title: CGH: FN0171855.08.01.01.10.M6_v_M92-220

source_name: DNA from soybean line FN0171855.08.01.01.10.M6


title: CGH: FN0176450.xx.xx.xx.xx.07.M7_v_M92-220

status: Public on Jun 04 2014

type: genomic

city: Saint Paul

first: Robert

middle: M

last: Stupar

state: MN

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

country: USA

institute: University of Minnesota

hyb_protocol: Genomic DNA were hybridized to the microarray according to the manufacturer instructions (NimbleGen CGH User Guide Ver 9.1)

scan_protocol: Slides were scanned on the NimbleGen MS 200 Scanner (Roche/NimbleGen, Madison,WI) according to the array manufacturer instructions (NimbleGen CGH User Guild Ver 9.1)

data_processing: Data was analyzed using the Roche NimbleGen DEVA software.

molecule: genomic DNA

organism: Glycine max

source_name: DNA from soybean line FN0176450.xx.xx.xx.xx.07.M7

label_protocol: 500 ng of genomic DNA was labeled and amplified using the NimbleGen Dual-Color Labeling Kit according to the NimbleGen CGH User Guide Ver 9.1.

growth_protocol: single plant leaf tissue

extract_protocol: Genomic DNA samples were isolated using the Qiagen Plant DNeasy protocol

tag: genotype

tag: tissue

value: single plant leaf

tag: strain

source_name: DNA from soybean line M92-220


title: SmoWT-MB_DMSO_2

type: RNA

city: Stanford

first: Yujie

last: Tang

state: CA

address: 265 Campus Dr SIM1 G3055

department: Neurology

institute: Stanford University School of Medicine

description: Sample 4.AVG_Signal

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Rank-invariant normalized data was generated using GenomeStudio v1.9.0 and converted to .gct file format, which was then collapsed to gene symbols using the GSEA desktop application (http://www.broadinstitute.org/gsea/index.jsp).

label: biotin

molecule: total RNA

organism: Mus musculus

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

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

tag: cell line

value: SmoWT-MB

tag: cell type

value: Ptch-deficient mouse medulloblastoma cell line

tag: treated with

value: DMSO for 6hrs


title: CGH: FN0176405.xx.xx.xx.xx.xx.08.M8_v_M92-220

source_name: DNA from soybean line FN0176405.xx.xx.xx.xx.xx.08.M8


title: CGH: FN0183480.xx.xx.xx.xx.x1.M7_v_M92-220

source_name: DNA from soybean line FN0183480.xx.xx.xx.xx.x1.M7


title: CGH: FN0176450.xx.xx.xx.xx.06.M7_v_M92-220

source_name: DNA from soybean line FN0176450.xx.xx.xx.xx.06.M7


title: SmoWT-MB_GDC-0449_1

description: Sample 3.AVG_Signal

value: SMOi GDC-0449 for 6hrs


title: SmoWT-MB_JQ1_1

description: Sample 2.AVG_Signal

value: BETi JQ1 for 6hrs


title: SmoWT-MB_DMSO_1

description: Sample 1.AVG_Signal


title: CGH: FN0180773.xx.xx.xx.xx.x1.M7_v_M92-220

source_name: DNA from soybean line FN0180773.xx.xx.xx.xx.x1.M7


title: PACD Unaffected 2_10

city: Los Angeles

first: Anthony

middle: J.

last: Aldave

address: 200 Stein Plaza DSERC 3-143

department: Ophthalmology

institute: Stein Eye Institute, UCLA

description: hybridized to CytoScan HD

hyb_protocol: as per Affymetrix CytoScanHD standard protocol

data_processing:
Data analysis results (.CYCHP files) for the 13 samples were generated using the ChAS analysis files for the CytoScan HD Array version NA32.3. The reference model file for the analysis was the CytoScanHD_Array.na32.3.v1.REF_MODEL. The annotation used for the analysis was CytoScanHD_Array.na32.3.annot.db.
The ChAS software implements the Command Console binary data format for building the .CYCHP files. Analysis results are incorporated into four data groups, three of which can be read and visualized on the ChAS software interface. Each data group contains one or more data sets. As a whole the three relevant data groups provide analysis results for each chromosome, analysis results for each probeset, and analysis results for segments. Details of each group and their corresponding data sets can be found at http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cychp.html.

organism: Homo sapiens

source_name: Leukocytes 2_10

extract_protocol: Genomic DNA was extracted from blood using the Qiagen FlexiGene DNA Kit

tag: affected status

value: unaffected

tag: gender

value: male


title: CGH: FN0113646.03.02.M4_v_M92-220

source_name: DNA from soybean line FN0113646.03.02.M4


title: 426_MIV_RA

status: Public on Jun 03 2014

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

description: Gonads RNA of Ruditapes decussatus

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 2 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v10.7.3.1 and normalized by quantile normalization using R statistical software

label: Cyanine 3

organism: Ruditapes decussatus

source_name: Male gonads at stage IV of Ruditapes decussatus sampled in Ria Aveiro

label_protocol: Amplified and labeled according to Agilent Low input One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Total RNA was isolated using Extract-all (Eurobio) procedure.

value: male gonads

tag: Stage

value: IV

tag: sample data and location

value: between July 2011 and July 2012 in Ria Aveiro


title: PACD Affected 2_3

description: hybridized to CytoScan HD

scan_protocol: as per Affymetrix CytoScanHD standard protocol

source_name: Leukocytes 2_3

value: affected


title: 484_FIV_RA

description: Gonads RNA of Ruditapes decussatus

source_name: Female gonads at stage IV of Ruditapes decussatus sampled in Ria Aveiro

value: female gonads


title: 445_MIV_RA

description: Gonads RNA of Ruditapes decussatus


title: PACD Affected 2_7

description: hybridized to CytoScan HD

source_name: Leukocytes 2_7

label_protocol: as per Affymetrix CytoScanHD standard protocol


title: 466_FIV_RA

description: Gonads RNA of Ruditapes decussatus


title: 468_MIV_RA

description: Gonads RNA of Ruditapes decussatus


title: PACD Affected 3_3

description: hybridized to CytoScan HD

source_name: Leukocytes 3_3


title: 430_FIV_RA

description: Gonads RNA of Ruditapes decussatus


title: CGH: FN0112885.02.06.03.M5_v_M92-220

source_name: DNA from soybean line FN0112885.02.06.03.M5


title: PACD Unaffected 1_25

description: hybridized to CytoScan HD

source_name: Leukocytes 1_25


title: 444_FIII_RA

description: Gonads RNA of Ruditapes decussatus

source_name: Female gonads at stage III of Ruditapes decussatus sampled in Ria Aveiro

value: III


title: PACD Unaffected 1_23

description: hybridized to CytoScan HD

source_name: Leukocytes 1_23

value: female


title: 432_MIII_RA

description: Gonads RNA of Ruditapes decussatus

source_name: Male gonads at stage III of Ruditapes decussatus sampled in Ria Aveiro


title: 442_MIII_RA

description: Gonads RNA of Ruditapes decussatus


title: 440_MIII_RA

description: Gonads RNA of Ruditapes decussatus


title: CGH: FN0176450.xx.xx.xx.xx.05.M7_v_M92-220

source_name: DNA from soybean line FN0176450.xx.xx.xx.xx.05.M7

source_name: DNA from soybean line M92-220


title: 433_FIII_RA

description: Gonads RNA of Ruditapes decussatus


title: 83_MIII_RA

description: Gonads RNA of Ruditapes decussatus


title: 398_FIII_RA

description: Gonads RNA of Ruditapes decussatus


title: 70_FIII_RA

description: Gonads RNA of Ruditapes decussatus


title: 436_FIII_RA

description: Gonads RNA of Ruditapes decussatus


title: 396_FIII_RA

description: Gonads RNA of Ruditapes decussatus


title: 441_FIII_RA

description: Gonads RNA of Ruditapes decussatus


title: 439_MIII_RA

description: Gonads RNA of Ruditapes decussatus


title: 364_FII_RA

description: Gonads RNA of Ruditapes decussatus

source_name: Female gonads at stage II of Ruditapes decussatus sampled in Ria Aveiro

value: II


title: 389_FII_RA

description: Gonads RNA of Ruditapes decussatus


title: CGH: FN0112228.06.02.01.M5_v_M92-220

source_name: DNA from soybean line FN0112228.06.02.01.M5


title: 342_MII_RA

description: Gonads RNA of Ruditapes decussatus

source_name: Male gonads at stage II of Ruditapes decussatus sampled in Ria Aveiro


title: 346_FII_RA

description: Gonads RNA of Ruditapes decussatus


title: 390_FII_RA

description: Gonads RNA of Ruditapes decussatus


title: 363_MII_RA

description: Gonads RNA of Ruditapes decussatus


title: 251_I_RA

description: Gonads RNA of Ruditapes decussatus

source_name: Gonads at stage I of Ruditapes decussatus sampled in Ria Aveiro

value: gonads

value: I

value: between July 2011 and July 2012 in Ria Formosa


title: 355_MII_RA

description: Gonads RNA of Ruditapes decussatus


title: 358_FII_RA

description: Gonads RNA of Ruditapes decussatus


title: CGH: FN0112871.04.03.M4_v_M92-220

source_name: DNA from soybean line FN0112871.04.03.M4

value: single plant leaf


title: 157_I_RA

description: Gonads RNA of Ruditapes decussatus


title: PACD Unaffected 1_24

description: hybridized to CytoScan HD

source_name: Leukocytes 1_24


title: CGH: FN0112351.04.01.M4_v_M92-220

source_name: DNA from soybean line FN0112351.04.01.M4


title: PACD Unaffected 1_17

description: hybridized to CytoScan HD

source_name: Leukocytes 1_17


title: 352_MII_RA

description: Gonads RNA of Ruditapes decussatus


title: 76_I_RA

description: Gonads RNA of Ruditapes decussatus


title: CGH: FN0112546.01.02.M4_v_M92-220

source_name: DNA from soybean line FN0112546.01.02.M4


title: PACD Affected 1_12

description: hybridized to CytoScan HD

source_name: Leukocytes 1_12


title: HEL_Control shRNA (Luc)_1

city: Cambridge

first: Fatima

last: Al-Shahrour

state: MA

address: 7 Cambridge Center

department: Cancer program

institute: Broad Institute of MIT and Harvard

description: Replicate 1 Luc

hyb_protocol: The cDNA was fragmented, labeled and hybridized to Affymetrix HG_U133AAofAv2 microarrays (Affymetrix, Santa Clara, CA)

scan_protocol: Standard Affymetrix protocol

data_processing: Raw expression values were normalized using Robust Multiarray Averaging (RMA) using quantile normalization

source_name: HEL cell line_Control shRNA (Luc)

label_protocol: Linear amplification of 20 ng of total RNA was performed using the Ovation Biotin RNA Amplification and Labeling   System   (Nugen)

extract_protocol: RNA was purified from HEL cells using Trizol (Invitrogen)

treatment_protocol: The JAK2V617F-mutant AML cell line HEL was treated with 2 independent shRNA lentiviruses for JAK2 in a pLKO-puromycin selectable vector as well as 2 non-targeting shRNA controls (sh-Luciferase and GFP vector control).

