title: PWBC_5_nuts.7

city: Pamplona

first: Ana

last: Arpón

address: Irunlarrea 1

institute: University of Navarra

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina hiScanSQ platform

data_processing: GenomeStudio Methylation Software Module v1.9.0

label: Cy5 and Cy3

source_name: Peripheral white blood cells five years MedDiet+nuts

extract_protocol: Genomic DNA was extracted and purified from samples using MasterPure™DNA Purification Kit for Blood according to standard instructions

value: Male

value: MedDiet+nuts


title: PWBC_5_nuts.12

status: Public on Nov 23 2017

type: genomic

country: Spain

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

tag: Sex

tag: diet


title: PWBC_5_nuts.11


title: PWBC_5_lowfat.8

source_name: Peripheral white blood cells five years low-fat

value: Low-fat diet


title: PWBC_5_EVOO.1

source_name: Peripheral white blood cells five years MedDiet+EVOO

value: Female

value: MedDiet+EVOO


title: PWBC_5_EVOO.7


title: PWBC_5_nuts.9


title: PWBC_5_nuts.6


title: PWBC_5_lowfat.11


title: PWBC_5_EVOO.10


title: PWBC_5_EVOO.2


title: PWBC_5_nuts.10


title: PWBC_5_nuts.5


title: PWBC_5_nuts.1


title: PWBC_5_nuts.4


title: PWBC_5_EVOO.12


title: PWBC_5_nuts.3


title: PWBC_5_EVOO.8


title: PWBC_5_lowfat.10


title: PWBC_5_nuts.2


title: PWBC_5_EVOO.9


title: PWBC_5_lowfat.12


title: PWBC_5_EVOO.3


title: PWBC_5_EVOO.4


title: PWBC_5_EVOO.11


title: PWBC_5_lowfat.7


title: PWBC_5_nuts.8


title: PWBC_5_lowfat.9


title: PWBC_5_EVOO.5


title: PWBC_5_EVOO.6


title: PWBC_5_lowfat.3


title: PWBC_5_lowfat.4


title: PWBC_5_lowfat.5


title: PWBC_5_lowfat.2


title: PWBC_base_lowfat.12

source_name: Peripheral white blood cells baseline low-fat


title: PWBC_base_nuts.11

source_name: Peripheral white blood cells baseline MedDiet+nuts


title: PWBC_5_lowfat.1


title: PWBC_base_nuts.8


title: PWBC_base_EVOO.10

source_name: Peripheral white blood cells baseline MedDiet+EVOO


title: PWBC_base_nuts.7


title: PWBC_base_EVOO.12


title: PWBC_base_lowfat.11


title: PWBC_base_nuts.12


title: PWBC_5_lowfat.6


title: PWBC_base_EVOO.11


title: PWBC_base_nuts.9


title: PWBC_base_lowfat.10


title: PWBC_base_lowfat.7


title: PWBC_base_EVOO.9


title: PWBC_base_nuts.10


title: PWBC_base_nuts.2


title: PWBC_base_lowfat.8


title: PWBC_base_nuts.5


title: PWBC_base_nuts.6


title: PWBC_base_nuts.3


title: PWBC_base_EVOO.7


title: PWBC_base_EVOO.8


title: PWBC_base_EVOO.5


title: PWBC_base_lowfat.9


title: PWBC_base_EVOO.4


title: PWBC_base_EVOO.3


type: RNA

city: Houston

first: Carl

last: Allen

state: TX

address: 6621 Fannin St

department: Pediatrics

country: USA

institute: Texas Children's Cancer Center/Baylor College of Medicine

description: LCH sorted CD207+, DMSO treated, biological paired sample 3 Gene Expression

hyb_protocol: All sampes were hybridized with Affymetrix Human Transcriptome Array 2.0 Genechips and scanned at Genome Explorations Inc.

scan_protocol: Chips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Affymetrix Expression Console using the default settings for SST-RMA

label: biotin

molecule: total RNA

source_name: Langerhans Cell Histiocytosis Lesion - Sorted CD207+ Cells

label_protocol: Amplified cDNA was fragmented and labeled with the FL-Ovation cDNA Biotin Module v2 (Nugen).

growth_protocol: Lesion or control cells were thawed and treated with Dnase and was left overnight in serum free media

extract_protocol: RNA was extracted with PicoPure RNA Isolation Kit (Molecular Devices). Quality was verified with the Agilent 6000 Picochip. RNA was then amplified with the WT-Ovation Pico System (Nugen)

treatment_protocol: Vemurafenib: 100uM  Trametinib: 10mM ( All treatment for 12 hours before the sorting)

tag: tissue

value: Langerhans cell histiocytosis lesion

tag: cell type

tag: agent

value: DMSO


description: LCH sorted CD207+, MEKi treated, biological paired sample 3 Gene Expression

value: MEKi


description: LCH sorted CD207+, BRAFi treated, biological paired sample 3 Gene Expression

value: BRAFi


title: PWBC_base_lowfat.6


title: PWBC_base_EVOO.6


title: CP19_LN1

status: Public on Nov 22 2017

city: Ann Arbor

first: Karin

last: Hardiman

state: Michigan

address: 2922F Taubman Center

department: General Surgery

institute: University of Michigan

hyb_protocol: Arrays were hybridized overnight (17 hrs). Then the arrays were washed with SSPE-based wash buffers and stained by stacking layers of streptavidin-phycoerithrin and biotinylated antistreptavidin antibody using parallel GeneChip Fluidics 450 stations.

scan_protocol: Oncoscan v3 scanning script, GeneChip Scanner 3000 7G, AGCC software

data_processing:
CEL files are combined by Affymetrix OncoScan Console v.1.1.0 software (ThermoFisher, Waltham, Massachusetts) to generate OSCHP files, which are analyzed by Nexus Copy Number v7.5 (Biodiscovry, El Segundo, California) using their SNP-FASST2 segmentation algorithm.
Probe intensity data at 50-100kb resolution across a set of 891 cancer genes and 300-400kb across the rest of the genome are generated, resulting in a median Log2 Ratio and a median B-allele frequency (BAF) measurement for each genomic segment.

source_name: Patient CP19, metastatic tumor sample, lymph node 1

label_protocol: Samples were labeled with biotin according to the Affymetrix protocol for Oncoscan (P/N 703175 Rev. 1).

extract_protocol: DNA was extracted from tissue using the Allprep mini kit (Qiagen, Valencia, California) and according to the manufacturer's instructions.

tag: gender

value: male

tag: age

tag: tumor stage

value: Colon cancer tumor CP19, metastasis , lymph node 1

tag: location

value: Sigmoid

tag: number of nodes positive

tag: tissue type

value: FFPE


title: CP19_T1

source_name: Patient CP19, primary tumor sample, location 1

value: Colon cancer tumor CP19, primary , location 1

value: fresh frozen


description: LCH sorted CD207+, MEKi treated, biological paired sample 4 Gene Expression


title: PWBC_base_nuts.1


description: LCH sorted CD207+, BRAFi treated, biological paired sample 4 Gene Expression


title: CP19_LN2

source_name: Patient CP19, metastatic tumor sample, lymph node 2

value: Colon cancer tumor CP19, metastasis , lymph node 2


title: PWBC_base_nuts.4


title: CP18_LN5

source_name: Patient CP18, metastatic tumor sample, lymph node 5

value: female

value: Colon cancer tumor CP18, metastasis , lymph node 5


title: CP18_T1

source_name: Patient CP18, primary tumor sample, location 1

value: Colon cancer tumor CP18, primary , location 1


description: LCH sorted CD207+, DMSO treated, biological paired sample 2 Gene Expression


description: LCH sorted CD207+, DMSO treated, biological paired sample 1 Gene Expression


description: LCH sorted CD207+, MEKi treated, biological paired sample 1 Gene Expression


title: CP18_LN8

source_name: Patient CP18, metastatic tumor sample, lymph node 8

value: Colon cancer tumor CP18, metastasis , lymph node 8


title: CP18_LN6

source_name: Patient CP18, metastatic tumor sample, lymph node 6

value: Colon cancer tumor CP18, metastasis , lymph node 6


title: PWBC_base_lowfat.5

value: Female

value: Low-fat diet


description: LCH sorted CD207+, BRAFi treated, biological paired sample 1 Gene Expression

value: Langerhans cell histiocytosis lesion


description: LCH sorted CD207+, DMSO treated, biological paired sample 4 Gene Expression

value: DMSO


title: CP19_LN4

source_name: Patient CP19, metastatic tumor sample, lymph node 4

value: Colon cancer tumor CP19, metastasis , lymph node 4


title: CP18_LN7

source_name: Patient CP18, metastatic tumor sample, lymph node 7

value: Colon cancer tumor CP18, metastasis , lymph node 7


title: CP15_LN2

source_name: Patient CP15, metastatic tumor sample, lymph node 2

value: male

value: Colon cancer tumor CP15, metastasis , lymph node 2

value: Cecum


title: CP17_LN1

source_name: Patient CP17, metastatic tumor sample, lymph node 1

value: Colon cancer tumor CP17, metastasis , lymph node 1

value: Sigmoid

value: FFPE


title: CP14_LN7

source_name: Patient CP14, metastatic tumor sample, lymph node 7

value: Colon cancer tumor CP14, metastasis , lymph node 7


title: CP14_LN9

source_name: Patient CP14, metastatic tumor sample, lymph node 9

value: Colon cancer tumor CP14, metastasis , lymph node 9


title: CP17_T1

source_name: Patient CP17, primary tumor sample, location 1

value: Colon cancer tumor CP17, primary , location 1

value: fresh frozen


title: CP14_LN2

source_name: Patient CP14, metastatic tumor sample, lymph node 2

value: Colon cancer tumor CP14, metastasis , lymph node 2


title: CP15_LN3

source_name: Patient CP15, metastatic tumor sample, lymph node 3

value: Colon cancer tumor CP15, metastasis , lymph node 3


title: CP19_T2

source_name: Patient CP19, primary tumor sample, location 2

value: Colon cancer tumor CP19, primary , location 2


title: CP17_T2

source_name: Patient CP17, primary tumor sample, location 2

value: Colon cancer tumor CP17, primary , location 2


title: PWBC_base_lowfat.2

source_name: Peripheral white blood cells baseline low-fat

value: Female

value: Low-fat diet


description: LCH sorted CD207+, BRAFi treated, biological paired sample 2 Gene Expression

