title: Hemin deplete vs hemin replete, experiment 3

description: Biological replicate 3 of 3.

data_processing: Normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. LIMMA was used. LIMMA ( Linear Models for Microarray Data) package for statistical inference. LIMMA includes pre-processing capabilities for two-colour spotted arrays such as normalization of cDNA data, and background subtraction. LOWESS was used to normalize the data.  Data were analyzed for significant differences using the Significance Analysis for Oral Pathogen Microarrays (SAOPMD).   SAOPMD combines all the repeats within and between arrays and generates statistics.  Data included were derived from three microarrays (biological replicates) each containing 4 technical replicates.

growth_protocol: Bacterial cells grown in hemin replete and hemin deplete conditions

treatment_protocol: no additional treatment performed

value: hemin deplete

source_name: RNA from whole bacteria grown under hemin deplete conditions

value: hemin replete


title: Hemin deplete vs hemin replete, experiment 2

status: Public on May 18 2015

type: RNA

city: Richmond

first: Janina

middle: P

last: Lewis

state: VA

address: 521 North 11th Street

department: Philips Institute of OCMB

country: USA

institute: Virginia Commonwealth University

description: Biological replicate 2 of 3.

hyb_protocol: Labeled cDNA probes were combined and mixed with hybridization buffer and applied to prehybridized array.  Array was placed in hybridization chamber and incubated ON at 42C.

scan_protocol: Scanned on an Axon 4200A microarray scanner. Images were quantified using GenePix software (v 6.0).

molecule: total RNA

organism: Porphyromonas gingivalis

source_name: RNA from whole bacteria

label_protocol: 10 µg of total RNA were primed with random DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of ArrayScript reverse transcriptase (Applied Biosystems/Ambion, Austin, TX).  Dyes were incorporated into the reverse transcribed cDNAs (Cy3 and Cy5, GE Healthcare).

extract_protocol: Total RNA extracted using Qiagen kit following manufacturer's instructions

tag: strain

tag: treatment

source_name: RNA from whole bacteriagrown under hemin deplete conditions


title: Iron deplete vs iron replete, experiment 1, technical replicate 1

description: Biological replicate 1 of 4. Technical replicate 1.

data_processing: Normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. LIMMA was used. LIMMA ( Linear Models for Microarray Data) package for statistical inference. LIMMA includes pre-processing capabilities for two-colour spotted arrays such as normalization of cDNA data, and background subtraction. LOWESS was used to normalize the data.  Data were analyzed for significant differences using the Significance Analysis for Oral Pathogen Microarrays (SAOPMD).   SAOPMD combines all the repeats within and between arrays and generates statistics.  Data included were derived from seven microarrays (biological replicates) each containing 4 technical replicates.

growth_protocol: Bacterial cells grown in iron replete and iron deplete conditions

treatment_protocol: No additional treatment performed

value: iron deplete

value: iron replete


title: Hemin deplete vs hemin replete, experiment 1

description: Biological replicate 1 of 3.


title: WT_control_3

status: Public on May 19 2015

city: Philadelphia

first: Wayne

middle: W

last: Hancock

state: PA

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

hyb_protocol: 10 microgram of labeled aRNA was fragmented, and 6.5 microgram of the fragmented aRNA was hybridized to the Affymetrix Mouse 430A_2 chips.  Hybridization conditions were 16hrs at 45C.

scan_protocol: The chips were washed using Fluidics protocol midiEuk2v3_450 on an Affymetrix GeneChip Fluidics Station 450 and scanned on an Affymetrix Genechip Scanner.

data_processing: Microarray experiments were performed using whole-mouse-genome oligoarrays (Mouse430a, Affymetrix). Array data were analyzed using MAYDAY version 2.12

label: biotin

organism: Mus musculus

source_name: WT_Regulatory T-cells CD4+CD25+

label_protocol: 100ng of totalRNA was labeled using Ambion's MessageAmp Premier RNA Amplification Kit (PN:4383452)

extract_protocol: Total RNA was isolated using Rneasy (Quiagen). RNA integrity and quantity was analyzed using a DU640 (Beckman-Coulter).

tag: strain background

tag: genotype/variation

value: Wild type

tag: cell type

value: Regulatory T-cells CD4+CD25+


title: WT_control_1


title: THP1-SP110b_DoxIFN_4D_rep2

city: Taipei

first: Bo-Shiun

last: Yan

address: No. 1, Sec. 1, Ren-Ai Road

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Taiwan University

description: Gene expression data from THP1-SP110b cells treated with Dox plus IFNγ for 4 days

hyb_protocol: The biotinylated RNA was fragmented and hybridized overnight to human genome U133 plus 2.0 array (Affymetrix).

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

data_processing: The raw data were processed using the GeneChip Robust Multiarray Averaging (GC-RMA) and analyzed by GeneSpring GX software (Agilent Technologies).

organism: Homo sapiens

label_protocol: 5 μg of total RNA was reverse-transcribed and the cDNA product was purified and then transcribed in vitro with biotin-labeled ribonucleotides (IVT Labeling Kit; Affymetrix).

growth_protocol: THP1-SP110b cells were cultured at 37°C in 5% CO2  in RPMI 1640 medium containing penicillin/streptomycin, 2 mM L-glutamine, and 7.5% tetracycline-free fetal bovine serum (Life Technologies).

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

tag: cell line

value: monocyte

tag: sp110b overexpression status

value: on


title: THP1-SP110b_IFN_2D_rep2

description: Gene expression data from THP1-SP110b cells treated with IFNγ for 2 days

value: off


title: THP1-SP110b_DoxIFN_4D_rep3

source_name: THP1-SP110b cells treated with Dox plus IFNγ for 4 days


title: THP1-SP110b_DoxIFN_4D_rep1


title: THP1-SP110b_IFN_4D_rep1

description: Gene expression data from THP1-SP110b cells treated with IFNγ for 4 days


title: WT_control_2


title: THP1-SP110b_IFN_4D_rep2

source_name: THP1-SP110b cells treated with IFNγ for 4 days


title: THP1-SP110b_IFN_2D_rep3

source_name: THP1-SP110b cells treated with IFNγ for 2 days


title: THP1-SP110b_IFN_2D_rep1


title: THP1-SP110b_DoxIFN_2D_rep1

description: Gene expression data from THP1-SP110b cells treated with Dox plus IFNγ for 2 days


title: THP1-SP110b_DoxIFN_2D_rep3

source_name: THP1-SP110b cells treated with Dox plus IFNγ for 2 days


title: THP1-SP110b_IFN_4D_rep3


title: THP1-SP110b_DoxIFN_2D_rep2


title: THP1-SP110b_CON_rep2

description: Gene expression data from untreated THP1-SP110b cells as control

source_name: Untreated THP1-SP110b cells


title: THP1-SP110b_CON_rep3


title: THP1-SP110b_CON_rep1


title: Regional lymph node No. 14-N

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

country: Germany

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: For Hybridization 12.5 µg fragmented cRNA were used. The arrays were incubated for 16h in the Affymetrix Hybidization Oven 640 at 45°C. Washing and staining steps were performed semi-automatic in the Affymetrix Fluidics Station 450, the single steps following the Affymetrix One Cycle Protocol for standard arrays.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G and the Command Console software at a wavelength of 570nm and a pixel size of 1.56µm.

data_processing: R statistical platform and simpleaffy package (Bioconductor) was used for background correction (RMA procedure) and normalization (quantile).

label: Biotin

source_name: pN0_regional lymph node

label_protocol: Labeling of the RNA was performed according to the standard Affymetrix One Cycle protocol for the GeneChip 3`IVT Expression Kit.

extract_protocol: RNA was extracted in several steps using trizol, chloroform, isopropanol and ethanol, followed by further purification with the RNeasy Mini Kit (Quiagen; Hilden; Germany) according to the manufacturer's instructions.

tag: subject

value: esophageal cancer patient

tag: tissue

value: Lymph node

tag: pn status

tag: lymph node location relative to tumor

value: regional


title: Distant lymph node No. 13-F

source_name: pN0_distant lymph node

value: distant


title: Regional lymph node No. 12-N


title: Regional lymph node No. 13-N


title: Distant lymph node No. 14-F


title: L_monocytogenes_LO28_delta_lhrC1-5_stressed_rep3

city: Odense

first: Birgitte

middle: Haar

last: Kallipolitis

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description: This sample is of stressed delta-lhrC1-5 mutant Listeria monocytogenes LO28. It is the third of three stressed delta-lhrC1-5 mutant biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed following NimbleGen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed using NimbleScan v2.6. 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), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Listeria monocytogenes LO28

source_name: Listeria monocytogenes LO28 delta-lhrC1-5, stressed.

label_protocol: Labeling was performed following NimbleGen standard operating protocol. See www.nimblegen.com.

growth_protocol: Cultures were grown in Brain Heart Infusion (BHI) medium at 37°C until an OD600 of 0.35.

extract_protocol: 10 mL of each sample were treated with 2 volumes of RNA protect reagent (Quagen) as recommended by the manufacturer. The samples were vortexed and incubated at room temperature for 5 min followed by centrifugation (10 min, 5000g). RNA was extracted by using TRIzol Reagent (Ambion) as described previously (Nielsen et al., 2010, Nucleic Acids Res. 38: 907-19). DNase treatment was performed using 20 units of DNase 1 recombinant RNase-free (Roche) in the presence of 200 units RNasin Plus (Promega). RNA was purified by one phenol-chloroform extraction and one chlorofrom extraction followed by RNA precipitation. RNA was re-suspended in RNase free water (Ambion). RNA was quantified using a NanoDrop 2000 and the quality was assessend by the Agilent 2100 Bioanalyzer utilizing the RNA 6000 LapChip kit.

