt

last: Wefers

address: Ingolstaedter Landstr. 1

department: Institute of Developmental Genetics

institute: Helmholtz Zentrum Muenchen

data_processing: The raw data were processed in R using beadarray and vsn for normalization

source_name: hippocampus, wildtype

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX, USA) according to the manufacturer’s instructions.

extract_protocol: Animals were killed with CO2, the complete hippocampal tissue was prepared, and total RNA was extracted with the Trizol protocol. The integrity and quality of the RNA samples were analyzed with an RNA electrophoresis chip (RNA 6000 Nano Kit, Agilent, Boeblingen, Germany).

tag: strain

tag: gender

value: male

tag: age

value: 6 months

tag: tissue

value: hippocampus


title: breast_165_nonR


title: CamkII-wt, biological replicate 6, technical replicate 2


title: breast_162_nonR


title: breast_167_nonR


title: 98/17386 N

value: Slide 16


title: 99/1378 N

value: Slide 18


title: breast_143_nonR


title: 99/9170 N

value: Slide 19


title: CamkII-Cre, biological replicate 5, technical replicate 2

source_name: hippocampus, Cre transgene


title: breast_141_nonR


title: 97/25412 N

value: Slide 15


title: breast_139_nonR

value: B-


title: 97/11387 N

value: Slide 14


title: breast_012_nonR


title: breast_119_nonR


title: CamkII-Cre, biological replicate 6, technical replicate 2


title: breast_183_nonR


title: CamkII-wt, biological replicate 4, technical replicate 2


title: CamkII-wt, biological replicate 3, technical replicate 2


title: breast_118_nonR

value: B+


title: 99-16095 N

value: Slide 9

value: IHC+


title: CamkII-Cre, biological replicate 4, technical replicate 2


title: 01-8021 N

value: Slide 8


title: breast_001_nonR


title: 14_Skin_2

description:
SDU_KG_BC_14_Skin
1_US45103081_13982855_S01_Cropped

tag: distant met or lymph node

value: distant

tag: metastasis site

value: skin

tag: patient

tag: prep code

tag: patient nr.


title: 13_Brain

description:
SDU_KG_BC_13_Brain
1_US45103081_13982852_S01_Cropped

value: brain

tag: operation date

tag: er status

tag: pgr status


title: 14_Breast

description:
SDU_KG_BC_14_Breast
1_US45103081_13982854_S02_Cropped

tag: age at diagnosis

tag: localisation of metastasis

value: Liver

tag: diameter of invasive carcinoma (mm)

tag: malignancygrade

tag: positive lymph nodes

value: N/K

tag: time to recurrence (years)


title: CamkII-wt, biological replicate 2, technical replicate 2

tag: strain

tag: gender

value: male

value: 6 months


title: CamkII-Cre, biological replicate 2, technical replicate 2

tag: age

tag: tissue

value: hippocampus


title: 98-13984 N

tag: slide id

value: Slide 5

tag: imagene id

tag: age at op

tag: size (mm)

tag: er-status

tag: pgr-status

tag: nodal-status, positive

tag: nodal-status, total removed

tag: duration of tamoxifen (years)

tag: time.to.recurrence (years)


title: 13_Lymph node

description:
SDU_KG_BC_13_Lymph node
1_US45103081_13982849_S01_Cropped

tag: distant met or lymph node

value: lymph node

tag: metastasis site

tag: patient

tag: prep code

value: SDU_KG_BC_13_Lymph node

tag: patient nr.

tag: operation date


title: 14_Liver

description:
SDU_KG_BC_14_Liver
1_US45103081_13982853_S01_Cropped

source_name: breast cancer, liver met

value: liver

tag: er status

tag: pgr status


title: 00-9843 N

tag: slide id

value: Slide 7

tag: imagene id


title: 13_Breast

description:
SDU_KG_BC_13_Breast
1_US45103081_13982851_S01_Cropped

tag: age at diagnosis

tag: localisation of metastasis

tag: diameter of invasive carcinoma (mm)

tag: malignancygrade

tag: positive lymph nodes

tag: time to recurrence (years)


title: 12_Lymph node

description:
SDU_KG_BC_12_Lymph node
1_US45103081_13982846_S02_Cropped

value: SDU_KG_BC_12_Lymph node


title: CamkII-Cre, biological replicate 3, technical replicate 2

tag: strain

tag: gender

tag: age

tag: tissue


title: 12_Brain_N

description:
SDU_KG_BC_12_Brain_N
1_US45103081_13982848_S02_Cropped

tag: distant met or lymph node

tag: metastasis site

tag: patient

tag: prep code


title: CamkII-Cre, biological replicate 1, technical replicate 2


title: 15_Breast

description:
SDU_KG_BC_15_Breast
1_US45103081_13982857_S01_Cropped

tag: patient nr.

tag: operation date

value: Brain

tag: er status

tag: pgr status


title: 16_Liver

description:
SDU_KG_BC_16_Liver
1_US45103081_13982862_S01_Cropped


title: CamkII-wt, biological replicate 1, technical replicate 2


title: breast_R-40

tag: slide id

tag: age at op

tag: size (mm)

tag: er-status

tag: pgr-status

tag: nodal-status, positive

tag: nodal-status, total removed

tag: duration of tamoxifen (years)

tag: time.to.recurrence (years)

tag: time.to.death (years)


title: CamkII-Cre, biological replicate 6, technical replicate 1

tag: strain

tag: gender

tag: age

tag: tissue


title: breast_R-39


title: 98-3227 N

value: Slide 6

tag: imagene id

value: IHC+


title: breast_R-37


title: CamkII-wt, biological replicate 6, technical replicate 1


title: 11_Breast2_N

description:
SDU_KG_BC_11_Breast2_N
1_US45103081_13982841_S02_Cropped

tag: distant met or lymph node

tag: metastasis site

tag: patient

tag: prep code

tag: patient nr.