source_name: Langerhans Cell Histiocytosis Lesion - Sorted CD207+ Cells

value: Langerhans cell histiocytosis lesion

value: BRAFi


title: CP17_LN7

source_name: Patient CP17, metastatic tumor sample, lymph node 7

value: male

value: Colon cancer tumor CP17, metastasis , lymph node 7


title: CP15_T1

source_name: Patient CP15, primary tumor sample, location 1

value: Colon cancer tumor CP15, primary , location 1

value: Cecum


title: CP15_T2

source_name: Patient CP15, primary tumor sample, location 2

value: Colon cancer tumor CP15, primary , location 2


title: CP11_LN7

source_name: Patient CP11, metastatic tumor sample, lymph node 7

value: Colon cancer tumor CP11, metastasis , lymph node 7

value: FFPE


title: PWBC_base_EVOO.1

source_name: Peripheral white blood cells baseline MedDiet+EVOO

value: MedDiet+EVOO


title: CP11_LN1

source_name: Patient CP11, metastatic tumor sample, lymph node 1

value: Colon cancer tumor CP11, metastasis , lymph node 1


title: PWBC_base_lowfat.4


title: CP11_T1

source_name: Patient CP11, primary tumor sample, location 1

value: Colon cancer tumor CP11, primary , location 1

value: fresh frozen


title: CP14_T2

source_name: Patient CP14, primary tumor sample, location 2

value: Colon cancer tumor CP14, primary , location 2


title: PWBC_base_EVOO.2


title: CP14_T3

source_name: Patient CP14, primary tumor sample, location 3

value: Colon cancer tumor CP14, primary , location 3


title: CP14_T1

source_name: Patient CP14, primary tumor sample, location 1

value: Colon cancer tumor CP14, primary , location 1


title: CP11_LN6

source_name: Patient CP11, metastatic tumor sample, lymph node 6

value: Colon cancer tumor CP11, metastasis , lymph node 6


title: PWBC_base_lowfat.3

value: Female

value: Low-fat diet


title: CP08_T1

source_name: Patient CP08, primary tumor sample, location 1

value: male

value: Colon cancer tumor CP08, primary , location 1

value: Transverse colon


title: CP08_T2

source_name: Patient CP08, primary tumor sample, location 2

value: Colon cancer tumor CP08, primary , location 2


title: CP11_T2

source_name: Patient CP11, primary tumor sample, location 2

value: Colon cancer tumor CP11, primary , location 2

value: Cecum


description: LCH sorted CD207+, MEKi treated, biological paired sample 2 Gene Expression

value: Langerhans cell histiocytosis lesion

value: MEKi


title: PEO1 CD90- CD133- Replicate 4

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

description:
289-1
Replicate 4

hyb_protocol: Fragmentized cRNA was hybridized to the GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). Washing and staining were performed using the Affymetrix Fluidics Station 450 as per manufacturer specifications.

scan_protocol: Microarrays were scanned on the Affymetrix GeneChip Scanner 3000.

data_processing: The intensity for a transcript is based by using Lowess (Yang et al., 2003) on the original probe intensities for the transcript (CEL files) and then the transcript intensities were used for normalization between different samples using Correlation method (Chua et al., 2006, PMID 16528099).

source_name: CD90- CD133- PEO1 Human Ovarian Cancer Cells

label_protocol: Biotin-labelled cRNA was prepared from total RNA samples according to the standard Affymetrix protocol.

growth_protocol: Cells were maintained in RPMI-1640 (Nacalai Tesque) containing 10% FBS (Sigma-Aldrich).

extract_protocol: Total RNA was extracted from all cells using the Absolutely RNA Nanoprep kit (Agilent) according to manufacturer instructions. RNA quality was assessed on the 2100 Bioanalyser (Agilent) using the RNA 6000 Nano Chip kit (Agilent) for intact 18S and 28S ribosomal peaks without significant degradation (RNA Integrity Number >8).

treatment_protocol: Trypsinised parental PEO1 cells were stained with anti-CD90-PE (Beckman Coulter), anti-CD133-APC (Miltenyi) antibodies and Sytox-blue dye (Thermo Fischer) according to company protocols and underwent cell sorting with the BD FACSAria cell sorter.

tag: cell line

value: Ovarian cancer cell line

tag: cd90 expression

tag: cd133 expression


title: PEO1 CD90- CD133- Replicate 2

description:
270-1
Replicate 2


title: PEO1 CD90+ CD133+ Replicate 2

description:
270-3R
Replicate 2

source_name: CD90+ CD133+ PEO1 Human Ovarian Cancer Cells


title: PWBC_base_lowfat.1

source_name: Peripheral white blood cells baseline low-fat


title: PEO1 CD90- CD133- Replicate 5

description:
289-4
Replicate 5


title: PEO1 CD90+ CD133- Replicate 3

description:
286-2
Replicate 3

source_name: CD90+ CD133- PEO1 Human Ovarian Cancer Cells


title: Medulloblastoma_Crebbp_knockout_rep3

city: Boston

first: Daniel

middle: Josef

last: Merk

state: MA

address: 450 Brookline Ave, Smith 1050

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description:
Math1CreERT2CrebbpSmoM2-3
Gene expression data from murine medulloblastoma with Crebbp knockout

hyb_protocol: Biotinylated fragmented ssDNA was hybridized onto the GeneChip® Mouse Gene 2.0 ST Array (Affymetrix) according to the manufacturer's recommendation. The hybridization was performed for 16 h at 45°C in the GeneChip® Hybridization Oven 640 (Affymetrix). Washing and staining of the arrays were done on the Gene Chip® Fluidics Station 450 (Affymetrix) according to the manufacturer's recommendation.

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed using R/Bioconductor, generating the RMA expression values with the oligo package.

organism: Mus musculus

label_protocol: For each experimental sample RNA quality was assessed by NanoDrop ND-1000 Spectrophotometer. The labeling reaction was performed by using the GeneChip® WT PLUS Reagent Kit from Affymetrix (Cat N° 902281) following manufacturer´s instructions.

growth_protocol: All animals were housed in cages in an animal facility, with water and food ad libitum.

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

treatment_protocol: All animal received an i.p. injection of 1mg tamoxifen, resuspended in corn oil, at postnatal day 5. Animals with clear tumor growth were sacrificed at postnatal day 60, and tumor tissue was collected.

tag: genotype/variation

value: postnatal day 5

value: medulloblastoma


title: PEO1 CD90+ CD133- Replicate 5

description:
289-5
Replicate 5


title: PEO1 CD90+ CD133+ Replicate 1

description:
255-3
Replicate 1


title: PEO1 CD90+ CD133+ Replicate 3

description:
286-3
Replicate 3


title: PEO1 CD90+ CD133+ Replicate 5

description:
289-6
Replicate 5


title: PEO1 CD90- CD133- Replicate 3

description:
286-1
Replicate 3


title: PEO1 CD90+ CD133+ Replicate 4

description:
289-3
Replicate 4


title: PEO1 CD90+ CD133- Replicate 2

description:
270-2R
Replicate 2


title: Medulloblastoma_Crebbp_wild_type_rep2

description:
Math1CreERT2SmoM2-2
Gene expression data from murine medulloblastoma with Crebbp wild type


title: Medulloblastoma_Crebbp_wild_type_rep1

description:
Math1CreERT2SmoM2-1
Gene expression data from murine medulloblastoma with Crebbp wild type


title: Medulloblastoma_Crebbp_knockout_rep1

description:
Math1CreERT2CrebbpSmoM2-1
Gene expression data from murine medulloblastoma with Crebbp knockout


title: Cerebellum_Crebbp_knockout_rep1

description:
Gene expression data from murine cerebellum with Crebbp knockout
Math1CreCrebbp-1

treatment_protocol: All animals were sacrificed at postnatal day 7, and cerebellar tissue was collected.

value: Crebbp knockout; Math1Cre::CrebbpFl/Fl

value: postnatal day 7

value: cerebellum


title: Medulloblastoma_Crebbp_wild_type_rep3

description:
Math1CreERT2SmoM2-3
Gene expression data from murine medulloblastoma with Crebbp wild type


title: Cerebellum_Crebbp_knockout_rep3

description:
Gene expression data from murine cerebellum with Crebbp knockout
Math1CreCrebbp-3


title: Cerebellum_Crebbp_wild_type_rep1

description:
Gene expression data from murine cerebellum with Crebbp wild type
Math1Cre-1

value: Crebbp wild type; Math1Cre


title: PEO1 CD90- CD133- Replicate 1

description:
255-1
Replicate 1


title: Cerebellum_Crebbp_knockout_rep2

description:
Gene expression data from murine cerebellum with Crebbp knockout
Math1CreCrebbp-2


title: Cerebellum_Crebbp_wild_type_rep2

description:
Gene expression data from murine cerebellum with Crebbp wild type
Math1Cre-2


title: PEO1 CD90+ CD133- Replicate 4

description:
289-2
Replicate 4


title: 3- Aml12-Zfp125

city: Chicago

first: Gustavo

middle: Werpel

last: Fernandes

state: IL

address: 5841 South Maryland Av.

department: Endocrinology

institute: University of Chicago

description: Expression Array derived from Expression Console software;

hyb_protocol: Samples were hybridized with GeneChip Mouse Exon 2.0 ST Arrays (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing: Raw data were processed with theExpression Console, followed byCA). Gene expression data were preprocessed using Affymetrix Expression Console. Differential expression analysis was performed in Affymetrix Transcriptome Analysis Console (TAC)

label: Polya spike-AFFX-r2-Bs

source_name: AML12- Zfp125

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: AMl12-Zfp125 or AML12-EV Cells were selected using G418 - Medium.

extract_protocol: RNA obtained from cells stably expressing Zfp125 was extracted with the RNeasy Mini Kit (Qiagen) and processed for microarray at the Joslin Diabetes Center Genomics Core Laboratory (Boston, MA).

treatment_protocol: Cells were kept on Control Medium

value: Hepatocytes

tag: expression


title: 2- Aml12-Zfp125


title: 4- Aml12-Zfp125


title: 1- Aml12-Zfp125


title: 2- Aml12-EV

source_name: AML12 - EV

value: empty vector


title: 4- Aml12-EV


title: 1- Aml12-EV


title: 3- Aml12-EV


title: PEO1 CD90+ CD133- Replicate 1

description:
255-2
Replicate 1


title: CP18_T2

source_name: Patient CP18, primary tumor sample, location 2

value: female

value: Colon cancer tumor CP18, primary , location 2

value: Sigmoid

value: fresh frozen


title: 2 µM TDCIPP-exposed embryo at 6 hpf, Biological rep-1, Technical rep-1

city: Riverside

first: David

last: Volz

state: CA

address: 900 University Ave.

