title: C2PL16V2

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: BL22

status: Public on Apr 01 2014

type: genomic

city: Nagoya

first: Miyuki

middle: Suguro

last: Katayama

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

department: Division of Molecular Medicine

country: Japan

institute: Aichi Cancer Center Research Institute

description: file with raw data for this sample: Burkitt_lymphoma01_to_26.txt

hyb_protocol: Labeled 1 μg of tested and reference DNA samples was mixed with 100 μg of Human Cot-1 DNA (Invitrogen) and precipitated, after which the pellet was resuspended in the 45-μl hybridization mixture, which consisted of 50% form amide, 10% dextran sulfate, 2× SSC, 4% SDS, and 10 μg/μl yeast tRNA (Invitrogen Life Technologies, Inc.) Hybridization was performed for 48 h in a container placed on a slowly rocking table containing 200 μl of 50% form amide and 2× SSC to control moisture.    It was followed by 15 min post hybridization washing in 50% form amide/2× SSC at 50°C, 30 min in 2× SSC/0.1% SDS at 50°C, 15 min in PN buffer consisting of 0.1 M NaH2PO4, 0.1 M Na2HPO4 at (pH 8.0), and 0.1% NP40 at room temperature, rinsing in 2× SSC at room temperature, and finally dehydration in 70%, 85%, 100% ethanol at room temperature for 2 min each and air-drying.

scan_protocol: Scanning analysis was carried out with the Agilent Micro Array Scanner (Agilent Technologies).

data_processing: Acquired array images were analyzed using Genepix Pro 4.1 (Axon Instruments, Inc., Foster City, CA). DNA spots were automatically segmented, the local background was subtracted, and the total intensities and fluorescence intensity ratio of the two dyes for each spot were calculated. Fluorescence intensity ratio of the two dyes (Cy3 intensity/Cy5 intensity) were converted into log2 intensity ratios (log2 ratio).  In order to remove the so-called probe effect, we first selected a subset of the samples whose Pearson's correlation coefficient r > 0.5 (p=2E-155), where correlation was computed after removing obvious genomic aberrations manually.   Then, at each probe, we considered the median value of those selected samples as the probe specific bias, and it was subtracted from the log2 ratios of the entire samples.

molecule: genomic DNA

organism: Homo sapiens

source_name: A tumor biopsy sample of a Burkitt lymphoma patient at diagnosis

label_protocol: Tested and reference(mixture of 10 healthy male) DNA (1 μg each) was digested with DpnII and labeled with the Bio prime DNA labeling system (Invitrogen) using cyanine3-dUTP and cyanine5-dUTP (GE Healthcare Life Sciences), respectively. Unincorporated fluorescent nucleotides were removed with the aid of Sephadex G-50 spin columns (GE Healthcare Life Sciences).

extract_protocol: Genomic DNA was extracted according to standard procedures using proteinase K digestion and phenol chloroform extraction. Normal DNA was prepared by using peripheral-blood lymphocytes from a normal male.

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

value: clonal heterogeneity (+)

tag: international prognostic index

value: high / high intermediate

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

value: loss

tag: follow up years

tag: dead or alive at the end of follow-up

value: Dead

source_name: healthy males

value: male


title: BL19

value: clonal heterogeneity (-)

tag: gender


title: BL18


title: BL17

value: low / low intermediate

value: Alive


title: BL21


title: BL20


title: BL14

value: loss / deletion


title: BL15


title: BL16


title: BL13


title: BL11


title: C2PL3V4

type: RNA

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

country: USA

institute: Baylor Institute for Immunology Research

hyb_protocol: 750 ng of amplified labeled RNA were hybridized overnight to Illumina HT12 V4 beadchips (Illumina, San Diego, CA)

scan_protocol: Following hybridization each chip was washed, blocked, stained, and scanned on an Illumina BeadStation 500 following the manufacturer’s protocols.

data_processing: Illumina GenomeStudio software was used for each sample to subtract background and scale average signal intensity to the global average signal intensity for all samples.

label: biotin

molecule: total RNA

source_name: Whole Blood

label_protocol: 250 ng of RNA from all samples passing quality control were then amplified and labeled using the Illumina TotalPrep-96 RNA amplification kit (Ambion, Austin, TX)

extract_protocol: RNA was isolated using the MagMAX™-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) according to the manufacturer's instructions

tag: group

value: SLE

tag: age

value: F

tag: race

value: White

tag: country of origin

value: France

tag: years since diagnosis of sle

tag: sledai

tag: skin

value: N

tag: joints

tag: hemato

tag: renal

value: Y

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: eosino


title: C1PL4V2

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes


title: BL09

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up


title: C2PL31V1

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

value: North Africa

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells

tag: eosino


title: C2PL31V2

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes


title: C2PL25V1

tag: group

tag: age

value: Asian

value: Philippines

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells

tag: eosino


title: C1PL10V1

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes


title: C2PL11V3

tag: group

tag: age

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: eosino


title: C2PL15V1

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: platelets

tag: leukocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: BL08

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

value: clonal heterogeneity (+)

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up

tag: gender


title: C2PL18V2

tag: group

tag: age

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: neutrophils

tag: lymphocytes

tag: eosino


title: BL12

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up

tag: gender


title: BL10

value: loss


title: C2PL36V2

tag: group

tag: age

tag: race

value: Black

tag: country of origin

value: Cuba

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: platelets

tag: leukocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: BL07

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up

tag: gender

value: male


title: BL06


title: BL04

value: clonal heterogeneity (-)

value: high / high intermediate


title: BL03

value: Alive


title: BL02

value: low / low intermediate

value: Dead


title: BL01


title: MALT31

description: file with raw data for this sample: MALT01_to_MALT31.txt

source_name: A tumor biopsy sample of a MALT lymphoma patient at diagnosis


title: MALT30


title: MALT29


title: C2PL22V2

tag: group

value: SLE

tag: age

value: F

tag: race

value: White

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: neutrophils

tag: lymphocytes

tag: eosino


title: MALT28

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up

tag: gender


title: C1PL15V1

tag: group

tag: age

tag: race

tag: country of origin

value: France

tag: years since diagnosis of sle

tag: sledai

tag: skin

value: N

tag: joints

value: Y

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: platelets

tag: leukocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: C1PL6V2

tag: group

tag: age

tag: gender

value: M

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: neutrophils

tag: lymphocytes

tag: eosino


title: C2PL4V2

tag: group

tag: age

value: North Africa

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: platelets

tag: leukocytes


title: MALT27

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up

tag: gender


title: C3VS18n1

tag: group

value: Healthy control of SLE

tag: age

tag: race

tag: country of origin


title: C1PL8V1

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: neutrophils

tag: lymphocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells

tag: eosino


title: C2PL3V1

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: cs mg/kg

tag: hcq

tag: platelets

tag: leukocytes


title: MALT26

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up


title: C2PL37V1

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: neutrophils

tag: lymphocytes

tag: eosino


title: C1PL13V2

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: cs mg/kg

tag: hcq

tag: platelets

tag: leukocytes


title: C2PL18V1

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: neutrophils

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: C2PL1V2

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: cs mg/kg

tag: hcq

tag: platelets

tag: leukocytes

tag: lymphocytes

tag: eosino


title: C3VS9n1

tag: group

tag: age


title: C2PL32V2

tag: gender

tag: race

tag: skin

tag: joints

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: hcq mg/d

tag: low c3

tag: low c4

tag: hb

tag: neutrophils


title: C1PL9V4

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: cs mg/kg

tag: hcq

tag: a-dsd

tag: platelets

tag: leukocytes

tag: lymphocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: MALT25

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up

tag: gender


title: MALT24


title: MALT23


title: MALT21


title: MALT22


title: MALT20


title: MALT19

value: clonal heterogeneity (+)


title: MALT18


title: MALT17


title: C2PL36V4

tag: group

tag: age

tag: race

value: Black

tag: country of origin

value: Cuba

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: low c3

tag: low c4

tag: hb

tag: neutrophils

tag: eosino


title: MALT15

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

value: clonal heterogeneity (-)