title: 11_Breast2_N_2

description:
SDU_KG_BC_11_Breast2_N
1_US45103081_13982842_S02_Cropped


title: breast_R-34

tag: slide id

tag: age at op

tag: size (mm)

tag: er-status

value: B+


title: 11_Breast1

description:
SDU_KG_BC_11_Breast1
1_US45103081_13982840_S02_Cropped

tag: operation date

tag: age at diagnosis

tag: localisation of metastasis

tag: diameter of invasive carcinoma (mm)

tag: malignancygrade

tag: positive lymph nodes

tag: er status

tag: pgr status

tag: time to recurrence (years)


title: 12_Breast

description:
SDU_KG_BC_12_Breast
1_US45103081_13982845_S02_Cropped

tag: distant met or lymph node

tag: metastasis site


title: breast_R-33

tag: pgr-status

value: IHC-

tag: nodal-status, positive

tag: nodal-status, total removed

tag: duration of tamoxifen (years)

tag: time.to.recurrence (years)

tag: time.to.death (years)


title: 11_Ovary

description:
SDU_KG_BC_11_Ovary
1_US45103081_13982837_S01_Cropped

source_name: breast cancer, ovary met

value: distant

value: ovary

tag: patient

tag: prep code

tag: patient nr.

tag: operation date


title: CamkII-wt, biological replicate 5, technical replicate 1

tag: strain

tag: gender

tag: age

tag: tissue


title: CamkII-Cre, biological replicate 5, technical replicate 1


title: breast_R-32

tag: slide id

tag: age at op

tag: size (mm)

tag: er-status


title: CamkII-wt, biological replicate 3, technical replicate 1


title: 10_Brain1

description:
SDU_KG_BC_10_Brain1
1_US45103081_13982836_S01_Cropped

tag: distant met or lymph node

tag: metastasis site

value: brain

tag: er status

tag: pgr status


title: 10_Lymph node

description:
SDU_KG_BC_10_Lymph node
1_US45103081_13982835_S02_Cropped

value: SDU_KG_BC_10_Lymph node


title: CamkII-Cre, biological replicate 4, technical replicate 1

value: male

value: 6 months


title: CamkII-wt, biological replicate 4, technical replicate 1

value: hippocampus


title: breast_R-28

tag: pgr-status

tag: nodal-status, positive

tag: nodal-status, total removed

tag: duration of tamoxifen (years)

tag: time.to.recurrence (years)


title: CamkII-Cre, biological replicate 3, technical replicate 1

tag: strain


title: 07_Brain

description:
SDU_KG_BC_07_Brain
1_US45103081_13982833_S01_Cropped

tag: patient

tag: prep code

tag: patient nr.

tag: operation date


title: CamkII-wt, biological replicate 2, technical replicate 1

tag: gender

tag: age

tag: tissue


title: 12_Brain

description:
SDU_KG_BC_12_Brain
1_US45103081_13982847_S01_Cropped

tag: distant met or lymph node


title: CamkII-Cre, biological replicate 2, technical replicate 1


title: 11_Ovary_N

description:
SDU_KG_BC_11_Ovary_N
1_US45103081_13982844_S02_Cropped

source_name: ovary normal

tag: metastasis site


title: breast_R-27

tag: slide id

tag: age at op

tag: size (mm)

tag: er-status

tag: time.to.death (years)


title: 11_Breast2_N_3

description:
SDU_KG_BC_11_Breast2_N
1_US45103081_13982843_S02_Cropped


title: 11_Liver

description:
SDU_KG_BC_11_Liver
1_US45103081_13982838_S02_Cropped

tag: er status

tag: pgr status


title: breast_R-26

tag: pgr-status

tag: nodal-status, positive

tag: nodal-status, total removed

tag: duration of tamoxifen (years)

tag: time.to.recurrence (years)


title: 07_Lymph node

description:
SDU_KG_BC_07_Lymph node
1_US45103081_13982832_S01_Cropped

value: lymph node

tag: patient

tag: prep code

value: SDU_KG_BC_07_Lymph node

tag: patient nr.

tag: operation date


title: 07_Breast

description:
SDU_KG_BC_07_Breast
1_US45103081_13982830_S01_Cropped

tag: distant met or lymph node

tag: metastasis site

tag: age at diagnosis

tag: localisation of metastasis

tag: diameter of invasive carcinoma (mm)

tag: malignancygrade

tag: positive lymph nodes

tag: time to recurrence (years)


title: breast_R-23

tag: slide id

tag: age at op

tag: size (mm)

tag: er-status

tag: pgr-status


title: 06_Lymph node_N

description:
SDU_KG_BC_06_Lymph node_N
1_US45103081_13982826_S02_Cropped

source_name: lymph node normal

tag: patient

value: SDU_KG_BC_06_Lymph node_N


title: breast_R-25

tag: nodal-status, positive

tag: nodal-status, total removed

tag: duration of tamoxifen (years)

tag: time.to.recurrence (years)

tag: time.to.death (years)


title: breast_R-22


title: 06_Breast1_N

description:
SDU_KG_BC_06_Breast1_N
1_US45103081_13982827_S02_Cropped

tag: distant met or lymph node

tag: metastasis site

tag: prep code

tag: patient nr.


