title: Bacteria_acid_rep2

source_name: bacterial cells, acidic shock

treatment_protocol: Cells grown overnight at 28 ºC and maintained at 28 ºC for the 30 min were used as control. For acidic shock experiments, cells grown overnight at 28 ºC were subjected to an acidic shock of pH 3 at 28 ºC for 30 min.

value: acidic shock


title: BEAS-2B, control baseline, Biological replicate3

status: Public on Dec 21 2015

type: RNA

city: Seattle

first: Richard

last: Gelinas

address: 401 Terry Avenue North

country: USA

institute: Institute for Systems Biology

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control baseline
Control_Baseline_rep3

hyb_protocol: Labeled target was hybridized overnight to Affymetrix U219-96 plates followed by washing, staining on the Affymetrix GeneTitan instrument following the manufacturer’s protocol.

scan_protocol: Scanning was also performed on the Affymetrix GeneTitan instrument following the manufacturer’s protocol.

data_processing: Cel files were preprocessed with RMA method from R/Bioconductor for background correction, quantile normalization and summarization

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: BEAS-2B, control baseline

label_protocol: Purified RNA was stored at -80°C until use in the Genechip experiments. For the Genechip experiments, 250 ng of total RNA was converted to Genechip targets using the Affymetrix HT 3’ IVT Express (Santa Clara, CA) protocol optimized for use on the Beckman Coulter Biomek FXp automation workstation (Indianapolis, IN).

growth_protocol: Human bronchial epithelial cells (BEAS-2B; ATCC® CRL-9609™) were seeded into 12-well plates at a density of 2.8 x 105 cells/well and placed overnight in the 37oC incubator with 5% CO2 and 90% humidity.

extract_protocol: Total RNA (including small RNAs) was isolated from BEAS-2B cells with QIAgen (Helden, Germany) miRNeasy Mini columns using the manufacturer’s protocol.  In brief, monolayer BEAS-2B cells were rinsed once with ice-cold phosphate buffered saline (pH 7.4) followed by extraction in QIAzol lysis reagent and brief vortexing.  Lysates were frozen at -80°C until RNA isolation.  For RNA isolation, lysates were thawed on ice and then extracted once in chloroform.  Ethanol was added to the aqueous phase of the extract and this mixture was added to RNeasy spin columns.  Columns were washed to remove contaminants and purified total RNA was eluted with nuclease-free water.  RNA quantity was determined using a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA).

treatment_protocol: On the day of infection, the rhinovirus strain RV16 (RV) and the influenza virus (IV) (H1N1, strain A/WS/33, ATCC IV-1520) stocks were removed from a -80oC freezer, and diluted in serum-free medium. After removing the cell culture medium from the BEAS-2B cells, 300 μl of the diluted virus (either RV, IV or RV+IV) was added to each well. A similar volume of medium alone was added to the control wells. A multiplicity of infection of 2 was used for each virus. All plates were incubated at 33oC with 5% CO2 and 90% humidity. All infected and uninfected (control) samples were collected at the scheduled time points (2, 4, 8, 12, 24, 36, 48, 60 and 78 hours post-infection) and processed according to a randomized schedule to minimize the possibility of experimentally induced batch effects.

tag: strain

tag: virus infection

value: uninfected

tag: virus serotype

tag: time point

value: baseline


title: Bacteria_acid_rep1

city: Evora

first: Marta

last: Laranjo

address: Apartado 94

department: ICAAM

country: Portugal

institute: Universidade de Evora

hyb_protocol: One-Color Microarray-Based Gene Expression Analysis (Agilent) - Manufacturer's protocol

data_processing: The signal intensity for each spot was extracted using QuantArray Analysis Software (GSI Lumonics). Analysis of raw data was performed using BRB-ArrayTools v3.4.0, where each gene’s measured intensity was median normalized to correct for differences in the labelling efficiency between samples. The normalized dataset was then subjected to statistical analysis and clustering using MeV software to identified the diferencially expressed genes. The same dataset was also used to calculate the M-value and Fold-change variation.

organism: Mesorhizobium japonicum MAFF 303099

label_protocol:
aRNA amplification protocol: MessageAmp™ II-Bacteria Kit (Ambion) - Manufacturer's protocol
Quick Amp Labeling Kit (Agilent) - Manufacturer's protocol

growth_protocol: 10 ml of cells with an OD(540 nm)=0.3, which corresponds to approximately 6x10exp8 cells per ml were used.

extract_protocol:
RNeasy Mini Kit (Qiagen) manufacturer's protocol
mRNA enrichment protocol: MICROBExpress™ Bacterial mRNA Enrichment Kit (Ambion) - Manufacturer's protocol

tag: treatment


title: Bacteria_acid_rep3

scan_protocol: One-Color Microarray-Based Gene Expression Analysis (Agilent) - Manufacturer's protocol


title: liver_patient_5_non_tumor_rep1 (mRNA)

city: Tokyo

first: Y-H.