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up

tag: gender

value: male


title: MALT16


title: MALT14


title: C2PL6V3

tag: group

tag: age

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: a-dsd

tag: platelets

tag: leukocytes

tag: lymphocytes


title: C1PL3V1

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: low c3

tag: low c4

tag: hb

tag: neutrophils

tag: eosino


title: MALT12

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up


title: MALT13

tag: gender


title: C2PL7V1

tag: group

tag: age

tag: race

tag: country of origin

value: Comorres

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: a-dsd

tag: platelets

tag: leukocytes

tag: lymphocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: C2PL33V2

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: low c3

tag: low c4

tag: hb

tag: neutrophils

tag: eosino


title: C2PL32V5

tag: group

tag: age

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: a-dsd

tag: platelets

tag: leukocytes

tag: lymphocytes


title: C2PL20V3

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: low c3

tag: low c4

tag: hb

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: MALT11

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up

tag: gender


title: C2PL14V2

tag: group

tag: age

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: a-dsd

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: eosino


title: C3VS6n1

tag: group

tag: age

tag: gender

tag: race

tag: country of origin


title: C1PL14V1

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: hcq mg/d

tag: low c3

tag: low c4

tag: hb

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: MALT10

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up

tag: gender


title: C2PL8V2

tag: group

tag: age

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: a-dsd

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: eosino


title: MALT09

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up

tag: gender


title: C1PL10V2

tag: group

tag: age

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: hcq mg/d

tag: low c3

tag: low c4

tag: hb

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: C2PL25V2

tag: group

tag: age

tag: gender

tag: race

value: Asian

tag: country of origin

value: Philippines

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: cs mg/kg

tag: hcq

tag: a-dsd

tag: platelets

tag: leukocytes


title: C2PL11V1

value: SLE

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: hcq mg/d

tag: low c3

tag: low c4

tag: hb

tag: neutrophils

tag: lymphocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: eosino


title: C2PL16V3

tag: group

tag: age

tag: gender

value: F

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: cs mg/kg

tag: hcq

tag: a-dsd

tag: platelets

tag: leukocytes

tag: nk cells


title: MALT07

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up


title: C2PL36V5

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: hcq mg/d

tag: low c3

tag: low c4

tag: hb

tag: neutrophils

tag: lymphocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: eosino


title: C3VS11n1

tag: group

tag: age

tag: gender

tag: race

value: White

tag: country of origin


title: MALT03

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up


title: C2PL41V1

value: France

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: nk cells


title: MALT04

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up

tag: gender


title: C1PL3V2

tag: group

tag: age

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

value: N

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: eosino


title: MALT06

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up

tag: gender


title: MALT08


title: MALT01


title: MALT02


title: C2PL32V3

tag: group

tag: age

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

value: Y

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: nk cells


title: C3VS12n1

tag: group

tag: age

tag: gender

value: M

tag: race

tag: country of origin


title: C2PL5V2

value: North Africa

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: eosino


title: C2PL2V1

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: nk cells


title: C2PL10V1

tag: group

tag: age

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: eosino


title: C1PL6V1

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: nk cells


title: C2PL10V4

tag: group

tag: age

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: eosino


title: C1PL2V2

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells


title: C2PL20V5

tag: group

tag: age

tag: gender

tag: race

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: nk cells

tag: eosino


title: C2PL2V3

tag: group

tag: age

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes


title: C1PL12V3

tag: gender

tag: race

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd


title: C2PL10V3

tag: group

tag: age

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells

tag: eosino


title: Mouse756_Cisplatin

city: Maastricht

first: Kasper

last: Derks

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Center

hyb_protocol: Labeled materials were hybridized to Custom Exiqon LNA probes for 16 hours at 60°C, subsequently washed and scanned

scan_protocol: Samples were finally scanned using the ScanArray Express HT (Tecan). Image generation and feature extraction were performed using Imagene 6.0.

data_processing:
The raw microRNA data, median signal minus median background, were normalized using quantile normalization. For the CsA, WY and CDDP exposed groups quality control discarded one outlier per group. Duplicate spots on the array were averaged and the normalized values were analyzed for differentially expressed microRNAs using a linear model (bioconductor package Limma; Smyth 2005) and corrected for multiple testing (Benjamini and Hochberg 1995) was applied.
Only the spots corresponding to mouse microRNAs were used.
Note: the annotation is updated for a couple of spots after signal extraction by Imagene. Therefore the annotation in the EL**.txt raw files are not completely correct. The new annotation is available in a separate text file (see  'annotation.txt' linked as supplementary file on Series record).

organism: Mus musculus

source_name: Mouse756 Liver cells

label_protocol: Total RNA was labeled using the Createch Cy3 label kit (Createch), 1ug of total RNA was used.

growth_protocol: Six-week-old male WT mice (C57BL/6J, n=4 per group) were acclimated for 2 weeks and subsequently treated for 7 days with a GTXC, NGTXC or NC through feed, gavage or i.p. injection. From the day of weaning, the health status of the mice was monitored daily and mice were weighed weekly starting at acclimation. Animals were kept in the same stringently controlled (specific pathogen-free, spf) environment, fed ad libitum and kept under a normal day/night rhythm. After 7 days of exposure, mice were sacrificed at a fixed time of the day. During autopsy, several organs (including the liver), were isolated and stored according to protocol using RNAlater (Qiagen, Valencia, CA, USA).

extract_protocol: Hepatic total RNA was isolated using the miRNeasy kit (Qiagen, Valencia, CA, USA) and the QIAcube (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. All samples passed RNA quality control using capillary gel electrophoresis (RIN > 7.6) (Bioanalyzer 2100; Agilent Technologies, Amstelveen, the Netherlands). The same total RNA isolates as used for mRNA were used for isolation of microRNAs. MicroRNA profiling was performed as previously described (Pothof et al. 2009).

treatment_protocol: For the chemicals used in this study, appropriate dosages were derived from previously performed dose range finding (DRF) studies (2-AAF, Phe, CsA, DEHP, DES, E2, PBB, Res, WY, D-man (van Kreijl et al. 2001; de Vries et al. 1997)) or if not known yet, identified by performing additional 28-day DRF studies prior to the short-term exposure studies (see supplemental information 1 for DRF studies using AFB1, CPPD, BPA, DIDP, SD and TBTO). In short, eight to ten weeks old male C57BL/6J mice (n = 10 per group) were exposed to chemicals, using multiple dosages based on literature or expert advice. Body weight dynamics during the first week and over the full 28-day exposure were monitored to extract suitable (non- or slightly cytotoxic) doses (Supplemental information 1). If body weight dynamics were not conclusive, the liver was studied macroscopically (data not shown). Exposure through feed was continuously during the experiment, application using i.p. injection occurred at day 0, 3 and 6 (autopsy on day 7) and exposure using gavage at day 0, 2, 4 and 6 (autopsy on day 7). Body weights were recorded during this 7-day exposure period (Supplemental information 2). Comparison of different control groups (gavage, i.p. injection or feed) showed no significant differential effect on transcriptional levels (Luijten et al. in preparation), hence only food administrated control samples were implemented in this study

tag: strain

tag: gender

tag: age

value: six-weeks-old

tag: compound

value: Cisplatin

tag: class

value: GTXC

tag: mouse number

tag: tissue

value: liver


title: MALT05

tag: total number of genomic aberrations

tag: with or without clonal heterogeneity

value: clonal heterogeneity (-)

tag: international prognostic index

tag: genomic loss/deletion for 9p21.3 (cdkn2a locus)

tag: genomic loss for 17p13.1 (tp53 locus)