value: JAK2V617F-mutant AML cell line HEL

tag: treatment

value: Control shRNA (Luc)


title: CGH: FN0111221.03.03.M4_v_M92-220

source_name: DNA from soybean line FN0111221.03.03.M4


title: HEL_Control shRNA (Luc)_2

description: Replicate 2 Luc


title: CGH: FN0111996.06.01.M4_v_M92-220

source_name: DNA from soybean line FN0111996.06.01.M4


title: HEL_Control shRNA (Luc)_3

description: Replicate 3 Luc


title: PACD Unaffected 1_7

description: hybridized to CytoScan HD

source_name: Leukocytes 1_7


title: PACD Unaffected 1_22

description: hybridized to CytoScan HD

source_name: Leukocytes 1_22


title: 454_MIV_RF

description: Gonads RNA of Ruditapes decussatus

source_name: Male gonads at stage IV of Ruditapes decussatus sampled in Ria Formosa


title: 452_MIV_RF

description: Gonads RNA of Ruditapes decussatus


title: HEL_JAK2 knockdown (Jak2-9 shRNA)_2

description: Replicate 2 Jak2-9 shRNA

source_name: HEL cell line_JAK2 knockdown (Jak2-9 shRNA)

value: JAK2 knockdown (Jak2-9 shRNA)


title: CGH: FN0110338.02.01.M4_v_M92-220

source_name: DNA from soybean line FN0110338.02.01.M4

source_name: DNA from soybean line M92-220


title: 67_I_RA

description: Gonads RNA of Ruditapes decussatus


title: HEL_JAK2 knockdown (Jak2-9 shRNA)_3

description: Replicate 3 Jak2-9 shRNA


title: 151_I_RA

description: Gonads RNA of Ruditapes decussatus


title: 453_FIV_RF

description: Gonads RNA of Ruditapes decussatus

source_name: Female gonads at stage IV of Ruditapes decussatus sampled in Ria Formosa


title: PACD Affected 1_5

description: hybridized to CytoScan HD

source_name: Leukocytes 1_5


title: HEL_JAK2 knockdown (Jak2-10 shRNA)_3

description: Replicate 3 Jak2-10 shRNA

source_name: HEL cell line_JAK2 knockdown (Jak2-10 shRNA)

value: JAK2 knockdown (Jak2-10 shRNA)


title: HEL_JAK2 knockdown (Jak2-9 shRNA)_1

description: Replicate 1 Jak2-9 shRNA


title: 448_FIV_RF

description: Gonads RNA of Ruditapes decussatus


title: 463_MIV_RF

description: Gonads RNA of Ruditapes decussatus


title: 418_MIII_RF

description: Gonads RNA of Ruditapes decussatus

source_name: Male gonads at stage III of Ruditapes decussatus sampled in Ria Formosa


title: HEL_Control shRNA (GFP)_1

description: Replicate 1 GFP

source_name: HEL cell line_Control shRNA (GFP)

value: Control shRNA (GFP)


title: Normal (TRG_1)

description: Gene expression data from peripheral blood granulocytes from a healthy donor.

source_name: Normal, Peripheral blood neutrophils

extract_protocol: RNA   was   purified   from   granulocytes   using   Trizol (Invitrogen).

value: Peripheral blood neutrophils

tag: diagnosis

value: Normal

tag: jak2 v617f quantitative genotyping

tag: calr status

tag: tet2 status

tag: mpl w515k/l status


title: CGH: FN0110495.02.03.M4_v_M92-220

source_name: DNA from soybean line FN0110495.02.03.M4


title: HEL_Control shRNA (GFP)_2

description: Replicate 2 GFP


title: HEL_Control shRNA (GFP)_3

description: Replicate 3 GFP


title: 50_FIII_RF

description: Gonads RNA of Ruditapes decussatus

source_name: Female gonads at stage III of Ruditapes decussatus sampled in Ria Formosa


title: 461_FIV_RF

description: Gonads RNA of Ruditapes decussatus

value: IV


title: 449_FIV_RF

description: Gonads RNA of Ruditapes decussatus


title: 450_FIV_RF

description: Gonads RNA of Ruditapes decussatus


title: 406_MIII_RF

description: Gonads RNA of Ruditapes decussatus

value: male gonads


title: CGH: FN0110332.02.02.M4_v_M92-220

source_name: DNA from soybean line FN0110332.02.02.M4


title: Normal (TRG_6)


title: 419_MIII_RF

description: Gonads RNA of Ruditapes decussatus


title: 391_MII_RA

description: Gonads RNA of Ruditapes decussatus

source_name: Male gonads at stage II of Ruditapes decussatus sampled in Ria Aveiro

value: between July 2011 and July 2012 in Ria Aveiro


title: 47_FIII_RF

description: Gonads RNA of Ruditapes decussatus

value: female gonads

value: III


title: PACD Unaffected 1_11

description: hybridized to CytoScan HD

source_name: Leukocytes 1_11

value: unaffected

value: female


title: 420_MII_RF

description: Gonads RNA of Ruditapes decussatus

source_name: Male gonads at stage II of Ruditapes decussatus sampled in Ria Formosa

value: II


title: 413_FIII_RF

description: Gonads RNA of Ruditapes decussatus

value: between July 2011 and July 2012 in Ria Formosa


title: HEL_JAK2 knockdown (Jak2-10 shRNA)_2

description: Replicate 2 Jak2-10 shRNA


title: 41_FIII_RF

description: Gonads RNA of Ruditapes decussatus


title: Normal (DGG_5DC)


title: Normal (DGG_4BL)


title: 44_FIII_RF

description: Gonads RNA of Ruditapes decussatus


title: Normal (TRG_2)


title: Normal (TRG_5)


title: 414_MII_RF

description: Gonads RNA of Ruditapes decussatus


title: 384_MII_RF

description: Gonads RNA of Ruditapes decussatus


title: Normal (TRG_9)


title: MPN patient sample (MPD_114)

description: Gene expression data from peripheral blood granulocytes from a patient with chronic MPN.

source_name: MPN patient sample, Peripheral blood neutrophils

value: ET

value: WT


title: Normal (DGG_3BH)


title: 374_FII_RF

description: Gonads RNA of Ruditapes decussatus

source_name: Female gonads at stage II of Ruditapes decussatus sampled in Ria Formosa


title: MPN patient sample (MPD_580)

value: MUT


title: Normal (TRG_8)


title: 416_MII_RF

description: Gonads RNA of Ruditapes decussatus


title: 380_MII_RF

description: Gonads RNA of Ruditapes decussatus


title: MPN patient sample (MPD_562)

value: Heterozygous


title: 370_FII_RF

description: Gonads RNA of Ruditapes decussatus


title: MPN patient sample (MPD_374)


title: 376_FII_RF

description: Gonads RNA of Ruditapes decussatus


title: HEL_JAK2 knockdown (Jak2-10 shRNA)_1

description: Replicate 1 Jak2-10 shRNA

value: JAK2V617F-mutant AML cell line HEL

value: JAK2 knockdown (Jak2-10 shRNA)


title: Normal (DGG_2ES)

value: Peripheral blood neutrophils


title: 383_FII_RF

description: Gonads RNA of Ruditapes decussatus


title: MPN patient sample (MPD_176)


title: 368_FII_RF

description: Gonads RNA of Ruditapes decussatus


title: 378_I_RF

description: Gonads RNA of Ruditapes decussatus

source_name: Gonads at stage I of Ruditapes decussatus sampled in Ria Formosa

value: gonads

value: I


title: MPN patient sample (MPD_102)


title: MPN patient sample (MPD_240)


title: MPN patient sample (MPD_146)


title: 375_I_RF

description: Gonads RNA of Ruditapes decussatus


title: MPN patient sample (MPD_5)


title: MPN patient sample (MPD_129)


title: 224_I_RF

description: Gonads RNA of Ruditapes decussatus


title: MPN patient sample (MPD_446)


title: Albendazole treated protoscolecevs protoscolece

city: Urumqi

first: Guodong

last: Lü

state: Xinjiang

address: Liyushan north road

department: State Key Lab Cultivation Base for Xinjiang Major Diseases Research and Xinjiang Key Laboratory of Echinococcosis

country: China

institute: First Affiliated Hospital of Xinjiang Medical University

description: compare gene expression profiles of control protoscolece

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

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

organism: Echinococcus granulosus

source_name: protoscolece treated with albendazole

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

growth_protocol: protoscoleces were cultured in RPMI 1640  (Life Technologies) supplemented with 10% fetal bovine serum (Invitrogen) at 37°C with 5% CO2.

extract_protocol: The protoscoleces of each group were harvest, and total RNA was extracted with Trizol Reagent (Invitrogen) and ethanol precipitation.

treatment_protocol: The protoscoleces of ABZ group were treated by saturation concentration of albendazole (ABZ) for 10 days and harested. The protoscoleces in the artemisinin (ART) group were treated with 100 μg/ml ART for 6 days and harested. ABZ and ART were dissolved in 1% DMSO, respectively. The protoscoleces of DMSO group were treated with 1% DMSO for 10 days and harested. The control group protoscoleces were cultured in  RPMI 1640  (Life Technologies) supplemented with 10% fetal bovine serum (Invitrogen) without any treatment.

value: protoscolece

source_name: protoscolece with normal culture


title: DMSO treated protoscolecevs protoscolece

source_name: protoscolece treated with DMSO

value: 1% DMSO for 10 days


title: Artemisinin treated protoscolecevs protoscolece

source_name: protoscolece treated with artemisinin

value: 100 ug/ml ART for 6 days


title: MPN patient sample (MPD_25)


title: human TGF-β treated protoscoleces for 8h Replicate 1

description: Biological replicate 1 of 3. protoscoleces treated with human TGF-β for 8 h

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed.Capitalbio software was used.

treatment_protocol: The protoscoleces were treated with 1  nM  of  recombinant  human  TGF-β for 24 h and harested at 0 h, 4 h, 8 h and 24 h. The experiment replicates 3 times.

value: 1 nM of recombinant human TGF-β

tag: time point

value: 8 h

source_name: protoscoleces treated with human TGF-β at 0 h

value: 0 h


title: MPN patient sample (MPD_197)


title: human TGF-β treated protoscoleces for 8h Replicate 3

description: Biological replicate 3 of 3. protoscoleces treated with human TGF-β for 8 h


title: human TGF-β treated protoscoleces for 8h Replicate 2

description: Biological replicate 2 of 3. protoscoleces treated with human TGF-β for 8 h


title: MPN patient sample (MPD_84)

value: MF


title: human TGF-β treated protoscoleces for 4h Replicate 3

description: Biological replicate 3 of 3. protoscoleces treated with human TGF-β for 4 h

value: 4 h


title: MPN patient sample (MPD_201)

value: ET


title: human TGF-β treated protoscoleces for 24 h Replicate 3

description: Biological replicate 3 of 3. protoscoleces treated with human TGF-β for 24 h


title: human TGF-β treated protoscoleces for 24 h Replicate 2

description: Biological replicate 2 of 3. protoscoleces treated with human TGF-β for 24 h


title: human TGF-β treated protoscoleces for 24 h Replicate 1

description: Biological replicate 1 of 3. protoscoleces treated with human TGF-β for 24 h


title: MPN patient sample (MPD_115)

value: WT


title: MPN patient sample (MPD_461)


title: MPN patient sample (MPD_605)

value: MUT


title: MPN patient sample (MPD_313)

value: Heterozygous


title: 341_I_RF

description: Gonads RNA of Ruditapes decussatus

value: between July 2011 and July 2012 in Ria Formosa


title: human TGF-β treated protoscoleces for 4h Replicate 2

description: Biological replicate 2 of 3. protoscoleces treated with human TGF-β for 4 h


title: human TGF-β treated protoscoleces for 4h Replicate 1

description: Biological replicate 1 of 3. protoscoleces treated with human TGF-β for 4 h


title: MPN patient sample (MPD_287)

value: Homozygous


title: MPN patient sample (MPD_11)

value: Peripheral blood neutrophils


title: MPN patient sample (MPD_285)


title: MPN patient sample (MPD_325)


title: MPN patient sample (MPD_242)

value: PV


title: MPN patient sample (MPD_271)


title: MPN patient sample (MPD_272)


title: MPN patient sample (MPD_149)


title: MPN patient sample (MPD_170)


title: MPN patient sample (MPD_298)


title: MPN patient sample (MPD_78)


title: MPN patient sample (MPD_328)


title: MPN patient sample (MPD_18)


title: MPN patient sample (MPD_29)


title: MPN patient sample (MPD_141)


title: MPN patient sample (MPD_247)


title: MPN patient sample (MPD_239)


title: MPN patient sample (MPD_241)


title: MPN patient sample (MPD_19)


title: MPN patient sample (MPD_218)


title: MPN patient sample (MPD_189)


title: MPN patient sample (MPD_49)


title: Tenofovir_disoproxil_5_dye_swap

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

description: Animal treated with tenofovir VS pooled samples from 10 animals treated with saline

hyb_protocol: Channel 1 sample was mixed with channel 2 sample, hybridization buffer was added (final concentration was 3xSSC, 0.2% SDS) and samples were denatured. Using LifterSlip cover glasses (Erie Scientific Company, Portsmouth, NH, USA) samples were hybridized for 16h at 65ºC in a water bath using humidified hybridization chambers (HybChambers, GeneMachines, San Carlos, CA, USA). Prior hybridizations Sterolgene v1 Mouse slides were pre-hybridized for 1 hour at 42ºC in 5xSSC, 0.1%SDS and 1%BSA, then washed at room temperature for 5 min in 2xSSC and 0.1%SDS, 3 min in 0.2xSSC and 2 min in MilliQ water and dried by centrifugation. After hybridization slides were washed at room temperature for 5 min in 2xSSC and 0.5%SDS, 5 min in 0.5xSSC, 5 min in 0.05xSSC, and then dried using vacuum centrifuge.