last: Taguchi

state: Non-US/Canada

address: 1-13-27 Kasuga,Bukyo-ku

department: Physics

country: Japan

institute: Chuo University

description:
non-tumor
mRNA_11

hyb_protocol: For miRNA microarray, 100 ng of RNA was labeled and hybridized using the Human microRNA Microarray Kit (Rel 14.0) (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microRNA microarrays Version 1.0.For mRNA micaroarray, 100 ng of RNA was labeled and hybridized using the SurePrint G3 Human GE microarray kit (G4851B) (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microarrays.

scan_protocol: For miRNA microarray, hybridization signals were detected with Agilent DNA microarray scanner G2539B and the scanned images were analyzed using Agilent feature extraction software (v10.10.1.1). For mRNA microarray, hybridization signals were detected with Agilent DNA microarray scanner G2539A and the scanned images were analyzed using Agilent feature extraction software (v10.10.1.1).

data_processing: For miRNA and mRNA microarray, gProcessedSignal was extracted and normalized so as to have zero mean and variance of 1.

source_name: liver mRNA non-tumor part

extract_protocol: RNA was prepared using the mirVana miRNA isolation kit (Life Technologies, CA, USA) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Surgically resected hepatocellular carcinoma (HCC) samples and surrounded non-tumor samples, and cholangiocarcinoma (CCC) samples and surrounded non-tumor samples

tag: patient

value: patient 5

tag: disease state

value: CCC

tag: tissue

value: liver_non-tumor part

tag: gender

value: male

tag: age

tag: date of birth

tag: afp

tag: pivka-ii

tag: cea

tag: tumor size

tag: hospotal id


title: Quiescent hepatic stellate cell Patient L4

type: genomic

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

hyb_protocol: Hybridization done by Nimblegen as per normal service protocol. MeDIP and input DNA samples were hybridized onto Roche-Nimblegen human HG18 RefSeq 720K Promoter arrays covering 5 kb of all human promoters (C4226-00-01; www.nimblegen.com).

scan_protocol: Scanning done by Nimblegen as per normal service protocol

data_processing: log2 (MeDIP/Input) with biweight mean of values subtracted

molecule: genomic DNA

source_name: Isolated non-cultured hepatic stellate cells_IP

label_protocol: Labeling done by Nimblegen as per normal service protocol

growth_protocol: Uncultured isolated cells

extract_protocol: MeDIP was performed in duplicate from 4 µg DNA as described (Sørensen and Collas, 2009). In brief, genomic DNA was treated with 30 µg/ml RNase A for 2 h at 37oC, and fragmented to ~200-800 base pairs by sonication. Sonicated DNA was ethanol-precipitated using glycogen as a carrier and dissolved in 60 µl MilliQ H2O. Two microgram sonicated DNA were diluted in 450 µl TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA), denatured for 10 min in boiling water and immediately chilled on ice for 10 min. Fifty-one microliters of 10x IP buffer (1x: 140 mM NaCl, 10 mM Na-Phosphate, pH 7.0, 0.05% Triton X-100) and 10 µl 5-methylcytosine antibodies (Diagenode) were added and incubated for 2 h at 4oC on a rotator. Pre-washed Dynabeads® M-280 sheep anti-mouse IgG (Invitrogen) in 40 µl IP buffer were added and incubated for 2 h at 4oC on a rotator. Samples were collected by magnetic separation, washed and immune complexes digested with Proteinase K for 3 h at 50oC. DNA was extracted with phenol-chloroform isoamylalcohol, ethanol-precipitated and dissolved in 15 µl H2O overnight. Input DNA was fragmented and treated as above except that no immunoprecipitation step was performed. Precipitated and input DNA was amplified using the WGA-2 Whole Genome Amplification kit (Sigma-Aldrich) and cleaned up using the Qiagen MinElute PCR Purification kit.

treatment_protocol: Genomic DNA was fragmented by sonication to 200-500 bp in a Bioruptor (Diagenode), and methylated fragments immunoprecipitated using the anti-5-methylC antibody.

tag: cell state / treatment

value: Freshly isolated cells, frozen and processed for meDIP

tag: medip antibody

value: Diagenode MAb-5MCYT

tag: cell type

value: hepatic stellate cell

value: liver

source_name: Isolated non-cultured hepatic stellate cells_input

treatment_protocol: Genomic DNA was fragmented by sonication to 200-500 bp in a Bioruptor (Diagenode).