tag: follow up years

tag: dead or alive at the end of follow-up


title: C2PL33V3

tag: group

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells


title: C2PL21V2

tag: group

tag: age

tag: gender

tag: race

value: Black

tag: country of origin

value: Zaire

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: nk cells

tag: eosino


title: C2PL20V1

tag: group

tag: age

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells


title: C2PL12V2

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: nk cells

tag: eosino


title: C2PL26V2

tag: group

tag: age

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes


title: C3VS4n1

value: Healthy control of SLE

tag: gender

tag: race

tag: country of origin


title: C2PL26V3

tag: group

tag: age

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells

tag: eosino


title: Mouse754_Cisplatin

source_name: Mouse754 Liver cells

tag: strain

tag: gender

value: male

tag: age

tag: compound

tag: class

tag: mouse number

tag: tissue


title: C3VS2n1

tag: group

tag: race

tag: country of origin


title: C3VS15n1

value: French West Indies


title: C2PL30V1

value: SLE

value: F

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes


title: C2PL31V3

tag: group

tag: age

tag: gender

tag: race

value: White

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: iv cs

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells

tag: eosino


title: C2PL6V4

tag: group

tag: age

value: N

tag: aza

tag: mmf

tag: csa

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes


title: C2PL29V1

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

value: France

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

value: Y

tag: iv cs

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells

tag: eosino


title: C1PL1V2

tag: group

tag: age

tag: aza

tag: mmf

tag: csa

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes


title: C2PL3V3

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: iv cs

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells

tag: eosino


title: Mouse753_Cisplatin

source_name: Mouse753 Liver cells

tag: strain

tag: age

tag: compound

tag: class

tag: mouse number

tag: tissue


title: Mouse654_Tributyl-tin-oxide

source_name: Mouse654 Liver cells

tag: gender

value: Tributyl-tin-oxide

value: NC


title: Mouse664_Bisphenol A

source_name: Mouse664 Liver cells

value: six-weeks-old

value: Bisphenol A


title: Mouse677_Sodium diclofenac

source_name: Mouse677 Liver cells

value: Sodium diclofenac

value: liver


title: Mouse684_2 AAF

source_name: Mouse684 Liver cells

value: 2 AAF

value: GTXC


title: Mouse564_D-Mannitol

source_name: Mouse564 Liver cells

value: D-Mannitol


title: Mouse563_D-Mannitol

source_name: Mouse563 Liver cells

value: male


title: Mouse683_2 AAF

source_name: Mouse683 Liver cells


title: Mouse535_Diethylstillbestrol

source_name: Mouse535 Liver cells

value: Diethylstillbestrol

value: NGTXC


title: C2PL13V3

tag: group

value: SLE

value: M

tag: race

tag: country of origin

value: North Africa

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: aza

tag: mmf

tag: csa

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes


title: C2PL5V1

tag: group

tag: age

tag: gender

value: F

tag: race

value: White

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

value: N

tag: hemato

tag: renal

tag: cyp

tag: iv cs


title: C3VS8n1

value: Healthy control of SLE


title: C2PL16V1

value: France

tag: aza

tag: mmf

tag: csa

value: Y

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells

tag: eosino


title: C2PL13V1

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: iv cs

tag: leukocytes

tag: neutrophils

tag: lymphocytes


title: Mouse631_Wyeth-14643

source_name: Mouse631 Liver cells

tag: strain

tag: age

value: six-weeks-old

tag: compound

tag: class

tag: mouse number

tag: tissue


title: C3VS13n1

tag: group

tag: gender

tag: race

tag: country of origin


title: Mouse542_17 B- Estradiol

source_name: Mouse542 Liver cells

value: Phenobarbital

value: liver


title: C1PL1V1

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: csa

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells

tag: eosino


title: Mouse653_Tributyl-tin-oxide

source_name: Mouse653 Liver cells

tag: strain

tag: gender

tag: age

tag: compound

value: Tributyl-tin-oxide

tag: class

value: NC

tag: mouse number

tag: tissue


title: Mouse672_Diisodecyl phthalate

source_name: Mouse672 Liver cells

value: male

value: Diisodecyl phthalate


title: C2PL35V1

source_name: Whole Blood

tag: group

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: leukocytes

tag: neutrophils

tag: lymphocytes


title: Mouse593_Benzo(a)pyrene

source_name: Mouse593 Liver cells

tag: strain

tag: gender

tag: age

tag: compound

value: Benzo(a)pyrene

tag: class

value: GTXC

tag: mouse number

tag: tissue


title: Mouse554_Reserpine

source_name: Mouse554 Liver cells

value: Reserpine

value: NGTXC


title: C2PL45V2

tag: group

value: SLE

value: F

tag: race

tag: country of origin

value: North Africa

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: eosino


title: Mouse560_DEPH

source_name: Mouse560 Liver cells

tag: strain

tag: gender

tag: age

tag: compound

value: DEPH

tag: class

tag: mouse number

tag: tissue


title: Mouse658_Aflatoxine B1

source_name: Mouse658 Liver cells

value: Aflatoxine B1


title: C2PL12V1

tag: group

tag: race

value: White

tag: country of origin

value: France

tag: years since diagnosis of sle

tag: sledai

tag: skin

value: N

tag: joints

value: Y

tag: hemato

tag: renal

tag: cyp

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: C2PL5V3

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: eosino


title: Mouse623_Cyclosporin

source_name: Mouse623 Liver cells

tag: strain

tag: age

value: six-weeks-old

tag: compound

value: Cyclosporin

tag: class

tag: mouse number

tag: tissue

value: liver


title: C3VS7n1

tag: group

value: Healthy control of SLE

tag: gender

tag: race

tag: country of origin


title: C2PL46V1

value: M

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: leukocytes


title: Mouse558_DEPH

source_name: Mouse558 Liver cells

tag: strain

tag: gender

value: male

tag: age

tag: compound

tag: class

tag: mouse number

tag: tissue


title: Mouse552_Reserpine

source_name: Mouse552 Liver cells

value: Reserpine


title: Mouse559_DEPH

source_name: Mouse559 Liver cells

value: NGTXC


title: C2PL6V2

tag: group

value: SLE

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: iv cs

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: neutrophils

tag: lymphocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells

tag: eosino


title: C2PL38V2

tag: group

tag: age

tag: gender

value: F

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: mmf

tag: csa

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: leukocytes


title: Mouse671_Diisodecyl phthalate

source_name: Mouse671 Liver cells

tag: strain

tag: age

tag: compound

value: Diisodecyl phthalate

tag: class

value: NC

tag: mouse number

tag: tissue


title: C2PL28V1

tag: group

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: iv cs

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: neutrophils

tag: lymphocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells

tag: eosino


title: Mouse666_Bisphenol A

source_name: Mouse666 Liver cells

tag: strain

tag: gender

tag: age

tag: compound

value: Bisphenol A

tag: class

tag: mouse number

tag: tissue


title: Mouse543_Phenobarbital

source_name: Mouse543 Liver cells

value: Phenobarbital


title: C2PL45V3

tag: group

tag: race

value: White

tag: country of origin

value: North Africa

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: leukocytes


title: C2PL33V5

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

value: France

tag: years since diagnosis of sle

tag: sledai

tag: skin

value: N

tag: joints

value: Y

tag: hb

tag: platelets

tag: neutrophils

tag: lymphocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells

tag: eosino


title: C2PL19V1

tag: group

tag: age

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: leukocytes


title: C2PL20V6

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hb

tag: platelets

tag: neutrophils

tag: lymphocytes

tag: eosino


title: C3VS1n1


title: Mouse522_Phenacetine

source_name: Mouse522 Liver cells

tag: strain

value: six-weeks-old

tag: compound

value: Phenacetine

tag: class

value: GTXC

tag: mouse number

tag: tissue

value: liver


title: Mouse561_D-Mannitol

source_name: Mouse561 Liver cells

tag: gender

value: male

tag: age

value: D-Mannitol


title: C2PL8V1

tag: group

value: SLE

tag: race

tag: country of origin

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: leukocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: C1PL9V2

tag: group

tag: age

tag: gender

value: F

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: hb

tag: platelets

tag: neutrophils

tag: lymphocytes

tag: eosino


title: C2PL26V4

tag: group

tag: age

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: leukocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: C3VS5n1

tag: group

value: Healthy control of SLE

tag: age

tag: gender

tag: race

tag: country of origin


title: C2PL9V1

value: M

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: hb

tag: platelets

tag: neutrophils

tag: lymphocytes

tag: eosino


title: Mouse630_Wyeth-14643

source_name: Mouse630 Liver cells

tag: strain

tag: gender

tag: age

tag: compound

tag: class

value: NGTXC

tag: mouse number

tag: tissue


title: Mouse557_DEPH

source_name: Mouse557 Liver cells

value: DEPH


title: Mouse670_Diisodecyl phthalate

source_name: Mouse670 Liver cells

value: Diisodecyl phthalate

value: NC


title: C2PL1V3

source_name: Whole Blood

tag: group

tag: race

value: White

tag: country of origin

value: France

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: leukocytes


title: Mouse540_17 B- Estradiol

source_name: Mouse540 Liver cells

tag: strain

tag: gender

tag: age

tag: compound

value: 17 B- Estradiol

tag: class

tag: mouse number

tag: tissue


title: Mouse539_17 B- Estradiol

source_name: Mouse539 Liver cells

value: six-weeks-old


title: Mouse523_Phenacetine

source_name: Mouse523 Liver cells

value: Phenacetine


title: Mouse624_Cyclosporin

source_name: Mouse629 Liver cells


title: C2PL26V1

tag: group

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

value: N

tag: joints

tag: hemato

tag: renal

tag: cyp

value: Y

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: hb

tag: platelets

tag: neutrophils

tag: lymphocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells

tag: eosino


title: Mouse665_Bisphenol A

source_name: Mouse665 Liver cells

tag: strain

tag: gender

value: male

tag: age

tag: compound

value: Bisphenol A

tag: class

tag: mouse number

tag: tissue

value: liver


title: Mouse562_D-Mannitol

source_name: Mouse562 Liver cells

value: D-Mannitol


title: C2PL24V1

tag: group

value: SLE

value: F

tag: race

tag: country of origin

value: North Africa

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: leukocytes


title: Mouse594_Benzo(a)pyrene

source_name: Mouse594 Liver cells

tag: strain

tag: gender

tag: age

tag: compound

value: Benzo(a)pyrene

tag: class

value: GTXC

tag: mouse number

tag: tissue


title: C2PL9V3

tag: group

value: M

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: hb

tag: platelets

tag: neutrophils

tag: lymphocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells

tag: eosino


title: Mouse520_Phenacetine

source_name: Mouse520 Liver cells

tag: strain

tag: gender

tag: age

tag: compound

tag: class

tag: mouse number

tag: tissue


title: C2PL43V1

tag: group

tag: race

value: White

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: leukocytes


title: C1PL7V2

tag: group

tag: age

tag: gender

tag: race

value: Black

tag: country of origin

value: New Caledonia

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hb

tag: platelets

tag: neutrophils

tag: lymphocytes

tag: eosino


title: C2PL13V2

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: Mouse503_control

source_name: Mouse503 Liver cells

tag: strain

tag: gender

tag: age

value: six-weeks-old

tag: compound

value: Control

tag: class

tag: mouse number

tag: tissue


title: C2PL32V1

tag: group

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

value: N

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: eosino


title: Mouse622_Cyclosporin

source_name: Mouse622 Liver cells

tag: strain

tag: gender

tag: age

tag: compound

value: Cyclosporin

tag: class

value: NGTXC

tag: mouse number

tag: tissue


title: Mouse551_Reserpine

source_name: Mouse551 Liver cells

value: male

value: Reserpine


title: C2PL17V1

tag: group

tag: race

tag: country of origin

value: France

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

value: Y

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: low c3

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: C1PL4V3

tag: group

value: SLE

tag: age

tag: gender

value: F

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: oral cs

tag: cs mg/d

tag: a-dsd

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: eosino


title: C1PL1V3

tag: group

tag: age

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: low c3


title: C1PL16V1

tag: gender

tag: race

tag: country of origin

value: North Africa

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: oral cs

tag: cs mg/d

tag: a-dsd

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: Mouse669_Diisodecyl phthalate