scan_protocol: Arrays scanned on an Tecan LS200 scanner; images analyzed using MediaCybernetics Array-Pro Analyzer software.

data_processing: Features were filtered out according to the following criteria: coefficient of variation (CV, ratio between standard deviation of the background and the median feature intensity) above 0.5 and foreground to background ratio above 1.5. Saturated features were removed. Log2 ratios were normalized using LOESS fit to spike in control RNAs and housekeeping controls. Filtration and normalization was done in Orange software. Normalized log ratios can be compared across samples. Data normalization and analysis was performed using Orange software (Demsar, 2006; Curk, 2005; http://www.ailab.si/orange).

source_name: Animal treated with tenofovir

label_protocol: cDNA synthesis and incorporation of aa-dUTP by reverse transcription was performed using SuperScript™ III Reverse Transcriptase (Invitrogen, USA), 100mM dNTPs (Promega, USA), amino-allyl dUTP (Sigma Aldrich, USA), oligo dT primers (Invitrogen, USA) and 20µg of total RNA, protected with RNase OUT  RNase inhibitor (Invitrogen, USA). Negative control group RNA was pooled from all mice and used as a reference in all hybridizations. Final dNTP concentration was of 25mM for dATP, dCTP and dGTP; dTTP and amino-allyl-dUTP were in ratio 3:2 (final concentration 15mM and 10mM, respectively). 250 pg of Firefly Luciferase mRNA (Promega, Madison, WI, USA), and 0.5 μL of test spike mix from Lucidea Universal ScoreCard kit were added as internal controls and calibrators. After the reverse transcription, RNA was alkaline-hydrolysed and amino-allyl cDNA was purified on MinElute PCR Purification Kit columns (Qiagen, Germany). Cy3 and Cy5 NHS esters were coupled to aa-cDNA (Cy3, resp. Cy5 Mono-Reactive Dye Pack (Amersham Biosciences, USA)). Uncoupled dye was removed on MinElute columns.

growth_protocol: Female mice of the inbred strain C57BL/6, 8-10 weeks old were kept in transparent plastic cages and maintained in an Independent Environmental Air Flow Animal Cabinet with lighting from 6AM  to 6PM, temperature 22 °C.

extract_protocol: Total RNA was isolated from liver tissue samples stored in RNAlater (Qiagen, Germany) using TRI REAGENT (MRC, USA). RNA concentration and purity was measured by spectrophotometry at 260, 280 and 230 nm using an Infinite M200 micro plate reader (Tecan, Switzerland). RNA integrity was determined on an Agilent 2100 Bioanalyzer using an RNA 6000 Nano LabChip kit (both Agilent Technologies, USA).

treatment_protocol: Animals were randomly separated into 4 groups of 5 and treated for three days by intraperitoneal injections as following: AD and TD groups were given 25 mg/kg of AD or TD intraperitoneally for three days. PC (positive control) group of four animals was treated with 60 mg/kg phenobarbital plus one dose of 80 mg/kg of β-naphthoflavone on day two. 5 animals of NC (negative control) group were injected 200µl of 0.9% saline solution. On day four, animals were killed by cervical dislocation.

value: liver

value: tenofovir disoproxil

tag: animal

source_name: Pooled samples from 10 animals treated with saline

value: saline


title: Normal (TRG_7)

source_name: Normal, Peripheral blood neutrophils

value: Normal


title: MPN patient sample (MPD_165)


title: MPN patient sample (MPD_282)


title: MPN patient sample (MPD_344)


title: MPN patient sample (MPD_288)


title: Tenofovir_disoproxil_4_dye_swap

tag: tissue


title: Tenofovir_disoproxil_3_dye_swap

tag: strain


title: Tenofovir_disoproxil_1_dye_swap


title: Tenofovir_disoproxil_2_dye_swap


title: Adefovir_dipivoxil_5_dye_swap

description: Animal treated with adefovir VS pooled samples from 10 animals treated with saline

source_name: Animal treated with adefovir

value: adefovir dipivoxil


title: Adefovir_dipivoxil_4_dye_swap


title: MPN patient sample (MPD_155)


title: MPN patient sample (MPD_196)


title: Positive_control_3

description: Animal treated with phenobarbital and beta-naphthoflavone VS pooled samples from 10 animals treated with saline

value: phenobarbital and beta-naphthoflavone


title: Positive_control_4

source_name: Animal treated with phenobarbital and beta-naphthoflavone


title: Positive_control_2


title: MPN patient sample (MPD_364)


title: MPN patient sample (MPD_369)


title: Adefovir_dipivoxil_1_dye_swap


title: Adefovir_dipivoxil_2_dye_swap


title: MPN patient sample (MPD_354)


title: Positive_control_1


title: MPN patient sample (MPD_88)


title: MPN patient sample (MPD_184)


title: MPN patient sample (MPD_117)


title: MPN patient sample (MPD_181)


title: MPN patient sample (MPD_424)


title: MPN patient sample (MPD_137)


title: MPN patient sample (MPD_153)


title: MPN patient sample (MPD_62)


title: Adefovir_dipivoxil_3_dye_swap


title: MPN patient sample (MPD_428)


title: 228_I_RF

description: Gonads RNA of Ruditapes decussatus

value: gonads

value: I


title: Tenofovir_disoproxil_5


title: Tenofovir_disoproxil_4


title: MPN patient sample (MPD_264)


title: Tenofovir_disoproxil_3


title: MPN patient sample (MPD_324)


title: Adefovir_dipivoxil_1


title: Adefovir_dipivoxil_5


title: Tenofovir_disoproxil_1


title: Adefovir_dipivoxil_4


title: Adefovir_dipivoxil_3


title: Adefovir_dipivoxil_2


title: Acrolein-3

city: Louisville

first: Timothy

last: O'Toole

state: KY

address: 302E. Muhammad Ali Blvd

institute: University of Louisville

description: miRNA expression at 4hours after treatement

hyb_protocol: resuspended RNA hybirdized to array in hybridization buffer at 550C for 20hr. Then slides washed in Agilent wash buffers 1 and 2.

scan_protocol: scanned with Agilent microarray scanner (G2505B); one color  images extracted with Feature Extraction Software (v9.5.1 Agilent)

data_processing: raw data files extracted from Agilent Feature extraction software were processed and analyzed with GeneSpring GX9.0 software

source_name: HUVEC

label_protocol: 100ng total RNA treated with CIP, denatured, and ligated to pCP-Cy3 with T4 RNA ligase, then purified on spin column, dried with Speed-vac

growth_protocol: HUVEC in log phase growth (passage 3-5) were maintained in EBM media (Lonza).

extract_protocol: Total RNA extracted using Qiagen kit

treatment_protocol: Cells were grown in media containing 0.1% serum overnight, incubated with 10uM acrolein or vehicle in HBSS for 2 hr, and allowed to recover in normal media for 4hr.

value: umbilical vein endothelial cells


title: MPN patient sample (MPD_120)

value: MF


title: MPN patient sample (MPD_256)

value: WT


title: Acrolein-1


title: Acrolein-2


title: Control-4


title: Tenofovir_disoproxil_2


title: MPN patient sample (MPD_209)

value: ET


title: MPN patient sample (MPD_111)

value: Heterozygous


title: MPN patient sample (MPD_537)

value: MUT


title: Control-3


title: MPN patient sample (MPD_161)

value: Homozygous


title: MPN patient sample (MPD_214)

value: Peripheral blood neutrophils


title: MPN patient sample (MPD_118)


title: MPN patient sample (MPD_283)

value: PV


title: Acrolein-4


title: Control-2


title: Control-1


title: MPN patient sample (MPD_459)


title: MPN patient sample (MPD_295)


title: MPN patient sample (MPD_52)


title: MPN patient sample (MPD_47)


title: MPN patient sample (MPD_376)


title: MPN patient sample (MPD_12)


title: MPN patient sample (MPD_310)


title: Serum DNA 282

city: London

first: Andrew

middle: E

last: Teschendorff

address: 72 Huntley Street

department: UCL Cancer Institute/Institute for Women's Health

country: United Kingdom

institute: University College London

description:
bi-sulphite converted genomic serum DNA from woman
serum DNA from healthy postmenopausal women, a number of which developed breast cancer (cases)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Biotin

source_name: genomic DNA from serum sample 282

label_protocol: Standard Illumina Protocol for Infinium 27k Chip

extract_protocol: DNA was extracted from serum at Tepnel (www.tepnel.com) using Qiagen QiAamp Blood Mini Kit (51106)

tag: subject

value: healthy postmenopausal women

tag: case/control

tag: ageatdraw (yrs)

tag: season

tag: dna conc. (ug/ml)

value: L


title: Serum DNA 281

source_name: genomic DNA from serum sample 281

value: J


title: MPN patient sample (MPD_281)

tag: cell type


title: MPN patient sample (MPD_17)


title: MPN patient sample (MPD_131)


title: Serum DNA 276

source_name: genomic DNA from serum sample 276

value: K


title: MPN patient sample (MPD_159)

source_name: MPN patient sample, Peripheral blood neutrophils


title: MPN patient sample (MPD_21)


title: MPN patient sample (MPD_359)


title: MPN patient sample (MPD_332)


title: Serum DNA 279

source_name: genomic DNA from serum sample 279

value: F


title: MPN patient sample (MPD_3)


title: Serum DNA 278

source_name: genomic DNA from serum sample 278

value: D


title: Serum DNA 277

source_name: genomic DNA from serum sample 277

value: B


title: MPN patient sample (MPD_434)


title: Serum DNA 274

source_name: genomic DNA from serum sample 274

value: G


title: MPN patient sample (MPD_230)


title: MPN patient sample (MPD_457)


title: MPN patient sample (MPD_208)


title: Serum DNA 272

source_name: genomic DNA from serum sample 272

value: C


title: Serum DNA 280

source_name: genomic DNA from serum sample 280

value: H


title: Serum DNA 273

source_name: genomic DNA from serum sample 273

value: E


title: Serum DNA 275

source_name: genomic DNA from serum sample 275

value: I


title: MPN patient sample (MPD_69)

value: WT


title: MPN patient sample (MPD_358)

value: ET


title: Serum DNA 270

source_name: genomic DNA from serum sample 270


title: Serum DNA 269

source_name: genomic DNA from serum sample 269


title: Serum DNA 267

source_name: genomic DNA from serum sample 267


title: Serum DNA 264

source_name: genomic DNA from serum sample 264


title: Serum DNA 262

source_name: genomic DNA from serum sample 262


title: Serum DNA 259

source_name: genomic DNA from serum sample 259


title: Serum DNA 258

source_name: genomic DNA from serum sample 258


title: Serum DNA 263

source_name: genomic DNA from serum sample 263


title: Serum DNA 271

source_name: genomic DNA from serum sample 271

value: A


title: Serum DNA 266

source_name: genomic DNA from serum sample 266


title: MPN patient sample (MPD_28)

source_name: MPN patient sample, Peripheral blood neutrophils

value: Peripheral blood neutrophils

value: MF

value: Homozygous

value: MUT


title: Serum DNA 256

source_name: genomic DNA from serum sample 256

value: healthy postmenopausal women


title: Serum DNA 261

source_name: genomic DNA from serum sample 261


title: NOD/LtJ mouse  liver, treated animal 1

city: Chapel Hill

first: Merrie

last: Mosedale

state: North Carolina

address: 301 Pharmacy Lane, Kerr Hall CB#7569

department: Division of Pharmacotherapy and Experimental Therapeutics

institute: UNC Eshelman School of Pharmacy

description: Sample name: 401

hyb_protocol: Samples were hybridized to the Affymetrix GeneChip Mouse Genome 430 2.0 Array using the Hybridization, Wash and Stain kit (Affymetrix). Following hybridization, arrays were washed and stained using standard Affymetrix procedures.

scan_protocol: GeneChips were scanned with an Affymetrix Gene Chip Scanner.

data_processing: Data were processed using the Affymetrix Power Tools program apt-probeset-summarize. Probes overlapping SNPs in MDP strains were removed and intensity ratios were RMA (Robust Multi-array Analysis) transformed.

source_name: NOD/LtJ liver, isoniazid treated

label_protocol: The GeneChip 3’ IVT Express Kit (Affymetrix) was utilized to generate fragmented, biotin-labeled aRNA.

growth_protocol: 8 female mice in each of 31 strains were 8-10 weeks old at the start of the study.