treatment_protocol: Each culture was split and 4 µg/mL cefuroxime was added to one of the samples. The samples were then incubated for 30 min.

tag: agent

value: cefuroxime

value: Deletion mutant delta-lhrC1-5


title: Distant lymph node No. 11-F


title: Distant lymph node No. 10-F


title: Regional lymph node No. 8-N

source_name: pN1_regional lymph node


title: Distant lymph node No. 9-F

source_name: pN1_distant lymph node


title: Distant lymph node No. 5-F


title: Distant lymph node No. 4-F


title: Regional lymph node No. 7-N


title: Regional lymph node No. 2-N


title: Regional lymph node No. 6-N


title: Regional lymph node No. 1-N


title: Iron deplete vs iron replete, experiment 3, technical replicate 2

description: Biological replicate 3 of 4. Technical replicate 2.


title: Distant lymph node No. 7-F

description: LK-22.08f / 5425 II


title: Distant lymph node No. 3-F


title: Distant lymph node No. 12-F


title: Regional lymph node No. 5-N


title: Distant lymph node No. 2-F


title: Regional lymph node No. 10-N


title: Regional lymph node No. 11-N


title: Distant lymph node No. 1-F


title: Regional lymph node No. 3-N


title: Regional lymph node No. 9-N


title: Distant lymph node No. 6-F


title: Regional lymph node No. 4-N


title: Distant lymph node No. 8-F


title: 704010195W8

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

hyb_protocol: Hybridize 12-Sample Beadchip

scan_protocol: SentrixScanVersion 2.3.0.13  (This information is in the .XML file)

data_processing: The data were analysed using BeadStudio version 1.5.1.3 using the average chip normalization method.

source_name: Whole blood

label_protocol: Biotinylated cRNA were generated following manufacturer protocols using the Illumina TotalPrep Amplification Kit from Ambion.

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

tag: illness

value: Healthy

tag: ethnicity

value: African

tag: race

value: African black

tag: age

tag: gender

value: Female

tag: week

tag: calculated viral set point

value: ND

tag: viral load

tag: cd4 count

tag: feibig stage

tag: dataset

value: Test Set


title: 702010104E

value: African Ngoni

value: Male

value: E

tag: treatment


title: 702010129E

value: African Lomwe


title: 702010039E


title: 702010165E

value: African Tonga


title: 706010214E


title: 704010187W8


title: 702010182W8

value: African Yao


title: 701010161E

value: US

value: White


title: 704010249E


title: 704010146W8


title: 702010064E


title: 706010208W8


title: 706010188E


title: 706010196W8


title: 700010530E


title: 702010012W8

value: African Chewa


title: 706010170W24

value: HIV

value: NO


title: 706010170W12


title: 700010496W1

value: Healthy


title: 700010488E


title: 706010164W4

value: African

value: Unstable


title: 706010164W12

value: African black


title: 706010170E


title: 706010170W4

value: ND


title: 706010164W1

value: Test Set


title: 706010164W24


title: 704010152W4


title: 703010200W24


title: 703010200W12


title: 704010152E


title: 703010200W1


title: 706010164E


title: 704010152W12


title: 700010451E

value: Female


title: 700010365E

value: African American

value: Male


title: 703010200E

value: E


title: 702010930E

value: African Ngoni

value: only 1 visit

value: Validation Set


title: 702011101E

value: African Lomwe


title: 702010176W12


title: 702010520E

value: African Sena


title: 702010824E

value: HIV


title: 703010200W2

value: African Chewa

value: NO


title: 702010176W2

value: African


title: 702010157W12


title: 702010176W4


title: 702010157W1


title: 703011165E


title: 702010852E


title: 702010176E


title: 703010200W4


title: 703010863E

value: unstable VL - no set point


title: 702010157E


title: 702010813E


title: 702010545E

value: Healthy


title: 703010976E


title: 702010846E


title: 702011143E

value: not enough visits to calculate


title: 701010145W12

value: US

value: White

value: ND

value: YES

value: Test Set


title: 701010172W4

value: Male


title: 702011099E

value: African Ngoni

value: Female

value: E


title: 703011157E

value: only 1 visit

value: Validation Set


title: 701010172W2

value: HIV


title: 701010145W24


title: 701010172W1


title: 701010172E

value: NO


title: 702010809E

value: African

value: African Sena


title: 701010145W4


title: 703011039E

value: Healthy

value: African Chewa


title: 702010984E

value: African Mang'anja

value: not enough visits to calculate


title: 702011184E

value: African Lomwe


title: 701010145E

value: US

value: White

value: ND


title: 702010992E

value: African Yao

value: Male


title: 701010137W24

value: YES

value: Test Set


title: 701010137W12


title: 701010137W1


title: 703010337E

value: E

value: Validation Set


title: 701010145W1

value: HIV


title: 701010145W2


title: 702010979E

value: African


title: 702011014E


title: 700010357E


title: 702010838E

value: Female

value: NO


title: 702010419E

value: African Khokhola


title: 702010634E

value: African Sena


title: 701010092W2

value: African American


title: 701010092W4


title: 702010968E

value: African Ngoni

value: not enough visits to calculate


title: 701010137W2

value: US

value: White


title: 701010092W12

value: ND


title: 702011241E

value: African Lomwe

value: Male


title: 701010092E

value: Test Set


title: 701010027W1

value: YES

value: Training Set


title: 700010382HE

value: Healthy

value: E


title: 701010137E

value: HIV


title: 703010144H8

value: African

value: African Chewa

value: Female


title: 703010256E

value: NO

value: Validation Set


title: 703011190E

value: African Nyanja


title: 701010092W24

value: US

value: African American


title: 703010178H8


title: 703010242E

value: African Ngoni


title: 706010065HE

value: African Black


title: 706010057HE

value: Male


title: 706010041HE

value: ND


title: 703011244E


title: 703010049HE


title: 702010955E

value: not enough visits to calculate


title: ZNF overexpression - NMuMG_4

city: San Francisco

first: Laurie

last: Littlepage

state: CA

address: 513 Parnassus Avenue, Box 0452

department: Anatomy

institute: University of California, San Francisco

hyb_protocol: Hybridize at 65°C for 14 to 18 hours.

scan_protocol: Axon Instruments (V1.00) AxImageIO, GenePix 4000B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Vector

label_protocol: Ambion MessageAmp II Amino Allyl kit

extract_protocol: Qiagen RNeasy kit

tag: expression

value: vector control

tag: cell line

value: NMuMG

value: ZNF217 overexpression


title: 706010033H8

value: Healthy

value: Training Set


title: 702011072E

value: African

value: E


title: 703010036H8


title: ZNF overexpression - NMuMG_2


title: 704010091H8

value: Female


title: 701010120HE


title: 705010031H8


title: 702010553E

value: African Sena

value: Validation Set


title: ZNF overexpression - NMuMG_1


title: 702011037E

value: African Lambia


title: ZNF overexpression - NMuMG_3


title: 704010083W12

value: HIV

value: NO


title: 703010115HE

value: African Lomwe


title: 703011322E

value: African Ngoni


title: 702010901E

value: Male

value: Increasing after 6 months

value: ND


title: 703011545E

value: African Chewa


title: 703010062HE


title: 704010083W4

value: African Black


title: 702010721E

value: unstable VL - no set point


title: 704010083W1

value: Training Set


title: 704010083W2

value: African


title: 704010042W24


title: 704010042W4


title: 704010083E

value: E


title: 704010042W12


title: 703011182E

value: Female


title: 702011045E

value: Healthy

value: African Yao


title: 704010042W2


title: 704010042W1


title: 702010943E

value: African Sena

value: not enough visits to calculate

value: Validation Set


title: 702010773E

value: HIV

value: African Lomwe

value: NO


title: 702010600E

value: African Ngoni

value: Male


title: 704010083W24

value: ND


title: Wy_48h_exp2

city: Maastricht

first: Linda

last: Rieswijk

address: Universiteitssingel 50

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

hyb_protocol: To adjust the volume to 200 μl, nuclease free water was added to the labeled samples. Thereafter 200 μl hybridization buffer provided in miRCURY LNA™ microRNA Array, 5th generation kit (Exiqon, Denmark) was added. In a total volume of 400 μl the sample was denatured for 2 minutes at 95ºC, incubated on ice for at least 15 minutes and then spun down. Manual hybridization was performed using an Agilent hybridization SureHyb chamber kit and gasket slide kit at 56 °C for 16h in a hybridization oven with rotation. Following manual hybridization the arrays were automatically washed in a Tecan HS4800 Pro Hybridization station according to Exiqon instructions. For each biological experiment, one hybridization per time point was conducted and one sample per array.

scan_protocol: After washing, the arrays were scanned using the GenePix 4000A scanner (Axon Instruments, Foster City, CA).