source_name: Mouse669 Liver cells

tag: strain

tag: gender

tag: age

tag: compound

value: Diisodecyl phthalate

tag: class

value: NC

tag: mouse number

tag: tissue

value: liver


title: C2PL32V4

tag: group

tag: race

value: White

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: low c3

tag: lymphocytes

tag: eosino


title: C2PL36V1

tag: group

tag: age

tag: gender

tag: race

value: Black

tag: country of origin

value: Cuba

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: a-dsd

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils


title: C2PL33V6

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: low c3

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: C1PL4V4

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: a-dsd

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: eosino


title: Mouse536_Diethylstillbestrol

source_name: Mouse536 Liver cells

tag: strain

tag: age

value: six-weeks-old

tag: compound

value: 17 B- Estradiol

tag: class

tag: mouse number

tag: tissue


title: Mouse660_Aflatoxine B1

source_name: Mouse660 Liver cells

tag: gender

value: Aflatoxine B1

value: GTXC


title: Mouse506_control

source_name: Mouse506 Liver cells

value: male

value: cControl

value: Control


title: Mouse534_Diethylstillbestrol

source_name: Mouse534 Liver cells

value: Diethylstillbestrol

value: NGTXC


title: Mouse675_Sodium diclofenac

source_name: Mouse675 Liver cells

value: Sodium diclofenac


title: C2PL42V3

source_name: Whole Blood

tag: group

value: SLE

value: M

tag: race

value: Asian

tag: country of origin

value: Vietnam

tag: years since diagnosis of sle

tag: sledai

tag: skin

value: N

tag: joints

tag: renal

value: Y

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: low c3

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: Mouse544_Phenobarbital

source_name: Mouse544 Liver cells

tag: strain

tag: gender

tag: age

tag: compound

value: Phenobarbital

tag: class

tag: mouse number

tag: tissue

value: liver


title: Mouse621_Cyclosporin

source_name: Mouse621 Liver cells

value: six-weeks-old

value: Cyclosporin


title: Mouse685_2 AAF

source_name: Mouse685 Liver cells

value: 2 AAF

value: GTXC


title: Mouse678_Sodium diclofenac

source_name: Mouse678 Liver cells

value: male

value: NC


title: Mouse652_Tributyl-tin-oxide

source_name: Mouse652 Liver cells

value: Tributyl-tin-oxide


title: Mouse545_Phenobarbital

source_name: Mouse545 Liver cells

value: NGTXC


title: Mouse533_Diethylstillbestrol

source_name: Mouse533 Liver cells

value: Diethylstillbestrol


title: C2PL9V4

tag: group

value: SLE

tag: race

value: White

tag: country of origin

value: France

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: a-dsd

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: eosino


title: C2PL12V3

tag: group

tag: age

tag: gender

value: F

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: low c3

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: Mouse546_Phenobarbital

source_name: Mouse546 Liver cells

tag: strain

tag: age

tag: compound

tag: class

tag: mouse number

tag: tissue


title: C2PL9V5

tag: group

tag: gender

value: M

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

value: N

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: a-dsd

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: eosino


title: C3VS3n1

tag: group

value: Healthy control of SLE

tag: age

tag: gender

tag: race

tag: country of origin


title: C2PL15V3

value: North Africa

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

value: Y

tag: mmf

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: low c3


title: Mouse592_Benzo(a)pyrene

source_name: Mouse592 Liver cells

tag: strain

tag: gender

tag: age

value: six-weeks-old

tag: compound

value: Benzo(a)pyrene

tag: class

tag: mouse number

tag: tissue

value: liver


title: Mouse553_Reserpine

source_name: Mouse553 Liver cells

value: male

value: Reserpine


title: C2PL45V1

tag: group

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: csa

tag: iv cs

tag: oral cs

tag: a-dsd

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: eosino


title: Mouse651_Tributyl-tin-oxide

source_name: Mouse651 Liver cells

tag: strain

tag: gender

tag: age

tag: compound

value: Tributyl-tin-oxide

tag: class

value: NC

tag: mouse number

tag: tissue


title: C2PL39V1

tag: group

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: low c3


title: C2PL1V1

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: oral cs

tag: a-dsd

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells

tag: eosino


title: Mouse591_Benzo(a)pyrene

source_name: Mouse591 Liver cells

tag: strain

tag: age

tag: compound

tag: class

value: GTXC

tag: mouse number

tag: tissue


title: C3VS10n1

tag: group

tag: gender

tag: race

tag: country of origin


title: C2PL2V2

value: SLE

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: leukocytes

tag: neutrophils


title: C2PL17V2

tag: group

tag: age

tag: gender

tag: race

value: White

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: lymphocytes

tag: eosino


title: C3VS16n1

value: France


title: C1PL9V5

value: F

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: Mouse659_Aflatoxine B1

source_name: Mouse659 Liver cells

tag: strain

tag: gender

tag: age

tag: compound

value: Aflatoxine B1

tag: class

tag: mouse number

tag: tissue


title: C1PL16V2

tag: group

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

value: N

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: eosino


title: C1PL2V3

tag: group

tag: age

tag: gender

value: M

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: Mouse676_Sodium diclofenac

source_name: Mouse676 Liver cells

tag: strain

tag: age

tag: compound

value: Sodium diclofenac

tag: class

tag: mouse number

tag: tissue


title: C2PL33V4

tag: group

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: hemato

tag: renal

value: Y

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: eosino


title: Mouse541_17 B- Estradiol

source_name: Mouse541 Liver cells

tag: strain

tag: gender

tag: age

value: six-weeks-old

tag: compound

value: 17 B- Estradiol

tag: class

value: NGTXC

tag: mouse number

tag: tissue


title: Mouse682_2 AAF

source_name: Mouse682 Liver cells

value: male

value: 2 AAF

value: liver


title: Mouse504_control

source_name: Mouse504 Liver cells

value: Control


title: Mouse521_Phenacetine

source_name: Mouse521 Liver cells

value: Phenacetine

value: GTXC


title: Mouse663_Bisphenol A

source_name: Mouse663 Liver cells

value: Bisphenol A

value: NC


title: Mouse657_Aflatoxine B1

source_name: Mouse657 Liver cells


title: 48F

city: Columbus

first: Cecilia

last: Fernandez

address: 460 12th street

institute: OSU

hyb_protocol: Liu C-G, Calin GA, Volinia S and Croce CM. MicroRNA expression profiling using microarrays. Nature Protocols, 3(4):563-578, 2008

data_processing: quantile normalization

source_name: liver metastasis

label_protocol: biotin end-labeled random-octamer oligonucleotide primers

extract_protocol: Trizol

tag: disease state

value: Colorectal carcinoma

tag: patient

value: liver metastasis


title: C2PL19V2

source_name: Whole Blood

tag: group

value: SLE

value: F

tag: race

value: White

tag: country of origin

value: North Africa

tag: years since diagnosis of sle

tag: sledai

tag: skin

value: N

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: 48T

scan_protocol: Liu C-G, Calin GA, Volinia S and Croce CM. MicroRNA expression profiling using microarrays. Nature Protocols, 3(4):563-578, 2008