title: breast_R-21_rep2


title: CamkII-wt, biological replicate 1, technical replicate 1

tag: strain

tag: gender

tag: age

tag: tissue


title: breast_R-21_rep1

tag: slide id

tag: age at op

tag: size (mm)


title: 06_Breast1

description:
SDU_KG_BC_06_Breast1
1_US45103081_13982823_S02_Cropped

tag: patient

tag: operation date

tag: age at diagnosis

tag: localisation of metastasis

tag: diameter of invasive carcinoma (mm)

tag: malignancygrade

tag: positive lymph nodes

tag: er status

tag: pgr status

value: N/K

tag: time to recurrence (years)


title: breast_R-19

tag: er-status

tag: pgr-status

tag: nodal-status, positive

tag: nodal-status, total removed

tag: duration of tamoxifen (years)

tag: time.to.recurrence (years)

tag: time.to.death (years)


title: breast_R-20

tag: slide id

tag: age at op

tag: size (mm)


title: breast_R-18


title: breast_R-16


title: Braf-cko, biological replicate 1, technical replicate 2

source_name: hippocampus, conditional knockout

tag: strain

tag: gender

tag: age

value: 4 months

tag: tissue


title: breast_R-11


title: 06_Lymph node

description:
SDU_KG_BC_06_Lymph node
1_US45103081_13982824_S01_Cropped

source_name: breast cancer, lymph node

tag: distant met or lymph node

tag: metastasis site

tag: patient

tag: prep code

value: SDU_KG_BC_06_Lymph node

tag: patient nr.

tag: operation date


title: Braf-flox, biological replicate 6, technical replicate 1

source_name: hippocampus, floxed control


title: Braf-cko, biological replicate 4, technical replicate 1


title: breast_R-8

tag: er-status

tag: pgr-status

tag: nodal-status, positive

tag: nodal-status, total removed


title: breast_R-5

tag: slide id

tag: duration of tamoxifen (years)

tag: time.to.recurrence (years)

tag: time.to.death (years)


title: breast_R-4

tag: age at op

tag: size (mm)


title: breast_R-3


title: CamkII-Cre, biological replicate 1, technical replicate 1

tag: strain

tag: gender

tag: age

tag: tissue


title: Braf-cko, biological replicate 5, technical replicate 1


title: Braf-flox, biological replicate 5, technical replicate 1


title: Braf-flox, biological replicate 3, technical replicate 1


title: Braf-cko, biological replicate 2, technical replicate 1


title: breast_R-10


title: Braf-flox, biological replicate 4, technical replicate 1


title: Braf-flox, biological replicate 2, technical replicate 1


title: breast_R-7


title: Braf-cko, biological replicate 3, technical replicate 1


title: Braf-cko, biological replicate 1, technical replicate 1


title: uterus containing embryos at blastocyst stage C4, biological rep 1

city: Sheffield

first: Carmen

last: Alminana

address: Tree Root Walk

department: Academic Unit of Reproductive and Developmental Medicine, Human Metabolism Department

institute: University of Sheffield

description: Gene expression data from uterus in response to embryos at balstocyst stage

hyb_protocol: 12 μg of cRNA molecules were heat fragmented and injected to the Porcine GeneChips in a hybridization solution according to the Affymetrix protocol. Hybridization took place overnight in a rotating hybridization oven at 60rpm, 45°C for 16 hours. The GeneChip arrays were washed using the Affymetrix Fluidics Station.

scan_protocol: After washing, the GeneChip arrays were scanned using Affymetrix GC3000 scanner.

data_processing: The resultant images were analysed using the Microarray Suite software version 5.1 (MAS 5.1 Affymetrix).

organism: Sus scrofa

source_name: uterus containing embryos at blastocyst stage, biological rep 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, Affymetrix,P/N 702232 Rev. 3 ).

extract_protocol: Total RNA was isolated using a standard procedure involving phenol:chloroform extraction followed by ethanol precipitation.

treatment_protocol: In order to identify the uterine gene expression modified in the presence of the embryo when compared to the oocyte we used a novel model that eliminated genetic variability. One oviduct was inseminated with spermatozoa and the contralateral oviduct was injected with diluent only, using laparoscopic insemination. This allowed us to obtain samples from the same sow, one uterine horn containing embryos at the blastocyst stage (6 days after insemination) and the contralateral uterine horn with oocytes. Uterine tissues were collected from both sides of the reproductive tract in each sow by hysterectomy at day 6 after laparoscopic inseminations. After evaluating embryos and oocytes in each uterine horn the reproductive tract was excised by hysterectomy operation and the uterine horns were opened longitudinally. Then, epithelial cells were isolated by scraping of the mucosal epithelial layer from the uterine horn in the first 10 cm of the horn adjacent to utero-tubal junction with a glass slide. Scraped cells from the uterine horn samples were transferred immediately to Tri Reagent (Sigma, Sigma-Aldrich Co, Madrid, Spain), homogenised, snap-frozen in liquid nitrogen and stored at -80ºC until further processing.

value: uterus

tag: sample type


title: Braf-flox, biological replicate 1, technical replicate 1


title: uterus containing embryos at blastocyst stage C6, biological rep 3

source_name: uterus containing embryos at blastocyst stage, biological rep 3


title: uterus containing oocytes C3, biological rep 3

description: Gene expression data from uterus in response to oocytes

source_name: uterus containing oocytes, biological rep 3

value: uterus containing oocytes


title: uterus containing embryos at blastocyst stage C5, biological rep 2

source_name: uterus containing embryos at blastocyst stage, biological rep 2


title: uterus containing oocytes C1, biological rep 1

source_name: uterus containing oocytes, biological rep 1


title: uterus containing oocytes C2, biological rep 2

source_name: uterus containing oocytes, biological rep 2


title: Turkmens Central Asia Male turkmE31

status: Public on Apr 18 2012

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

description: Genomic DNA extracted from blood was genotyped using Human610-Quad v1.0  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:
Genomic DNA extracted from blood was genotyped using Infinium Human610-Quad v1.0  Genotyping BeadChips (Illumina).
Image data was analyzed using Genomestudio v2009.2 with GT module 1.5.16 (Illumina).