department: Environmental Sciences

institute: University of California, Riverside

hyb_protocol: Amplified and labeled samples were hybridized onto duplicate Zebrafish Gene 1.0 ST Arrays (Affymetrix) for 16 h at 45°C using a GeneChip Hybridization Oven 640 and a GeneChip Hybridization, Wash, and Stain Kit (Affymetrix); these arrays were constructed by Affymetrix based on the danRer6/Zv9 genome build and contained 1,255,682 probes representing 59,302 unique genes.

scan_protocol: Arrays (24 total) were then scanned using a GeneChip Scanner 3000 7G system and computer workstation equipped with GeneChip Command Console 4.0 software (Affymetrix).

data_processing: Following completion of array scans, probe cell intensity (CEL) files (24 total) were imported into Expression Console Software (Affymetrix) and processed at the gene-level using Affymetrix’s ZebGene-1_0-st library file and Robust Multichip Analysis (RMA) algorithm to generate CHP files. After confirming data quality within Expression Console, CHP files containing log2 expression signals for each probe were then imported into Transcriptome Analysis Console Software (Affymetrix) and R (www.r-project.org) to analyze treatment-specific transcriptional responses using volcano plots and one-way between-subject analysis of variance (ANOVA). Affymetrix transcript cluster IDs for differentially expressed genes with False Discovery Rates (FDR) of p < 0.1 were imported into DAVID Bioinformatics Resources 6.8 for Gene Ontology (GO) enrichment analysis against zebrafish genome assembly GRCz10.

organism: Danio rerio

source_name: Zebrafish embryos exposed to 2 µM TDCIPP from 0.75 to 6 hpf

label_protocol: Total RNA samples were amplified and biotinylated using GeneChip WT PLUS Reagent Kit (Affymetrix).  Briefly, 100 ng of total RNA per sample was reverse-transcribed into ds-cDNA using NNN random primers containing a T7 RNA polymerase promoter sequence; cDNA quality was then confirmed using an Agilent 2100 Bioanalyzer system. T7 RNA polymerase was then added to cDNA samples to amplify RNA, and then RNA was reverse-transcribed to ss-DNA and degraded using RNase H. ss-DNA molecules were then fragmented and terminally labelled with biotin.

growth_protocol: Embryos were collected and sorted based on their stages, exposed to treatment solutions in glass beakers at 0.75 hpf (2-cell stage) and incubated at 28°C under artificial light till 2 or 6 hpf.

extract_protocol: Total RNA was extracted from pooled embryos using a SV Total RNA Isolation System (Promega). After elution of RNA in 100 μL nuclease-free water, total RNA concentrations, 260/280 ratios, and 260/230 ratios were quantified using a NanoDrop ND-2000 spectrophotometer (ThermoFisher Scientific) and then stored at -80°C; total RNA quality was also confirmed using an Agilent 2100 Bioanalyzer system.

treatment_protocol: Treated with 0.1% DMSO (Control) or 2 µM TDCIPP (Treatment)

value: whole embryo

value: TDCIPP

tag: time

value: 0.75 to 6 hpf


title: 2 µM TDCIPP-exposed embryo at 6 hpf, Biological rep-3, Technical rep-1


title: 0.1% DMSO-exposed embryo at 6 hpf, Biological rep-1, Technical rep-2

source_name: Zebrafish embryos exposed to 0.1% DMSO from 0.75 to 6 hpf

value: control


title: 2 µM TDCIPP-exposed embryo at 6 hpf, Biological rep-3, Technical rep-2


title: 2 µM TDCIPP-exposed embryo at 2 hpf, Biological rep-2, Technical rep-2

source_name: Zebrafish embryos exposed to 2 µM TDCIPP from 0.75 to 2 hpf

value: 0.75 to 2 hpf


title: 0.1% DMSO-exposed embryo at 6 hpf, Biological rep-2, Technical rep-1


title: 0.1% DMSO-exposed embryo at 6 hpf, Biological rep-2, Technical rep-2


title: 0.1% DMSO-exposed embryo at 6 hpf, Biological rep-3, Technical rep-1


title: 0.1% DMSO-exposed embryo at 6 hpf, Biological rep-3, Technical rep-2


title: 2 µM TDCIPP-exposed embryo at 6 hpf, Biological rep-2, Technical rep-1


title: 2 µM TDCIPP-exposed embryo at 6 hpf, Biological rep-2, Technical rep-2


title: 0.1% DMSO-exposed embryo at 6 hpf, Biological rep-1, Technical rep-1


title: 2 µM TDCIPP-exposed embryo at 6 hpf, Biological rep-1, Technical rep-2


title: 2 µM TDCIPP-exposed embryo at 2 hpf, Biological rep-3, Technical rep-1


title: Cerebellum_Crebbp_wild_type_rep3

description:
Gene expression data from murine cerebellum with Crebbp wild type
Math1Cre-3


title: 0.1% DMSO-exposed embryo at 2 hpf, Biological rep-1, Technical rep-1

source_name: Zebrafish embryos exposed to 0.1% DMSO from 0.75 to 2 hpf


title: 2 µM TDCIPP-exposed embryo at 2 hpf, Biological rep-1, Technical rep-2


title: CP08_LN3

source_name: Patient CP08, metastatic tumor sample, lymph node 3

value: male

value: Colon cancer tumor CP08, metastasis , lymph node 3

value: Transverse colon

value: FFPE


title: Medulloblastoma_Crebbp_knockout_rep2

description:
Math1CreERT2CrebbpSmoM2-2
Gene expression data from murine medulloblastoma with Crebbp knockout

value: postnatal day 5

value: medulloblastoma


title: 0.1% DMSO-exposed embryo at 2 hpf, Biological rep-1, Technical rep-2


title: 2 µM TDCIPP-exposed embryo at 2 hpf, Biological rep-3, Technical rep-2


title: 2 µM TDCIPP-exposed embryo at 2 hpf, Biological rep-1, Technical rep-1


title: 0.1% DMSO-exposed embryo at 2 hpf, Biological rep-2, Technical rep-2


title: 0.1% DMSO-exposed embryo at 2 hpf, Biological rep-3, Technical rep-1


title: 0.1% DMSO-exposed embryo at 2 hpf, Biological rep-3, Technical rep-2


title: 2 µM TDCIPP-exposed embryo at 2 hpf, Biological rep-2, Technical rep-1


title: 0.1% DMSO-exposed embryo at 2 hpf, Biological rep-2, Technical rep-1


title: Normal lung fibroblast 2

city: Seoul

first: Hyun Sub

last: Cheong

address: #1007, Teihard Hall, Sogang Univ. Baekbum-ro 35, Mapo-gu

department: Genetic Epidemiology

country: South Korea

institute: SNP Genetics, Inc.

description: fibroblast 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio.

source_name: Lung fibroblast

label_protocol: DNAs were bisulfite covnerted with Zymo Bisulfite Conversion Kit and Cy3/Cy5 labeled DNAs were prepared using Illumina standard protocol.

extract_protocol: DNA was extracted with QIAGEN DNeasy Tissue kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Victor2.

value: fibroblast

tag: disease state

value: normal

value: Lung


title: H2O2_24

status: Public on Nov 21 2017

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

country: China

institute: College of Life Sciences, Zhejiang University

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 24 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°. The arrays were then scanned at wavelengths of 635 and 532 nm using the GenePix scanner and the GenePix Pro software using settings recommended by the manufacturer.Microarrays could be re-used approximately 4-6 times by removing the hybridized labeled DNA sequences from the oligonucleotides. Microarrays and gasket slides were stripped separately in 1x stripping buffer (10 mM potassium phosphate, pH6.6). The slides were slowly heated to the boiling point in the stripping buffer for 30-45 minutes. After stripping, they were transferred to deionized water, and then slowly removed and stored in a nitrogen cabinet. The gasket slides were centrifuged at 500 rpm to remove excess liquid. Labels on microarrays were removed prior to stripping.

scan_protocol: The data generated by GenePix Pro were exported as .gpr files and analyzed with a homemade software pipeline. Probes that were flagged by the software were deleted from the analysis.

data_processing: The data generated by GenePix Pro were exported to text files and analyzed with Microsoft Excel. The 635 nm/532 nm ratio was analyzed for each oligonucleotide. The average value of the median ratios of the control probes was calculated and used to normalize the ratios of the experimental probes to a value of 1 by dividing each probe ratio by the average control probe ratio.

organism: Saccharomyces cerevisiae

source_name: cell culture of strain HOS24

label_protocol: DNA from these colonies was labeled with Cy5, and mixed with control DNA (DNA from the strain JSC24) labeled with Cy3. The two samples were mixed and competitively hybridized to the SNP microarrays.

growth_protocol: Yeast cells were grown in YPD medium at 30 degree.

extract_protocol: Genomic DNA were prepared by standard procedures (St. Charles et al., 2012)

treatment_protocol: To allow accumulation of recombination events, 30 JSC25-1-derived isolated colonies were independently treated with H2O2 (100 mM) for 20 passages. In each passage, cells were treated with 100 mM H2O2 for 1 h, washed, and then plated on YPD medium to form colonies. After 20 sequential treatments of H2O2, 30 JSC25-1-derived mutants (named as HOS1-30) from the last treatment were examined by whole genome SNP microarrays.