source_name: tumor

tag: disease state

tag: patient

tag: tissue

value: colorectal carcinoma tumor


title: 48N

source_name: lymph node metastasis

value: lymph node metastasis


title: 38T


title: 47F


title: 38F


title: 47T


title: 47N


title: C2PL27V2

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

value: France

tag: years since diagnosis of sle

tag: sledai

tag: skin

value: Y

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: eosino


title: C1PL11V2

tag: group

tag: age

tag: gender

value: M

tag: race

tag: country of origin

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: 46F

tag: disease state

tag: patient

tag: tissue


title: C2PL29V3

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: leukocytes

tag: neutrophils

tag: lymphocytes

tag: eosino


title: C2PL40V1

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets


title: C2PL20V2

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: leukocytes

tag: neutrophils

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: C2PL33V1

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: lymphocytes

tag: eosino


title: C2PL9V2

tag: group

tag: age

tag: skin

tag: joints

tag: hemato

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: leukocytes

tag: neutrophils

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: 45T

tag: disease state

tag: patient

tag: tissue


title: 45N


title: 44F


title: 46T


title: 45F


title: 46N


title: 43F


title: 44T


title: 43N


title: 43T


title: 41T


title: 39F


title: 40T


title: 41N


title: 40N


title: 40F


title: 44N


title: 39N


title: 35T


title: 39T


title: 35N


title: 37T


title: 37F


title: 31T


title: 31N


title: 34N


title: 34F


title: 34T


title: 42F


title: 30T


title: 29N


title: 41F


title: 42T


title: 36T


title: 36F


title: 30N


title: 33N


title: 35F


title: 32N


title: 32T


title: 33T


title: 27T


title: 27N


title: 28T


title: 42N


title: 25T


title: 25N


title: C2PL28V2

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: joints

tag: hemato

tag: csa

tag: iv cs

tag: oral cs

tag: cs mg/d

tag: a-dsd

tag: low c3

tag: low c4

tag: hb

tag: platelets

tag: lymphocytes

tag: eosino


title: 24T

tag: disease state

tag: patient

tag: tissue


title: 26T


title: 26N


title: 21N


title: 21T


title: C2PL14V1

tag: group

tag: age

tag: gender

tag: race

tag: country of origin

tag: years since diagnosis of sle

tag: sledai

tag: skin

tag: renal

tag: cyp

tag: aza

tag: mmf

tag: cs mg/kg

tag: hcq

tag: hcq mg/d

tag: leukocytes

tag: neutrophils

tag: cd4 tcells

tag: cd8 t cells

tag: b cells

tag: nk cells


title: 24N

tag: disease state

tag: patient

tag: tissue


title: 29T


title: C20N


title: C19N


title: C19T


title: C18N


title: 28N


title: C17T


title: C18T


title: C17N


title: C16N


title: C16T


title: C20T


title: C15N


title: C13T


title: C14T


title: C15T


title: C14N


title: C12N


title: C13N


title: C12T


title: C10T


title: C8N


title: C9T


title: C11T


title: C8T


title: C9N


title: C6N


title: C7N


title: C7T


title: C6T


title: C4T


title: C4N


title: C11N


title: C5T


title: C3N


title: C5N


title: C2N


title: C2T


title: C1N


title: C1T


title: C3T


title: 5 uM finasteride 3

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

hyb_protocol: Xenopus tropicalus microarrays were manufactured with Agilent Sure Print Technology in Fall 2012.  RNA labeling, microarray hybridization, and microarray analysis were performed according to Agilent’s One-Color Microarray-Gene Based Expression Analysis protocol (May 2010) using an Agilent kit (Agilent, Mississauga, ON, CAN).  After hybridization for 17 hours, microarray slides were washed and scanned using Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology and raw expression data along with tif images were extracted by the Feature Extraction Software 10.7.3.1.

data_processing: Normalized signal intensity provided here is Quantile Normalization

organism: Xenopus tropicalis

source_name: Testis tissue

label_protocol: Agilent one color protocol for Cy3

extract_protocol: RNA extracted by TRIzol (Invitrogen)

tag: agent

value: 5 uM finasteride

tag: gender

value: male

tag: developmental stage

value: juveniles


title: 0 uM control 2

scan_protocol: After hybridization for 17 hours, microarray slides were washed and scanned using Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology and raw expression data along with tif images were extracted by the Feature Extraction Software 10.7.3.1.

value: 0 uM control


title: Liver PRKAR1A ko rep3

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

description:
rep3
8521433055_F

hyb_protocol: Biotin-labeled cRNA was synthesized by the total prep RNA amplification kit from Ambion (Austin, TX). cRNA was quantified and normalized to 150 ng/ul, and then 750 ng was hybridized to each BeadChip.

scan_protocol: The image data was then acquired by scanning the chips on an Illumina iScan.

data_processing: The raw idat files were uploaded into the Illumina Genomestudio software and the data exported for analysis. Sample and control probe signal intensities were exported from GenomeStudio. These files were imported into R version 2.15.0, quantile normalized, and log2 transformed using the Bioconductor beadarray package, version 2.6.0, and Illumina probe IDs were annotated using the Bioconductor illuminaMousev2.db package, version 1.16.0.

source_name: Liver

growth_protocol: We disinhibited cAMP-PKA signaling in vivo in mouse liver by ablating hepatic protein kinase A regulatory subunit 1A (prkar1a). Tail vein injection of adenovirus driving CRE recombinase under control of the CMV promoter (AdvCRE) successfully ablated prkar1a and activated PKA-dependent signaling in prkar1afl/fl 14 mice (L-Δprkar1a mice). In contrast, wild-type mice, which were intravenously cannulated and continuously infused for 3 days with D-glucose to achieve fasting glucose levels to match those measured in L-Δprkar1a mice.

tag: genotype

value: PRKAR1A ko

value: Liver

tag: genetic background


title: Liver ctrl rep4

description:
rep4
8521433055_G

label_protocol: Biotin-labeled cRNA was synthesized by the total prep RNA amplification kit from Ambion (Austin, TX). cRNA was quantified and normalized to 150 ng/ul, and then 750 ng was hybridized to each BeadChip.

extract_protocol: We disinhibited cAMP-PKA signaling in vivo in mouse liver by ablating hepatic protein kinase A regulatory subunit 1A (prkar1a). Tail vein injection of adenovirus driving CRE recombinase under control of the CMV promoter (AdvCRE) successfully ablated prkar1a and activated PKA-dependent signaling in prkar1afl/fl 14 mice (L-Δprkar1a mice). In contrast, wild-type mice, which were intravenously cannulated and continuously infused for 3 days with D-glucose to achieve fasting glucose levels to match those measured in L-Δprkar1a mice.

value: ctrl


title: Liver ctrl rep8

description:
rep8
8521433085_F

treatment_protocol: We disinhibited cAMP-PKA signaling in vivo in mouse liver by ablating hepatic protein kinase A regulatory subunit 1A (prkar1a). Tail vein injection of adenovirus driving CRE recombinase under control of the CMV promoter (AdvCRE) successfully ablated prkar1a and activated PKA-dependent signaling in prkar1afl/fl 14 mice (L-Δprkar1a mice). In contrast, wild-type mice, which were intravenously cannulated and continuously infused for 3 days with D-glucose to achieve fasting glucose levels to match those measured in L-Δprkar1a mice.


title: Liver PRKAR1A ko rep5

description:
rep5
8521433085_C


title: 5 uM finasteride 1


title: 0 uM control 3


title: Liver PRKAR1A ko rep2

description:
rep2
8521433055_E


title: 0 uM control 1


title: Liver ctrl rep6

description:
rep6
8521433085_D


title: Liver PRKAR1A ko rep8

description:
rep8
8521433085_H


title: Liver ctrl rep3

description:
rep3
8521433055_D


title: 0 uM control 4


title: Liver ctrl rep1

description:
rep1
8521433055_A


title: Liver ctrl rep7

description:
rep7
8521433085_E


title: 5 uM finasteride 2


title: Liver PRKAR1A ko rep1

description:
rep1
8521433055_B


title: Liver PRKAR1A ko rep4

description:
rep4
8521433085_B


title: Liver ctrl rep5

description:
rep5
8521433085_A


title: 5 uM finasteride 4


title: Liver PRKAR1A ko rep7

description:
rep7
8521433085_G


title: Liver ctrl rep2

description:
rep2
8521433055_C


title: Dengue Patient Timepoint1 114

city: Singapore

first: Ahmad Nazri

last: Mohamed Naim

address: 60 Biopolis Street, Genome, #02-01

department: Infectious disease

country: Singapore

institute: Genome institute of Singapore

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were analysed in Genespring GX11.5 software. Measurements less than 0.01 was set to 0.01. Data was then normalised at the 80th percentile.

source_name: Human whole blood

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep -96 RNA Amplification Kit for Illumina arrays

extract_protocol: Total RNA was extracted from whole blood drawn in pax-gene vacutainer tubes by PAX-gene RNA kit (Qiagen). Quality control was performed with NanoDrop 1000 instrument