value: hepatic stellate cells


title: BEAS-2B, control baseline, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control baseline
Control_Baseline_rep2

tag: strain

tag: virus infection

tag: virus serotype


title: liver_patient_4_non_tumor_rep1 (mRNA)

description:
non-tumor
mRNA_8

label_protocol: For miRNA microarray, 100 ng of RNA was labeled and hybridized using the Human microRNA Microarray Kit (Rel 14.0) (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microRNA microarrays Version 1.0.For mRNA micaroarray, 100 ng of RNA was labeled and hybridized using the SurePrint G3 Human GE microarray kit (G4851B) (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microarrays.

tag: patient

value: patient 4


title: BEAS-2B, control baseline, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control baseline
Control_Baseline_rep1

tag: time point


title: liver_patient_2_non_tumor_rep1 (mRNA)

description:
non-tumor
mRNA_4

value: patient 2

tag: disease state

tag: tissue


title: liver_patient_3_non_tumor_rep1 (mRNA)

description:
non-tumor
mRNA_6

value: patient 3

tag: gender

tag: age


title: liver_patient_1_non_tumor_rep1 (mRNA)

description:
non-tumor
mRNA_2

value: patient 1

tag: histol information

value: moderate tubular

tag: date of birth

tag: afp


title: C1_M_Macrophages_Normal_Donor_1

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

description:
without bome marrow involvement
C1_M

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A_2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GCOS 4.1 (MAS 5.0 algorithm ) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

source_name: Macrophages isolated from primary long-term bone marrow culture

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from approximately 1 ug total RNA (Expression Analysis Technical Manual v2, Affymetrix).

growth_protocol: Primary long-term bone marrow cultures (Dexter et al., 1977)

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

treatment_protocol: untreated cultured cells

tag: individual

value: Normal Donor 1

tag: cell culture

value: primary long-term bone marrow cultures (LTBMC)

tag: cell population isolated from ltbmc

value: Macrophages

value: control

tag: diagnosis

value: Primary Central Nervous System Lymphoma


title: rt embryo heart_retene_14d_rep2

city: Jyväskylä

first: Eeva-Riikka

last: Vehniäinen

address: Survontie 9, POB 35

country: Finland

institute: University of Jyväskylä

description: Gene expression in hearts of rainbow trout embryos exposed to 32 µg/l retene for 14d

hyb_protocol: 600 ng  Cy-3 labeled sample was hybridized on an Agilent 8x60K custom array (Design ID 036352) in  65 C overnight using Gene Expression Hybridization kit (Agilent). The washes were performed with Gene Expression Wash Pack (Agilent) following the manufacturer's instructions.

scan_protocol: Slides were scanned with Agilent Technologies Scannerilla (G2565CA), the scan profile was AgilentG3_GX_1Color.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1 (Agilent) using protocol GE1_107_Sep09 and Grid: 036352_D_F_20110902 to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The data were normalized using quantile normalisation with limma in R

organism: Oncorhynchus mykiss

source_name: rainbow trout embryo heart, 14d, 32 µg/l retene, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 250 ng RNA using the One-Color Low Input Quick Amp Labeling (Agilent) according to the manufacturer's instructions, and processed with RNA Spike in kit  (Agilent) Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer and quality checekd with Agilent 2100 bioanalyzer RNA 6000 Nano kit.

extract_protocol: Total RNA was extracted with Trizol according to manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Newly hatched rainbow trout (O. mykiss) embryos were exposed to retene (32 µg/l) or control (0.032 % DMSO; the same concentration as in retene treatment) waters in 1 l glass bowls, 15 embryos in each bowl. 600 ml of the exposure waters was changed daily. The exposures were terminated after 1, 3, 7, and 14 days, and the hearts of the embryos were dissected under microscope and frozen in liquid nitrogen. One sample was pooled from hearts of 15 or 45 embryos (pooled from embryos in three bowls). The samples pooled from 15 hearts were used if the quality of the RNA from 45 embryos was not good enough.

value: heart

tag: number of hearts pooled for the sample

tag: developmental stage

value: embryo

tag: treatment

value: 32 µg/l retene


title: C2_M_Macrophages_Normal_Donor_2

value: Normal Donor 2

value: female

value: Iron Deficiency


title: rt embryo heart_retene_14d_rep3

source_name: rainbow trout embryo heart, 14d, 32 µg/l retene, replicate 3


title: A4_M-Macrophages_AML-Patient_4

value: Patient  4

value: AML

value: FAB:M2, karyotype:normal


title: C3_M_Macrophages_Normal_Donor_3

description:
without bome marrow involvement
C3_M

value: Normal Donor 3

value: male

value: Cutaneous Follicular Lymphoma


title: rt embryo heart_retene_14d_rep1

source_name: rainbow trout embryo heart, 14d, 32 µg/l retene, replicate 1


title: rt embryo heart_DMSO control_14d_rep3

description: Gene expression in hearts of rainbow trout embryos exposed to DMSO (used as a carrier in the experiment) for 14d