data_processing: To quantify the signals, the images were processed in to GPR (5th) and TXT (7th) files through the GenePix Pro Sofware Suite version 3.0 by using the GAL file for probe annotation, as obtained from Exiqon. The GAL file is based on miRBase version 20.0. These GPR or TXT files were then imported in to R 2.11.0, for quality control and statistical analysis. First, the quality of all arrays was inspected using arrayQC, an in-house quality control pipeline that generates virtual images, boxplots, correlation plots, clustering images, MvA and PCA plots. Spike-ins were used for all arrays as an extra quality check. Within this dataset, no arrays were deviated technically. During data analysis the spot intensities were background-corrected and then filtered for low signals (i.e. intensity < 10). Only the mouse microRNA reporter intensities (661 unique reporters x 4 technical replicates) were used for further analyses. If for a reporter less than 3 of the 4 technical replicates were left, then the reporter intensity on that specific reporter was set to NA. The data were log2 transformed, followed by a quantile normalization and a summarization step. In the summarization step, the median intensity from the remaining technical replicates per condition was calculated. Finally, for each reporter a cut-off filtering was applied using the median of the three biological replicates. Only reporters that had a median intensity ≥50 for at least one condition of the 9 compounds tested, or their respective controls, passed this filtering per time point. After filtering, log2 ratios were calculated between average intensities of the treatment of its respective control.

label_protocol: The miRCURYTM locked-nuclei acid array (LNA), 5th and 7th generation (Exiqon, Denmark) contains probes that detect mature forms of all microRNAs present in miRBase 20.0 (http://www.mirbase.org/) (Griffiths-Jones et al, 2008). The Exiqon platform has been validated and is shown to reliably detect microRNA expression. The 5th and 7th generation microarray contains 9,360 and 14,708 reporters, which represent several control probes and sequences of mature human/mouse/rat specific microRNA (4 technical replicates). In our analysis, 661 unique mouse reporters (measurable on both generation arrays) were used. cDNA was generated using 1 μg of total RNA per sample. RNA was labeled only with Hy3 containing dye (single color) using the mercury LNA™ microRNA Hy3 Power labeling kit (Exiqon, Denmark) according to the manufacturer’s protocol in a total volume of 12.5 μl.

growth_protocol: PMH were isolated from adult male C57BL/6 mice using a perfusion method and cultured between a collagen-collagen sandwich formation in two six wells plates as described by Mathijs et al., 2010.

extract_protocol: At the end of treatment the medium was removed and PMH were harvested in Qiazol (QIAGEN Benelux B.V., Venlo, The Netherlands). Total RNA was isolated using a miRNeasy Mini Kit (QIAGEN Benelux B.V., Venlo, The Netherlands) according to the manufacturer’s protocol and followed by DNase I (Qiagen, Inc) treatment. Following purification, RNA concentrations were measured by means of a NanoDrop® ND-1000 spectrophotometer (Thermo Scientific, Wilmington, USA) at 260 and 280 nm. RNA quality and integrity were assessed by using automated gel electrophoresis on an Agilent 2100 Bioanalyzer system (Agilent Technologies Netherlands B.V., Amstelveen, The Netherlands). Only RNA samples which showed clear 18S and 28S peaks and with an RNA integrity number (RIN) higher than 8 were used. Samples were stored at -80ºC until RNA hybridization.

treatment_protocol: After a recovery period of 40-42h, the Dulbecco's Modified Eagle's (Gibco BRL, Breda, The Netherlands) culture medium was replaced by culture medium containing either one of the 6 compounds or a vehicle control (0.5% of DMSO or PBS). All chemicals were obtained through Sigma-Aldrich, except for TCDD (Cerilliant). A dose causing minimal cytotoxicity after 24h of exposure thus resulting in ±80% viability, was established by the MTT assay (Mosmann, 1983). Next, cells were treated with an IC20-24h dose of aflatoxin B1 (AFB1), benzo(a)pyrene (BaP), cisplatin (CisPl), 2,3,7,8-tetrachloordibenzodioxine (TCDD), cyclosporin A (CsA) or Wy-14,643 (Wy) (as shown in Table 1) for 24 or 48 h before being harvested. Independent biological experiments (at least in triplicate) with hepatocytes from different mice were obtained for every time point.

tag: studytype

value: Single Dose Toxicity

tag: assaytype

value: ex vivo

tag: strain

tag: compound

tag: dose

tag: doseunit

value: µM

tag: doseduration

tag: durationunit

value: h

tag: dosefrequency

value: once

tag: vehicle

value: DMSO

tag: route

value: medium

tag: tissue source

value: liver

tag: cell type

value: primary hepatocytes


title: 703010159W4

tag: illness

tag: ethnicity

value: African

tag: race

value: African Chewa

tag: age

tag: gender

value: Female

tag: week

tag: calculated viral set point

tag: viral load

tag: cd4 count

tag: feibig stage

tag: dataset

value: Training Set


title: eWAT_HFD_IL37TG_replicate4

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.28.2).

source_name: IL-37-overexpresssing_HFD 16wks_epidydimal white adipose tissue

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: The IL-37tg mice on a C57Bl/6 background have been reported before (Nold et al, Nat Immunol, 2010; PMID: 20935647). Wild type C57BL/6 mice were purchased from the Jackson Laboratories. All animal procedures were conducted under protocols approved by the animal experimentation committee of Radboud University Medical Centre, Nijmegen, the Netherlands.

extract_protocol: Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: After a 2 week run-in period on a low fat diet (LFD), male mice were given a high-fat diet (HFD) diet for 16 weeks. The LFD and HFD contained 10% respecytively 45% of energy derived from fat (diet formulations according to D12450B resp. D12451; Research Diets, Inc). After the 16 week diet intervention, epididymal white adipose tissue (eWAT) was removed, and stored at -800 until analysis.

tag: strain

value: male

tag: genotype/variation

value: IL37-overexpressing transgenic mice

tag: diet

value: high fat diet (HFD) for 16 wks

tag: tissue

value: epidydimal white adipose tissue


title: 703010159E

value: HIV

value: E

tag: treatment

value: NO


title: Wy_24h_exp3

tag: studytype

value: Single Dose Toxicity

tag: assaytype

value: ex vivo

tag: compound

tag: dose

tag: doseunit

value: µM

tag: doseduration

tag: durationunit

value: h

tag: dosefrequency

tag: vehicle

tag: route

tag: tissue source

tag: cell type


title: 703010131W12

tag: illness

tag: ethnicity

tag: race

value: African Lomwe

tag: age

tag: gender

value: Male

tag: week

tag: calculated viral set point

tag: viral load

tag: cd4 count

tag: feibig stage

value: ND

tag: dataset


title: eWAT_HFD_IL37TG_replicate3

tag: strain

tag: genotype/variation

tag: diet

tag: tissue


title: 703010159W24

value: African

value: African Chewa

tag: treatment


title: Wy_48h_exp1

tag: studytype

tag: assaytype

tag: compound

tag: dose

tag: doseunit

tag: doseduration

tag: durationunit

tag: dosefrequency

value: once

tag: vehicle

value: DMSO

tag: route

value: medium

tag: tissue source

value: liver

tag: cell type

value: primary hepatocytes


title: 703010159W12

tag: illness

value: HIV

tag: ethnicity

tag: race

tag: age

tag: gender

value: Female

tag: week

tag: calculated viral set point

tag: viral load

tag: cd4 count

tag: feibig stage

tag: dataset

value: Training Set


title: 704010042E

value: African Black

value: E

tag: treatment

value: NO


title: 703010159W1


title: 703010131W4


title: eWAT_HFD_IL37TG_replicate2

tag: strain

value: male

tag: genotype/variation

value: IL37-overexpressing transgenic mice

tag: diet

value: high fat diet (HFD) for 16 wks

tag: tissue

value: epidydimal white adipose tissue


title: 702011086E

value: Healthy

value: African

value: African Mang'anja

value: Validation Set


title: Wy_48h_Exp3

hyb_protocol: Amplified, biotinylated and fragmented targets were then hybridized on to the arrays. After hybridization, arrays were washed and stained using an Affymetrix fluidics station and scanned by use of an Affymetrix GeneArray scanner. A total of 60 RNA samples was prepared and analyzed on GeneChip arrays (treated and control samples from each time point were at least in triplicate). Normalization quality controls, including scaling factors, average intensities, present calls, background intensities, noise, and raw Q values, appeared to be within acceptable limits for all chips. Hybridization controls BioB, BioC, BioD, and CreX were called present on all chips and yielded the expected increases in intensities.

scan_protocol: standard Affymetrix protocol

data_processing: All raw datasets from generated CEL files were first imported into R2.11.0 and run through an in-house quality control pipeline (available through ArrayAnalysis.org (Eijssen et al, 2013)) and then used for statistical analysis. R package is freely available for academic use from the Comprehensive R Archive Network (http://www.cran.r-project.org/). The probe sets were re-annotated by use of custom Cell Definition Files (CDF) (version 12.1.0. http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/17.0.0/entrezg.asp). This resulted in a list of 16,331 unique gene IDs. After re-annotation, data were normalized by Robust Multichip Average (RMA) normalization and log2 transformed using the R package “affy”. Low expression genes were filtered out by using a log[intensity cutoff] >5. This cutoff was based on the 1st quartile of the distribution of average intensities of all reporters.

label_protocol: High-density oligonucleotide GeneChips from Affymetrix were used to measure gene expression levels (Mouse Genome 430 2.0 array (45101 probes)). Targets for these arrays were prepared from 250 ng of total RNA by means of the GeneChip 3’ IVT Express Kit according to the Affymetrix protocol (Affymetrix UK Ltd, High Wycombe, UK).