tag: ploidy

value: diploid strain

tag: background strain

value: JSC25-1 (also called W303-1AⅹYJM789)

source_name: cell culture of control strain JSC24

tag: strain


title: H2O2_29

source_name: cell culture of strain HOS29


title: H2O2_25

source_name: cell culture of strain HOS25


title: H2O2_26

source_name: cell culture of strain HOS26


title: H2O2_28

source_name: cell culture of strain HOS28


title: Normal lung fibroblast 4

description: fibroblast 4

tag: cell type

tag: tissue


title: H2O2_21

source_name: cell culture of strain HOS21


title: H2O2_18

source_name: cell culture of strain HOS18


title: H2O2_22

source_name: cell culture of strain HOS22


title: H2O2_16

source_name: cell culture of strain HOS16


title: H2O2_13

source_name: cell culture of strain HOS13


title: H2O2_17

source_name: cell culture of strain HOS17


title: H2O2_19

source_name: cell culture of strain HOS19


title: H2O2_30

source_name: cell culture of strain HOS30


title: H2O2_14

source_name: cell culture of strain HOS14


title: H2O2_23

source_name: cell culture of strain HOS23


title: H2O2_27

source_name: cell culture of strain HOS27


title: IPF Rapidly lung fibroblast 1-2

description: fibroblast 1-2

source_name: Lung fibroblast

value: Idiopathic pulmonary fibrosis - rapid

tag: age


title: H2O2_20

source_name: cell culture of strain HOS20

source_name: cell culture of control strain JSC24


title: IPF Rapidly lung fibroblast 1-1

description: fibroblast 1-1


title: Normal lung fibroblast 3

description: fibroblast 3


title: H2O2_15

source_name: cell culture of strain HOS15


title: IPF Slowly lung fibroblast 2-3

description: fibroblast 2-3

value: Idiopathic pulmonary fibrosis - slow


title: IPF Slowly lung fibroblast 2-2

description: fibroblast 2-2


title: Normal lung fibroblast 1

description: fibroblast 1


title: H2O2_12

source_name: cell culture of strain HOS12


title: IPF Slowly lung fibroblast 2-1

description: fibroblast 2-1


title: IPF Rapidly lung fibroblast 1-3

description: fibroblast 1-3


title: IPF Rapidly lung fibroblast 1-4

description: fibroblast 1-4


title: IPF Slowly lung fibroblast 2-4

description: fibroblast 2-4


title: H2O2_8

source_name: cell culture of strain HOS8


title: H2O2_3

source_name: cell culture of strain HOS3


title: Tumor_Mouse3

city: Madison

first: Jennifer

last: Pleiman

state: Wisconsin

address: 1111 Highland Ave

department: Genetics

institute: University of Wisconsin-Madison

hyb_protocol: Agilent One-Color Microarray-Based Gene Expression Analysis 17hrs 65 deg celcius Surehyb chamber

scan_protocol: Agilent Technologies Scanner G2505B US22502567 3um 16bit

data_processing: Agilent Feature extraction version 10.7.3.1 for background subtraction - Background and Multiplicitive detrending. Data analyzed in R using Limma.  Threshold: 1.0   Logbase: 2   Technology: Agilent.SingleColor.28005  Normalization: Quantile

source_name: colon

label_protocol: Total RNA was amplified and labeled according to manufactures instructions. Agilent One Color Microarray-Based Gene Expression Analysis Agilent low RNA input linear amplification kit, PLUS

growth_protocol: Ad lib feeding and drinking.  12hours light:12hours dark.

extract_protocol: Qiagen Qiashredder columns followed by Qiagen Allprep DNA/RNA Extraction Kit with optional on-the-column Dnase treatment

treatment_protocol: Sacrificed and dissected at 100 days, samples homogenized in RLTplus and stored at -80C

value: BTBR/Pas x C57BL/6J)F1-Min

value: colon

value: colonic adenoma

tag: genotype

value: Apc-Min/+

tag: Sex

value: 100 days


title: H2O2_9

source_name: cell culture of strain HOS9


title: H2O2_4

source_name: cell culture of strain HOS4


title: Normal_Mouse2

value: normal colonic epithelium

value: male


title: H2O2_1

source_name: cell culture of strain HOS1


title: Normal_Mouse4


title: H2O2_2

source_name: cell culture of strain HOS2


title: Normal_Mouse1


title: H2O2_5

source_name: cell culture of strain HOS5


title: H2O2_7

source_name: cell culture of strain HOS7


title: siha_shtw2_4

city: Shanghai

first: ai

middle: ping

last: jiang

address: No.151, Libing Rd., Zhangjiang Hi-tech Park, Pudong

institute: Shanghai Biotechnology Corporation

description: miRNA expression of SiHa cells with downregulation of TWIST2

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US) .

source_name: SiHa-shtw2 cells

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit without phenol (Cat # AM1561, Ambion, Austin, TX, US), following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: SiHa-tw2 cells overexpressed TWIST2 and SiHa-shtw2 cells down-expressed TWIST2 in SiHa cells, which were cultured in DMEM (Gibco) supplemented with 10% heat-inactivated FBS.

value: SiHa


title: Tumor_Mouse2


title: Normal_Mouse3


title: H2O2_11

source_name: cell culture of strain HOS11


title: Tumor_Mouse4


title: siha_tw2_10

description: miRNA expression of SiHa cells with overexpression of TWIST2

source_name: SiHa-tw2 cells


title: YB14_Ctrl

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix Mouse Gene 2.0 ST Array microarrays.  The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.

label: Biotin

source_name: adipose_previously infected mouse with PBS

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Mouse HuGene-1_0-st-v1 GeneChips (Affymetrix, Inc).  DNase treatment was included as part of isolation to remove possible contaminating DNA.  Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling.  300 ng of total RNA was used for labeling with theAmbion WT Expression Kit (cat#4411974)  and Affymetrix kit (Cat # 900652).After hybridization,  the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

extract_protocol: Trizol (Invitrogen) and RNaseazy (Qiagen) kits were used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: Naïve or previously infected mice (>4 weeks Y. pseudotuberculosis) were injected iv with YopE peptide or vehicle control and mAT was isolated at the indicated time points

value: adipose tissues

value: WT

tag: diet

value: previously infected mouse with PBS


title: YB16_Ctrl


title: YB13_Ctrl


title: Siha

description: miRNA expression of SiHa

source_name: SiHa cells


title: YB12_18hr_pep

source_name: adipose_previously infected mouse with peptide 18 hours


title: YB15_Ctrl


title: H2O2_6

source_name: cell culture of strain HOS6

source_name: cell culture of control strain JSC24


title: YB07_4hr_pep

source_name: adipose_previously infected mouse with peptide 4 hours


title: Tumor_Mouse1


title: YB03_Naive+pep

source_name: adipose_naive with peptide (from bacteria)

value: naive with peptide (from bacteria)


title: YB05_4hr_pep

value: previously infected mouse with peptide 4 hours


title: YB01_Naive+pep


title: YB11_18hr_pep

value: previously infected mouse with peptide 18 hours


title: YB06_4hr_pep


title: YB10_18hr_pep


title: YB08_4hr_pep


title: H2O2_10

source_name: cell culture of strain HOS10

value: diploid strain

value: JSC25-1 (also called W303-1AⅹYJM789)


title: YB02_Naive+pep


title: Dgcr8-/--shctrl_sample_1

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

description: expression data of Dgcr8-/- ESCs

hyb_protocol: cDNA was fragmented and 10ug hybridized to an Affymetrix GeneChip Mouse Gene 2.0 ST Array for 16 hours. Arrays were washed and stained using the Affy 450 Fluidics Station according to the manufacturer's protocol.

scan_protocol: Arrays were scanned using a GeneChip 3000 scanner according to the manufacturers recommendation.

data_processing:
Raw microarray signal intensities were robust multiarray average (RMA)-summarized and quantile-normalized using R/BioConductor.
Log2 transformed Dgcr8-/--shctrl verse Dgcr8-/--302 ESCs groups ratio

source_name: Dgcr8 knockout embryonic stem cells

label_protocol: Total RNA was isolated with the DirectZol RNA kit (Zymo Research) and cDNA were synthesized by the Verso cDNA Synthesis Kit (Thermo Fisher).

extract_protocol: Trizol isolation followed by Rneasy (Qiagen) column purification were performed according to manufacturer's specifications.

value: Dgcr8-/- ESCs

tag: shRNA

value: a control hairpin


title: Dgcr8-/--302_sample_3

description: expression data of Dgcr8-/- ESCs expressing miR-302

source_name: Dgcr8 knockout embryonic stem cells expressing mimics of miR-302


title: Dgcr8-/--shctrl_sample_2

description: expression data of Dgcr8-/- ESCs


title: Dgcr8-/--shctrl_sample_3

description: expression data of Dgcr8-/- ESCs


title: Dgcr8-/--302_sample_2


title: ExVivoWEHI231cell_4hr_0ug/ml_rep1

city: Nanjing

first: Xiu

middle: Li

last: Feng

address: No.1, Weigang

institute: Nanjing Agricultural University

description: Gene expression after 4hr in 0ug/ml BP9-treated WEHI231 cell

hyb_protocol: The synthesized Cy3-labelled cRNA was diluted in 2X GEx Hyb Buffer (HI-RPM) at 45°C for overnight following the manufacturers instructions, and then washed with 0.2% SDS，2×SSC buffer at 42°C for 5 min, and then washed in 0.2×SSC at room temperature for 5 min, and then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent G2565CA Microarray Scanner using one color scan setting for 8x60k array slides.

data_processing: The resulting text files extracted from Agilent Feature Extraction Software (version 10.5.1.1) were imported into the Agilent GeneSpring GX software (version 11.0) for further analysis. The microarray data sets were normalized with percentile shift, and detected the differential genes by Flag labeled with Absolute Fold change over 2.

source_name: WEHI231 cell, 4hr, 0ug/ml, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from total RNAs according to the manufacturer's instructions, followed by NucleoSpinExtract II Kit (MN).  Random Primer was used as the primer for KLENOW enzyme labeling with Cy3-dCTP (GE Healthcare Cat. No.PA53021).

growth_protocol: WEHI231 cells were cultured with RPMI 1640 supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen) at 37℃ with 5% CO2.

extract_protocol: Total RNAs are harvested using Trizol (Invitrogen, Gaithersburg, MD, USA) according to manufacturer’s instructions, and were purified with  NucleoSpin® RNA clean-up kit (MACHEREY-NAGEL,Germany), and then total RNAs were quantified  with spectrophotometerand quality was monitored with formaldehyde denaturing gel electrophoresis.

treatment_protocol: WEHI231 cell was treated by BP9 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated with or without 0.01ug/mL BP9 for 4 hours at 37 ºC in a humidified incubator with 5% CO2.