tag: sample type

value: blood

tag: collection time

value: Less than 72 hour after symptoms

tag: igg

value: Pos


title: Dengue Patient Timepoint3 112

value: 2 to 5 weeks after symptoms

value: Neg


title: Dengue Patient Timepoint2 112

value: 3 to 7 dys after symptoms


title: Dengue Patient Timepoint3 113


title: Dengue Patient Timepoint2 113


title: Dengue Patient Timepoint1 113


title: C10N

value: Colorectal carcinoma

value: lymph node metastasis


title: Dengue Patient Timepoint2 105


title: Dengue Patient Timepoint1 112


title: Dengue Patient Timepoint2 111


title: Dengue Patient Timepoint1 111


title: Dengue Patient Timepoint2 110


title: Dengue Patient Timepoint1 109


title: Dengue Patient Timepoint3 104


title: Dengue Patient Timepoint3 111


title: Dengue Patient Timepoint1 110


title: Dengue Patient Timepoint1 108


title: Dengue Patient Timepoint3 106


title: Dengue Patient Timepoint1 106


title: Dengue Patient Timepoint1 107


title: Dengue Patient Timepoint3 107


title: Dengue Patient Timepoint2 108


title: Dengue Patient Timepoint3 109


title: Dengue Patient Timepoint2 107


title: Dengue Patient Timepoint1 104


title: Dengue Patient Timepoint1 105


title: Dengue Patient Timepoint3 110


title: Dengue Patient Timepoint2 106


title: Dengue Patient Timepoint2 103


title: Dengue Patient Timepoint3 102


title: Dengue Patient Timepoint2 109


title: Dengue Patient Timepoint3 101


title: Dengue Patient Timepoint2 101


title: Dengue Patient Timepoint1 103


title: Dengue Patient Timepoint3 105


title: Dengue Patient Timepoint1 102


title: Dengue Patient Timepoint3 100


title: Dengue Patient Timepoint2 102


title: Dengue Patient Timepoint1 101


title: Dengue Patient Timepoint1 99


title: Dengue Patient Timepoint1 100


title: Dengue Patient Timepoint2 100


title: Dengue Patient Timepoint2 98


title: Dengue Patient Timepoint1 96


title: Dengue Patient Timepoint2 99


title: Dengue Patient Timepoint3 99


title: Dengue Patient Timepoint1 98


title: Dengue Patient Timepoint3 97


title: Dengue Patient Timepoint3 95


title: Dengue Patient Timepoint2 96


title: Dengue Patient Timepoint3 96


title: Dengue Patient Timepoint1 97


title: Dengue Patient Timepoint1 95


title: Dengue Patient Timepoint2 95


title: Dengue Patient Timepoint2 94


title: Dengue Patient Timepoint3 94


title: Dengue Patient Timepoint1 94


title: Dengue Patient Timepoint1 93


title: Dengue Patient Timepoint1 92


title: Dengue Patient Timepoint3 93


title: Dengue Patient Timepoint2 92


title: Dengue Patient Timepoint3 91


title: Dengue Patient Timepoint3 92


title: Dengue Patient Timepoint2 93


title: Dengue Patient Timepoint2 97


title: Dengue Patient Timepoint3 90


title: Dengue Patient Timepoint1 91


title: Dengue Patient Timepoint1 87


title: Dengue Patient Timepoint1 90


title: Dengue Patient Timepoint3 89


title: Dengue Patient Timepoint3 86


title: Dengue Patient Timepoint2 90


title: Dengue Patient Timepoint2 88


title: Dengue Patient Timepoint2 91


title: Dengue Patient Timepoint3 85


title: Dengue Patient Timepoint2 86


title: Dengue Patient Timepoint1 85


title: Dengue Patient Timepoint2 85


title: Dengue Patient Timepoint3 88


title: Dengue Patient Timepoint1 89


title: Dengue Patient Timepoint3 84


title: Dengue Patient Timepoint1 88


title: Dengue Patient Timepoint3 87


title: Dengue Patient Timepoint2 89


title: Dengue Patient Timepoint1 86


title: Dengue Patient Timepoint2 87


title: Dengue Patient Timepoint2 83


title: Dengue Patient Timepoint1 84


title: Dengue Patient Timepoint1 83


title: Dengue Patient Timepoint3 83


title: Dengue Patient Timepoint3 82


title: Dengue Patient Timepoint1 82


title: Dengue Patient Timepoint2 82


title: Dengue Patient Timepoint2 84


title: Dengue Patient Timepoint2 81


title: Dengue Patient Timepoint3 81


title: Dengue Patient Timepoint2 80


title: Dengue Patient Timepoint1 80


title: Dengue Patient Timepoint3 79


title: Dengue Patient Timepoint1 79


title: Dengue Patient Timepoint2 79


title: Dengue Patient Timepoint3 78


title: Dengue Patient Timepoint2 78


title: Dengue Patient Timepoint3 80


title: Dengue Patient Timepoint3 76


title: Dengue Patient Timepoint1 81


title: Dengue Patient Timepoint2 77


title: Dengue Patient Timepoint1 77


title: Dengue Patient Timepoint1 78


title: Dengue Patient Timepoint1 76


title: Dengue Patient Timepoint2 76


title: Dengue Patient Timepoint3 77


title: Dengue Patient Timepoint2 75


title: C16 vs. WT

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

hyb_protocol: Hybridization was performerd according to the Agilent two-color microarray protocol

scan_protocol: Microarays were scanned using the Agilent DNA microarray scanner. Raw data was collected using the Agilent feature extraction software v10.7.

data_processing: Median values of Cy3 and Cy5 channel were processed in the R environment using the limma package. Backround correction was performed using the normexp method, Cy3 and Cy5 channels were loess normalized, Quantil-normalization was used for seperate microarrays.

organism: Dinoroseobacter shibae DFL 12 = DSM 16493

source_name: wild-type OD600 0.4

label_protocol: total RNA was labelled using the Universal Linker System (Kreatech) according to the manufacturers  protocol

growth_protocol: DFL 12 was grown in a defined minimal medium with succinate as sole carbon source. Growth temperature was 30°C, cells were kept in the dark

extract_protocol: Samples were collected in RNAprotect (Qiagen). RNA was extracted using the Rneasy Mini kit (Qiagen) with on column DNA digestion according to the manufacturers protocol followed by a second DNA digestion step in solution using DnaseI (Quiagen) and RNA purification using the RNeasy mini kit.

treatment_protocol: DFL 12 ∆luxI1 was supplemented with 500 nM AHL at cultivation start

tag: strain

value: wild-type

tag: treatment

tag: growth phase (od600)


title: Dengue Patient Timepoint3 75


title: Dengue Patient Timepoint3 98


title: Dengue Patient Timepoint2 74


title: C12 vs. WT


title: C16 vs. luxI1

source_name: ∆luxI1 OD600 0.4


title: Dengue Patient Timepoint1 74


title: C8 vs. WT


title: C12 vs. luxI1


title: Dengue Patient Timepoint3 74


title: C8 vs. luxI1


title: Dengue Patient Timepoint1 75


title: luxI1 vs. WT


title: WT vs. C16en

value: C16en 500nM


title: Dengue Patient Timepoint1 73


title: luxI1 vs. C16


title: 3-oxo-C16en vs. luxI1

value: 3-oxo-C16en 500nM


title: Dengue Patient Timepoint3 73


title: C14en vs. 3-oxo-C14

value: C14en 500nM


title: 3-oxo-C14 vs. 3-oxo-C14en

value: 3-oxo-C14en 500nM


title: 3-oxo-C14en vs. luxI1


title: C16en vs. 3-oxo-C16en


title: Dengue Patient Timepoint2 73


title: Dengue Patient Timepoint1 72


title: WT vs. 3-oxo-C14


title: luxI1 vs. C14en


title: C14 vs. 3-oxo-C14en


title: Dengue Patient Timepoint3 72


title: C14en vs. C14


title: 3-oxo-C12h vs. 3-oxo-C12l


title: WT vs. 3-oxo-C12h


title: C14 vs. WT


title: 3-oxo-C12l vs. luxI1


title: Dengue Patient Timepoint3 70


title: Dengue Patient Timepoint2 71


title: Dengue Patient Timepoint2 72


title: Dengue Patient Timepoint1 71


title: Dengue Patient Timepoint1 70


title: A3_DHT

city: Sendai

first: Rika

last: Fujii

address: 2-1, Seiryo-machi, Aoba-ku

department: Molecular and functional dynamics

institute: Tohoku University

description: Gene expression after 24hr

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >17 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2xGE Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G2519F#26652) for 17 hours at 65Â°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 37Â°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 using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: breast cancer cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy Mini Kit (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were grown in phenol red free-RPMI1640 with 5% dextran-coated charcoal-treated fetal calf serum for 3 days, and then 1 nM DHT was added. After incubating for 24 h, total RNA was extracted

extract_protocol: Total RNA was extracted with ISOGEN (Nippon Gene Co., LTD., Toyama, Japan), according to the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell line

value: DHT 1nM


title: A3_DHT_Bic

description: Gene expression after 24hr

value: DHT 1nM,Bicalutamide 10microM


title: Dengue Patient Timepoint3 71


title: CDC1551 kasB T334D T336D Transcriptome Replicate 3

city: Saranac Lake

first: Brian

last: Weinrick

state: NY

address: 154 Algonquin Avenue

institute: Trudeau Institute

description: effect of kasB T334D T336D

hyb_protocol: Slide was hybridized for 16 hours at 42 in water bath with volume of 60 uL in solution of standard gene expression hybridization solution, and blocked in standard prehybridization solution. After hybridization, the slide was washed with standard wash protocol. refer to PFGRC protocol SOP#M008

scan_protocol: scanned with PMT voltage adjusted for maximum dynamic range

data_processing: In MIDAS, lowess normalization, standard deviation regularization, in-slide replicate analysis, one bad channel policy set to generous, all flags on

organism: Mycobacterium tuberculosis

source_name: whole_organism from Mycobacterium tuberculosis CDC1551 labeled with Cy3.