tag: tissue source

tag: cell type

tag: studytype

value: Single Dose Toxicity

tag: assaytype

value: ex vivo

tag: compound

tag: dose

tag: doseunit

value: µM

tag: doseduration

tag: durationunit

value: h

tag: dosefrequency

value: once

tag: vehicle

value: DMSO

tag: route

value: medium


title: Wy_24h_exp1

value: liver

value: primary hepatocytes


title: eWAT_HFD_IL37TG_replicate1

tag: gender

value: male


title: eWAT_HFD_WT_replicate4

source_name: WT_HFD 16wks_epidydimal white adipose

tag: strain

value: wild type


title: 703010131W2

tag: illness

value: HIV

tag: ethnicity

tag: race

value: African Lomwe

tag: age

value: Male

tag: week

tag: calculated viral set point

tag: treatment

value: NO

tag: viral load

tag: cd4 count

value: ND

tag: feibig stage

tag: dataset

value: Training Set


title: 703010131W1

value: African


title: eWAT_HFD_WT_replicate3

tag: genotype/variation

tag: diet

value: high fat diet (HFD) for 16 wks

tag: tissue

value: epidydimal white adipose tissue


title: 703010131W24


title: Wy_24h_exp2

tag: studytype

value: Single Dose Toxicity

tag: assaytype

value: ex vivo

tag: compound

tag: dose

tag: doseunit

value: µM

tag: doseduration

tag: durationunit

value: h

tag: dosefrequency

tag: vehicle

tag: route

tag: tissue source

tag: cell type


title: Ct_DMSO_48h_exp3

tag: strain

value: DMSO

value: once

value: medium

value: liver


title: Wy_48h_Exp2

value: primary hepatocytes


title: eWAT_HFD_WT_replicate2

tag: gender

value: male

value: wild type


title: 703010131E

tag: illness

value: HIV

tag: ethnicity

tag: race

value: African Lomwe

tag: age

value: Male

tag: week

value: E

tag: calculated viral set point

tag: treatment

value: NO

tag: viral load

tag: cd4 count

tag: feibig stage

tag: dataset


title: Wy_48h_Exp1

tag: studytype

tag: assaytype

tag: compound

tag: dose

tag: doseunit

tag: doseduration

tag: durationunit

tag: dosefrequency

tag: vehicle


title: Ct_DMSO_48h_exp2

tag: strain

tag: route

tag: tissue source

tag: cell type


title: 703011432E

tag: illness

tag: ethnicity

value: African

tag: race

value: African Chewa

tag: age

tag: gender

tag: week

tag: calculated viral set point

value: unstable VL - no set point

tag: treatment

tag: viral load

value: Validation Set


title: eWAT_HFD_WT_replicate1

tag: genotype/variation

tag: diet

value: high fat diet (HFD) for 16 wks

tag: tissue

value: epidydimal white adipose tissue


title: 703010054W2

value: African Tumbuka

tag: cd4 count

tag: feibig stage

value: ND

tag: dataset

value: Training Set


title: 702011053E

value: Healthy

value: African Ngoni


title: WAT_Sel1l-/-_repl4

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.26.6).

source_name: adipose tissue, Sel1l-/- mouse, fed high fat diet for 5 weeks

growth_protocol: Sel1L-flox/flox mice were crossed with adiponectin promoter driven Cre mice to create adipose tissue-specific Sel1L-/- mice.

treatment_protocol: Male wildtype C57Bl/6 mice and adipose tissue-specific Sel1l-/- mice were fed a high fat diet (Research Diets D12492) for 5 weeks.

tag: strain

value: C57BL/6 (C57BL/6N and C57BL/6J mixed)

tag: Sex

value: male

tag: mouseid

value: high fat diet (Research Diets D12492)

value: white adipose tissue

tag: genotype

value: Adipocyte Sel1l-/-


title: 703010159W2

tag: illness

value: HIV

tag: ethnicity

tag: race

value: Female

value: NO


title: Ct_DMSO_48h_exp1

tag: studytype

value: Single Dose Toxicity

tag: assaytype

value: ex vivo

tag: compound

value: DMSO

tag: dose

tag: doseunit

tag: doseduration

tag: durationunit

value: h

tag: dosefrequency

value: once

tag: vehicle

tag: route

value: medium

tag: tissue source

value: liver

tag: cell type

value: primary hepatocytes


title: Ct_DMSO_24h_exp3

tag: strain


title: Ct_DMSO_24h_exp1


title: Wy_48h_exp3

value: µM


title: Ct_DMSO_24h_exp2


title: Wy_24h_Exp4


title: TCDD_48h_exp3

value: uM


title: Wy_24h_Exp3


title: Wy_24h_Exp2


title: Wy_24h_Exp1


title: WAT_Sel1l-/-_repl3

value: C57BL/6 (C57BL/6N and C57BL/6J mixed)

tag: Sex

value: male

tag: mouseid

tag: tissue

tag: genotype


title: 703010054W12

tag: illness

tag: ethnicity

value: African

tag: race

value: African Tumbuka

tag: age

tag: gender

value: Male

tag: week

tag: calculated viral set point

tag: treatment

tag: viral load

tag: cd4 count

tag: feibig stage

value: ND

tag: dataset

value: Training Set


title: 703010054W4

value: HIV

value: NO


title: 703010054W1


title: WAT_Sel1l-/-_repl1

tag: strain

value: high fat diet (Research Diets D12492)

value: white adipose tissue

value: Adipocyte Sel1l-/-


title: 703010010W12


title: 703010054E

value: E


title: WAT_WT_repl3

source_name: adipose tissue, wildtype mouse, fed high fat diet for 5 weeks

tag: Sex

value: wildtype


title: WAT_WT_repl4

tag: mouseid


title: WAT_WT_repl2

tag: tissue


title: TCDD_48h_Exp1

tag: tissue source

value: liver

tag: cell type

value: primary hepatocytes

tag: studytype

value: Single Dose Toxicity

tag: assaytype

value: ex vivo

tag: compound

tag: dose

tag: doseunit

tag: doseduration

tag: durationunit

value: h

tag: dosefrequency

value: once

tag: vehicle

value: DMSO

tag: route

value: medium


title: WAT_Sel1l-/-_repl2

value: C57BL/6 (C57BL/6N and C57BL/6J mixed)

value: male

tag: genotype


title: 703010010W24

tag: illness

value: HIV

tag: ethnicity

value: African

tag: race

value: African Tumbuka

tag: age

tag: gender

value: Male

tag: week

tag: calculated viral set point

tag: treatment

tag: viral load

tag: cd4 count

value: ND

tag: feibig stage

tag: dataset

value: Training Set


title: 703010054W24

value: NO


title: TCDD_48h_exp1

tag: studytype

tag: assaytype

tag: strain

tag: compound

tag: dose

tag: doseunit

value: uM

tag: doseduration

tag: durationunit

tag: tissue source

value: liver

tag: cell type


title: TCDD_48h_Exp2

value: primary hepatocytes

value: Single Dose Toxicity

tag: dosefrequency

tag: vehicle

tag: route


title: TCDD_24h_Exp3

value: ex vivo

value: h


title: WAT_WT_repl1

tag: Sex

tag: mouseid

value: high fat diet (Research Diets D12492)