extract_protocol: 24 hours after the final dose, mice were sacrificed, livers were excised, and left liver lobe tissue was flash frozen in liquid nitrogen. Total liver RNA was isolated with the RNeasy total RNA isolation kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: 4 mice per strain were dosed with vehicle (sterile water) and 4 with isoniazid (100 mg/kg) once daily by oral gavage for 3 days.

tag: gender

value: female

tag: age

value: left liver lobe

value: NOD/LtJ

value: Isoniazid

tag: steatosis

value: No

tag: scan date


title: Serum DNA 257

source_name: genomic DNA from serum sample 257

value: F


title: NOD/LtJ mouse  liver, control animal 3

description: Sample name: 399

source_name: NOD/LtJ liver, vehicle treated

tag: treatment

value: Vehicle


title: NOD/LtJ mouse  liver, control animal 2

description: Sample name: 398


title: Serum DNA 265

source_name: genomic DNA from serum sample 265

value: B


title: Serum DNA 260

source_name: genomic DNA from serum sample 260


title: NOD/LtJ mouse  liver, treated animal 2

description: Sample name: 402


title: NOD/LtJ mouse  liver, control animal 1

description: Sample name: 397


title: NOD/LtJ mouse  liver, treated animal 4

description: Sample name: 404


title: A/J mouse  liver, treated animal 1

description: Sample name: 394

source_name: A/J liver, isoniazid treated

value: A/J


title: Serum DNA 255

source_name: genomic DNA from serum sample 255


title: A/J mouse  liver, control animal 4

description: Sample name: 392

source_name: A/J liver, vehicle treated


title: Serum DNA 254

source_name: genomic DNA from serum sample 254

value: K


title: A/J mouse  liver, treated animal 2

description: Sample name: 395


title: NOD/LtJ mouse  liver, treated animal 3

description: Sample name: 403


title: Serum DNA 253

source_name: genomic DNA from serum sample 253

value: I


title: Serum DNA 268

source_name: genomic DNA from serum sample 268

value: H


title: NOD/LtJ mouse  liver, control animal 4

description: Sample name: 400


title: A/J mouse  liver, control animal 3

description: Sample name: 391


title: MPN patient sample (MPD_532)

value: Peripheral blood neutrophils

tag: diagnosis

value: PV

tag: jak2 v617f quantitative genotyping

tag: calr status

value: WT

tag: tet2 status


title: Serum DNA 250

source_name: genomic DNA from serum sample 250

value: A


title: A/J mouse  liver, control animal 2

description: Sample name: 390

tag: tissue


title: 129S1/SvImJ mouse  liver, treated animal 3

description: Sample name: 387

source_name: 129S1/SvImJ liver, isoniazid treated

tag: strain


title: A/J mouse  liver, control animal 1

description: Sample name: 389


title: Serum DNA 248

source_name: genomic DNA from serum sample 248

tag: subject

value: healthy postmenopausal women


title: 129S1/SvImJ mouse  liver, treated animal 2

description: Sample name: 386

value: female


title: 129S1/SvImJ mouse  liver, treated animal 4

description: Sample name: 388

value: left liver lobe


title: Serum DNA 251

source_name: genomic DNA from serum sample 251

tag: case/control

value: C


title: 129S1/SvImJ mouse  liver, control animal 4

description: Sample name: 384

source_name: 129S1/SvImJ liver, vehicle treated


title: 129S1/SvImJ mouse  liver, treated animal 1

description: Sample name: 385

value: Isoniazid


title: Serum DNA 246

source_name: genomic DNA from serum sample 246

tag: ageatdraw (yrs)


title: Serum DNA 252

source_name: genomic DNA from serum sample 252

tag: season

value: G


title: Serum DNA 243

source_name: genomic DNA from serum sample 243

tag: dna conc. (ug/ml)


title: Serum DNA 247

source_name: genomic DNA from serum sample 247


title: Serum DNA 249

source_name: genomic DNA from serum sample 249

value: J


title: Serum DNA 245

source_name: genomic DNA from serum sample 245


title: Serum DNA 244

source_name: genomic DNA from serum sample 244

value: E


title: Serum DNA 240

source_name: genomic DNA from serum sample 240

value: D


title: SEA/GnJ mouse  liver, treated animal 1

description: Sample name: 369

source_name: SEA/GnJ liver, isoniazid treated

value: SEA/GnJ

value: No


title: Serum DNA 242

source_name: genomic DNA from serum sample 242

value: L


title: 129S1/SvImJ mouse  liver, control animal 2

description: Sample name: 382

value: Vehicle


title: SEA/GnJ mouse  liver, treated animal 2

description: Sample name: 371


title: 129S1/SvImJ mouse  liver, control animal 1

description: Sample name: 381


title: 129S1/SvImJ mouse  liver, control animal 3

description: Sample name: 383


title: SEA/GnJ mouse  liver, control animal 2

description: Sample name: 366

source_name: SEA/GnJ liver, vehicle treated


title: SEA/GnJ mouse  liver, control animal 4

description: Sample name: 368


title: SEA/GnJ mouse  liver, control animal 3

description: Sample name: 367


title: SEA/GnJ mouse  liver, control animal 1

description: Sample name: 365


title: Serum DNA 239

source_name: genomic DNA from serum sample 239

value: B


title: Serum DNA 237

source_name: genomic DNA from serum sample 237


title: RIIIS/J mouse  liver, treated animal 3

description: Sample name: 364

source_name: RIIIS/J liver, isoniazid treated

value: RIIIS/J


title: Serum DNA 241

source_name: genomic DNA from serum sample 241

value: F


title: Serum DNA 238

source_name: genomic DNA from serum sample 238

value: I


title: Serum DNA 235

source_name: genomic DNA from serum sample 235

value: healthy postmenopausal women


title: Serum DNA 234

source_name: genomic DNA from serum sample 234

value: A


title: RIIIS/J mouse  liver, treated animal 2

description: Sample name: 362

value: female

value: left liver lobe


title: Serum DNA 232

source_name: genomic DNA from serum sample 232


title: RIIIS/J mouse  liver, control animal 4

description: Sample name: 360

source_name: RIIIS/J liver, vehicle treated


title: RIIIS/J mouse  liver, control animal 3

description: Sample name: 359


title: Serum DNA 233

source_name: genomic DNA from serum sample 233


title: RIIIS/J mouse  liver, treated animal 1

description: Sample name: 361

value: Isoniazid


title: RIIIS/J mouse  liver, control animal 2

description: Sample name: 358


title: RIIIS/J mouse  liver, control animal 1

description: Sample name: 357


title: Serum DNA 230

source_name: genomic DNA from serum sample 230


title: PWK/PhJ mouse  liver, treated animal 4

description: Sample name: 356

source_name: PWK/PhJ liver, isoniazid treated

value: PWK/PhJ


title: Serum DNA 236

source_name: genomic DNA from serum sample 236


title: Serum DNA 231

source_name: genomic DNA from serum sample 231


title: Serum DNA 228

source_name: genomic DNA from serum sample 228

value: G


title: PWK/PhJ mouse  liver, treated animal 2

description: Sample name: 354


title: Serum DNA 227

source_name: genomic DNA from serum sample 227

value: C


title: PWK/PhJ mouse  liver, treated animal 1

description: Sample name: 353


title: PWK/PhJ mouse  liver, control animal 2

description: Sample name: 350

source_name: PWK/PhJ liver, vehicle treated


title: PWK/PhJ mouse  liver, control animal 4

description: Sample name: 352


title: Serum DNA 223

source_name: genomic DNA from serum sample 223

value: D


title: PWK/PhJ mouse  liver, control animal 3

description: Sample name: 351


title: Serum DNA 222

source_name: genomic DNA from serum sample 222


title: Serum DNA 218

source_name: genomic DNA from serum sample 218

value: K


title: Serum DNA 225

source_name: genomic DNA from serum sample 225


title: Serum DNA 220

source_name: genomic DNA from serum sample 220

value: J


title: PWK/PhJ mouse  liver, control animal 1

description: Sample name: 349

value: No


title: Serum DNA 221

source_name: genomic DNA from serum sample 221

value: L


title: Serum DNA 216

source_name: genomic DNA from serum sample 216


title: Serum DNA 226

source_name: genomic DNA from serum sample 226


title: MA/MyJ mouse  liver, control animal 4

description: Sample name: 336

source_name: MA/MyJ liver, vehicle treated

value: MA/MyJ

value: Vehicle


title: Serum DNA 217

source_name: genomic DNA from serum sample 217


title: Serum DNA 229

source_name: genomic DNA from serum sample 229


title: PWK/PhJ mouse  liver, treated animal 3

description: Sample name: 355

source_name: PWK/PhJ liver, isoniazid treated


title: Serum DNA 219

source_name: genomic DNA from serum sample 219


title: LG/J mouse  liver, treated animal 1

description: Sample name: 329

source_name: LG/J liver, isoniazid treated

value: LG/J

value: Yes


title: Serum DNA 224

source_name: genomic DNA from serum sample 224

value: healthy postmenopausal women

value: F


title: MA/MyJ mouse  liver, control animal 2

description: Sample name: 334

value: female


title: MA/MyJ mouse  liver, control animal 1

description: Sample name: 333

value: left liver lobe


title: MA/MyJ mouse  liver, treated animal 1

description: Sample name: 339

source_name: MA/MyJ liver, isoniazid treated

value: Isoniazid


title: MA/MyJ mouse  liver, treated animal 2

description: Sample name: 340


title: LG/J mouse  liver, treated animal 3

description: Sample name: 331


title: Serum DNA 214

source_name: genomic DNA from serum sample 214

value: H


title: LG/J mouse  liver, treated animal 2

description: Sample name: 330


title: Serum DNA 215

source_name: genomic DNA from serum sample 215

value: E


title: Serum DNA 213

source_name: genomic DNA from serum sample 213

value: I


title: Serum DNA 212

source_name: genomic DNA from serum sample 212

value: A


title: LG/J mouse  liver, control animal 4

description: Sample name: 328

source_name: LG/J liver, vehicle treated


title: Serum DNA 211

source_name: genomic DNA from serum sample 211


title: Serum DNA 207

source_name: genomic DNA from serum sample 207


title: LG/J mouse  liver, control animal 3

description: Sample name: 327


title: Serum DNA 209

source_name: genomic DNA from serum sample 209

value: D


title: Serum DNA 208

source_name: genomic DNA from serum sample 208

value: G


title: LG/J mouse  liver, control animal 1

description: Sample name: 325


title: LG/J mouse  liver, control animal 2

description: Sample name: 326


title: NON/LtJ mouse  liver, treated animal 1

description: Sample name: 322

source_name: NON/LtJ liver, isoniazid treated

value: NON/LtJ

value: No


title: Serum DNA 206

source_name: genomic DNA from serum sample 206

value: L


title: NON/LtJ mouse  liver, control animal 2

description: Sample name: 318

source_name: NON/LtJ liver, vehicle treated

value: Vehicle


title: NON/LtJ mouse  liver, treated animal 3

description: Sample name: 324


title: Serum DNA 204

source_name: genomic DNA from serum sample 204


title: NON/LtJ mouse  liver, control animal 1

description: Sample name: 317


title: NON/LtJ mouse  liver, control animal 4

description: Sample name: 320


title: KK/HIJ mouse  liver, treated animal 4

description: Sample name: 316

source_name: KK/HIJ liver, isoniazid treated

value: KK/HIJ


title: KK/HIJ mouse  liver, treated animal 3

description: Sample name: 315


title: NON/LtJ mouse  liver, treated animal 2

description: Sample name: 323


title: Serum DNA 210

source_name: genomic DNA from serum sample 210


title: Control_rep5

first: Iordanis

last: Karagiannidis

address: 675 Charles E. Young Dr. South

institute: UCLA, David Geffen School of Medicine

description: Gene expression after 35 days of chronic unpredictable stress

hyb_protocol: Clinical microarray core, UCLA

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting (Clinical microarray core, UCLA)

data_processing: Agilent Feature Extraction and version # is 11.5.1.1

organism: Rattus norvegicus

source_name: Epididymal Adipocytes, control, replicate 5

label_protocol: Clinical microarray core, UCLA

extract_protocol: RNA was isolated from preadipocytes using the RNeasy kit (QIAGEN, Hilden, Germany) . RNA was quantified using a NanoDrop-1000 spectrophotometer and further quality control tests were performed at the UCLA Clinical microarray core