label_protocol: 2 ug total RNA was used as template for reverse transcription with random hexamer primers and aminoallyl-dUTP in a 2:3 ratio to dTTP in the nucleotide mix.  After overnight incubation at 42°C, the reaction was stopped, RNA was hydrolyzed, and unincorporated nucleotides and free amines were removed with the Qiagen MinElute kit as per protocol, with amine-free phosphate wash and elution buffers.  cDNA concentration and purity were measured by Nanodrop.  Cy3 and Cy5 dyes were coupled to the aminoallyl-cDNA, which was then purified using a MinElute kit.  Probe concentration, purity, and dye incorporation were measured by Nanodrop.

extract_protocol: Cells are collected by centrifugation and resuspended in 1mL buffer RLT from a Qiagen RNeasy kit.  The suspension is transferred to Fast-Prep Blue Cap tubes and processed for 45 seconds at speed 6.5 in a Fast-Prep apparatus.  After a brief incubation on ice the debris is spun down and the supernatant (~750uL) is removed to a fresh microcentrifuge tube.  525uL absolute ethanol is added and the samples are applied to RNeasy columns in two applications.  At this point the RNA is purified as recommended by the Qiagen protocol.

treatment_protocol: nucleic_acid_extraction: total RNA prep

tag: media

value: liquid

value: parental wildtype

source_name: whole_organism from Mycobacterium tuberculosis CDC1551 labeled with Cy5.

value: kasB T334D T336D


title: CDC1551 kasB T334A T336A Transcriptome Replicate 5

description: effect of kasB T334A T336A

value: kasB T334A T336A


title: CDC1551 kasB T334D T336D Transcriptome Replicate 4

description: effect of kasB T334D T336D


title: CDC1551 kasB T334A T336A Transcriptome Replicate 4

description: effect of kasB T334A T336A


title: CDC1551 kasB KO Transcriptome Replicate 4

description: effect of kasB KO

value: kasB KO


title: Dengue Patient Timepoint3 69

value: blood

value: 2 to 5 weeks after symptoms

value: Pos


title: CDC1551 kasB KO Transcriptome Replicate 5

description: effect of kasB KO


title: CDC1551 kasB T334D T336D Transcriptome Replicate 5

description: effect of kasB T334D T336D


title: T47D_Bic

description: Gene expression after 24hr

value: DHT 1nM,Bicalutamide 10 microM


title: Dengue Patient Timepoint1 68

value: Less than 72 hour after symptoms


title: Dengue Patient Timepoint2 69

value: 3 to 7 dys after symptoms


title: Dengue Patient Timepoint1 67

value: Neg


title: T47D_DHT

description: Gene expression after 24hr


title: Dengue Patient Timepoint1 69


title: Dengue Patient Timepoint2 66


title: Dengue Patient Timepoint1 66


title: Dengue Patient Timepoint1 65


title: Mouse630_Wyeth-14643_STW

city: Leiden

first: Joost

last: Melis

address: Postbus 9600

department: Toxicogenetics

institute: Leiden University Medical Center

description: Quality Control: Approved

hyb_protocol: Amplified materials were hybridized to Mouse Genome 430 2.0 Array for 16 hours at 45°C, subsequently washed and stained with the EukGE-WS2v5_450 protocol

scan_protocol: Samples were finally scanned using the GeneChip Scanner 3000-7G (Affymetrix Inc., Santa Clara, CA, USA). Image generation and feature extraction were performed using Affymetrix GCOS Software v1.4.0.036.

data_processing: Quality control and correction (correcting significant hybridization and experimental blocking effects), annotation, RMA normalization and subsequent data analysis was performed as previously described (Schaap et al. 2012). Only the annotated Entrez genes were used for further analysis. Functional genomics analyses, using the top 1000 FDR-ranked genes, were performed using Metacore (version 6.11 build 41105, GeneGo Inc. St. Joseph, MI, USA) to assess the biological response upon each chemical exposure

source_name: Mouse630 Liver cells

label_protocol: MRNA was amplified and labeled with the GeneChip Expression 3'-Amplification One-Cycle cDNA Synthesis Kit and GeneChip Expression 3'-Amplification Reagents For IVT Labeling according to the manufacturer’s instructions  (Eukaryotic Sample and Array Processing 701025 Rev.5; Affymetrix Inc., Santa Clara, CA, USA).