value: WEHI231 cells


title: Dgcr8-/--302_sample_1


title: YB04_Naive+pep


title: Staurosporine 30 nM negative

city: Washington

first: Henghong

state: DC

address: 3970 Reservoir Rd., NW

department: Biochemistry

institute: Georgetown University

description: Staurosporine 30 nM negative

hyb_protocol: Labelled cRNA samples (325 ng of cyanine-3 labelled cRNA and 325 ng of cyanine-5 labelled cRNA) were hybridized to Agilent SurePrint G3 Human GE 8x60K oligonucleotide microarrays (Agilent Catalogue No: G4851A, Agilent Microarray Design ID: 028004; Agilent Technologies, Santa Clara, CA) at 65oC for 17 hours.

scan_protocol: Slides were washed according to the manufacturer’s specifications and scanned using an Agilent G2505C DNA Microarray Scanner at 3 μm resolution. Agilent Feature Extraction (version 11.0.1.1) was used for data extraction purposes from the generated image files and to generate QC reports for each array.

data_processing: Agilent Feature Extraction version 9.1was used to background subtraction, LOWESS normalization, and calculate the signal intensities and Cy5/Cy3 ratios.

source_name: TK6 lymphoblastoid cell line

label_protocol: Gene expression profiles were generated using a two-colour dye swap design.  RNA from treated and vehicle control was labeled with Agilent Fairplay III Microarray labeling kit (Agilent, Santa Clara, CA), according to the manufacturer’s instructions.

growth_protocol: TK6 cells, a human lymphoblastoid cell line, were obtained from American Type Culture Collection (ATCC# CRL-8015; ATCC, Manassas, VA, USA). TK6 cells were maintained as described elsewhere [Ellinger-Ziegelbauer et al., 2009]. Briefly, TK6 cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum. The cell culture density was maintained at 1-10x105 cells/ml, and was tested periodically for mycoplasma contamination; all mycoplasma results were negative. Exponentially growing cells were treated at a density of 4-5x105 cells/ml.

extract_protocol: RNA was extracted using the Trizol protocol (Invitrogen) followed by RNA cleanup with an RNeasy column (Qiagen). Total RNA was quantified and assessed for purity and integrity using a NanoDrop® ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer. Only high quality total RNA samples, with RNA Integrity Numbers (RINs) ranging from 8.6 to 10 and A260/280 absorbance ratios >2.0 were used for gene expression analysis.

treatment_protocol: TK6 cells were exposed to the compounds of the indicated concentration, which was previously identified as either responsive or the high concentration. At the end of each 4h exposure, the exposed and vehicle control  cells were harvested for RNA extraction.

tag: treatment

value: Staurosporine

tag: concentration

value: 30 nM

tag: group

value: treatment

value: vehicle control


title: Sunitinib 20 uM positive

description: Sunitinib 20 uM positive

value: Sunitinib

value: 20 uM


title: Sorafenib 20 uM positive

description: Sorafenib 20 uM positive

value: Sorafenib


title: Topotecan 400 nM negative

description: Topotecan 400 nM negative

value: Topotecan


title: YB09_18hr_pep

value: adipose tissues

value: WT


title: ExVivoWEHI231cell_4hr_0.01ug/ml_rep1

description: Gene expression after 4hr in 0.01ug/ml BP9-treated WEHI231 cell

source_name: WEHI231 cell, 4hr, 0.01ug/ml, replicate 1


title: Olmesartan  0.16 uM negative

description: Olmesartan  0.16 uM negative

value: Olmesartan


title: Progesterone 1 mM positive

description: Progesterone 1 mM positive

value: Progesterone

value: 1 mM


title: Phenobarbital 1 mM negative

description: Phenobarbital 1 mM negative

value: Phenobarbital


title: Nocodazole 30 uM positive

description: Nocodazole 30 uM positive

value: Nocodazole

value: 30 uM


title: Rabeprazole 0.8 uM positive

description: Rabeprazole 0.8 uM positive

value: Rabeprazole


title: Norfloxacin 1 mM positive

description: Norfloxacin 1 mM positive

value: Norfloxacin


title: Staurosporine 30 nM positive

description: Staurosporine 30 nM positive

value: Staurosporine

value: 30 nM


title: Progesterone 1 mM negative

description: Progesterone 1 mM negative

value: treatment

value: vehicle control


title: Nitrogen Mustard 200 nM negative

description: Nitrogen Mustard 200 nM negative

value: Nitrogen Mustard


title: Rotigotin 100 uM positive

description: Rotigotin 100 uM positive

value: Rotigotin


title: Nocodazole 30 uM negative

description: Nocodazole 30 uM negative


title: Olmesartan 0.16 uM positive

description: Olmesartan 0.16 uM positive


title: Methyl Carbamate 1 mM positive

description: Methyl Carbamate 1 mM positive

value: Methyl Carbamate


title: Melamine 1 mM negative

description: Melamine 1 mM negative

value: Melamine


title: Sorafenib 20 uM negative

description: Sorafenib 20 uM negative

value: Sorafenib

value: 20 uM


title: N butyl chloride 1 mM positive

description: N butyl chloride 1 mM positive

value: N butyl chloride


title: Norfloxacin 1 mM negative

description: Norfloxacin 1 mM negative

value: 1 mM


title: Rotigotin 100 uM negative

description: Rotigotin 100 uM negative


title: Rabeprazole 0.8 uM negative

description: Rabeprazole 0.8 uM negative


title: MMC 10 uM negative

description: MMC 10 uM negative

value: MMC

value: 10 uM


title: Imatinib 400 uM positive

description: Imatinib 400 uM positive

value: Imatinib


title: Phenobarbital 1 mM positive

description: Phenobarbital 1 mM positive

value: Phenobarbital


title: Hydroquinone 20 uM positive

description: Hydroquinone 20 uM positive

value: Hydroquinone


title: Melamine 1 mM positive

description: Melamine 1 mM positive


title: Methyl Carbamate 1 mM negative

description: Methyl Carbamate 1 mM negative


title: N butyl chloride 1 mM negative

description: N butyl chloride 1 mM negative


title: Genistein 20 uM negative

description: Genistein 20 uM negative

value: Genistein


title: Nitrogen Mustard 200 nM positive

description: Nitrogen Mustard 200 nM positive


title: Sunitinb 20 uM negative

description: Sunitinb 20 uM negative

value: Sunitinb


title: Hydroquinone 20 uM negative

description: Hydroquinone 20 uM negative

value: treatment


title: Imatinib 400 uM negative

description: Imatinib 400 uM negative

value: vehicle control


title: MMC 10 uM positive

description: MMC 10 uM positive


title: Genistein 20 uM positive

description: Genistein 20 uM positive


title: Topotecan 400 nM positive

description: Topotecan 400 nM positive

value: Topotecan


title: Esomeprazole 200 uM positive

description: Esomeprazole 200 uM positive

value: Esomeprazole


title: Dexamethasone 1 mM negative

description: Dexamethasone 1 mM negative

value: Dexamethasone


title: Ciprofloxacin 100 uM negative

description: Ciprofloxacin 100 uM negative

value: Ciprofloxacin


title: EMS 2 mM negative

description: EMS 2 mM negative

value: EMS

value: 2 mM


title: Esomeprazole 200 uM negative

description: Esomeprazole 200 uM negative


title: Erythromycin 500 uM negative

description: Erythromycin 500 uM negative

value: Erythromycin


title: Cycloheximide positive

description: Cycloheximide positive

value: Cycloheximide


title: D-Mannitol 1 mM negative

description: D-Mannitol 1 mM negative

value: D-Mannitol

value: 1 mM


title: Diethylstilbestrol 40 uM negative

description: Diethylstilbestrol 40 uM negative

value: Diethylstilbestrol

value: 40 uM


title: Dexamethasone 1 mM positive

description: Dexamethasone 1 mM positive


title: Ciprofloxacin 100 uM positive

description: Ciprofloxacin 100 uM positive


title: EMS 2 mM positive

description: EMS 2 mM positive


title: Dasatinib 20 uM negative

description: Dasatinib 20 uM negative

value: Dasatinib

value: 20 uM


title: Doxorubicin 1.2 uM negative

description: Doxorubicin 1.2 uM negative

value: Doxorubicin


title: D-Mannitol 1 mM positive

description: D-Mannitol 1 mM positive

value: treatment


title: Doxorubicin 1.2 uM positive

description: Doxorubicin 1.2 uM positive

value: vehicle control


title: ENU 500 uM negative

description: ENU 500 uM negative

value: ENU


title: Cycloheximide negative

description: Cycloheximide negative

value: 10 uM


title: Gefitinib 100 uM negative

description: Gefitinib 100 uM negative

value: Gefitinib


title: Gefitinib 100 uM positive

description: Gefitinib 100 uM positive


title: Donepezil 1 mM negative

description: Donepezil 1 mM negative

value: Donepezil


title: Donepezil 1 mM positive

description: Donepezil 1 mM positive


title: Diethanolamine 1 mM negative

description: Diethanolamine 1 mM negative

value: Diethanolamine


title: Diethanolamine 1 mM positive

description: Diethanolamine 1 mM positive


title: Erythromycin 500 uM positive

description: Erythromycin 500 uM positive


title: ENU 500 uM positive

description: ENU 500 uM positive


title: Exemastan 100 uM negative

description: Exemastan 100 uM negative

value: Exemastan


title: Dasatinib 20 uM positive

description: Dasatinib 20 uM positive


title: Diethylstilbestrol 40 uM positive

description: Diethylstilbestrol 40 uM positive


title: Busulfan 20 uM negative

description: Busulfan 20 uM negative

value: Busulfan


title: Busulfan 20 uM positive

description: Busulfan 20 uM positive


title: AZT 1 mM positive

description: AZT 1 mM positive

value: AZT


title: AZT 1 mM negative

description: AZT 1 mM negative


title: Bleomycin 10 uM negative

description: Bleomycin 10 uM negative

value: Bleomycin


title: 5FU 400 uM negative

description: 5FU 400 uM negative


title: 5FU 400 uM positive

description: 5FU 400 uM positive


title: Ampicillin 1 mM negative

description: Ampicillin 1 mM negative

value: Ampicillin

value: 1 mM


title: 24DNP 1 mM positive

description: 24DNP 1 mM positive


title: 6MP 1 mM positive

description: 6MP 1 mM positive


title: Chlorambucil 4 uM positive

description: Chlorambucil 4 uM positive

value: Chlorambucil

value: 4 uM


title: Ampicillin 1 mM positive

description: Ampicillin 1 mM positive


title: 6MP 1 mM negative

description: 6MP 1 mM negative


title: 6-TG 4 uM negative

description: 6-TG 4 uM negative


title: Chlorambucil 4 uM negative

description: Chlorambucil 4 uM negative


title: Benomyl 1 mM positive

description: Benomyl 1 mM positive

value: Benomyl


title: Bleomycin 10 uM positive

description: Bleomycin 10 uM positive


title: O7_3

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 7 replicate 3

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: Data processed using limma package in R version 3.2.0