tag: tissue

value: white adipose tissue

tag: genotype

value: wildtype


title: 703010010W4

tag: illness

tag: ethnicity

tag: race

tag: age

tag: gender

tag: week

tag: calculated viral set point

tag: treatment

tag: viral load

tag: cd4 count

tag: feibig stage

tag: dataset


title: TCDD_24h_exp3

tag: studytype

tag: assaytype

tag: strain

tag: compound

tag: dose

tag: doseunit

tag: doseduration

tag: durationunit

tag: dosefrequency

value: once

tag: vehicle

value: DMSO

tag: route

value: medium

tag: tissue source

tag: cell type


title: TCDD_24h_exp2


title: TCDD_48h_exp2


title: TCDD_24h_exp1


title: TCDD_24h_Exp1


title: TCDD_24h_Exp2


title: 703010010W2

tag: illness

value: HIV

tag: ethnicity

value: African

tag: race

value: African Tumbuka

tag: age

tag: gender

tag: week

tag: calculated viral set point

tag: treatment

tag: viral load


title: PBS_48h_exp3

tag: studytype

tag: assaytype

tag: strain

tag: compound

value: PBS

tag: dose

tag: doseunit


title: PBS_48h_exp2

tag: doseduration

tag: durationunit

tag: dosefrequency

tag: vehicle

tag: route

tag: tissue source


title: PBS_48h_exp1

tag: cell type


title: PBS_24h_exp3


title: PBS_48h_Exp3


title: PBS_48h_Exp2


title: PBS_24h_exp2


title: DMSO.2_48h_exp3


title: PBS_24h_exp1


title: TCDD_48h_Exp3


title: PBS_24h_Exp3


title: 702010047W24

tag: illness

tag: ethnicity

tag: race

value: African Ngoni

tag: age

tag: gender

value: Male

tag: week

value: NO

tag: cd4 count

value: ND

tag: feibig stage

tag: dataset

value: Training Set


title: 702010047W12

tag: calculated viral set point

tag: treatment

tag: viral load


title: PBS_24h_Exp2

value: liver

value: primary hepatocytes

tag: studytype

value: Single Dose Toxicity

tag: assaytype

value: ex vivo

tag: strain

tag: compound

tag: dose

tag: doseunit

tag: doseduration

tag: durationunit

tag: dosefrequency


title: PBS_48h_Exp1

tag: tissue source

tag: cell type

value: h

tag: vehicle

tag: route


title: DMSO.2_48h_exp2

value: once


title: PBS_24h_Exp1


title: DMSO.2_48h_exp1

value: DMSO


title: 702010047W2

tag: illness

tag: ethnicity

tag: race

tag: age

tag: gender

tag: week

tag: cd4 count

tag: feibig stage

tag: dataset


title: 702010047W1

tag: calculated viral set point

tag: treatment

tag: viral load


title: DMSO_48h_Exp3_PvK-5

tag: studytype

tag: assaytype

tag: strain

tag: compound

tag: dose

tag: doseunit

tag: doseduration

tag: durationunit

tag: dosefrequency

value: medium


title: 702010047E

tag: illness

value: HIV

tag: ethnicity

tag: race

tag: age

tag: gender

value: E


title: DMSO.2_24h_exp3

tag: vehicle

tag: route

tag: tissue source

tag: cell type


title: 703010010W1

value: African

value: African Tumbuka

tag: week

tag: calculated viral set point

tag: treatment

tag: viral load

tag: cd4 count

tag: feibig stage

tag: dataset


title: 701010068W8

value: US

value: White

value: YES


title: DMSO.2_24h_exp2

tag: studytype

tag: assaytype

tag: strain

tag: compound

tag: dose

tag: doseunit

tag: doseduration

tag: durationunit

tag: dosefrequency


title: DMSO_48h_Exp3_LR-10075

tag: tissue source

tag: cell type

tag: vehicle

tag: route


title: 701010068W24

tag: illness

tag: ethnicity

tag: race

tag: age

tag: gender

value: Male

tag: week

tag: calculated viral set point

tag: treatment

tag: viral load

value: ND


title: DMSO_48h_Exp3_LR-10090

value: liver

tag: studytype

tag: assaytype

tag: strain

tag: compound

tag: dose

tag: doseunit


title: DMSO_48h_Exp2_LR-10078

tag: tissue source

tag: cell type

value: primary hepatocytes

tag: doseduration

tag: durationunit

tag: dosefrequency

tag: vehicle


title: DMSO_48h_Exp1_PvK-1

value: Single Dose Toxicity

tag: route


title: DMSO_48h_Exp2_PvK-2

value: ex vivo


title: 702010047W4

tag: illness

tag: ethnicity

tag: race

value: African Ngoni

tag: age

tag: gender

tag: week

value: NO

tag: cd4 count

tag: feibig stage

tag: dataset

value: Training Set


title: 701010068W4

tag: calculated viral set point

tag: treatment

tag: viral load


title: DMSO.2_24h_exp1

tag: studytype

tag: assaytype

tag: strain

tag: compound

value: DMSO

tag: dose

tag: doseunit

tag: doseduration

value: h

value: once

value: medium

tag: tissue source

tag: cell type


title: DMSO.1_48h_exp3

tag: durationunit

tag: dosefrequency

tag: vehicle

tag: route


title: DMSO.1_48h_exp2


title: 701010068W2

tag: illness

value: HIV

tag: ethnicity

tag: race

tag: age

tag: gender

tag: week

tag: cd4 count

tag: feibig stage

tag: dataset


title: DMSO.1_48h_exp1

tag: studytype

tag: assaytype

tag: strain

tag: compound

tag: dose

tag: doseunit


title: 701010068W1

value: US

tag: calculated viral set point

tag: treatment

tag: viral load


title: DMSO_24h_Exp5_PvK-5

tag: tissue source

tag: cell type

tag: doseduration

tag: durationunit

tag: dosefrequency

tag: vehicle

tag: route


title: DMSO.1_24h_exp3


title: DMSO.1_24h_exp2


title: DMSO_48h_Exp1_LR-10067


title: DMSO_24h_Exp4_PvK-6


title: DMSO_24h_Exp3_LR-10089


title: DMSO.1_24h_exp1


title: CsA_48h_exp2

value: cyclosporin A

value: uM


title: 701010068E

tag: illness

tag: ethnicity

tag: race

value: White

tag: age

tag: gender

value: Male

tag: week

value: E

tag: cd4 count

tag: feibig stage

tag: dataset


title: CsA_48h_exp3

tag: studytype

tag: assaytype

tag: strain

tag: compound

tag: dose

tag: doseunit

value: liver

value: primary hepatocytes


title: DMSO_24h_Exp3_LR-10074

tag: tissue source

tag: cell type

value: Single Dose Toxicity

value: ex vivo

tag: doseduration

tag: durationunit

tag: dosefrequency

tag: vehicle


title: DMSO_24h_Exp2_PvK-2

tag: route


title: DMSO_24h_Exp2_LR-10077


title: CsA_48h_exp1


title: 701010043W4

tag: illness

tag: ethnicity

tag: race

value: African American

tag: age

tag: gender

value: Female

tag: week

tag: calculated viral set point

tag: treatment

value: YES

tag: viral load

value: ND


title: 701010043W12

tag: cd4 count

tag: feibig stage

tag: dataset

value: Training Set


title: DMSO_24h_Exp1_PvK-1

tag: tissue source

tag: cell type

tag: studytype

tag: assaytype

tag: strain

tag: compound

value: DMSO

tag: dose

tag: doseunit

tag: doseduration

value: h

value: once

value: medium


title: 701010043W24

tag: illness

value: HIV

tag: ethnicity

value: US

tag: race

tag: age

tag: gender


title: DMSO_24h_Exp2_LR-10002

tag: durationunit

tag: dosefrequency

tag: vehicle

tag: route


title: 701010027W24

value: White

value: Male

tag: week

tag: calculated viral set point

tag: treatment

tag: viral load

tag: cd4 count

tag: feibig stage

tag: dataset


title: 701010043W2


title: 701010043E

value: E

value: NO


title: 701010027W2


title: 701010027W4


title: 701010027W12


title: DMSO_24h_Exp1_LR-10066

tag: tissue source

value: liver

tag: cell type

value: primary hepatocytes

tag: studytype

value: Single Dose Toxicity

tag: assaytype

tag: strain

tag: compound

tag: dose

tag: doseunit

tag: doseduration


title: CsA_24h_exp3

value: ex vivo

value: cyclosporin A

value: uM

tag: durationunit

tag: dosefrequency

tag: vehicle

tag: route


title: CsA_24h_exp2


title: 701010027E

tag: illness

tag: ethnicity

tag: race

tag: age

tag: gender

tag: week

tag: calculated viral set point

tag: treatment

tag: viral load

value: Training Set


title: CisPl_48h_exp3

tag: studytype

tag: assaytype

tag: strain

tag: compound

value: cisplatin

value: PBS

tag: tissue source

tag: cell type


title: 703010010E

value: African

value: African Tumbuka

tag: cd4 count

tag: feibig stage

tag: dataset


title: CisPl_48h_exp2

tag: dose

tag: doseunit

tag: doseduration

tag: durationunit

value: h

tag: dosefrequency

value: once

tag: vehicle

tag: route

value: medium


title: CisPl_48h_exp1


title: CsA_48h_Exp3

value: DMSO


title: CsA_48h_Exp1


title: CsA_48h_Exp2


title: DMSO_24h_Exp1_LR-10001


title: CsA_24h_Exp3


title: CisPl_24h_exp3


title: CsA_24h_exp1


title: CisPl_24h_exp2


title: CisPl_24h_exp1


title: CsA_24h_Exp1


title: BaP_48h_exp3

value: benzo(a)pyrene


title: 700010246W2

tag: illness

value: HIV

tag: ethnicity

value: US

tag: race

value: White

tag: age

tag: gender

value: Male

tag: week

tag: calculated viral set point

tag: treatment

value: YES

tag: viral load

value: ND


title: CsA_24h_Exp2

tag: tissue source

value: liver

tag: cell type

value: primary hepatocytes

tag: studytype

value: Single Dose Toxicity

tag: assaytype

value: ex vivo

tag: strain

tag: compound

value: cyclosporin A

value: uM


title: 700010246W4

tag: cd4 count

tag: feibig stage

tag: dataset

value: Training Set


title: 700010246W12

tag: illness

tag: ethnicity


title: 700010246W1

tag: race

tag: age


title: BaP_48h_exp2

tag: dose

tag: doseunit

tag: doseduration

tag: durationunit

value: h

tag: dosefrequency

value: once

tag: vehicle

tag: route


title: CisPl_48h_Exp2

tag: tissue source

tag: cell type

tag: studytype

tag: assaytype

value: cisplatin

value: PBS

value: medium


title: CisPl_48h_Exp3

tag: strain

tag: compound


title: CisPl_48h_Exp1


title: 700010246E

tag: illness

value: HIV

value: US

tag: gender

tag: week

value: E

tag: calculated viral set point

tag: treatment

value: NO

tag: viral load

tag: cd4 count

tag: feibig stage

tag: dataset


title: 700010246W24

tag: ethnicity

tag: race

value: White

tag: age

value: Male

value: YES

value: ND


title: 700010238W24

value: African American


title: CisPl_24h_Exp3

tag: tissue source

value: liver

tag: cell type

value: primary hepatocytes