treatment_protocol: Rats are exposed to a variable sequence of stressors, 2 per day, for 35 days (see supplementary data). This stress model has been validated in numerous reports and is a well-characterized model of depression in human with high face and predictive validity (4, 21, 38, 47). Briefly, stressors were applied based on a computer generated randomized sequence. Control animals were handled every 2 days during weighing.    Schedule of stressors 2/day for 35 days (computer randomized sequence).    Swim stress 18°C 10 min (between 10am-2pm) Day 25, 27, 29, 30, 32, 33, 34  Rotation 1 hour (between 10am-2pm) Day 1, 2, 4, 6, 9, 11, 14, 20, 31  Isolation overnight  Day 7, 12  Food/water deprivation overnight  Day 2, 3, 6, 10, 13, 15, 16, 19, 24, 28, 32  Light on overnight  Day 1, 4, 7, 8, 13, 18, 22, 23  Light off 3 hours (between 10am-2pm) Day 5, 8, 11, 20, 21, 24, 26, 28, 31  Stroboscope overnight  Day 5, 15, 16, 17, 19, 21, 26, 27, 29, 33, 34, 35  Wet bedding overnight  Day 3, 12, 14,   Crowding overnight  Day 9, 10, 17, 18, 22, 23, 25, 30, 35

value: Fisher 344

tag: cell type

value: Epididymal adipocytes

value: male


title: NON/LtJ mouse  liver, control animal 3

description: Sample name: 319

tag: gender

value: female


title: Control_rep6

source_name: Epididymal Adipocytes, control, replicate 6


title: Serum DNA 201

source_name: genomic DNA from serum sample 201

value: healthy postmenopausal women


title: Serum DNA 205

source_name: genomic DNA from serum sample 205

value: J


title: Serum DNA 202

source_name: genomic DNA from serum sample 202

value: K


title: Control_rep3

source_name: Epididymal Adipocytes, control, replicate 3


title: Control_rep4

source_name: Epididymal Adipocytes, control, replicate 4


title: Serum DNA 203

source_name: genomic DNA from serum sample 203

value: B


title: Control_rep2

source_name: Epididymal Adipocytes, control, replicate 2


title: KK/HIJ mouse  liver, treated animal 2

description: Sample name: 314

tag: age

value: left liver lobe

value: Isoniazid


title: Stress_rep5

source_name: Epididymal Adipocytes, chronic stress, replicate 5

value: after 35 days of chronic unpredictable stress


title: Serum DNA 198

source_name: genomic DNA from serum sample 198

value: A


title: KK/HIJ mouse  liver, treated animal 1

description: Sample name: 313

tag: steatosis


title: Stress_rep6

source_name: Epididymal Adipocytes, chronic stress, replicate 6


title: Stress_rep2

source_name: Epididymal Adipocytes, chronic stress, replicate 2


title: KK/HIJ mouse  liver, control animal 3

description: Sample name: 311

source_name: KK/HIJ liver, vehicle treated

tag: scan date


title: Stress_rep4

source_name: Epididymal Adipocytes, chronic stress, replicate 4

tag: treatment


title: Control_rep1

source_name: Epididymal Adipocytes, control, replicate 1


title: KK/HIJ mouse  liver, control animal 4

description: Sample name: 312


title: Stress_rep3

source_name: Epididymal Adipocytes, chronic stress, replicate 3


title: Serum DNA 199

source_name: genomic DNA from serum sample 199

value: C


title: Serum DNA 197

source_name: genomic DNA from serum sample 197


title: KK/HIJ mouse  liver, control animal 2

description: Sample name: 310

value: No


title: 3691_CSCs_shGrem1_2456

city: Cleveland

first: Kenneth

last: Yan

state: OH

address: 2111 E. 96th Street

department: Stem Cell Biology & Regenerative Medicine

institute: Cleveland Clinic Lerner Research Institute

description: Gene expression data from glioma CSCs (patient 3691) following transduction of shRNAs targeting Grem1

hyb_protocol: Following fragmentation, 180 ng of cDNA were hybridized for 16 hr at 48C onto the GeneChip HuGene 2.1 PEG Array. GeneChips were washed and stained in the GeneTitan Multichannel Instrument.

scan_protocol: GeneChips were scanned using the GeneTitan Multichannel Instrument using AGCC 4.0 software

data_processing: The data was analyzed using robust multi-array average (RMA) analysis using the Bioconductor oligo R package

source_name: 3691 glioma CSCs treated with grem1 knockdown shRNA

label_protocol: Biotinylated cDNA fragments were prepared according to the standard Affymetrix protocol from 100-150 ng total RNA (GeneAtlas WT Expression Kit Manual, 2012, Affymetrix).

growth_protocol: Glioma tumors were dissociated from patient specimens and passaged in a mouse xenograft model.  Mouse xenografts were dissociated and sorted based on CD133 marker expression.  Glioma cancer stem cell-enriched populations (CD133+) were cultured in neurobasal media supplemented with B27 without vitamin A, with added L-glutamine, sodium pyruvate, and 10 ng/mL of epidermal growth factor (EGF) and basic fibroblast growth factor (bFGF) for less than 5 passages

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

treatment_protocol: Transduction with gremlin1 shRNAs was performed by adding lentivirus directly to the media.   Cells were lysed in Trizol three days post-infection.

tag: individual

value: patient 3691

value: brain

tag: specimen

value: patient-derived tumor specimen maintained briefly in mouse subcutaneous xenografts, tissue culture passage <5

value: glioma cancer stem cell (CSC)

tag: genotype/variation

value: grem1 knockdown (shGrem1_2456)


title: Serum DNA 196

source_name: genomic DNA from serum sample 196


title: 3691_CSCs_shGrem1_485

value: grem1 knockdown (shGrem1_485)


title: KK/HIJ mouse  liver, control animal 1

description: Sample name: 309

value: female

value: KK/HIJ

value: Vehicle


title: 3691_CSCs_NT

description: Gene expression data from glioma CSCs (patient 3691) following transduction of scrambled non-targeting shRNAs

source_name: 3691 glioma CSCs treated with non-targeting scrambled shRNA

value: control


title: Serum DNA 194

source_name: genomic DNA from serum sample 194

value: healthy postmenopausal women

value: D


title: 528_CSCs_shGrem1_2456

description: Gene expression data from glioma CSCs (patient 528) following transduction of shRNAs targeting Grem1

source_name: 528 glioma CSCs treated with grem1 knockdown shRNA

value: patient 528


title: CE/J mouse  liver, treated animal 4

description: Sample name: 300

source_name: CE/J liver, isoniazid treated

value: left liver lobe

value: CE/J

value: Isoniazid

value: Yes


title: Serum DNA 193

source_name: genomic DNA from serum sample 193

value: B


title: Serum DNA 195

source_name: genomic DNA from serum sample 195

value: F


title: Serum DNA 200

source_name: genomic DNA from serum sample 200

value: E


title: Stress_rep1

source_name: Epididymal Adipocytes, chronic stress, replicate 1

value: Fisher 344

value: Epididymal adipocytes

value: male

value: after 35 days of chronic unpredictable stress


title: 528_CSCs_NT

description: Gene expression data from glioma CSCs (patient 528) following transduction of scrambled non-targeting shRNAs

source_name: 528 glioma CSCs treated with non-targeting scrambled shRNA

value: brain

value: patient-derived tumor specimen maintained briefly in mouse subcutaneous xenografts, tissue culture passage <5

value: glioma cancer stem cell (CSC)


title: Il23r-/- T cells rep5

city: Oxford

first: Chris

last: Schiering

address: John Radcliffe Hospital

department: Nuffield Department of Clinical Medicine

institute: University of Oxford

description: SAMPLE 11

hyb_protocol: Illumina Direct Hybridisation Assay used for Whole-genome gene expression profiling

scan_protocol: Illumina BeadArray Reader used to capture images with default settings

data_processing: llumina Inc. GenomeStudio version 1.6.0 was used to generate background substracted non-normalized data and normalization was carried out using 75th percentile normalisation in GeneSpring. Non-normalized values in supplementary file have only had background subtraction.

source_name: TCRβ+CD4+ T cells from colon

label_protocol: Illumina TotalPrep™ RNA Amplification Kit

extract_protocol: RNA was extracted using RiboPure RNA Purification Kit (Ambion)

treatment_protocol: Colitis was induced by co-transfer of WT and Il23r-/- naïve CD4 T cells into Rag1-/- recipients. Upon development of clinical signs of inflammation WT and Il23r-/- CD4+ T cells were sort-purified from the colon lamina propria on the basis of congenic markers. Total RNA was extracte immediately after the sort without further manipulation.

tag: source

value: colon lamina propria

value: TCRβ+CD4+ T cells from colon

tag: genotype


title: Serum DNA 192

source_name: genomic DNA from serum sample 192

value: healthy postmenopausal women

value: K


title: CE/J mouse  liver, treated animal 3

description: Sample name: 299

value: female

tag: tissue

value: left liver lobe

tag: strain

value: CE/J


title: 528_CSCs_shGrem1_485

value: patient 528

value: grem1 knockdown (shGrem1_485)


title: Il23r-/- T cells rep3

description: SAMPLE 9


title: Il23r-/- T cells rep2

description: SAMPLE 8


title: Serum DNA 191

source_name: genomic DNA from serum sample 191

tag: subject

tag: case/control

value: G


title: CE/J mouse  liver, treated animal 2

description: Sample name: 298

value: Isoniazid

value: Yes


title: CE/J mouse  liver, treated animal 1

description: Sample name: 297


title: MA/MyJ mouse  liver, control animal 3

description: Sample name: 335

source_name: MA/MyJ liver, vehicle treated

value: MA/MyJ

value: Vehicle

value: No


title: Il23r-/- T cells rep1

description: SAMPLE 7


title: WT T cells rep5

description: SAMPLE 5

value: wild type


title: WT T cells rep6

description: SAMPLE 6


title: Il23r-/- T cells rep4

description: SAMPLE 10


title: Serum DNA 188

source_name: genomic DNA from serum sample 188

tag: ageatdraw (yrs)

tag: season

value: F


title: Serum DNA 189

source_name: genomic DNA from serum sample 189

tag: dna conc. (ug/ml)

value: J


title: WT T cells rep4

description: SAMPLE 4

value: colon lamina propria

tag: cell type

value: TCRβ+CD4+ T cells from colon


title: CE/J mouse  liver, control animal 4

description: Sample name: 296

source_name: CE/J liver, vehicle treated

tag: gender

tag: age


title: WT T cells rep3

description: SAMPLE 3


title: CE/J mouse  liver, control animal 2

description: Sample name: 294

tag: steatosis

tag: scan date


title: Serum DNA 190

source_name: genomic DNA from serum sample 190

value: healthy postmenopausal women

value: C


title: Serum DNA 187

source_name: genomic DNA from serum sample 187

value: K


title: C58/J mouse  liver, treated animal 3

description: Sample name: 291

source_name: C58/J liver, isoniazid treated

value: female

value: left liver lobe

tag: treatment


title: CE/J mouse  liver, control animal 1

description: Sample name: 293

value: CE/J


title: C58/J mouse  liver, treated animal 4

description: Sample name: 292


title: WT T cells rep2

description: SAMPLE 2


title: cLP Foxp3+ Treg rep3

description: SAMPLE 6

source_name: TCRβ+CD4+Foxp3+ from colon lamina propria (cLP)

label_protocol: TargetAmp2-Round Biotin-aRNA Amplification Kit 3.0 (Epicentre, Illumina) and RNA quality was assessed using the Agilent 2100 Bioanalyzer

extract_protocol: RNA was extracted using the RNAqueous®-Micro Total RNA Isolation Kit (Ambion)

treatment_protocol: steady state mice were used as source for all samples


title: Serum DNA 185

source_name: genomic DNA from serum sample 185

value: G


title: Serum DNA 186

source_name: genomic DNA from serum sample 186

value: I


title: CE/J mouse  liver, control animal 3

description: Sample name: 295

value: Yes


title: WT T cells rep1

description: SAMPLE 1


title: MSN Foxp3+ Treg rep1

description: SAMPLE 1

source_name: TCRβ+CD4+Foxp3+ from mesenteric lymph node (MLN)

value: mesenteric lymph node


title: Serum DNA 184

source_name: genomic DNA from serum sample 184

value: E


title: DCLPS_rep2

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

data_processing: The data were normalised using quantile normalisation with lumi in R

source_name: CD8 T Cell

label_protocol: Preparation of cDNA, cRNA, and labeling were carried out by the Yale Center for Genomic Analysis using the standard Illumina protocols.   Hybridization buffer from the BeadChip kit (Illumina) was mixed with 1500 ng of biotin-labeled cRNA, heated to 65°C for 5 minutes, and then loaded onto the BeadChip.  The BeadChips were sealed in a hybridization chamber and placed in an oven at 58°C with a rocker for 16-20 hours.  After the hybridization, the BeadChips were washed and stained in a series of washes and stains as outlined in the Illumina protocol.  The BeadChips were scanned on the Illumina Iscan.