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C 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 blood was performed using standard extraction protocols.

value: Male

tag: population

value: Turkmens

tag: region

value: Central Asia

value: blood


title: Kurds Central Asia Male kurd1198

value: Kurds


title: Turkmens Central Asia Male turkm3661


title: Turkmens Central Asia Male turkm537


title: Turkmens Central Asia Male turkmG33


title: Kurds Central Asia Male kurd1101


title: Tajiks Central Asia Female tad838

value: Female

value: Tajiks


title: Kurds Central Asia Male kurd1160


title: Turkmens Central Asia Male turkm1820


title: Turkmens Central Asia Male turkmV32


title: Turkmens Central Asia Male turkmH6


title: Turkmens Central Asia Male turkmu26


title: Turkmens Central Asia Male turkmG31


title: Turkmens Central Asia Female turkmu33


title: Kurds Central Asia Male kurd1156


title: Turkmens Central Asia Female turkmE42


title: Turkmens Central Asia Female turkm7529


title: Armenians Caucasus Male armenia106

value: Armenians

value: Caucasus


title: Armenians Caucasus Male armenia162


title: Armenians Caucasus Male armenia279


title: Armenians Caucasus Male armenia139


title: Armenians Caucasus Male armenia191


title: Armenians Caucasus Male armenia91


title: Kurds Central Asia Male kurd1173


title: Kumyks Caucasus Female Kumyk22

value: Kumyks


title: Armenians Caucasus Male armenia102


title: Kurds Central Asia Male kurd1159


title: Armenians Caucasus Male armenia293


title: Armenians Caucasus Male armenia176


title: Turkmens Central Asia Male turkmBe24


title: Armenians Caucasus Male armenia80


title: Armenians Caucasus Male armenia86


title: Armenians Caucasus Male armenia73


title: Kumyks Caucasus Male kumyks15


title: North_Ossetians Caucasus Male NorthOssetia19


title: Kumyks Caucasus Male kumyks7


title: Kumyks Caucasus Female kumyks11


title: Kumyks Caucasus Male kumyks111


title: Kumyks Caucasus Male kumyks10


title: Kumyks Caucasus Male kumyks8


title: Armenians Caucasus Male armenia7


title: Kumyks Caucasus Female kumyks13


title: North_Ossetians Caucasus Male NorthOssetia12


title: Kumyks Caucasus Male kumyks5


title: North_Ossetians Caucasus Male NorthOssetia16


title: Armenians Caucasus Male armenia3


title: Kumyks Caucasus Male kumyks4


title: Kumyks Caucasus Male kumyks110


title: North_Ossetians Caucasus Male NorthOssetia20


title: North_Ossetians Caucasus Male NorthOssetia17


title: North_Ossetians Caucasus Male NorthOssetia11


title: Armenians Caucasus Male armenia36


title: North_Ossetians Caucasus Male NorthOssetia14


title: Kumyks Caucasus Male kumyks1


title: Kumyks Caucasus Male kumyks108


title: Kumyks Caucasus Male kumyks6


title: North_Ossetians Caucasus Male NorthOssetia13


title: North_Ossetians Caucasus Male NorthOssetia8


title: Armenians Caucasus Male armenia71


title: North_Ossetians Caucasus Male NorthOssetia5


title: North_Ossetians Caucasus Male NorthOssetia3


title: North_Ossetians Caucasus Male NorthOssetia9


title: North_Ossetians Caucasus Male NorthOssetia1


title: Ukrainians East Europe Male UkrainePol19

value: Ukrainians

value: East Europe


title: Ukrainians East Europe Male Ukraine97


title: North_Ossetians Caucasus Male NorthOssetia2


title: Ukrainians East Europe Female UkrBel736


title: Ukrainians East Europe Male Ukraine94


title: Ukrainians East Europe Male Ukraine130


title: Ukrainians East Europe Male UkrainePol25


title: Ukrainians East Europe Male Ukraine141


title: Ukrainians East Europe Male UkrBel614


title: Ukrainians East Europe Male Ukraine133


title: Bulgarians East Europe Male Bulgaria37

value: Bulgarians


title: Ukrainians East Europe Male UkrLv215


title: North_Ossetians Caucasus Male NorthOssetia4


title: Ukrainians East Europe Male Ukraine136


title: Ukrainians East Europe Male UkrLv240


title: Bulgarians East Europe Male Bulgaria39


title: Ukrainians East Europe Male UkrLv228


title: Ukrainians East Europe Male UkrLv237


title: Ukrainians East Europe Male UkrLv223


title: Ukrainians East Europe Male UkrBel620


title: Ukrainians East Europe Female UkrBel733


title: Bulgarians East Europe Male Bulgaria33


title: Ukrainians East Europe Male UkrBel622


title: Bulgarians East Europe Male Bulgaria25


title: Bulgarians East Europe Male Bulgaria8


title: Bulgarians East Europe Male Bulgaria26


title: Ukrainians East Europe Male UkrLv226


title: Ukrainians East Europe Male UkrBel618