source_name: genomic RNA from CD73+CD90+CD105+ WJ MSC

growth_protocol: WJ-MSCs were grown on plastic in 10% FBS/DMEM

extract_protocol: genomic RNA was extracted using Qiagen columns; each sample of 100 ng/μl RNA

value: Multipotent, undifferentiated CD73+CD90+CD105+ WJ MSC

value: obese

tag: donor

tag: replicate


title: 6-TG  4 uM positive

description: 6-TG  4 uM positive

value: vehicle control

value: treatment


title: O6_3

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 6 replicate 3


title: Benomyl 1 mM negative

description: Benomyl 1 mM negative


title: O7_1

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 7 replicate 1


title: 5AzaC 10 uM negative

description: 5AzaC 10 uM negative

value: 10 uM


title: O7_2

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 7 replicate 2


title: O6_1

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 6 replicate 1


title: O6_2

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 6 replicate 2


title: O5_3

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 5 replicate 3


title: 24DNP 1 mM negative

description: 24DNP 1 mM negative


title: Exemastan 100 uM positive

description: Exemastan 100 uM positive


title: 5AzaC 10 uM positive

description: 5AzaC 10 uM positive


title: O5_1

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 5 replicate 1


title: O4_2

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 4 replicate 2


title: O1_3

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 1 replicate 3


title: O3_3

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 3 replicate 3


title: O5_2

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 5 replicate 2


title: O2_1

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 2 replicate 1


title: O1_1

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 1 replicate 1


title: N7_2

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 7 replicate 2

value: non-obese


title: O4_1

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 4 replicate 1


title: O2_3

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 2 replicate 3


title: O4_3

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor  4 replicate 3


title: O2_2

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 2 replicate 2


title: O1_2

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 1 replicate 2


title: O3_1

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 3 replicate 1


title: N7_3

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 7 replicate 3


title: N5_3

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 5 replicate 3


title: O3_2

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 3 replicate 2


title: N7_1

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 7 replicate 1


title: N4_3

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 4 replicate 3


title: N6_1

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 6 replicate 1


title: N3_3

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 3 replicate 3


title: N5_2

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 5 replicate 2


title: N6_2

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 6 replicate 2


title: N6_3

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 6 replicate 3


title: N4_2

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 4 replicate 2


title: N5_1

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 5 replicate 1


title: N3_1

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 3 replicate 1


title: N3_2

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 3 replicate 2


title: N2_2

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 2 replicate 2


title: N4_1

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 4 replicate 1


title: fumarate-limited chemostat, replicate 3

city: Wageningen

first: Ye

last: Tian

address: Stippeneng 4

department: AFSG

country: Netherlands

institute: Wageningen University

description:
US22502548_SLOT02_S01_GE2_107_Sep09_2_4
I used only one dye Cy3 to label all my samples individually, then I only hybridized one sample (one condition) on one single Array, afterwards I analysed the relative ratio between 2 samples under different condition

hyb_protocol: For each labelled sample, 600 ng of purified dye-coupled cDNA  was hybridized to the oligo-microarray at 65 ºC for 16 h following the one-colour microarray-based prokaryote analysis FairPlay III labelling protocol (Agilent Technologies, ver.1.3).

scan_protocol: Slides were scanned on an Agilent DNA Microarray Scanner G2505C

data_processing:
Outlier spots and spot intensity were extracted with Agilent Feature Extraction software version 10.7.3.1. After background subtraction, mexp and quantile normalization method for within-and inter-array normalization, respectively, were applied using the R-Bioconductor package. Moreover,  the normalized values were used of averaging probes replicates and genes replicates.
All the values are presented as transcript intensity  transformations of log2 ratio at a given limiting condition to batch condition.

organism: Desulfitobacterium hafniense Y51

source_name: fumarate-limited chemostat, replicate 3

label_protocol: Five micrograms of total RNA was first reverse-transcribed to cDNA, labelled, and purified using a FairPlay Microarray Labeling Kit according to the one-colour microarray-based prokaryote analysis FairPlay III labelling protocol (Agilent Technologies, ver.1.3).

extract_protocol: Modified version of Macaloid based RNA isolation protocol (Zoetendal et al., 2006: http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2006.05056.x/full).

tag: cultivation

value: chemostat

tag: electron acceptor (concentration)

value: Fumarate (35mM)

tag: electron donor (concentration)

value: Lactate (30mM)

tag: medium flow

tag: volume


title: ammonium-deprived, replicate 3

description:
US22502548_SLOT02_S01_GE2_107_Sep09_1_1
I used only one dye Cy3 to label all my samples individually, then I only hybridized one sample (one condition) on one single Array, afterwards I analysed the relative ratio between 2 samples under different condition

source_name: ammonium-deprived, replicate 3

value: Fumarate (65mM)

value: Lactate (40mM)


title: ammonium-deprived, replicate 2

description:
US22502548_SLOT01_S01_GE2_107_Sep09_2_2
I used only one dye Cy3 to label all my samples individually, then I only hybridized one sample (one condition) on one single Array, afterwards I analysed the relative ratio between 2 samples under different condition

source_name: ammonium-deprived, replicate 2


title: fumarate-limited chemostat, replicate 2

description:
US22502548_SLOT02_S01_GE2_107_Sep09_2_3
I used only one dye Cy3 to label all my samples individually, then I only hybridized one sample (one condition) on one single Array, afterwards I analysed the relative ratio between 2 samples under different condition

source_name: fumarate-limited chemostat, replicate 2

value: Fumarate (25mM)

value: Lactate (20mM)


title: batch culture, replicate 2

description:
US22502548_SLOT02_S01_GE2_107_Sep09_1_3
I used only one dye Cy3 to label all my samples individually, then I only hybridized one sample (one condition) on one single Array, afterwards I analysed the relative ratio between 2 samples under different condition

source_name: batch culture, replicate 2

value: batch

value: irrelevant


title: batch culture, replicate 1

description:
US22502548_SLOT02_S01_GE2_107_Sep09_1_2
I used only one dye Cy3 to label all my samples individually, then I only hybridized one sample (one condition) on one single Array, afterwards I analysed the relative ratio between 2 samples under different condition

source_name: batch culture, replicate 1


title: ammonium-deprived, replicate 1

description:
US22502548_SLOT01_S01_GE2_107_Sep09_2_1
I used only one dye Cy3 to label all my samples individually, then I only hybridized one sample (one condition) on one single Array, afterwards I analysed the relative ratio between 2 samples under different condition

source_name: ammonium-deprived, replicate 1

value: Fumarate (60mM)


title: lactate-limited chemostat, replicate 1

description:
US22502548_SLOT01_S01_GE2_107_Sep09_2_3
I used only one dye Cy3 to label all my samples individually, then I only hybridized one sample (one condition) on one single Array, afterwards I analysed the relative ratio between 2 samples under different condition

source_name: lactate-limited chemostat, replicate 1


title: N2_3

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 2 replicate 3

tag: cell type


title: lactate-limited chemostat, replicate 2

description:
US22502548_SLOT01_S01_GE2_107_Sep09_2_4
I used only one dye Cy3 to label all my samples individually, then I only hybridized one sample (one condition) on one single Array, afterwards I analysed the relative ratio between 2 samples under different condition

source_name: lactate-limited chemostat, replicate 2


title: N1_1

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 1 replicate 1


title: fumarate-limited chemostat, replicate 1

description:
US22502548_SLOT01_S01_GE2_107_Sep09_1_3
I used only one dye Cy3 to label all my samples individually, then I only hybridized one sample (one condition) on one single Array, afterwards I analysed the relative ratio between 2 samples under different condition

source_name: fumarate-limited chemostat, replicate 1

value: Fumarate (30mM)


title: N1_2

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 1 replicate 2

value: Multipotent, undifferentiated CD73+CD90+CD105+ WJ MSC


title: N1_3

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 1 replicate 3


title: N2_1

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 2 replicate 1


title: daf-2(e1370)_rep 4

status: Public on Nov 20 2017

city: Amsterdam

first: Arwen

last: Gao

address: Meibergdreef 9

institute: Academic Medical Center of Amsterdam

hyb_protocol: hybridized using the Agilent Gene Expression Hybridization Kit (Agilent Technologies)

scan_protocol: An ArrayXS-200108 with WormBase WS241 genome build (OakLabs) was used and fluorescence signals were detected by the SureScan microarray Scanner (Agilent Technologies)

data_processing: Data of all samples were quantile normalized using the ranked median quantiles as described previously in Bolstad 2003 A comparison of normalization methods for high desity oligonucleotide array data based on variance and bias. Bioinformatics. 19, 185-193

organism: Caenorhabditis elegans

source_name: daf-2 mutant_HT115_replicate 4

label_protocol: RNA was amplified and labeled using a Low Input QuickAmp Labeling Kit (Agilent Technologies)

growth_protocol: C. elegans were routinely grown and maintained on nematode growth media (NGM) at 20ºC. Worms of each strain were cultured on plates seeded with E. coli OP50, then eggs were obtained by alkaline hypochlorite treatment of gravid adults and placed onto plates seeded with E. coli HT115. At the young adult stage, each strain was collected by washing them off the culture plates with M9 buffer and the worm pellet was washed with dH2O for three times before collection in a 2 mL Eppendorf tube, snap-frozen in liquid N2 and lyophilized overnight. For RNA extraction, 500 worms/tube was collected in four replicates per worm strain

extract_protocol: Total RNA was extracted using the standard Trizol method, followed by phenol-chloroform purification and further processing by OakLabs Gmbh (Germany);In short, RNA quality and quantity was assessed after DNase clean-up using a 2100 Bioanalyzer (Agilent Technologies). All samples had a RNA integrity value of ≥7.2

tag: genotype/variation

value: daf-2 mutant (e1370)

tag: tissue

value: whole worm

tag: developmental stage

value: young adult


title: eat-2(ad465)_rep 3

source_name: eat-2 mutant_HT115_replicate 3

value: eat-2 mutant (ad465)


title: daf-2(e1370)_rep 3

source_name: daf-2 mutant_HT115_replicate 3


title: eat-2(ad465)_rep 1

source_name: eat-2 mutant_HT115_replicate 1


title: daf-2(e1370)_rep 1

source_name: daf-2 mutant_HT115_replicate 1


title: daf-2(e1370)_rep 2

source_name: daf-2 mutant_HT115_replicate 2


title: Neutrophil-derived Ezh2-/- HoxB8-ER cells replicate 1

status: Public on Nov 18 2017

city: La Jolla

first: RAFAEL

last: BEJAR

address: 3855 Heatlh Sciences Dr

department: MOORES CANCER CENTER

institute: UNIVERSITY OF CALIFORNIA SAN DIEGO

hyb_protocol: Samples were hybridized at VA/VMRF Microarray and NGS Core at UCSD.