extract_protocol: Total RNA samples was extracted using the RNeasy mini kit (Qiagen, CA)

value: CD8 T cells

value: immunized with DC-33 LPS

tag: background strain


title: C58/J mouse  liver, treated animal 2

description: Sample name: 290

value: Isoniazid

value: No


title: MSN Foxp3+ Treg rep2

description: SAMPLE 2

value: TCRβ+CD4+Foxp3+ from mesenteric lymph node (MLN)


title: DCMPLA_rep1

value: immunized with DC-33 MPLA


title: cLP Foxp3+ Treg rep1

description: SAMPLE 4

value: colon lamina propria

value: TCRβ+CD4+Foxp3+ from colon lamina propria (cLP)


title: MSN Foxp3+ Treg rep3

description: SAMPLE 3


title: cLP Foxp3+ Treg rep2

description: SAMPLE 5


title: DCMPLA_rep2


title: C58/J mouse  liver, treated animal 1

description: Sample name: 289


title: CNDT2 cells infected (AI) biological rep 2

city: Stockholm

first: Aldona

last: Dlugosz

address: Karolinska Huddinge

department: Gastroenterology and hepatology

country: Sweden

institute: Karolinska Institutet

hyb_protocol: GeneChip® ST Arrays (GeneChip® Human Gene 1.0 ST Array) were hybridized for 16 hours in a 45 °C incubator, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev 2, Affymetrix Inc., USA) the arrays were then washed and stained using the Fluidics Station 450

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

data_processing: Analysis of the gene expression data was carried out using the freely available statistical computing software R (http://www.r-project.org) together with available packages from the Bioconductor project (www.bioconductor.org). Raw data was normalized using the robust multi-array average (RMA) method.

source_name: CNDT2 cells infected (AI)

label_protocol: 250 ng of total RNA from each sample were used to generate amplified and biotinylated cDNA according to the Ambion WT Expression Kit (P/N 4425209 Rev B 05/2009) and Affymetrix GeneChip® WT Terminal Labeling and Hybridization User Manual (P/N 702808 Rev. 1, Affymetrix Inc., USA).

growth_protocol: LCC-18 cells were maintained in RPMI 1640 (Invitrogen, Life Technologies)  supplemented with 5% fetal bovine serum (FBS) (Hyclone, Thermo Scientific) 0.04 mg/ml transferrin (Sigma-Aldrich), 1.09 ng/ml β-estradiol (Sigma-Aldrich), 100U/ml insulin (please add supplier), 2.6 ng/ml hydrocortisone (Sigma-Aldrich), 30nM sodium selenite (Sigma-Aldrich,) and 25 mM HEPES (Invitrogen, Life Technologies). CNDT-2 cells were cultured in Advanced DMEM/F12 medium (Gibco, Life Technologies ) supplemented with 10 % FBS, 1x MEM vitamin solution (Gibco, Life Technologies), 2 mM L-glutamine (Hyclone, Thermo Scientific) and 25 mM HEPES (Invitrogen, Life Technologies)Both cell lines were grown at 37 °C in a 5 % CO2 humidified environment. LCC-18 are non-adherent and CNDT-2 cells grow adherent.

extract_protocol: Qiagen extraction ef total RNA was prformed according to the manufacturer's instructions

treatment_protocol: For infection, LCC-18 and CNDT-2 cells were inoculated with Chlamydia at a multiplicity of infection (MOI) of 0.5-1 for 1 h at 37°C. Monolayers of infected CNDT-2 cells were washed with PBS (Phosphate buffered saline) and incubated in fresh media containing 8µg/ml gentamycin (Invitrogen, Life Technologies ) for 24 h. Infected LCC-18 cells were spun at 500 x g for 5 min to pellet the cells. The inoculum was removed and fresh media containing 8 µg/ml gentamycin (Invitrogen, Life Technologies) to kill off extracellular bacteria was added. Infected LCC-18 cells were then incubated for 24 h. In order to induce persistent infection, LCC-18 and CNDT-2 cells were infected as described above and then incubated in medium containing 100 U/ml penicillin G  (Sigma-Aldrich) for 24 h at 37°C.

tag: cell line

value: enteroendcrine cell line

tag: cell line source

value: small intestinal carcinoid

tag: infection status

value: active infected


title: DCAlone_rep2

value: immunized with DC-33 alone


title: DCLPS_rep1


title: CNDT2 cells infected (AI) biological rep 1


title: Serum DNA 180

source_name: genomic DNA from serum sample 180

value: healthy postmenopausal women

value: B


title: C58/J mouse  liver, control animal 3

description: Sample name: 287

source_name: C58/J liver, vehicle treated

value: female

tag: tissue

value: left liver lobe

value: Vehicle


title: CNDT2 cells non infected (WT) biological rep 2

source_name: CNDT2 cells non infected (WT)

value: uninfected (WT control)


title: Serum DNA 182

source_name: genomic DNA from serum sample 182

value: A


title: DCAlone_rep1

value: CD8 T cells


title: Serum DNA 183

source_name: genomic DNA from serum sample 183

value: C


title: C58/J mouse  liver, control animal 2

description: Sample name: 286

tag: strain

value: No


title: CNDT2 cells persistently infected (PI) biological rep 1

description: CNDT2-L2-PenG 1

source_name: CNDT2 cells persistently infected (PI)

value: persistently infected


title: C58/J mouse  liver, control animal 4

description: Sample name: 288


title: C57BR/cdJ mouse  liver, treated animal 4

description: Sample name: 284

source_name: C57BR/cdJ liver, isoniazid treated

value: Isoniazid


title: Serum DNA 178

source_name: genomic DNA from serum sample 178

tag: subject


title: CNDT2 cells persistently infected (PI) biological rep 2

description: CNDT2-L2-PenG 2


title: LCC cells persistently infected (PI) biological rep 2

source_name: LCC cells persistently infected (PI)

value: neuroendocrine colonic tumour


title: LCC cells non infected (WT) biological rep 1

source_name: LCC cells non infected (WT)

value: enteroendcrine cell line


title: LCC cells persistently infected (PI) biological rep 1


title: LCC cells non infected (WT) biological rep 2


title: LCC cells infected (AI) biological rep 1

source_name: LCC cells infected (AI)


title: Serum DNA 179

source_name: genomic DNA from serum sample 179

tag: case/control


title: LCC cells infected (AI) biological rep 2


title: Serum DNA 181

source_name: genomic DNA from serum sample 181

tag: ageatdraw (yrs)

value: J


title: CNDT2 cells non infected (WT) biological rep 1

value: small intestinal carcinoid


title: C58/J mouse  liver, control animal 1

description: Sample name: 285


title: Serum DNA 177

source_name: genomic DNA from serum sample 177

tag: season

value: H


title: C57BR/cdJ mouse  liver, treated animal 3

description: Sample name: 283


title: C57BR/cdJ mouse  liver, treated animal 2

description: Sample name: 282


title: C57BR/cdJ mouse  liver, control animal 4

description: Sample name: 280

source_name: C57BR/cdJ liver, vehicle treated


title: 80 ppm H2S ventilated 27_28

city: Freiburg

first: Sashko

last: Spassov

address: Breisacher Straße 64

department: Department of Anaesthesiology and Intensive Care Medicine

country: Germany

institute: UCM-Freiburg

description: Gene expression data from mice ventilated with 80 ppm H2S for 6 hours

hyb_protocol: Labelled fragments were hybridized to the arrays for 16 h at 45°C with 60 rpm in an Affymetrix Hybridization Oven 640

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

data_processing: CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software Version 3.0. Genedata Expressionist software (Genedata AG, Basel, Switzerland) was used for further data analysis. CEL files were imported into the Refiner (Version 6.1) module of Expressionist. GC background subtraction was performed using anti-genomic background probes. Subsequently, quantile normalization and probe summarization was performed using the Bioconductor RMA condensing algorithm as implemented in Refiner (Irizarry et. al., Biostatistics 2003). To identify differentially expressed genes between the groups, the unpaired Bayes T-test (CyberT) (Baldi  and Long, Bioinformatics 2001) with the Bayes Confidence Estimate Value set to 15 and a window size of 101 genes as well as 100% valid values in each group was used with the Analyst module (version 2.2.6b). To control the false discovery rate (FDR), the Benjamini-Hochberg q-value was calculated (Benjamini and Hochberg, J Royal Stat Soc 1995). We then used the Effect size activity of Analyst to calculate the paired Effect size score between the experimental groups. Only genes from the categories main and unmapped (see Affymetrix transcript annotation NA32) were included in the analysis.

source_name: inferior right lung lobe

label_protocol: 500 ng of total RNA were reverse transcribed with (N6)-random primers coupled to a T7 RNA Polymerase promoter sequence. After second-strand synthesis, the double-stranded cDNAs were amplified overnight by in-vitro-transcription using T7 RNA Polymerase. The cRNA was purified and used as a template for a second cycle of reverse transcription with (N6) random primers. Here, dUTP was incorporated into the cDNA. After hydrolysis of the cRNA with RNAse H, the cDNA was purified and subsequently fragmented using the enzymes Uracil-DNA Glycosylase (UDG) and human apurinic/apyrimidinic Endonuclease 1 (APE1). The cDNA fragments were then labeled at their 3'-end with biotin using Terminal Deoxynucleotidyl Transferase (TdT).

growth_protocol: Male C57BL/6N mice (24-26 g body weight) were obtained from Charles River Laboratories (Sulzburg, Germany), acclimated for at least 5 days in the housing room under a 12 h light/dark cycle at about 23 °C and 39–43% relative humidity. Water and food were available ad libitum.

extract_protocol: The inferior right lung lobe was homogenized in Trizol reagent (Invitrogen Corporation, Burlington, Canada). RNA was purified using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions

treatment_protocol: After induction of anesthesia with 90 mg/kg ketamine and 1 mg/kg acepromazine intraperioneally (i.p.), animals were placed on a heating pad, and insertion of an arterial line as well as a tracheal tube was performed. Mice were randomized into 4 groups with n=5 per group. The control group was allowed to breathe spontaneously either synthetic air for 6 hours prior surgury. Two groups were ventilated with synthetic air or synthetic air with 80 ppm H2S for 6 hours using a rodent ventilator (Voltekenterprises, Toronto, ON, Canada) set to a tidal volume of 12 ml/kg, a frequency of 80-90 breaths/minute, and a positive end-expiratory pressure (PEEP) of 2 cm H2O.

value: inferior right lung lobe

tag: genotype

value: 24-26 g body weight

tag: treatment group

value: 80 ppm H2S ventilated


title: 80 ppm H2S ventilated 4_8


title: 80 ppm H2S ventilated 15_20


title: Serum DNA 176

source_name: genomic DNA from serum sample 176

value: healthy postmenopausal women

tag: dna conc. (ug/ml)

value: F


title: 80 ppm H2S ventilated 1_4

tag: age


title: C57BR/cdJ mouse  liver, treated animal 1

description: Sample name: 281

tag: gender

value: female

value: left liver lobe

tag: steatosis


title: C57BR/cdJ mouse  liver, control animal 3

description: Sample name: 279

tag: treatment

value: Vehicle

tag: scan date


title: Serum DNA 175

source_name: genomic DNA from serum sample 175

value: I


title: Serum DNA 172

source_name: genomic DNA from serum sample 172


title: 80 ppm H2S ventilated 9_12


title: Serum DNA 171

source_name: genomic DNA from serum sample 171

value: D


title: BUB/BnJ mouse  liver, treated animal 2

description: Sample name: 274

source_name: BUB/BnJ liver, isoniazid treated

value: BUB/BnJ

value: Yes


title: C57BR/cdJ mouse  liver, control animal 2

description: Sample name: 278

value: No


title: C57BR/cdJ mouse  liver, control animal 1

description: Sample name: 277


title: BUB/BnJ mouse  liver, treated animal 3

description: Sample name: 275

value: Isoniazid


title: Serum DNA 173

source_name: genomic DNA from serum sample 173

value: A


title: Serum DNA 170

source_name: genomic DNA from serum sample 170

value: B


title: Serum DNA 168

source_name: genomic DNA from serum sample 168

value: E


title: air ventilated 35_26

description: Gene expression data from mice ventilated with synthetic air for 6 hours

value: inferior right lung lobe

value: air ventilated


title: BUB/BnJ mouse  liver, treated animal 4

description: Sample name: 276


title: air ventilated 6_2

value: 24-26 g body weight


title: air ventilated 11_6


title: air ventilated 34_22


title: air ventilated 12_10


title: Serum DNA 174

source_name: genomic DNA from serum sample 174

value: healthy postmenopausal women

value: G


title: Serum DNA 169

source_name: genomic DNA from serum sample 169

value: K


title: BUB/BnJ mouse  liver, treated animal 1

description: Sample name: 273

value: female

value: left liver lobe


title: Serum DNA 167

source_name: genomic DNA from serum sample 167

value: C


title: Serum DNA 166

source_name: genomic DNA from serum sample 166


title: Control 5_1

description: Gene expression data from mice allowed to breathe spontaneously synthetic air for 6 hours prior surgury

value: control


title: BUB/BnJ mouse  liver, control animal 4

description: Sample name: 272

source_name: BUB/BnJ liver, vehicle treated

value: BUB/BnJ

value: Vehicle


title: Control 7_9


title: BUB/BnJ mouse  liver, control animal 3

description: Sample name: 271

value: Yes


title: Control 13_25


title: Serum DNA 165

source_name: genomic DNA from serum sample 165

value: L


title: Empty vector transformant_line Cont2-3

city: Higashi-Hiroshima

first: Kazuya

last: Koyama

state: Hiroshima

address: 3-7-1, Kagamiyama

department: Fundamental Reesearch Division

country: Japan

institute: National Research Institute of Brewing

description: This sample is of Arabidopsis thaliana ecotype Columbia transformed with empty vector. It is the second of three biological replicates used in this experiment, each from separate cultures (line Cont2-3).