title: Bulgarians East Europe Male Bulgaria7


title: Bulgarians East Europe Male Bulgaria3


title: Balkars Caucasus Male bal88

value: Balkars


title: Bulgarians East Europe Male Bulgaria4


title: Bulgarians East Europe Male Bulgaria2


title: Bulgarians East Europe Male Bulgaria6


title: Balkars Caucasus Male bal80


title: Balkars Caucasus Male bal7


title: Bulgarians East Europe Male Bulgaria1


title: Balkars Caucasus Male bal97


title: Balkars Caucasus Male bal31


title: Bulgarians East Europe Male Bulgaria5


title: Balkars Caucasus Male bal50


title: Balkars Caucasus Male bal14


title: Balkars Caucasus Male bal45


title: Balkars Caucasus Male bal115


title: Balkars Caucasus Male bal124


title: Balkars Caucasus Male bal136


title: Balkars Caucasus Male bal26


title: Balkars Caucasus Male bal108


title: Abkhazians Caucasus Male abh71

value: Abkhazians


title: Abkhazians Caucasus Male abh74


title: Balkars Caucasus Male bal22


title: Abkhazians Caucasus Male abh9


title: Abkhazians Caucasus Male abh45


title: Abkhazians Caucasus Male abh53


title: Abkhazians Caucasus Male abh41


title: Abkhazians Caucasus Male abh60


title: Abkhazians Caucasus Male abh24


title: Abkhazians Caucasus Male abh27


title: Abkhazians Caucasus Male abh85


title: Abkhazians Caucasus Male abh165


title: Abkhazians Caucasus Male abh154


title: Balkars Caucasus Male bal32


title: Abkhazians Caucasus Male abh107


title: Balkars Caucasus Male bal42


title: Abkhazians Caucasus Male abh100


title: Abkhazians Caucasus Male abh119


title: Abkhazians Caucasus Male abh122


title: Abkhazians Caucasus Male abh135


title: Balkars Caucasus Male bal64


title: Abkhazians Caucasus Male abh133


title: Mordovians East Europe Male mordovia15

value: Mordovians


title: Mordovians East Europe Male mordovia14


title: Mordovians East Europe Male mordovia13


title: Mordovians East Europe Male mordovia12


title: Mordovians East Europe Male mordovia11


title: Abkhazians Caucasus Male abh147


title: Mordovians East Europe Male mordovia5


title: Mordovians East Europe Male mordovia4


title: Abkhazians Caucasus Male abh137


title: Mordovians East Europe Male mordovia10


title: Balkars Caucasus Male bal149


title: Mordovians East Europe Male mordovia8


title: Balkars Caucasus Male bal102


title: Mordovians East Europe Male mordovia7


title: Mordovians East Europe Male mordovia6


title: Tajiks Central Asia Male tadjik15


title: Mordovians East Europe Male mordovia3


title: Tajiks Central Asia Male tadjik2


title: Tajiks Central Asia Male tadjik4


title: Tajiks Central Asia Male tadjik3


title: Tajiks Central Asia Female tadjik13


title: Tajiks Central Asia Female tadjik9


title: Tajiks Central Asia Male tadjik6


title: Tajiks Central Asia Male tadjik12


title: Tajiks Central Asia Male tadjik7


title: Tajiks Central Asia Female tadjik8


title: Tajiks Central Asia Female tadjik10


title: Tajiks Central Asia Female tadjik11


title: Mordovians East Europe Male mordovia2


title: Mordovians East Europe Male mordovia9


title: Tajiks Central Asia Male tadjik5


title: Chechens Caucasus Male ch193

value: Chechens


title: Tajiks Central Asia Male tadjik14

value: Male


title: DBF 6h3-chem

city: Lausanne

first: Edith

last: Coronado

state: Vaud

address: UNIL-Sorge

department: Microbiologie Fondamental

country: Switzerland

institute: UNIL

description: Gene expression of cells after 6h exposure to dibenzofuran in chemostat

hyb_protocol: Sixty ng of labeled cDNA were loaded onto each microarray, hybridized for 17 hours at 65°C, and washed and scanned as described for labeled cRNA in the One-Color Microarray-Based Gene Expression Analysis Manual (Agilent). The fragmentation step (heating to 60°C for 30 minutes) was omitted.

scan_protocol: Microarray slides were scanned using an Agilent High-Resolution Microarray Scanner (G2505), immediately after hybridization using the One-Color microarray -based gene expression analysis protocol provided by Agilent (scan area 61x21.6mm XDRHi:100% XDRLo:10%).

data_processing: Hybridization signal intensities were quantified from microarray image scans using AGILENT FEATURE EXTRACTION software version 10.5.1.1 (Agilent). Microarray data were normalized and globally scaled over the array using GENESPRING GX software with the RMA algorithm and quantile normalization. The samples corresponding to the cells that were exposed to dibenzofuran were compared to the ones growing on phenylalanine or exposed to phenylalanine media.