scan_protocol: Array scanning was performed at VA/VMRF Microarray and NGS Core at UCSD.

data_processing:
Differential expression analysis were subjected to One-Way Between-Subject ANOVA (impaired) algorithm and data was filtered under ANOVA p-value <0.05 and a fold change <-2 or >2.  Hierarchical cluster for the complete arrays was performed with Affymetrix Transcriptome Analysis Console Software with ANOVA p-value (all conditions) <0.001.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = MTA-1_0
program-name = Expression Console
program-version = 1.4.1.46

source_name: Ezh2-/- HoxB8-ER

label_protocol: Labeling protocol was conducted by VA/VMRF Microarray and NGS Core at UCSD following manufacturer's instructions.

growth_protocol: Bone marrow cells from Ezh2 null (Ezh2-/-) and littermate control mice (WT) were transduced with HOXB8 fused to the estrogen receptor ligand-binding domain (HOXB8-ER) to produce immortalized myeloid progenitor cells. HoxB8-ER cells were grown in the presence of 0,5µM of estradiol, which maintained them in an immortalized promyelocytic state. Estradiol was removed from media allowing cells to differentiate into neutrophils in 6 days.

extract_protocol: RNA was extracted with the NucleoSpin RNA Plus from Macherey-Nagel following manufacturer's instructions.

tag: strain background

tag: differentiation stage

value: neutrophil-derived


title: Neutrophil-derived HoxB8-ER cells + vehicle replicate 2

source_name: WT HoxB8-ER

value: Wild type; PMID:22396593

tag: treated with

value: vehicle


title: HoxB8-ER undifferentiated cells replicate 2

value: undifferentiated


title: Neutrophil-derived HoxB8-ER cells replicate 1


title: Neutrophil-derived Ezh2-/- HoxB8-ER cells replicate 2


title: Neutrophil-derived HoxB8-ER cells + vehicle replicate 1


title: Neutrophil-derived HoxB8-ER cells + GSK343 replicate 2

value: 0,5µM GSK343 for 9 days


title: eat-2(ad465)_rep 2

source_name: eat-2 mutant_HT115_replicate 2


title: Neutrophil-derived HoxB8-ER cells + GSK343 replicate 1


title: ZR-75-1_sh-LMO2

city: Tianjin

first: Wei

last: Sun

address: No.94 Weijin Road

department: School of Medicine

institute: Nankai University

description: cell were infected by lentivirus with LMO2 knocking-down cassette

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner.

data_processing: Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 12.1) for further analysis.

label_protocol: One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

growth_protocol: Cells were regularly cultured in RPMI 1640 medium supplied with 10% FBS.

extract_protocol: total RNA extraction with Trizol reagent (Invitrogen, Austin, TX, USA)

treatment_protocol: Cells were infected by packaged LMO2 overexpression, control or LMO2-shRNA lentivirus for 24 hrs. Stable cell strains were selected in medium supplemented with 2 μg/mL puromycin three days after lentiviral infection and maintained in medium supplemented with 1 μg/mL puromycin till harvested.

value: breast cancer cell line


title: SKBR-3_LMO2

description: cell were infected by lentivirus with LMO2 overexpression cassette


title: SKBR-3_ctrl

description: cell were infected by lentivirus with control cassette (EGFP)


title: 91399_Placebo_Week_8

status: Public on Nov 17 2017

city: New Orleans

first: Tianhua

last: Niu

state: Louisiana

address: 1430 Tulane Avenue #8643

department: Biochemistry and Molecular Biology

institute: Tulane University School of Medicine

description:
RNA expression data from whole blood sample
EA05064_33752_H133_Plus_91399_3

hyb_protocol: The labelled cRNAs were hybridized to the Affymetrix Human Genome U-133 Plus 2.0 (HG-U133plus2.0) arrays using standard Affymetrix hybridization, washing and staining kits according to the manufacturer's instructions by Expression Analysis Inc. (Durham, NC).

scan_protocol: GeneChips were scanned using standard Affymetrix GeneChip Scanner 3000 7G by Expression Analysis Inc. (Durham, NC).

data_processing: The data were analyzed with Bioconductor packages, such that data pre-processing and normalization were conducted by the Robust Multi-array Average (RMA) algorithm (Irizarry RA, et al., Nucleic Acids Res. 2003, PMID: 12582260).

label_protocol: Total RNAs were converted cDNAs and in vitro transcribed to biotin-labeled cRNAs according to the standard Affymetrix protocols by Expression Analysis Inc. (Durham, NC).

growth_protocol: This study was based on a previously published double-blind, multi-center, placebo-controlled, randomized, parallel-group study among 140 METH-dependent outpatients that were treated by either topiramate (N = 69) or placebo (N = 71) for 13 weeks (a dose titration phase: weeks 1-5; a maintenance phase: weeks 6-12; and a taper phase: week 13).

extract_protocol: Blood for RNA isolation were collected at approximately the same time of day for each individual at the three time points (i.e., baseline, Week 8, and Week 12) to control for potential circadian rhythm effects on expression. Total RNAs were extracted from the blood samples using the PAXgene Blood RNA Isolation Kit according to the manufacturer's instructions by Expression Analysis Inc. (Durham, NC).

treatment_protocol: Subjects meeting the eligibility criteria after a 14-day screening period and a baseline assessment were randomized into equivalent-size groups for oral treatment with TPM or placebo daily for 91 days (i.e., 13 weeks). There was a dose titration phase (Weeks 1-5) to a maximum tolerated dose of TPM not to exceed 200 mg/day, a maintenance phase (Weeks 6-12), and a taper phase (Week 13). To continue in the study, subjects had to maintain a minimum daily dose of 50 mg. Blood samples were collected on Day 1 (considered the baseline) and at the end of Weeks 8 and 12 from every participant who consented to participate in the genetics/expression study.

tag: individual id

tag: gender

value: Male

tag: age

tag: race

value: White

tag: ethnicity

value: Non-Hispanic

tag: treatment

value: Placebo

tag: time point

value: Week 8

value: whole blood


title: Ezh2-/- HoxB8-ER undifferentiated cells replicate 1


title: 91842_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_33699_H133_Plus_91842_2

value: Baseline


title: 91556_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_33832_H133_Plus_91556_3


title: 91562_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_33435_H133_Plus_91562_2

value: Female

value: Topiramate


title: 91389_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_33320_H133_Plus_91389_3

value: Hispanic


title: eat-2(ad465)_rep 4

source_name: eat-2 mutant_HT115_replicate 4

value: eat-2 mutant (ad465)

value: whole worm

value: young adult


title: Ezh2-/- HoxB8-ER undifferentiated cells replicate 2


title: Neutrophil-derived HoxB8-ER cells replicate 2

value: Wild type; PMID:22396593

value: neutrophil-derived


title: 91842_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_34701_H133_Plus_91842_3


title: HoxB8-ER undifferentiated cells replicate 1

value: undifferentiated


title: ZR-75-1_ctrl

value: breast cancer cell line


title: 91186_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31764_H133_Plus_91186_2

value: Male


title: 91186_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_33107_H133_Plus_91186_3

value: White


title: 91389_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_32645_H133_Plus_91389_2


title: 91186_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_33697_H133_Plus_91186_4

value: Non-Hispanic

value: Week 12


title: 91191_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_33626_H133_Plus_91191_4


title: 91041_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_32994_H133_Plus_91041_4

value: Placebo


title: 88970_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_31716_H133_Plus_88970_3

value: Week 8

value: whole blood


title: 88970_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31161_H133_Plus_88970_2

value: Baseline


title: 91191_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31765_H133_Plus_91191_2

value: Female

value: Topiramate


title: 89418_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31163_H133_Plus_89418_2

value: Hispanic


title: 88880_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_31078_H133_Plus_88880_4


title: 91399_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_32646_H133_Plus_91399_2


title: 91041_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31474_H133_Plus_91041_2


title: 91185_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_33005_H133_Plus_91185_3


title: 91185_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31739_H133_Plus_91185_2


title: 91191_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_32995_H133_Plus_91191_3


title: 91041_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_32607_H133_Plus_91041_3


title: 89190_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_31717_H133_Plus_89190_3


title: 89190_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31086_H133_Plus_89190_2


title: 89030_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31158_H133_Plus_89030_2


title: 88880_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31073_H133_Plus_88880_2


title: 89418_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_31001_H133_Plus_89418_4


title: 89084_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31079_H133_Plus_89084_2


title: 77440_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_35134_H133_Plus_77440_4


title: 89007_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31160_H133_Plus_89007_2


title: 77440_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_32212_H133_Plus_77440_2


title: 77440_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_35133_H133_Plus_77440_3


title: 89190_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_31900_H133_Plus_89190_4


title: 88970_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_31899_H133_Plus_88970_4


title: 77307_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_30645_H133_Plus_77307_2


title: 77269_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31092_H133_Plus_77269_2

value: Unknown


title: 77238_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31166_H133_Plus_77238_2


title: 77173_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31091_H133_Plus_77173_2


title: 76573_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_31168_H133_Plus_76573_3


title: 76483_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31069_H133_Plus_76483_2


title: 67471_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_35658_H133_Plus_67471_2


title: 77388_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31701_H133_Plus_77388_2


title: 76573_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31093_H133_Plus_76573_2


title: 91556_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_32801_H133_Plus_91556_2


title: 77236_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31461_H133_Plus_77236_2


title: 66753_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_33696_H133_Plus_66753_4


title: 66715_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31514_H133_Plus_66715_2


title: 67466_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_39759_H133_Plus_67466_4


title: 76673_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31473_H133_Plus_76673_2


title: 76573_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_31702_H133_Plus_76573_4