value: Single Dose Toxicity

value: ex vivo

tag: dose

tag: doseunit

tag: doseduration

tag: durationunit

tag: dosefrequency

tag: vehicle

tag: route


title: 700010238W12

tag: illness

tag: gender

tag: week

tag: calculated viral set point

tag: treatment

value: Training Set


title: BaP_48h_exp1

tag: studytype

tag: assaytype

tag: strain

tag: compound

value: benzo(a)pyrene

value: uM

value: h

value: once

value: DMSO


title: 700010238E

value: HIV

tag: ethnicity

value: US

tag: race

tag: age

value: E

tag: viral load

tag: cd4 count

tag: feibig stage

tag: dataset


title: BaP_24h_exp3

tag: dose

tag: doseunit

tag: doseduration

tag: durationunit

tag: dosefrequency

tag: vehicle

tag: route

value: medium

tag: tissue source

tag: cell type


title: BaP_24h_exp2

tag: studytype

tag: assaytype

tag: strain

tag: compound


title: 700010238W1

tag: illness

tag: ethnicity

tag: race

tag: age

tag: gender

value: Male

tag: week

tag: calculated viral set point

tag: treatment

value: YES

tag: viral load


title: 700010238W2

value: African American

tag: cd4 count

tag: feibig stage

value: ND

tag: dataset


title: BaP_24h_exp1

tag: dose

tag: doseunit

tag: doseduration

tag: durationunit

tag: dosefrequency

tag: vehicle

tag: route

tag: tissue source

value: liver

tag: cell type

value: primary hepatocytes


title: CisPl_24h_Exp2

tag: studytype

value: Single Dose Toxicity

tag: assaytype

value: ex vivo

tag: strain

tag: compound

value: cisplatin

value: PBS


title: BaP_48h_Exp1

value: benzo(a)pyrene

value: uM

value: h


title: BaP_48h_Exp2

value: once

value: DMSO


title: BaP_48h_Exp3


title: CisPl_24h_Exp1


title: 700010224W12

tag: illness

value: HIV

tag: ethnicity

value: US

tag: race

value: White

tag: age

tag: gender

tag: week

tag: calculated viral set point

tag: treatment

tag: viral load

value: Training Set


title: 700010224W24

value: Male

value: YES

tag: cd4 count

tag: feibig stage

tag: dataset


title: 700010224W1

value: ND


title: 700010224W4


title: AFB1_48h_exp1

value: aflatoxin B1

tag: dose

tag: doseunit

tag: doseduration

tag: durationunit

tag: dosefrequency

tag: vehicle

tag: route

value: medium

tag: tissue source

value: liver

tag: cell type

value: primary hepatocytes


title: AFB1_48h_exp3

tag: studytype

value: Single Dose Toxicity

tag: assaytype

value: ex vivo

tag: strain

tag: compound


title: AFB1_24h_exp2

value: uM


title: AFB1_24h_exp3

value: h


title: AFB1_48h_exp2

value: once


title: BaP_24h_Exp2

value: benzo(a)pyrene

value: DMSO


title: BaP_24h_Exp1


title: 700010224W2

tag: illness

value: HIV

tag: ethnicity

value: US

tag: race

tag: age

tag: gender

tag: week

tag: calculated viral set point

tag: treatment

tag: viral load


title: 700010150W12

value: White

tag: cd4 count

tag: feibig stage

tag: dataset

value: Training Set


title: AFB1_24h_exp1

tag: dose

tag: doseunit

tag: doseduration

tag: durationunit

tag: dosefrequency

tag: vehicle

tag: route

tag: tissue source

tag: cell type


title: AFB1_48h_Exp2

tag: studytype

tag: assaytype

tag: strain

tag: compound


title: AFB1_48h_Exp3


title: 700010150W4

tag: illness

tag: ethnicity

tag: race

tag: age

tag: gender

value: Male

tag: week

tag: calculated viral set point

tag: treatment

value: YES

tag: viral load


title: AFB1_24h_Exp1

value: aflatoxin B1

tag: dose

tag: doseunit

tag: doseduration

tag: durationunit

tag: dosefrequency

tag: vehicle


title: AFB1_24h_Exp2

tag: tissue source

tag: cell type

tag: studytype

tag: assaytype

tag: strain

tag: route

value: medium


title: AFB1_24h_Exp3

value: liver

tag: compound


title: untreated mouse 3

city: Boston

first: Aldo

last: Roccaro

state: MA

address: 450 Brookline Av

institute: Dana-Farber Cancer Institute

description: murine bone marrow cell gene expression profiling

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis. The data is transferred to a file-system from which it can be downloaded via a password-protected URL

data_processing: d-Chip

source_name: bone marrow cells

label_protocol: synthesis of double-stranded cDNA which then serves as a template for the synthesis of biotinylated cRNA by in vitro transcription

growth_protocol: Whole bone marrow cells have been collected from SCID/Bg mice

extract_protocol: RNA has been extracted using Qiagen kit

treatment_protocol: NOX-A12 has been administered to mice. Untreated mice have been used as control.

value: SCID/Bg


title: 700010150W24

tag: illness

tag: ethnicity

tag: race

tag: age

tag: gender

tag: week

tag: cd4 count

tag: feibig stage

value: ND

tag: dataset


title: 700010106W4

tag: calculated viral set point

tag: treatment

tag: viral load


title: AFB1_48h_Exp1

tag: tissue source

tag: cell type

value: primary hepatocytes

tag: studytype

value: Single Dose Toxicity

value: ex vivo

tag: dose

tag: doseunit

tag: doseduration

tag: durationunit

tag: dosefrequency

tag: vehicle


title: Glomerular compartment from E1 LN human kidney (European Renal cDNA bank) ERCB_IgAN_27

city: Ann Arbor

first: Celine

middle: C

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

description: Gene expression data from the glomerular compartment of human LN kidney

hyb_protocol: Biotin labeled cDNA was fragmented and hybridized to Affymetrix Human Genome U133Plus2 GeneChip arrays for the Toronto cohort and HG-U133A for the ERCB cohort (Santa Clara, CA) according to the manufacturer protocol.

data_processing: The data were analyzed using GenePattern pipeline: RMA method and Human Entrez Gene custom CDF annotation version 15 were used for the normalization; and Combat for batch correction.

source_name: Kidney biopsy from human LN

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, Affymetrix). GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

extract_protocol: Total RNA was isolated using the RNeasy mini kit from Qiagen, following the manufacturer’s instructions.

tag: tissue

value: Glomeruli from kidney biopsy

tag: phenotype

value: endocapillary proliferation E1


title: 700010224E

tag: illness

tag: ethnicity

tag: race

tag: age

tag: gender

tag: week

value: E

value: NO

tag: cd4 count


title: 700010150W2

value: HIV

value: US

tag: calculated viral set point

tag: treatment

tag: viral load

tag: feibig stage

tag: dataset


title: 700010106W12

value: White

value: Training Set


title: Glomerular compartment from E1 LN human kidney (European Renal cDNA bank) ERCB_IgAN_25

scan_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.


title: treated mouse 1

tag: strain


title: treated mouse 2


title: Glomerular compartment from E0 LN human kidney (European Renal cDNA bank) ERCB_IgAN_26

value: endocapillary proliferation E0


title: 700010106E

value: Male


title: 700010150E


title: Glomerular compartment from E1 LN human kidney (European Renal cDNA bank) ERCB_IgAN_24


title: 700010150W1

value: YES


title: treated mouse 3


title: untreated mouse 2


title: 700010106W1


title: 700010106W2


title: 700010106W24


title: Glomerular compartment from E0 LN human kidney (European Renal cDNA bank) ERCB_IgAN_20


title: Glomerular compartment from E0 LN human kidney (European Renal cDNA bank) ERCB_IgAN_23


title: Glomerular compartment from E1 LN human kidney (European Renal cDNA bank) ERCB_IgAN_19


title: Glomerular compartment from E0 LN human kidney (European Renal cDNA bank) ERCB_IgAN_17


title: Glomerular compartment from E1 LN human kidney (European Renal cDNA bank) ERCB_IgAN_18


title: Glomerular compartment from LN human kidney (European Renal cDNA bank) ERCB_IgAN_22

value: unknown


title: Glomerular compartment from E0 LN human kidney (European Renal cDNA bank) ERCB_IgAN_15


title: untreated mouse 1

value: SCID/Bg


title: Glomerular compartment from E0 LN human kidney (European Renal cDNA bank) ERCB_IgAN_21


title: Glomerular compartment from E0 LN human kidney (European Renal cDNA bank) ERCB_IgAN_13


title: Glomerular compartment from E0 LN human kidney (European Renal cDNA bank) ERCB_IgAN_14


title: 700010081E


title: 700010081W1

value: ND


title: 700010081W4


title: 700010081W12


title: 700010077W12

value: African American


title: BaP_24h_Exp3

tag: tissue source

value: liver

tag: cell type

value: primary hepatocytes

tag: studytype

value: Single Dose Toxicity

tag: assaytype

tag: compound

value: benzo(a)pyrene

tag: dose

tag: doseunit

value: uM

tag: doseduration

tag: durationunit

value: h

tag: dosefrequency

value: once

value: DMSO

tag: route

value: medium


title: 700010077W24

tag: illness

value: HIV

tag: ethnicity

value: US

tag: race

tag: age

tag: gender

tag: week

tag: calculated viral set point

value: NO

tag: cd4 count

value: Training Set


title: 700010081W24

value: White

value: Male

tag: treatment

value: YES

tag: viral load

tag: feibig stage

tag: dataset


title: 701010084HE

value: Healthy

value: Female

value: E

value: ND


title: Glomerular compartment from E0 LN human kidney (European Renal cDNA bank) ERCB_IgAN_11

tag: tissue

value: Glomeruli from kidney biopsy

tag: phenotype

value: endocapillary proliferation E0


title: Glomerular compartment from E0 LN human kidney (European Renal cDNA bank) ERCB_IgAN_16


title: 700010077E

value: African American


title: 700010081W2


title: 198_PD

city: Hangzhou

first: Xuefeng

last: Fang

address: 86 jiefang road

department: College of Medcine

country: China

institute: Zhejiang University

hyb_protocol: according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technologies, Santa Clara, USA) with minor modifications.