organism: Rhizorhabdus wittichii RW1

source_name: 6h after dibenzofuran exp, replica3

label_protocol: cDNA was synthesized from total RNA and directly labeled with cyanine-3-dCTP. Briefly, each 50-μL reaction contained 5 μg of total RNA, 1.25 μg of random hexanucleotide primers (Promega), 100 μM each of unlabeled dATP, dGTP, and dTTP (Invitrogen), 25 μM of unlabeled dCTP (Invitrogen), 25 μM of cyanine-3-labeled dCTP (Perkin-Elmer), 25 U SUPERase•In (Ambion), and 400 U Superscript II reverse transcriptase (Invitrogen). Reactions were performed by heating at 42°C for 2 hours followed by 70°C for 10 min. RNA was then removed by adding 100 mM NaOH, heating to 65°C for 20 min, and neutralized with 100 mM HCl and 300 mM sodium acetate (pH 5.2). Labeled cDNA products were purified using the MinElute PCR purification kit (Qiagen) and the quantity and incorporation of cyanine-3- labeled dCTP were calculated using the MICROARRAY function on a NanoDrop Spectrophotometer.

growth_protocol: Batch cultures of Sphingomonas wittichii RW1 were grown in 100 ml erlenmeyer flasks containing 20 ml of minimal medium with phenylalanine (5mM) or dibenzofuran (dosage of 5umol/ml) as carbon source. All cultures were started at an initial culture turbidity of 0.005 (at 600 nm, OD600) and incubated at 30°C with rotary shaking. Continuous culturing in carbon limited mode (chemostats) of strain RW1 was carried out in triplicate 500-ml working volume reactors (Infors-HT), containing 400 ml MM with 5 mM PHE as carbon and energy source. Reactors were inoculated with 100 ml of a preculture of RW1, grown on minimal media plus phenylalanine and grown until stationary phase (OD600 ~1). The triplicate fermentors were then first operated in batch mode at 30°C and with a stirring speed of 200 rpm. The pH and partial oxygen pressure (pO2) were monitored online and maintained at 7 and 90%, respectively. When the culture turbidity reached a steady value of OD600 = 1, the inflow of fresh MM with 5 mM Phe was started. The flow rate set was 23.8 ml/hr, giving a dilution rate of 0.05 hr-1, which corresponds to a doubling time of 14.6 h. The calculated maximal specific growth rate of strain RW1 in batch culture in MM with 5 mM PHE is 0.24 hr-1. The culture turbidity was measured at regular time intervals and culture samples were plated on LB agar to verify culture purity. Silicon based antifoam suspension (AntifoamB emulsion, Sigma-Aldrich) was added at a rate of 0.025 ml/hr to avoid excessive culture foaming. The continuous culture was considered in equilibrium after five reactor volume changes and when the measured parameters (culture turbidity and pO2) were stable.

extract_protocol: Total RNA was isolated and purified from S.wittichii RW1 frozen cells on the filters or pellets by hot-phenol extraction as described elsewhere (Johnson et al, 2008). Briefly, each 2-ml microcentrifuge tube that contained a frozen filter or cell pellet was filled with 250 ml lysis buffer (50 mM sodium acetate, 10 mM EDTA [pH 5.1]), 100 ul 10% sodium dodecyl sulfate, 1.0 ml buffer-equilibrated phenol (pH 4.3) (Sigma-Aldrich, St. Louis, MO), and 1 g 100 um-diameter silica beads (Sigma-Aldrich, St. Louis, MO). Cells were lysed by heating to 65°C for 2 min, bead beating for 2 min, incubating at 65°C for 8 min, and bead beating again for an additional 2 min. Cellular debris were collected by centrifugation (5 min at 13,000 rpm), and the aqueous lysate was transferred to a new nuclease-free microcentrifuge tube. The lysate was extracted twice with 1 volume of phenol-chloroform-isoamyl alcohol (pH 4.3) (125:24:1,vol/vol) and once with 1 volume of chloroform-isoamyl alcohol (24:1, vol/vol)(Sigma-Aldrich). RNA was precipitated by adding 0.1 volume of 3 M sodium acetate and 2 volumes of 100% ethanol. The precipitate was collected by centrifugation, washed once with 80% ethanol, and resuspended in nuclease-free water. RNA was purified from contaminating DNA by DNase I treatment using the DNA-free kit (Ambion, Austin, TX) according to the manufacturer’s instructions. Purified RNA was stored at -80°C prior to further use.

treatment_protocol: 1. dibenzofuran induction of S. wittichii RW1 cells in batch cultures: An overnight culture of RW1 was used to inoculate four different erlenmeyer flasks containing 20ml of minimal media+Phenylalanine (5mM) and they were incubated at 30°C until culture reached an OD600 of 0.2. The cultures were centrifuged during 2 min at 6000rpm at RT, the supernatant discarded and the cell pellets were immediately resuspended in either MM+DBF in crystals or MM+Phenylalanine. The cultures were incubated during 30 min at 30°C with rotary shaking after which the cells were filtered, the filters introduced in screw cap centrifuge tubes and immediately frozen with liquid N2. Protocol 2. Dibenzofuran induction of S. wittichii RW1 in continous cultures: RW1 cells were grown in fermentors (in triplicate) using MM+phenylalanine as growth media, until a steady state was observed. A pulse of dibenzofuran (2 mg in 1ml of heptamethylnonane per 400 ml working volume) was given to each fermentor and the media was immediately changed to MM+phenylalanine+DBF in crystals. Cell samples were extracted from the fermentors after dibenzofuran induction (time 0) and 30min, 1h, 2h and 6h after induction. Cell cultures were centrifuged (1min, 13,000rpm), the supernatant discarded and the cell pellets frozen with liquid N2. Protocol 3. Growth on DBF of S.wittichii RW1 compared to growth on Phe: An overnight culture of RW1 was used to inoculate two sets of three 100ml erlenmeyer flasks containing 20 ml of either mm+phenylalanine or mm+DBF (dosage of 5umol/ml). Cultures were incubated at 30°C on a rotary shaker, and let to grow until an O600 of 0.2 was reached. After this the cultures were filtered, the filters introduced in screw cap centrifuge tubes and immediately submerged in liquid N2.