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

scan_protocol: Scanning was performed by NimbleGen MS200 Microarray Scanner, following NimbleGen standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) and background correction as implemented in the NimbleScan software package, version 2.6 (Roche NimbleGen, Inc.).

organism: Arabidopsis thaliana

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

growth_protocol: Transgenic Arabidopsis seeds were surface-sterized and sown on GM agar plates (Valvekens et al., 1988) containing 30 mg l-1 kanamycin. The plants were grown in a growth cabinet with 16 h of light illumination per day with 80 µmol m-2 s-1 at 22°C and 60% humidity. Three-week old plants were harvested from GM agar plates for microarray analysis.

extract_protocol: Total RNA was prepared from 3-week old Arabidopsis whole plants, using Trizol reagent (Invitrogen Corp., Carlsbad, CA, USA) and further purified using an RNeasy plant mini kit (Qiagen Inc., Valencia, CA, USA) with the addition of an on-column DNase I digestion. Quality control was performed with the Agilent 2100 Bioanalyser. Ds-cDNA was synthesized using the Invitrogen Superscipt Double-Stranded cDNA Synthesis Kit.

tag: ecotype

value: Columbia

tag: genotype/variation

value: Empty vector transformant

tag: line


title: Control 12_21

tag: tissue


title: Empty vector transformant_line Cont5-1

description: This sample is of Arabidopsis thaliana ecotype Columbia transformed with empty vector. It is the third of three biological replicates used in this experiment, each from separate cultures (line Cont5-1).


title: Control 6_5


title: SWR/J mouse  liver, treated animal 4

description: Sample name: 268

source_name: SWR/J liver, isoniazid treated

tag: strain

value: SWR/J

value: Isoniazid


title: Serum DNA 163

source_name: genomic DNA from serum sample 163

tag: subject

value: H


title: BUB/BnJ mouse  liver, control animal 1

description: Sample name: 269


title: Serum DNA 164

source_name: genomic DNA from serum sample 164

tag: case/control

value: J


title: Empty vector transformant_line Cont1-1

description: This sample is of Arabidopsis thaliana ecotype Columbia transformed with empty vector. It is the first of three biological replicates used in this experiment, each from separate cultures (line Cont1-1).


title: MYBPAR expressing Arabidopsis_line PAR36-4

description: This sample is of Arabidopsis thaliana ecotype Columbia transformed with 35S::VvMYBPAR. It is the third of three biological replicates used in this experiment, each from separate cultures (line PAR36-4).

source_name: Arabidopsis thaliana ecotype Columbia transformed with 35S::VvMYBPAR construct

value: Plant transformed with 35S::VvMYBPAR construct


title: BUB/BnJ mouse  liver, control animal 2

description: Sample name: 270


title: siERK5E2 2

city: Urbana

first: Zeynep

last: Madak Erdogan

state: IL

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

description: Gene expression data from MCF-7 cells, siERK5 treatment 72h, 10 nM E2 for 24h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GCS 3000.

data_processing: The data were analyzed with  GCOS2.1 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

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

growth_protocol: MCF-7 cells were maintained in MEM media with 5% Calf serum

treatment_protocol: MCF-7 human breast cancer cells were transfected with 20 nM of siGENOME ctrl (siGL3) or ERK5 (Thermo Scientific) using Dharmafect1 following the manufacturer’s instructions. After 72 h of transfection, cells were treated with 0.1% control ethanol vehicle or 10 nM E2 for 24h

value: Breast adenocarcinoma


title: Serum DNA 161

source_name: genomic DNA from serum sample 161

value: healthy postmenopausal women

tag: ageatdraw (yrs)

value: B


title: Serum DNA 160

source_name: genomic DNA from serum sample 160

tag: season

value: I


title: MYBPAR expressing Arabidopsis_line PAR9-2

description: This sample is of Arabidopsis thaliana ecotype Columbia transformed with 35S::VvMYBPAR. It is the second of three biological replicates used in this experiment, each from separate cultures (line PAR9-2).


title: SWR/J mouse  liver, treated animal 2

description: Sample name: 266

value: female

value: left liver lobe


title: SWR/J mouse  liver, treated animal 3

description: Sample name: 267


title: siERK5Veh 2

description: Gene expression data from MCF-7 cells, siERK5 treatment 72h, 0.1%EtOH for 24h


title: siERK5E2 1

source_name: MCF-7 cells, siERK5 treatment 72h, 10 nM E2 for 24h


title: Serum DNA 162

source_name: genomic DNA from serum sample 162

value: D


title: Serum DNA 159

source_name: genomic DNA from serum sample 159

value: E


title: Serum DNA 157

source_name: genomic DNA from serum sample 157


title: siERK5Veh 1

source_name: MCF-7 cells, siERK5 treatment 72h, 0.1%EtOH for 24h


title: SWR/J mouse  liver, treated animal 1

description: Sample name: 265

value: Yes


title: siGL3E2 1

description: Gene expression data from MCF-7 cells, siGL3 treatment 72h, 10 nM E2 for 24h


title: MYBPAR expressing Arabidopsis_line PAR18-2

description: This sample is of Arabidopsis thaliana ecotype Columbia transformed with 35S::VvMYBPAR. It is the first of three biological replicates used in this experiment, each from separate cultures (line PAR18-2).


title: Serum DNA 158

description:
bi-sulphite converted genomic serum DNA from woman
serum DNA from healthy postmenopausal women, a number of which developed breast cancer (cases)

source_name: genomic DNA from serum sample 158

value: A


title: wild type-drought_rep2

city: Wuhan, Hubei Province

first: Zhulong

last: Chan

address: Moshan, Wuchang District

department: Wuhan Botanic Garden

institute: Chinese Academy of Sciences

description: wild type after drought treatment rep2

hyb_protocol: After purification, 12.5 μg of labeled and fragmented cRNA probes were hybridized to the Arabidopsis arrays with Hybrization, Wash and Stain Kit (Affymetrix, #900720) according to manufacturer’s instruction.

scan_protocol: The arrays were scanned using GeneChip® Scanner 3000 (Affymetrix, #3000). The scanned images were saved as DAT files and transformed to JPG image. The signal intensities were extracted from the JPG image with Affymetrix® GeneChip® Command Console® Software (AGCC software) and saved as CEL files.

data_processing: affylmGUI package (Wettenhall et al., 2006) rooted in R (Gentleman et al., 2004) Significant analysis of microarray (SAM) R software (Irizarry et al., 2003) was used to calculate the intensity ratios and fold changes. All the differential expressed genes with p-value below 0.05 and log2 fold change above 1 or below -1 were chosen for further analysis.

organism: Arabidopsis

source_name: wild type, drought treatment, replicate 2

label_protocol: For array hybridization, 200 ng of total RNA was used for first-strand cDNA synthesis and second-strand cDNA synthesis. Then aRNA cRNA was labeled with biotinylated ribonucleotide analog and was fragmented with fragmentation buffer using MessageAmpTM Premier RNA Amplification Kit (Ambion, #1792).

growth_protocol: Two transgenic Arabidopsis lines (nNOS-2 and nNOS-25) with the nNOS gene under the control of the cauliflower mosaic virus (CaMV) 35S promoter (Shi et al., 2012c), as well as Col-0 (WT), were used in this research. After stratificated in deionized water at 4°C for 3 days in darkness, the Arabidopsis seeds were sown in the plastic container filled with soil in the growth chamber. The growth chamber was controlled at an irradiance of about 120-150 µmol quanta m-2 s-1, 22-25°C, with 65% relative humidity under 16 h light and 8 h dark cycles. To keep the well growth condition, nutrient solution was irrigated twice every week.

extract_protocol: For RNA isolation, 2-week-old WT and transgenic plants (nNOS-25) in pots were subjected to control condition (well-watered) and drought condition (soil water deficit) by withholding water for 14 d, respectively. The leaf samples of two replications at 14 d under control and drought conditions were harvested from at least 20 seedlings per genotype. Total RNA was extracted with TRIzol reagent (Invitrogen) and quantified as previously described (Shi et al., 2012c), .then RNA was quantified and RNA quality was also determined using formaldehyde agarose gel and a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s protocol.

treatment_protocol: To conduct drought stress treatment, 2-week-old WT and transgenic plants in soil were subjected to drought condition (soil water deficit) by withholding water for 21 d and then re-watered.

value: leaf

value: wild-type


title: siGL3Veh 2

description: Gene expression data from MCF-7 cells, siGL3 treatment 72h, 0.1%EtOH for 24h


title: wild type-control_rep2

description: wild type without drought treatment rep2

source_name: wild type, control, replicate 2


title: Serum DNA 155

source_name: genomic DNA from serum sample 155

value: F


title: siGL3E2 2

source_name: MCF-7 cells, siGL3 treatment 72h, 10 nM E2 for 24h


title: SWR/J mouse  liver, control animal 2

description: Sample name: 262

source_name: SWR/J liver, vehicle treated

value: SWR/J

value: Vehicle


title: wild type-drought_rep1

description: wild type after drought treatment rep1

source_name: wild type, drought treatment, replicate 1


title: SWR/J mouse  liver, control animal 4

description: Sample name: 264


title: SWR/J mouse  liver, control animal 3

description: Sample name: 263


title: siGL3Veh 1

source_name: MCF-7 cells, siGL3 treatment 72h, 0.1%EtOH for 24h


title: Serum DNA 154

source_name: genomic DNA from serum sample 154


title: SM/J mouse  liver, treated animal 1

description: Sample name: 257

source_name: SM/J liver, isoniazid treated

value: SM/J

value: Isoniazid

value: No


title: SWR/J mouse  liver, control animal 1

description: Sample name: 261


title: SM/J mouse  liver, treated animal 2

description: Sample name: 259


title: wild type-control_rep1

description: wild type without drought treatment rep1

source_name: wild type, control, replicate 1


title: Serum DNA 152

source_name: genomic DNA from serum sample 152

value: healthy postmenopausal women


title: SM/J mouse  liver, control animal 4

description: Sample name: 256

source_name: SM/J liver, vehicle treated


title: Serum DNA 151

source_name: genomic DNA from serum sample 151

value: K


title: nNOS-drought_rep2

description: transgenic after drought treatment rep2

source_name: nNOS, drought treatment, replicate 2

value: nNOS gene under the control of the cauliflower mosaic virus (CaMV) 35S promoter