scan_protocol: scanned with using the Agilent DNA Microarray Scanner (part number G2505C)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies, Santa Clara, USA)

source_name: patients experienced PD with cisplatin based chemotherapy

extract_protocol: Total RNA was extracted with Trizol

treatment_protocol: lung SCC from patients having either partial response or progressive disease after cisplatin based chemotherapy

value: lung squamous cell carcinoma

value: progressive disease with cisplatin based chemotherapy


title: LP-1-eGFP bortezomib 10nM 24h rep2

city: Uppsala

first: Prasoon

last: Agarwal

state: Sweden

address: Dag Hammarshkojlds vag 20

department: IGP

country: Sweden

institute: Rudbeck Laboratory, Uppsala University

hyb_protocol: 600 ng Cyanine 3-CTP labelled c-RNA was used for 17-hour hybridzation at 65 degree C to the SurePrint G3 Human GE V2 8X60k microarrays (Agilent Technologies)

scan_protocol: The hybridized arrays were washed and then scanned with the Agilent DNA microarray scanner G2505C. Signal intensities were quantified from the scanned image by using Feature Extraction Software version 10.7.3.1 (Agilent Technologies)

data_processing: Quantile normalization with median of all samples baseline transformation using GeneSpring v 12.1.

label: Cyanine 3-CTP

source_name: LP-1-eGFP bortezomib 10nM 24h

label_protocol: 200 ng of total RNA was amplified and labelled using Low Input Quick Amp Labelling Kit according to the manufacturer's instructions (Agilent technologies).

growth_protocol: 37C, 5% CO2, humidity, 10% fetal bovine serum (Biochrom AG, Berlin, Germany), glutamine (2mM) and antibiotics (penicillin 100 U/mL and streptomycin 50g/mL) (Lonza)

extract_protocol:
Cells were cleared of medium, frozen on dry ice and maintained at -80C. All samples were used for RNA extraction simultaneously.
Total RNA isolation was performed using illustra RNAspin mini RNA isolation kit (GE Healthcare, Uppsala, Sweden)

treatment_protocol: LP-1 cells wtih cIAP2 overexpression, (using lentiviral transduction) LP-1-cIAP2-eGFP, cells and control (mock), LP-1-eGFP cells were treated with bortezomib for 6 and 24 hours.

tag: cell line

tag: cell type

value: humn MM (multiple myeloma) cell line

tag: genotype/variatoin

value: control (endogenous cIAP2 level)

tag: treated with

value: 10nM bortezomib for 24hrs


title: LP-1-eGFP untreated 24h rep2

source_name: LP-1-eGFP untreated 24h

value: none (untreated control)


title: 700010040W12

tag: illness

value: HIV

tag: ethnicity

value: US

value: NO

value: Training Set


title: 700010077W1

tag: race

tag: age

value: Male


title: 165_PD

label_protocol: according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technologies, Santa Clara, USA) with minor modifications


title: LP-1-cIAP2-eGFP bortezomib 10nM 6h rep2

source_name: LP-1-cIAP2-eGFP bortezomib 10nM 6h

value: cIAP2 overexpression

value: 10nM bortezomib for 6hrs


title: LP-1-eGFP untreated 6h rep2

source_name: LP-1-eGFP untreated 6h


title: 169_PD


title: 141_PR

source_name: patients experienced PR with cisplatin based chemotherapy

value: partial response with cisplatin based chemotherapy


title: LP-1-eGFP bortezomib 10nM 6h rep2

source_name: LP-1-eGFP bortezomib 10nM 6h


title: 177_PD


title: LP-1-eGFP bortezomib 10nM 24h rep1


title: 700010040W24

value: White

tag: gender

tag: week

value: ND


title: 83_PR


title: 69_PR


title: 700010040W4

tag: calculated viral set point

tag: cd4 count


title: LP-1-cIAP2-eGFP untreated 6h rep2

source_name: LP-1-cIAP2-eGFP untreated 6h


title: 80_PR


title: LP-1-cIAP2-eGFP untreated 24h rep2

source_name: LP-1-cIAP2-eGFP untreated 24h


title: LP-1-cIAP2-eGFP bortezomib 10nM 24h rep2

source_name: LP-1-cIAP2-eGFP bortezomib 10nM 24h


title: 700010040E

source_name: Whole blood

value: E

tag: treatment

tag: viral load


title: 700010163H8

value: Healthy

value: African American

tag: feibig stage

tag: dataset


title: Ctrl.Norm.Rep5_vs_Flax.Norm.Rep5

city: Carbondale

first: Dale

middle: Buchanan

last: Hales

state: Illinois

address: 1125 Lincoln Drive,Life Science II, Room 245 (M/C 6512), Southern Illinois University

department: Physiology

institute: School of Medicine, Southern Illinois University

description: Control diet, Normal tissue, replicate 5 versus Flaxseed diet, Normal tissue, replicate 5

hyb_protocol: Samples were hybridized in an Agilent Hybridization Cassette according to standard protocols.

scan_protocol: Scanned on an Axon GenePix 4000B scanner; Images were quantified using Axon GenePix 6.0.

data_processing: Median foreground intensites (no background subtraction) were normalized in R (version 2.7.2) using the vsn method in limma (version 2.14.7) . Spots with -100 flags were weighted zero before normalization.

organism: Gallus gallus

source_name: Control diet, Normal tissue

label_protocol: 1 microgram of total RNA was labeled using the Agilent two color QuickAmp labeling kit according to the manufacturers protocol.

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

treatment_protocol: Three hundred eighty-seven 2.5-year-old white leghorn hens were randomly divided into Control and Flax groups. Control hens were fed with standard diet, while Flax was with diet supplemented with 10% flaxseed for 1 year. Upon necropsy, ovaries were removed and small yellow follicles (6–8 mm) and pre-ovulatory follicles (9–35 mm) were removed from ovaries. Suspected abnormal ovarian tissues were noted and confirmed as cancerous or normal ovarian tissue by histology. Tumors were characterized based on the size of the ovarian tumor, oviductal involvement, and if there was any ascites fluid and peritoneal metastases present by gross observation. The ovarian tissue consisting of the stroma, cortical (< 1 mm), small and large white follicles (1–5 mm), was cut into smaller portions and stored in RNAlater for RNA extraction. Confirmed cancer and normal ovarian samples were used for further analysis.

value: Female

value: 3.5 Years

tag: tissue

value: Ovary

tag: strain

value: White Leghorn

tag: diet

value: control

tag: disease state

value: healthy

source_name: Flaxseed diet, Normal tissue

value: flaxseed


title: Flax.Cancer.Rep4_vs_Ctrl.Norm.Rep4

description: Flaxseed diet, Cancer tissue, replicate 4 versus Control diet, Normal tissue, replicate 4

source_name: Flaxseed diet, Cancer tissue

value: ovarian cancer


title: 164_PR

value: lung squamous cell carcinoma

tag: phenotype

value: progressive disease with cisplatin based chemotherapy


title: Ctrl.Cancer.Rep5_vs_Flax.Cancer.Rep5

description: Control diet, Cancer tissue, replicate 5 versus Flaxseed diet, Cancer tissue, replicate 5

source_name: Control diet, Cancer tissue


title: Flax.Cancer.Rep6_vs_Ctrl.Cancer.Rep6

description: Flaxseed diet, Cancer tissue, replicate 6 versus Control diet, Cancer tissue, replicate 6


title: LP-1-eGFP untreated 24h rep1

tag: cell line

tag: cell type

value: humn MM (multiple myeloma) cell line

tag: genotype/variatoin

value: control (endogenous cIAP2 level)

tag: treated with

value: none (untreated control)


title: Flax.Norm.Rep6_vs_Ctrl.Norm.Rep6

description: Flaxseed diet, Normal tissue, replicate 6 versus Control diet, Normal tissue, replicate 6

tag: gender

tag: age


title: Glomerular compartment from E0 LN human kidney (Toronto Glomerulonephritis Registry Biobank) H_IgA_21

value: Glomeruli from kidney biopsy

value: endocapillary proliferation E0


title: Ctrl.Norm.Rep3_vs_Ctrl.Cancer.Rep3

description: Control diet, Normal tissue, replicate 3 versus Control diet, Cancer tissue, replicate 3


title: 175_PD


title: Flax.Norm.Rep4_vs_Flax.Cancer.Rep3

description: Flaxseed diet, Normal tissue, replicate 4 versus Flaxseed diet, Cancer tissue, replicate 3


title: Glomerular compartment from E1 LN human kidney (Toronto Glomerulonephritis Registry Biobank) H_IgA_18

value: endocapillary proliferation E1


title: Glomerular compartment from E0 LN human kidney (Toronto Glomerulonephritis Registry Biobank) H_IgA_13