tag: protocol

value: chemostat


title: Chechens Caucasus Male ch113


title: Chechens Caucasus Male ch174


title: Chechens Caucasus Male ch179


title: Chechens Caucasus Male ch126


title: Chechens Caucasus Male ch131


title: Chechens Caucasus Male ch86


title: DBF 6h1-chem

source_name: 6h after dibenzofuran exp, replica1


title: DBF 6h2-chem

source_name: 6h after dibenzofuran exp, replica2


title: Chechens Caucasus Male ch150


title: Chechens Caucasus Male ch109


title: Chechens Caucasus Male ch55


title: DBF 2h3-chem

description: Gene expression of cells after 2h exposure to dibenzofuran in chemostat

source_name: 2h after dibenzofuran exp, replica3


title: DBF 1h3-chem

description: Gene expression of cells after 1h exposure to dibenzofuran in chemostat

source_name: 1h after dibenzofuran exp, replica3


title: DBF 2h1-chem

source_name: 2h after dibenzofuran exp, replica1


title: Chechens Caucasus Male ch34


title: Chechens Caucasus Male ch101


title: Chechens Caucasus Male ch60


title: DBF 1h2-chem

source_name: 1h after dibenzofuran exp, replica2


title: Chechens Caucasus Male ch170


title: Chechens Caucasus Male ch21


title: DBF 2h2-chem

source_name: 2h after dibenzofuran exp, replica2


title: Mordovians East Europe Male mordovia1


title: DBF 1h1-chem

source_name: 1h after dibenzofuran exp, replica1


title: Chechens Caucasus Male ch31


title: Uveal melanoma 23

city: Genova

first: Valentina

last: Mirisola

address: Largo Benzi 10

department: Functiona Genomics

country: Italy

institute: National Cancer Institute

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Affymetrix Expression Console

source_name: Uveal melanoma

label_protocol: Standard Affymetrix procedures

extract_protocol:
Tumour samples were homogenized in the tissue lyser Mixer Mill in total RNA extraction lysis buffer Qiazol (Qiagen).
Total RNA was extracted from the tissue lysate using an miRNeasy mini kit (Qiagen).

value: uveal melanoma

value: female

tag: eye

value: right


title: Chechens Caucasus Male ch76

value: blood


title: Uveal melanoma 20

value: left


title: Uveal melanoma 18

value: male


title: Uveal melanoma 21


title: DBF 30m3-chem

description: Gene expression of cells after 30min exposure to dibenzofuran in chemostat

source_name: 30 min after dibenzofuran exp, replica3


title: Uveal melanoma 36


title: Turkmens Central Asia Male turkmen1

value: Turkmens

value: Central Asia


title: DBF 30m2-chem

source_name: 30 min after dibenzofuran exp, replica2


title: Nogays Caucasus Male nogay21

value: Nogays

value: Caucasus


title: Nogays Caucasus Male nogay24


title: Uveal melanoma 2


title: Chechens Caucasus Male ch16


title: Chechens Caucasus Male ch3


title: Uveal melanoma 32


title: Uveal melanoma 40


title: Turkmens Central Asia Male turkmen2


title: Nogays Caucasus Male nogay25


title: Nogays Caucasus Male nogay38


title: Nogays Caucasus Male nogay33


title: Phe ctrl4-chem

description: Gene expression of cells grown in phenylalanine in chemostat

source_name: phenylalanine-grown cells in chemostat, replica4


title: Nogays Caucasus Male nogay39


title: Uveal melanoma 31


title: Phe ctrl2-chem

source_name: phenylalanine-grown cells in chemostat, replica2


title: Phe ctrl3-chem

source_name: phenylalanine-grown cells in chemostat, replica3


title: Chechens Caucasus Male ch11


title: Uveal melanoma 33


title: Phe ctrl1-chem

source_name: phenylalanine-grown cells in chemostat, replica1


title: DBF3_long

description: Gene expression of cells grown in dibenzofuran media

source_name: dibenzofuran grown cells replica3

value: batch


title: Uveal melanoma 25


title: Uveal melanoma 34


title: Uveal melanoma 7

extract_protocol: Tumour samples were homogenized in the tissue lyser Mixer Mill in total RNA extraction lysis buffer Qiazol (Qiagen).


title: Uveal melanoma 6


title: Uveal melanoma 17


title: Uveal melanoma 5


title: DBF2_long

source_name: dibenzofuran grown cells replica2


title: Uveal melanoma 8


title: Uveal melanoma 22


title: DBF1_long

source_name: dibenzofuran grown cells replica1


title: Uveal melanoma 4


title: Nogays Caucasus Male nogay35

source_name: blood


title: Nogays Caucasus Male nogay34


title: Uveal melanoma 12


title: Phe3_long

description: Gene expression of cells grown in phenylalanine media

source_name: phenylalanine grown cells replica3


title: Uveal melanoma 11


title: Nogays Caucasus Male nogay31


title: Phe2_long

source_name: phenylalanine grown cells replica2


title: Phe1_long

source_name: phenylalanine grown cells replica1


title: Uveal melanoma 10


title: Uveal melanoma 1


title: Uveal melanoma 9


title: DBF3_shock

description: Gene expression of cells resuspended in dbf media

source_name: dibenzofuran shock exp, replica 6


title: Uveal melanoma 13


title: Nogays Caucasus Male nogay47


title: HepG2 treated with BF Array 3

city: Seoul

first: Mi-Kyung

last: Song

address: 39-1 Hwawol-gok-dong, Wolsong-gil5, Seongbuk-gu-seoul

country: South Korea

institute: Korea Institute of Science & Technology

hyb_protocol: Hybridization was performed by incubation in a hybridization oven at 62°C for 12 h. After washing (2× SSC/0.1% SDS for 2 min at 58°C, 1× SSC for 2 min at RT, and 0.2× SSC for 3 min at room temperature [RT]), slides were dried by centrifugation at 800 rpm for 3 min at RT.