title: 66714_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_34315_H133_Plus_66714_4


title: 66753_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_33106_H133_Plus_66753_3


title: 66715_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_32725_H133_Plus_66715_3


title: 66753_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31850_H133_Plus_66753_2


title: 66714_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_33695_H133_Plus_66714_3


title: 66715_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_33025_H133_Plus_66715_4


title: 67466_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_35317_H133_Plus_67466_2


title: 66649_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_37455_H133_Plus_66649_4


title: 66714_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_32606_H133_Plus_66714_2


title: 66649_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_36747_H133_Plus_66649_3


title: 66649_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_35078_H133_Plus_66649_2


title: 66644_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31246_H133_Plus_66644_2


title: 67466_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_37456_H133_Plus_67466_3


title: 66630_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_34314_H133_Plus_66630_4


title: 66598_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_31157_H133_Plus_66598_4


title: 66562_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31083_H133_Plus_66562_2


title: 77138_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31460_H133_Plus_77138_2


title: 66630_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31920_H133_Plus_66630_2


title: 66598_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31070_H133_Plus_66598_2


title: 66562_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_31479_H133_Plus_66562_3


title: 66521_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31495_H133_Plus_66521_2


title: 66397_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_31898_H133_Plus_66397_3


title: 66397_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_32800_H133_Plus_66397_4


title: 66397_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31154_H133_Plus_66397_2


title: 66258_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_37454_H133_Plus_66258_4


title: 66360_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_32605_H133_Plus_66360_2


title: 66258_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_36746_H133_Plus_66258_3


title: 66518_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_31082_H133_Plus_66518_3


title: 66258_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_35077_H133_Plus_66258_2


title: 66360_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_33693_H133_Plus_66360_3


title: 66146_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31071_H133_Plus_66146_2


title: 66360_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_34313_H133_Plus_66360_4


title: 66562_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_31763_H133_Plus_66562_4


title: 66518_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_31087_H133_Plus_66518_4


title: 66186_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31085_H133_Plus_66186_2


title: 67471_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_37457_H133_Plus_67471_3


title: 66186_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_31803_H133_Plus_66186_4


title: 66186_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_31494_H133_Plus_66186_3


title: 66109_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_31721_H133_Plus_66109_4


title: 66630_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_33694_H133_Plus_66630_3


title: 66109_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_30534_H133_Plus_66109_2


title: 66082_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_32724_H133_Plus_66082_4


title: 206PNJ

city: Malaga

first: Angela

last: Santonja

state: Malaga

address: Campus de teatinos s/n

department: Hospital Universitario Virgen de la Victoria

institute: Instituto de Investigación Biomédica de Málaga (IBIMA)

description: Gene expression data from pretreatment biopsies of a triple negative breast cancer patient

hyb_protocol: Sample was hybridized to Affymetrix Human Transcriptome Array 2.0 array using a Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were using the RMA algorithm

source_name: Total RNA from pretreatment biopsies of a triple negative breast cancer patient

label_protocol: 200ng of total RNA from each sample was amplified and labelled according to the Affymetrix SensationPlus FFPE protocol

extract_protocol: RNA was extracted with the RNeasy FFPE Kit (Qiagen) from 3-6 sections of 10µm formalin-fixed paraffin-embedded tumor tissue

value: breast cancer

value: Anthracyclines and/or taxanes

tag: pathological complete response

value: yes


title: 201PNJ


title: 207PNJ


title: 199PNJ

value: Anthracyclines and/or taxanes + carboplatin


title: 66082_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_31912_H133_Plus_66082_3


title: 66086_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31153_H133_Plus_66086_2


title: 202PNJ

value: no


title: 200PNJ


title: 203PNJ


title: 66020_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_33105_H133_Plus_66020_3


title: 66082_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31244_H133_Plus_66082_2

value: Male


title: 65982_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_33024_H133_Plus_65982_3

value: White


title: 194PNJ


title: 66020_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31851_H133_Plus_66020_2

value: Non-Hispanic


title: 197PNJ


title: 66020_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_33692_H133_Plus_66020_4

value: Week 12


title: 65982_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31722_H133_Plus_65982_2

value: Placebo


title: 198PNJ


title: 44060_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_50895_H133_Plus_44060_4


title: 195PNJ


title: 44060_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_39790_H133_Plus_44060_3

value: Week 8


title: 191PNJ


title: 44060_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_37459_H133_Plus_44060_2

value: whole blood


title: 192PNJ


title: 65982_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_33691_H133_Plus_65982_4


title: 193PNJ


title: 44058_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_34934_H133_Plus_44058_2

value: Baseline


title: 190PNJ


title: 186PNJ


title: 43997_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_36359_H133_Plus_43997_4


title: 43997_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_35646_H133_Plus_43997_3


title: 187PNJ


title: 184PNJ


title: 44019_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_35075_H133_Plus_44019_2

value: Female


title: 182PNJ

description: Gene expression data from pretreatment biopsies of a triple negative breast cancer patient


title: 43997_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_34271_H133_Plus_43997_2

value: Topiramate


title: 179PNJ


title: 43960_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_36784_H133_Plus_43960_4


title: 180PNJ


title: 173PNJ


title: 185PNJ


title: 43923_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_33445_H133_Plus_43923_2


title: 43923_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_34933_H133_Plus_43923_4


title: 44019_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_37044_H133_Plus_44019_3


title: 43905_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_34932_H133_Plus_43905_4


title: 43923_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_34550_H133_Plus_43923_3


title: 178PNJ


title: 68HNVV


title: 160PNJ


title: 63V


title: 43960_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_35750_N2_H133_Plus_43960_3


title: 43905_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_33429_H133_Plus_43905_2


title: 43905_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_34549_H133_Plus_43905_3


title: 43883_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_33751_H133_Plus_43883_3


title: 138PNJ


title: 176PNJ


title: 59V


title: 43883_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_32604_H133_Plus_43883_2


title: 43880_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_32602_H133_Plus_43880_2

value: Hispanic


title: 54V


title: 60V


title: 56V


title: 55V


title: 43676_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_29546_F2_H133_Plus_43676_2


title: 43784_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_31088_H133_Plus_43784_4


title: 57V


title: 43706_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_31162_H133_Plus_43706_3


title: 62V

description: Gene expression data from pretreatment biopsies of a triple negative breast cancer patient


title: 43676_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_31243_H133_Plus_43676_3


title: 58V


title: 43706_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31075_H133_Plus_43706_2


title: 43676_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_31700_H133_Plus_43676_4


title: 49PNVV


title: 43669_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_31471_H133_Plus_43669_4


title: 43686_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31072_H133_Plus_43686_2


title: 43706_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_31472_H133_Plus_43706_4


title: 48


title: 43669_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_31089_H133_Plus_43669_3


title: 43784_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_31081_H133_Plus_43784_3


title: 43749_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31165_H133_Plus_43749_2


title: 52V


title: 54PNVV


title: 62HVV


title: 43669_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31074_H133_Plus_43669_2


title: 48V


title: 49V


title: 46


title: 43545_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_33451_H133_Plus_43545_4


title: 43484_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_32731_H133_Plus_43484_3


title: 46V


title: 43


title: 43218_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_33689_H133_Plus_43218_3


title: 40V


title: 43484_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31493_H133_Plus_43484_2


title: 42


title: 39V


title: 42V


title: 43334_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_33750_H133_Plus_43334_3


title: 43545_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31718_H133_Plus_43545_2


title: 40

description: Gene expression data from pretreatment biopsies of a triple negative breast cancer patient


title: 43218_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_34250_H133_Plus_43218_4


title: 38V


title: 45


title: 37


title: 36B


title: 39


title: 43151_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_33004_H133_Plus_43151_3


title: 43052_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31849_H133_Plus_43052_2


title: 43151_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_33509_H133_Plus_43151_4


title: 38


title: 43151_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31737_H133_Plus_43151_2


title: 43218_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31951_H133_Plus_43218_2


title: 36V


title: 35V


title: 33782_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_33442_H133_Plus_33782_3


title: 34


title: 33746_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_33759_H133_Plus_33746_4


title: 35


title: 33746_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31911_H133_Plus_33746_2


title: 33


title: 34V


title: 32


title: 33782_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31913_H133_Plus_33782_2


title: 33630_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_32424_H133_Plus_33630_2


title: 33673_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_33840_H133_Plus_33673_4


title: 31V


title: 33673_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_32156_H133_Plus_33673_2


title: 43052_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_33444_H133_Plus_43052_3


title: 33746_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_33447_H133_Plus_33746_3


title: 33617_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_35547_H133_Plus_33617_2


title: 33630_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_33995_H133_Plus_33630_4


title: 30V

description: Gene expression data from pretreatment biopsies of a triple negative breast cancer patient


title: 33673_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_33628_H133_Plus_33673_3


title: 32V


title: 33630_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_33627_H133_Plus_33630_3


title: 33V


title: 33274_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_33104_H133_Plus_33274_4


title: 43545_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_32978_H133_Plus_43545_3


title: 33244_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_31470_H133_Plus_33244_3


title: 27


title: 25


title: 26


title: 33346_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_35643_H133_Plus_33346_2


title: 24


title: 32942_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_32921_H133_Plus_32942_3


title: 30


title: 33274_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_32660_H133_Plus_33274_3


title: 33244_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_31909_H133_Plus_33244_4


title: 29V


title: 23V


title: 32942_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_33324_H133_Plus_32942_4


title: 31


title: 28V


title: 25V


title: 28B


title: 26V


title: 33119_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_37261_H133_Plus_33119_3


title: 33213_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31512_H133_Plus_33213_2


title: 33244_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31167_H133_Plus_33244_2


title: 33119_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_38356_H133_Plus_33119_4


title: 33119_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_35099_H133_Plus_33119_2


title: 32789_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31478_H133_Plus_32789_2


title: 32942_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31720_H133_Plus_32942_2


title: 32682_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31159_H133_Plus_32682_2


title: 32789_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_32483_H133_Plus_32789_3


title: 23

description: Gene expression data from pretreatment biopsies of a triple negative breast cancer patient


title: 22V


title: 21V


title: 19V


title: 18V


title: 19


title: 20V


title: 18


title: 32595_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31077_H133_Plus_32595_2


title: 32641_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_31080_H133_Plus_32641_2


title: 17V


title: 16V


title: 32568_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_31084_H133_Plus_32568_4