title: Glomerular compartment from E1 LN human kidney (Toronto Glomerulonephritis Registry Biobank) H_IgA_12


title: LP-1-eGFP bortezomib 10nM 6h rep1

value: 10nM bortezomib for 6hrs


title: LP-1-cIAP2-eGFP bortezomib 10nM 24h rep1

value: cIAP2 overexpression

value: 10nM bortezomib for 24hrs


title: LP-1-eGFP untreated 6h rep1


title: Ctrl.Cancer.Rep4_vs_Flax.Norm.Rep3

description: Control diet, Cancer tissue, replicate 4 versus Flaxseed diet, Normal tissue, replicate 3

value: Female

value: 3.5 Years

value: Ovary


title: Ctrl.Norm.Rep2_vs_Flax.Cancer.Rep2

description: Control diet, Normal tissue, replicate 2 versus Flaxseed diet, Cancer tissue, replicate 2

value: White Leghorn

value: control

value: healthy


title: LP-1-cIAP2-eGFP bortezomib 10nM 6h rep1


title: Flax.Cancer.Rep1_vs_Flax.Norm.Rep2

description: Flaxseed diet, Cancer tissue, replicate 1 versus Flaxseed diet, Normal tissue, replicate 2

value: flaxseed

value: ovarian cancer


title: Ctrl.Cancer.Rep1_vs_Ctrl.Norm.Rep1

description: Control diet, Cancer tissue, replicate 1 versus Control diet, Normal tissue, replicate 1


title: Glomerular compartment from E0 LN human kidney (Toronto Glomerulonephritis Registry Biobank) H_IgA_7


title: LP-1-cIAP2-eGFP_untreated_6h rep1

value: humn MM (multiple myeloma) cell line


title: Glomerular compartment from E0 LN human kidney (Toronto Glomerulonephritis Registry Biobank) H_IgA_9


title: A2_0627

status: Public on May 17 2015

city: South San Francisco

first: James

last: Diggans

address: 7000 Shoreline Ct

institute: Veracyte Inc.

description: Gene expression data from BEC specimen

hyb_protocol: GeneChip Fluidics (Affymetrix)

scan_protocol: Scanner 3000 (Affymetrix)

data_processing: RMA normalization

source_name: BEC specimen

label_protocol: GeneChip WT terminal labeling kit (Affymetrix)

growth_protocol: not applicable

extract_protocol: Total RNA isolated using miRNeasy kit from Qiagen, quantified using Nanodrop and quality determined using Bioanalyzer 2100 (Life Technologies). RNA was amplified using Ambion WT expression kit (Life Technologies).

treatment_protocol: not applicable

value: BEC specimen

value: Male

value: N


title: A2_0633

description: Gene expression data from BEC specimen

value: Y


title: A2_0624

description: Gene expression data from BEC specimen


title: Flax.Norm.Rep1_vs_Ctrl.Cancer.Rep2

description: Flaxseed diet, Normal tissue, replicate 1 versus Control diet, Cancer tissue, replicate 2


title: A2_0630

description: Gene expression data from BEC specimen


title: A2_0628

description: Gene expression data from BEC specimen


title: A2_0623

description: Gene expression data from BEC specimen


title: A2_0634

description: Gene expression data from BEC specimen


title: A2_0635

description: Gene expression data from BEC specimen


title: A2_0625

description: Gene expression data from BEC specimen


title: A2_0638

description: Gene expression data from BEC specimen


title: A2_0626

description: Gene expression data from BEC specimen


title: A2_0629

description: Gene expression data from BEC specimen


title: A2_0636

description: Gene expression data from BEC specimen


title: A2_0632

description: Gene expression data from BEC specimen


title: A2_0631

description: Gene expression data from BEC specimen


title: A2_0639

description: Gene expression data from BEC specimen


title: A2_0620

description: Gene expression data from BEC specimen


title: A2_0621

description: Gene expression data from BEC specimen


title: LP-1-cIAP2-eGFP untreated 24h rep1

value: none (untreated control)


title: A2_0618

description: Gene expression data from BEC specimen


title: A2_0617

description: Gene expression data from BEC specimen


title: A2_0614

description: Gene expression data from BEC specimen


title: A2_0619

description: Gene expression data from BEC specimen


title: A2_0603

description: Gene expression data from BEC specimen


title: A2_0615

description: Gene expression data from BEC specimen


title: A2_0616

description: Gene expression data from BEC specimen


title: A2_0604

description: Gene expression data from BEC specimen


title: A2_0613

description: Gene expression data from BEC specimen


title: A2_0637

description: Gene expression data from BEC specimen


title: A2_0605

description: Gene expression data from BEC specimen


title: A2_0608

description: Gene expression data from BEC specimen


title: A2_0611

description: Gene expression data from BEC specimen


title: A2_0602

description: Gene expression data from BEC specimen


title: A2_0609

description: Gene expression data from BEC specimen


title: A2_0610

description: Gene expression data from BEC specimen


title: A2_0601

description: Gene expression data from BEC specimen


title: A2_0600

description: Gene expression data from BEC specimen


title: A2_0599

description: Gene expression data from BEC specimen


title: A2_0612

description: Gene expression data from BEC specimen


title: A2_0595

description: Gene expression data from BEC specimen


title: A2_0606

description: Gene expression data from BEC specimen


title: A2_0596

description: Gene expression data from BEC specimen


title: A2_0597

description: Gene expression data from BEC specimen


title: A2_0594

description: Gene expression data from BEC specimen


title: A2_0607

description: Gene expression data from BEC specimen


title: A2_0591

description: Gene expression data from BEC specimen


title: A2_0593

description: Gene expression data from BEC specimen


title: A2_0598

description: Gene expression data from BEC specimen


title: A2_0592

description: Gene expression data from BEC specimen


title: A2_0590

description: Gene expression data from BEC specimen


title: A2_0582

description: Gene expression data from BEC specimen


title: A2_0577

description: Gene expression data from BEC specimen


title: A2_0584

description: Gene expression data from BEC specimen


title: A2_0581

description: Gene expression data from BEC specimen


title: A2_0580

description: Gene expression data from BEC specimen


title: A2_0578

description: Gene expression data from BEC specimen


title: A2_0576

description: Gene expression data from BEC specimen


title: A2_0586

description: Gene expression data from BEC specimen


title: A2_0572

description: Gene expression data from BEC specimen


title: A2_0579

description: Gene expression data from BEC specimen


title: A2_0588

description: Gene expression data from BEC specimen


title: A2_0574

description: Gene expression data from BEC specimen


title: A2_0575

description: Gene expression data from BEC specimen


title: A2_0570

description: Gene expression data from BEC specimen


title: A2_0583

description: Gene expression data from BEC specimen


title: A2_0585

description: Gene expression data from BEC specimen


title: A2_0587

description: Gene expression data from BEC specimen


title: A2_0573

description: Gene expression data from BEC specimen


title: A2_0571

description: Gene expression data from BEC specimen


title: A2_0569

description: Gene expression data from BEC specimen


title: A2_0566

description: Gene expression data from BEC specimen


title: A2_0567

description: Gene expression data from BEC specimen


title: A2_0563

description: Gene expression data from BEC specimen


title: A2_0568

description: Gene expression data from BEC specimen


title: A2_0562

description: Gene expression data from BEC specimen


title: A2_0565

description: Gene expression data from BEC specimen


title: A2_0561

description: Gene expression data from BEC specimen


title: A2_0560

description: Gene expression data from BEC specimen


title: A2_0557

description: Gene expression data from BEC specimen


title: A2_0552

description: Gene expression data from BEC specimen


title: A2_0554

description: Gene expression data from BEC specimen


title: A2_0558

description: Gene expression data from BEC specimen


title: A2_0555

description: Gene expression data from BEC specimen


title: A2_0551

description: Gene expression data from BEC specimen


title: A2_0549

description: Gene expression data from BEC specimen


title: A2_0550

description: Gene expression data from BEC specimen


title: A2_0559

description: Gene expression data from BEC specimen


title: A2_0548

description: Gene expression data from BEC specimen


title: A2_0547

description: Gene expression data from BEC specimen


title: A2_0546

description: Gene expression data from BEC specimen


title: A2_0543

description: Gene expression data from BEC specimen


title: A2_0539

description: Gene expression data from BEC specimen


title: A2_0545

description: Gene expression data from BEC specimen


title: A2_0541

description: Gene expression data from BEC specimen


title: A2_0544

description: Gene expression data from BEC specimen


title: A2_0540

description: Gene expression data from BEC specimen


title: A2_0556

description: Gene expression data from BEC specimen


title: A2_0538

description: Gene expression data from BEC specimen


title: A2_0535

description: Gene expression data from BEC specimen


title: A2_0537

description: Gene expression data from BEC specimen


title: A2_0542

description: Gene expression data from BEC specimen


title: A2_0536

description: Gene expression data from BEC specimen


title: A2_0534

description: Gene expression data from BEC specimen


title: A2_0553

description: Gene expression data from BEC specimen


title: A2_0531

description: Gene expression data from BEC specimen


title: A2_0528

description: Gene expression data from BEC specimen


title: A2_0532

description: Gene expression data from BEC specimen


title: A2_0530

description: Gene expression data from BEC specimen


title: A2_0523

description: Gene expression data from BEC specimen


title: A2_0526

description: Gene expression data from BEC specimen


title: A2_0522

description: Gene expression data from BEC specimen


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