scan_protocol: Images of the hybridized slides were captured using a GenePix 4000B scanner (Axon Instruments, USA). Scanned images were analyzed with GenePix 5.1 software (Axon Instruments) to obtain gene expression ratios.

data_processing: After analysis of scanned images, spots judged as substandard by visual examination of each slide were flagged and excluded from further analysis. Spots with dust artifacts or spatial defects were manually flagged and excluded. In an attempt to filter out unreliable data, spots with signal-to-noise ratios were also excluded. Data were normalized by global, lowless, print-tip, and scaled normalization methods. A volcano plot of genes that behaved similarly across BF treatments was created using GeneSpring GX 7.3.1 software. We utilized an algorithm based on Pearson's correlation to separate genes with similar patterns

source_name: HepG2 treated BF labeled with Cy5

label_protocol: Platinum Biochip Reagent Kit

extract_protocol: Trizol extraction

tag: agent

value: BF

tag: cell line

value: HepG2 (hepatocellular carcinoma)

source_name: HepG2 treated DMSO labeled with Cy3

value: DMSO


title: Uveal melanoma 16

source_name: Uveal melanoma


title: DBF 30m1-chem

source_name: 30 min after dibenzofuran exp, replica1


title: Adeno-Cre vs. Adeno-GFP infected Cdk7lox/lox MEFs rep 10

city: Madrid

first: David

last: Santamaría

state: Madrid

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

hyb_protocol: Samples were hybridized to Mouse WMG 4X44K (Agilent).

scan_protocol: Microarrays were scanned on a G2565C DNA microarray scanner (Agilent).

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 10.1.1).
Bioconductor's limma package was employed for preprocessing and normalization, thus, background was corrected using normexp method and data were normalized using loess and quantiles method for within-array and inter-array normalization, respectively
Normalized log2 ratio representing KO/WT in all cases including dye-swap experiment column (Sample 4).

source_name: WT

label_protocol: 1µg per sample was labeled with Two-Color Microarray-Based Gene Expression Analysis (Agilent) and purified with silica-based RNeasy spin columns (Qiagen).

growth_protocol: MEFs were grown in DMEM supplemented with 10% fetal bovine serum in 5%CO2 incubator. Following adenoviral infection MEFs were splitted when necessary to maintain sub-confluent cultures.

extract_protocol: RNA was extracetd using RNeasy kit (Quiagen) 7 days after adenoviral infection. RNA integrity was assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer.

treatment_protocol: MEFs were infected with 100MOI of Ad5-CMVCre or Ad5-CMVGFP.

tag: cell type

value: Adeno-GFP infected Cdk7lox/lox MEFs

value: Mixed (129 x C57Bl/6)

tag: genotype

value: WT

source_name: KO

value: Adeno-Cre infected Cdk7lox/lox MEFs

value: KO


title: HepG2 treated with BF Array 2


title: DBF2_shock

source_name: dibenzofuran shock exp, replica 5


title: Adeno-Cre vs. Adeno-GFP infected Cdk7lox/lox MEFs rep 9


title: Adeno-Cre vs. Adeno-GFP infected Cdk7lox/lox MEFs rep 7


title: Uveal melanoma 15

value: uveal melanoma


title: Adeno-Cre vs. Adeno-GFP infected Cdk7lox/lox MEFs rep 8


title: Adeno-Cre vs. Adeno-GFP infected Cdk7lox/lox MEFs rep 6


title: DBF1_shock

source_name: dibenzofuran shock exp, replica 4


title: Nogays Caucasus Male nogay48

value: Male

value: blood


title: HepG2 treated with BA Array 2

data_processing: After analysis of scanned images, spots judged as substandard by visual examination of each slide were flagged and excluded from further analysis. Spots with dust artifacts or spatial defects were manually flagged and excluded. In an attempt to filter out unreliable data, spots with signal-to-noise ratios were also excluded. Data were normalized by global, lowless, print-tip, and scaled normalization methods. A volcano plot of genes that behaved similarly across BA treatments was created using GeneSpring GX 7.3.1 software. We utilized an algorithm based on Pearson's correlation to separate genes with similar patterns

source_name: HepG2 treated BA labeled with Cy5

value: BA


title: Phe3_shock

description: Gene expression of cells resuspended in phenylalanine media

source_name: phenylalanine shock exp, replica 3


title: Uveal melanoma 3

value: male

value: right


title: HepG2 treated with BA Array 3

source_name: HepG2 teated BA labeled with Cy5


title: Nogays Caucasus Male nogay46

value: Nogays


title: HepG2 treated with BA Array 1


title: Nogays Caucasus Male nogay45

value: Caucasus


title: HepG2 treated with BF Array 1


title: Phe2_shock

source_name: phenylalanine shock exp, replica 2

value: batch


title: Phe1_shock

source_name: phenylalanine shock exp, replica 1