value: male

tag: age

value: six-weeks-old

tag: classification

value: NGTXC

tag: mouse number

value: liver


title: Dengue Patient Timepoint1 64


title: Mouse631_Wyeth-14643_STW

description: Quality Control: Approved

source_name: Mouse631 Liver cells

tag: tissue


title: Mouse624_Cyclosporin_STW

description: Quality Control: Approved

source_name: Mouse624 Liver cells

value: Cyclosporin


title: Mouse629_Wyeth-14643_STW

description: Quality Control: Approved

source_name: Mouse629 Liver cells


title: Mouse628_Wyeth-14643_STW

description: Quality Control: Approved

source_name: Mouse628 Liver cells


title: Mouse623_Cyclosporin_STW

description: Quality Control: Approved

source_name: Mouse623 Liver cells


title: Dengue Patient Timepoint1 63


title: Dengue Patient Timepoint2 63


title: Dengue Patient Timepoint3 63


title: Mouse563_D-Mannitol_STW

description: Quality Control: Approved

source_name: Mouse563 Liver cells

value: D-Mannitol

value: NC


title: Mouse561_D-Mannitol_STW

description: Quality Control: Approved

source_name: Mouse561 Liver cells


title: Mouse593_Benzo(a)pyrene_STW

description: Quality Control: Approved

source_name: Mouse593 Liver cells

value: Benzo(a)pyrene

value: GTXC


title: Mouse560_DEPH_STW

description: Quality Control: Approved

source_name: Mouse560 Liver cells

value: DEPH


title: Mouse594_Benzo(a)pyrene_STW

description: Quality Control: Approved

source_name: Mouse594 Liver cells


title: Mouse591_Benzo(a)pyrene_STW

description: Quality Control: Approved

source_name: Mouse591 Liver cells


title: Mouse621_Cyclosporin_STW

description: Quality Control: Approved

source_name: Mouse621 Liver cells


title: Mouse592_Benzo(a)pyrene_STW

description: Quality Control: Approved

source_name: Mouse592 Liver cells


title: Dengue Patient Timepoint2 62

source_name: Human whole blood

value: blood


title: Mouse564_D-Mannitol_STW

description: Quality Control: Approved

source_name: Mouse564 Liver cells


title: Mouse622_Cyclosporin_STW

description: Quality Control: Approved

source_name: Mouse622 Liver cells


title: Dengue Patient Timepoint1 62


title: Dengue Patient Timepoint3 62

value: 2 to 5 weeks after symptoms


title: Mouse554_Reserpine_STW

description: Quality Control: Approved

source_name: Mouse554 Liver cells

value: Reserpine


title: Dengue Patient Timepoint3 61

value: Pos


title: Mouse559_DEPH_STW

description: Quality Control: Approved

source_name: Mouse559 Liver cells


title: Mouse557_DEPH_STW

description: Quality Control: Approved

source_name: Mouse557 Liver cells


title: Mouse558_DEPH_STW

description: Quality Control: Approved

source_name: Mouse558 Liver cells


title: Mouse562_D-Mannitol_STW

description: Quality Control: Approved

source_name: Mouse562 Liver cells


title: Mouse552_Reserpine_STW

description: Quality Control: Approved

source_name: Mouse552 Liver cells


title: Mouse551_Reserpine_STW

description: Quality Control: Approved

source_name: Mouse551 Liver cells


title: Mouse546_Phenobarbital_STW

description: Quality Control: Approved

source_name: Mouse546 Liver cells

value: Phenobarbital


title: Dengue Patient Timepoint3 60


title: Dengue Patient Timepoint1 61

value: Less than 72 hour after symptoms


title: Mouse553_Reserpine_STW

description: Quality Control: Approved

source_name: Mouse553 Liver cells


title: Dengue Patient Timepoint2 61

value: 3 to 7 dys after symptoms


title: Mouse536_Diethylstillbestrol_STW

description: Quality Control: Approved

source_name: Mouse536 Liver cells

value: male

value: Diethylstillbestrol


title: Dengue Patient Timepoint3 59

value: Neg


title: Mouse545_Phenobarbital_STW

description: Quality Control: Approved

source_name: Mouse545 Liver cells

value: six-weeks-old

value: NGTXC

value: liver


title: Dengue Patient Timepoint2 59


title: Dengue Patient Timepoint1 60


title: Mouse539_17 B- Estradiol_STW

description: Quality Control: Approved

source_name: Mouse539 Liver cells

value: 17 B- Estradiol


title: Mouse535_Diethylstillbestrol_STW

description: Quality Control: Approved

source_name: Mouse535 Liver cells


title: Mouse541_17 B- Estradiol_STW

description: Quality Control: Approved

source_name: Mouse541 Liver cells


title: Dengue Patient Timepoint2 60

source_name: Human whole blood


title: Mouse542_17 B- Estradiol_STW

description: Quality Control: Approved

source_name: Mouse542 Liver cells


title: Mouse533_Diethylstillbestrol_STW

description: Quality Control: Approved

source_name: Mouse533 Liver cells


title: Mouse534_Diethylstillbestrol_STW

description: Quality Control: Approved

source_name: Mouse534 Liver cells


title: Mouse543_Phenobarbital_STW

description: Quality Control: Approved

source_name: Mouse543 Liver cells


title: Mouse540_17 B- Estradiol_STW

description: Quality Control: Approved

source_name: Mouse540 Liver cells


title: Mouse544_Phenobarbital_STW

description: Quality Control: Approved

source_name: Mouse544 Liver cells


title: Dengue Patient Timepoint1 59


title: Mouse522_Phenacetine_STW

description: Quality Control: Approved

source_name: Mouse522 Liver cells

value: Phenacetine


title: Mouse523_Phenacetine_STW

description: Quality Control: Approved

source_name: Mouse523 Liver cells

value: GTXC


title: Dengue Patient Timepoint3 58


title: Mouse520_Phenacetine_STW

description: Quality Control: Approved

source_name: Mouse520 Liver cells


title: Mouse521_Phenacetine_STW

description: Quality Control: Approved

source_name: Mouse521 Liver cells


title: Mouse503_control_STW

description: Quality Control: Approved

source_name: Mouse503 Liver cells

value: control


title: Mouse506_control_STW

description: Quality Control: Approved

source_name: Mouse506 Liver cells


title: Dengue Patient Timepoint1 58

value: blood


title: Mouse504_control_STW

description: Quality Control: Approved

source_name: Mouse504 Liver cells


title: Mouse761_control_Lever

description: Quality Control: Approved

source_name: Mouse761 Liver cells


title: Mouse505_control_STW

description: Quality Control: Approved

source_name: Mouse505 Liver cells


title: Dengue Patient Timepoint3 57

value: 2 to 5 weeks after symptoms


title: Mouse683_2 AAF_Lever

description: Quality Control: Approved

source_name: Mouse683 Liver cells

value: 2 AAF


title: Mouse759_control_Lever

description: Quality Control: Approved

source_name: Mouse759 Liver cells


title: Mouse764_control_Lever

description: Quality Control: Approved

source_name: Mouse764 Liver cells


title: Mouse754_Cisplatin_Lever

description: Quality Control: Approved

source_name: Mouse754 Liver cells

value: Cisplatin


title: Mouse755_Cisplatin_Lever

description: Quality Control: Approved

source_name: Mouse755 Liver cells


title: Mouse756_Cisplatin_Lever

description: Quality Control: Approved

source_name: Mouse756 Liver cells


title: Dengue Patient Timepoint2 57

source_name: Human whole blood


title: Mouse753_Cisplatin_Lever

description: Quality Control: Approved

source_name: Mouse753 Liver cells


title: Mouse685_2 AAF_Lever

description: Quality Control: Approved

source_name: Mouse685 Liver cells


title: Dengue Patient Timepoint2 58


title: Mouse682_2 AAF_Lever

description: Quality Control: Approved

source_name: Mouse682 Liver cells


title: Mouse678_Sodium diclofenac_Lever

description: Quality Control: Approved

source_name: Mouse678 Liver cells

value: Sodium diclofenac

value: NC


title: Mouse763_control_Lever

description: Quality Control: Approved

source_name: Mouse763 Liver cells


title: Dengue Patient Timepoint2 56

value: 3 to 7 dys after symptoms

value: Pos


title: Dengue Patient Timepoint1 56

value: Less than 72 hour after symptoms


title: Dengue Patient Timepoint2 55


title: Dengue Patient Timepoint1 57

value: Neg


title: Mouse676_Sodium diclofenac_Lever

description: Quality Control: Approved

source_name: Mouse676 Liver cells

value: male

value: six-weeks-old


title: Dengue Patient Timepoint1 55


title: Mouse677_Sodium diclofenac_Lever

description: Quality Control: Approved

source_name: Mouse677 Liver cells

value: liver


title: Dengue Patient Timepoint3 55


title: Mouse672_Diisodecyl phthalate_Lever

description: Quality Control: Approved

source_name: Mouse672 Liver cells

value: Diisodecyl phthalate


title: Mouse684_2 AAF_Lever

description: Quality Control: Approved

source_name: Mouse684 Liver cells


title: Mouse675_Sodium diclofenac_Lever

description: Quality Control: Approved

source_name: Mouse675 Liver cells


title: Dengue Patient Timepoint1 54


title: Dengue Patient Timepoint3 54


title: Mouse669_Diisodecyl phthalate_Lever

description: Quality Control: Approved

source_name: Mouse669 Liver cells


title: Mouse671_Diisodecyl phthalate_Lever

description: Quality Control: Approved

source_name: Mouse671 Liver cells


title: Mouse659_Aflatoxine B1_Lever

description: Quality Control: Approved

source_name: Mouse659 Liver cells

value: Aflatoxine B1


title: Dengue Patient Timepoint2 54


title: Mouse664_Bisphenol A_Lever

description: Quality Control: Approved

source_name: Mouse664 Liver cells

value: Bisphenol A


title: Dengue Patient Timepoint2 53


title: Mouse658_Aflatoxine B1_Lever

description: Quality Control: Approved

source_name: Mouse658 Liver cells

value: GTXC


title: Mouse666_Bisphenol A_Lever

description: Quality Control: Approved

source_name: Mouse666 Liver cells


title: Mouse663_Bisphenol A_Lever

description: Quality Control: Approved

source_name: Mouse663 Liver cells


title: Mouse660_Aflatoxine B1_Lever

description: Quality Control: Approved

source_name: Mouse660 Liver cells


title: Dengue Patient Timepoint3 52

source_name: Human whole blood

value: blood


title: Mouse670_Diisodecyl phthalate_Lever

description: Quality Control: Approved

source_name: Mouse670 Liver cells


title: Mouse665_Bisphenol A_Lever

description: Quality Control: Approved

source_name: Mouse665 Liver cells


title: Mouse657_Aflatoxine B1_Lever

description: Quality Control: Approved

source_name: Mouse657 Liver cells


title: Mouse654_Tributyl-tin-oxide_Lever

description: Quality Control: Approved

source_name: Mouse654 Liver cells

value: Tributyl-tin-oxide


title: Dengue Patient Timepoint3 53

value: 2 to 5 weeks after symptoms


title: Dengue Patient Timepoint2 52


title: Mouse653_Tributyl-tin-oxide_Lever

description: Quality Control: Approved

source_name: Mouse653 Liver cells


title: Dengue Patient Timepoint3 51


title: Dengue Patient Timepoint1 53


title: Dengue Patient Timepoint1 50


title: Mouse652_Tributyl-tin-oxide_Lever

description: Quality Control: Approved

source_name: Mouse652 Liver cells


title: Mouse563_D-Mannitol_Lever

description: Quality Control: Approved

source_name: Mouse563 Liver cells

value: D-Mannitol


title: Mouse628_Wyeth-14643_Lever

description: Quality Control: Approved

source_name: Mouse628 Liver cells

value: NGTXC


title: Mouse651_Tributyl-tin-oxide_Lever

description: Quality Control: Approved

source_name: Mouse651 Liver cells

value: NC


title: Dengue Patient Timepoint1 52


title: Mouse623_Cyclosporin_Lever

description: Quality Control: Approved

source_name: Mouse623 Liver cells

value: Cyclosporin


title: Mouse558_DEPH_Lever

description: Quality Control: Approved

source_name: Mouse558 Liver cells

value: DEPH


title: Mouse593_Benzo(a)pyrene_Lever

description: Quality Control: Approved

source_name: Mouse593 Liver cells

value: Benzo(a)pyrene


title: Dengue Patient Timepoint1 51

value: Less than 72 hour after symptoms

value: Pos


title: Mouse621_Cyclosporin_Lever

description: Quality Control: Approved

source_name: Mouse621 Liver cells

value: male

value: six-weeks-old


title: Mouse631_Wyeth-14643_Lever

description: Quality Control: Approved

source_name: Mouse631 Liver cells

value: liver


title: Dengue Patient Timepoint3 49


title: Mouse594_Benzo(a)pyrene_Lever

description: Quality Control: Approved

source_name: Mouse594 Liver cells


title: Dengue Patient Timepoint2 49

value: 3 to 7 dys after symptoms


title: Mouse546_Phenobarbital_Lever

description: Quality Control: Approved

source_name: Mouse546 Liver cells

value: Phenobarbital


title: Mouse557_DEPH_Lever

description: Quality Control: Approved

source_name: Mouse557 Liver cells


title: Mouse562_D-Mannitol_Lever

description: Quality Control: Approved

source_name: Mouse562 Liver cells


title: Mouse552_Reserpine_Lever

description: Quality Control: Approved

source_name: Mouse552 Liver cells

value: Reserpine


title: Dengue Patient Timepoint2 48

source_name: Human whole blood

value: blood

value: Neg


title: Mouse543_Phenobarbital_Lever

description: Quality Control: Approved

source_name: Mouse543 Liver cells


title: Dengue Patient Timepoint3 48

value: 2 to 5 weeks after symptoms