title: Serum DNA 150

source_name: genomic DNA from serum sample 150

value: G


title: SM/J mouse  liver, control animal 3

description: Sample name: 255

value: female

value: left liver lobe


title: SM/J mouse  liver, control animal 1

description: Sample name: 253


title: nNOS-drought_rep1

description: transgenic after drought treatment rep1

source_name: nNOS, drought treatment, replicate 1


title: Serum DNA 153

source_name: genomic DNA from serum sample 153

value: B


title: nNOS-control_rep1

description: transgenic without drought treatment rep1

source_name: nNOS, control, replicate 1


title: PL/J mouse  liver, treated animal 2

description: Sample name: 250

source_name: PL/J liver, isoniazid treated

value: PL/J


title: Serum DNA 148

source_name: genomic DNA from serum sample 148

value: A


title: PL/J mouse  liver, treated animal 1

description: Sample name: 249


title: Serum DNA 145

source_name: genomic DNA from serum sample 145


title: Serum DNA 146

source_name: genomic DNA from serum sample 146

value: H


title: nNOS-control_rep2

description: transgenic without drought treatment rep2

source_name: nNOS, control, replicate 2

value: leaf


title: PL/J mouse  liver, control animal 3

description: Sample name: 247

source_name: PL/J liver, vehicle treated


title: PL/J mouse  liver, treated animal 3

description: Sample name: 251


title: Serum DNA 149

source_name: genomic DNA from serum sample 149

value: C


title: Serum DNA 143

source_name: genomic DNA from serum sample 143


title: Serum DNA 156

source_name: genomic DNA from serum sample 156


title: Serum DNA 147

source_name: genomic DNA from serum sample 147

value: J


title: PL/J mouse  liver, control animal 2

description: Sample name: 246

value: Vehicle


title: Serum DNA 144

source_name: genomic DNA from serum sample 144

value: D


title: SM/J mouse  liver, control animal 2

description: Sample name: 254

source_name: SM/J liver, vehicle treated

value: SM/J


title: NZW/LacJ mouse  liver, treated animal 4

description: Sample name: 244

source_name: NZW/LacJ liver, isoniazid treated

value: NZW/LacJ

value: Isoniazid

value: Yes


title: PL/J mouse  liver, control animal 4

description: Sample name: 248

value: No


title: Serum DNA 139

source_name: genomic DNA from serum sample 139

value: healthy postmenopausal women


title: NZW/LacJ mouse  liver, treated animal 3

description: Sample name: 243

value: female


title: Serum DNA 141

source_name: genomic DNA from serum sample 141

value: G


title: NZW/LacJ mouse  liver, treated animal 2

description: Sample name: 242

value: left liver lobe


title: Serum DNA 140

source_name: genomic DNA from serum sample 140

value: E


title: NZW/LacJ mouse  liver, treated animal 1

description: Sample name: 241


title: Serum DNA 142

source_name: genomic DNA from serum sample 142

value: I


title: NZW/LacJ mouse  liver, control animal 4

description: Sample name: 240

source_name: NZW/LacJ liver, vehicle treated


title: Serum DNA 137

source_name: genomic DNA from serum sample 137

value: B


title: Serum DNA 138

source_name: genomic DNA from serum sample 138


title: Serum DNA 136

source_name: genomic DNA from serum sample 136


title: Serum DNA 135

source_name: genomic DNA from serum sample 135


title: Serum DNA 134

source_name: genomic DNA from serum sample 134


title: NZW/LacJ mouse  liver, control animal 1

description: Sample name: 237


title: NZW/LacJ mouse  liver, control animal 2

description: Sample name: 238


title: Serum DNA 132

source_name: genomic DNA from serum sample 132

value: F


title: NOR/LtJ mouse  liver, treated animal 2

description: Sample name: 226

source_name: NOR/LtJ liver, isoniazid treated

value: NOR/LtJ


title: NOR/LtJ mouse  liver, control animal 3

description: Sample name: 223

source_name: NOR/LtJ liver, vehicle treated


title: Serum DNA 131

source_name: genomic DNA from serum sample 131


title: NOR/LtJ mouse  liver, treated animal 3

description: Sample name: 227


title: Serum DNA 133

source_name: genomic DNA from serum sample 133

value: H


title: Serum DNA 130

source_name: genomic DNA from serum sample 130


title: Serum DNA 127

source_name: genomic DNA from serum sample 127

value: C


title: NZW/LacJ mouse  liver, control animal 3

description: Sample name: 239

value: Vehicle


title: NOR/LtJ mouse  liver, control animal 2

description: Sample name: 222


title: Serum DNA 129

source_name: genomic DNA from serum sample 129


title: NOR/LtJ mouse  liver, control animal 4

description: Sample name: 224


title: Serum DNA 125

source_name: genomic DNA from serum sample 125


title: Serum DNA 128

source_name: genomic DNA from serum sample 128


title: Serum DNA 124

source_name: genomic DNA from serum sample 124

value: D


title: Serum DNA 123

source_name: genomic DNA from serum sample 123

value: K


title: MRL/MpJ mouse  liver, treated animal 4

description: Sample name: 220

source_name: MRL/MpJ liver, isoniazid treated

value: MRL/MpJ

value: Isoniazid


title: MRL/MpJ mouse  liver, treated animal 3

description: Sample name: 219

value: No


title: Serum DNA 119

source_name: genomic DNA from serum sample 119

value: healthy postmenopausal women

value: J


title: Serum DNA 126

source_name: genomic DNA from serum sample 126

value: L


title: Serum DNA 121

source_name: genomic DNA from serum sample 121

value: G


title: MRL/MpJ mouse  liver, control animal 1

description: Sample name: 213

source_name: MRL/MpJ liver, vehicle treated

value: female

value: left liver lobe


title: Serum DNA 120

source_name: genomic DNA from serum sample 120

value: E


title: Serum DNA 122

source_name: genomic DNA from serum sample 122

value: I


title: MRL/MpJ mouse  liver, treated animal 2

description: Sample name: 218


title: LP/J mouse  liver, treated animal 3

description: Sample name: 212

source_name: LP/J liver, isoniazid treated

value: LP/J


title: MRL/MpJ mouse  liver, control animal 2

description: Sample name: 214


title: Serum DNA 118

source_name: genomic DNA from serum sample 118

value: F


title: Serum DNA 116

source_name: genomic DNA from serum sample 116

value: B


title: MRL/MpJ mouse  liver, control animal 4

description: Sample name: 216

value: Vehicle


title: NOR/LtJ mouse  liver, treated animal 1

description: Sample name: 225

source_name: NOR/LtJ liver, isoniazid treated

value: NOR/LtJ

value: Yes


title: LP/J mouse  liver, treated animal 2

description: Sample name: 211


title: NOR/LtJ mouse  liver, treated animal 4

description: Sample name: 228


title: Serum DNA 114

source_name: genomic DNA from serum sample 114


title: Serum DNA 113

source_name: genomic DNA from serum sample 113


title: Serum DNA 115

source_name: genomic DNA from serum sample 115

value: K


title: LP/J mouse  liver, treated animal 1

description: Sample name: 210

value: Isoniazid


title: LP/J mouse  liver, control animal 4

description: Sample name: 208

source_name: LP/J liver, vehicle treated

value: No


title: Serum DNA 117

source_name: genomic DNA from serum sample 117

value: healthy postmenopausal women

value: D


title: LP/J mouse  liver, control animal 2

description: Sample name: 206


title: LP/J mouse  liver, control animal 3

description: Sample name: 207


title: Serum DNA 109

source_name: genomic DNA from serum sample 109

value: H


title: Serum DNA 111

source_name: genomic DNA from serum sample 111

value: A


title: C57BLKS/J mouse  liver, treated animal 3

description: Sample name: 203

source_name: C57BLKS/J liver, isoniazid treated

value: female


title: C57BLKS/J mouse  liver, treated animal 2

description: Sample name: 202

value: left liver lobe


title: Serum DNA 110

source_name: genomic DNA from serum sample 110

value: L


title: C57BLKS/J mouse  liver, control animal 3

description: Sample name: 199

source_name: C57BLKS/J liver, vehicle treated


title: Serum DNA 107

source_name: genomic DNA from serum sample 107


title: Serum DNA 105

source_name: genomic DNA from serum sample 105

value: G


title: C57BLKS/J mouse  liver, control animal 2

description: Sample name: 198


title: Serum DNA 106

source_name: genomic DNA from serum sample 106

value: I


title: C57BLKS/J mouse  liver, control animal 4

description: Sample name: 200


title: C57BLKS/J mouse  liver, treated animal 4

description: Sample name: 204


title: LP/J mouse  liver, control animal 1

description: Sample name: 205

value: LP/J


title: Serum DNA 112

source_name: genomic DNA from serum sample 112

value: C


title: BTBR T+ tf/J mouse  liver, treated animal 4

description: Sample name: 196

source_name: BTBR T+ tf/J liver, isoniazid treated

value: BTBR T+ tf/J


title: Serum DNA 102

source_name: genomic DNA from serum sample 102

value: F


title: Serum DNA 108

source_name: genomic DNA from serum sample 108

value: B


title: Serum DNA 101

source_name: genomic DNA from serum sample 101


title: Serum DNA 103

source_name: genomic DNA from serum sample 103


title: BTBR T+ tf/J mouse  liver, treated animal 2

description: Sample name: 194

value: Yes


title: Serum DNA 100

source_name: genomic DNA from serum sample 100


title: NOR/LtJ mouse  liver, control animal 1

description: Sample name: 221

source_name: NOR/LtJ liver, vehicle treated

value: NOR/LtJ

value: Vehicle


title: C57BLKS/J mouse  liver, control animal 1

description: Sample name: 197


title: BTBR T+ tf/J mouse  liver, treated animal 1

description: Sample name: 193

value: Isoniazid


title: Serum DNA 104

source_name: genomic DNA from serum sample 104

value: healthy postmenopausal women

value: E


title: BTBR T+ tf/J mouse  liver, control animal 4

description: Sample name: 192

source_name: BTBR T+ tf/J liver, vehicle treated


title: Serum DNA 96

source_name: genomic DNA from serum sample 96

value: H


title: MRL/MpJ mouse  liver, control animal 3

description: Sample name: 215

source_name: MRL/MpJ liver, vehicle treated

value: female

value: MRL/MpJ

value: No


title: C57BLKS/J mouse  liver, treated animal 1

description: Sample name: 201

source_name: C57BLKS/J liver, isoniazid treated

value: left liver lobe


title: Serum DNA 97

source_name: genomic DNA from serum sample 97

value: J


title: BTBR T+ tf/J mouse  liver, control animal 1

description: Sample name: 189


title: Serum DNA 95

source_name: genomic DNA from serum sample 95


title: BTBR T+ tf/J mouse  liver, control animal 2

description: Sample name: 190


title: BTBR T+ tf/J mouse  liver, control animal 3

description: Sample name: 191


title: MRL/MpJ mouse  liver, treated animal 1

description: Sample name: 217

source_name: MRL/MpJ liver, isoniazid treated


title: AKR/J mouse  liver, treated animal 3

description: Sample name: 187

source_name: AKR/J liver, isoniazid treated

value: AKR/J


title: Serum DNA 94

source_name: genomic DNA from serum sample 94

value: K


title: Serum DNA 99

source_name: genomic DNA from serum sample 99

value: A


title: AKR/J mouse  liver, treated animal 1

description: Sample name: 185


title: Serum DNA 91

source_name: genomic DNA from serum sample 91


title: AKR/J mouse  liver, treated animal 2

description: Sample name: 186


title: BTBR T+ tf/J mouse  liver, treated animal 3

description: Sample name: 195

source_name: BTBR T+ tf/J liver, isoniazid treated

value: BTBR T+ tf/J


title: PL/J mouse  liver, control animal 1

description: Sample name: 245

source_name: PL/J liver, vehicle treated

value: PL/J


title: SJL/J mouse  liver, treated animal 3

description: Sample name: 179

source_name: SJL/J liver, isoniazid treated

value: SJL/J

value: Yes


title: AKR/J mouse  liver, control animal 2

description: Sample name: 182

source_name: AKR/J liver, vehicle treated

value: Vehicle


title: AKR/J mouse  liver, control animal 4

description: Sample name: 184


title: Serum DNA 90

source_name: genomic DNA from serum sample 90


title: AKR/J mouse  liver, control animal 3

description: Sample name: 183


title: Serum DNA 89

source_name: genomic DNA from serum sample 89


title: AKR/J mouse  liver, treated animal 4

description: Sample name: 188

value: Isoniazid


title: Serum DNA 92

source_name: genomic DNA from serum sample 92

value: healthy postmenopausal women

value: G


title: Serum DNA 86

source_name: genomic DNA from serum sample 86

value: D


title: Serum DNA 85

source_name: genomic DNA from serum sample 85

value: B


title: SJL/J mouse  liver, control animal 4

description: Sample name: 176

source_name: SJL/J liver, vehicle treated

value: female