source_name: rainbow trout embryo heart, 14d, DMSO, replicate 3

value: DMSO


title: A2_M_Macrpophages_AML-Patient_6

value: Patient  6

value: primary long-term bone marrow cultures (LTBMC)


title: C4_M_Macrophages_Normal_Donor_4

description:
without bome marrow involvement
C4_M

value: Normal Donor 4

value: Macrophages

value: control

value: Marginal Zone Lymphoma


title: A3_M_Macrophages_AML-Patient_3

value: Patient  3

value: FAB:M4, karyotype:t(1;5)(p32;q35)


title: A1_M_Macrophages_AML-Patient_5

value: Patient  5

value: female


title: rt embryo heart_DMSO control_14d_rep1

source_name: rainbow trout embryo heart, 14d, DMSO, replicate 1

value: heart

value: embryo


title: rt embryo heart_retene_7d_rep3

description: Gene expression in hearts of rainbow trout embryos exposed to 32 µg/l retene for 7d

source_name: rainbow trout embryo heart, 7d, 32 µg/l retene, replicate 3

value: 32 µg/l retene


title: rt embryo heart_DMSO control_14d_rep2

source_name: rainbow trout embryo heart, 14d, DMSO, replicate 2


title: A4_F_Fibroblasts_AML-Patient_4

source_name: Fibroblasts isolated from primary long-term bone marrow culture

value: Patient  4

value: Fibroblasts

value: AML

value: FAB:M2, karyotype:normal


title: rt embryo heart_DMSO control_7d_rep3

description: Gene expression in hearts of rainbow trout embryos exposed to DMSO (used as a carrier in the experiment) for 7d

source_name: rainbow trout embryo heart, 7d, DMSO, replicate 3

value: DMSO


title: C3_F_Fibroblasts_Normal_Donor_3

description:
without bome marrow involvement
C3_F

value: Normal Donor 3

value: male

value: primary long-term bone marrow cultures (LTBMC)

value: Cutaneous Follicular Lymphoma


title: C2_F_Fibroblasts_Normal_Donor_2

value: Normal Donor 2

value: control

value: Iron Deficiency


title: C4_F_Fibroblasts_Normal_Donor_4

description:
without bome marrow involvement
C4_F

value: Normal Donor 4

value: Marginal Zone Lymphoma


title: rt embryo heart_retene_7d_rep2

source_name: rainbow trout embryo heart, 7d, 32 µg/l retene, replicate 2

value: heart


title: A2_F_Fibroblasts_AML-Patient_2

value: Patient  2

value: female

value: FAB:M5, karyotype:normal


title: C1_Fibroblasts_Normal_Donor_1

description:
without bome marrow involvement
C1_F

value: Normal Donor 1

value: Fibroblasts

value: Primary Central Nervous System Lymphoma


title: rt embryo heart_DMSO control_7d_rep2

source_name: rainbow trout embryo heart, 7d, DMSO, replicate 2

value: embryo

value: DMSO


title: A3_F_Fiboblasts_AML-Patient_3

value: Patient  3

value: AML

value: FAB:M4, karyotype:t(1;5)(p32;q35)


title: liver_patient_11_non_tumor_rep1 (mRNA)

description:
non-tumor
mRNA_22

value: patient 11

value: CCC

value: liver_non-tumor part

value: moderate tubular

tag: pivka-ii

tag: cea

tag: tumor size

tag: hospotal id


title: rt embryo heart_retene_7d_rep1

source_name: rainbow trout embryo heart, 7d, 32 µg/l retene, replicate 1

tag: tissue

value: 32 µg/l retene

tag: time point


title: rt embryo heart_retene_3d_rep2

description: Gene expression in hearts of rainbow trout embryos exposed to 32 µg/l retene for 3d

source_name: rainbow trout embryo heart, 3d, 32 µg/l retene, replicate 2

value: heart


title: SG-4

city: Toon

first: Koh-ichi

last: Nakashiro

state: Ehime

address: 454 Shitsukawa

department: Oral and Maxillofacial Surgery

institute: Ehime University Graduate School of Medicine

hyb_protocol: Ten mg of labelled cRNA was hybridized to each pre-hybridized microarray at 55℃ for 16 hours.

scan_protocol: After Chemiluminescence detection using Applied Biosystems Chemiluminescence Detection Kit, images were collected by the AB1700 Chemiluminescent Microarray Analyzer.

data_processing: The quantile method was used for background correction and normalization.

label: digoxigenin

source_name: Salivary gland

label_protocol: Digoxigenin-UTP-labelled cRNA was generated and amplified from 1 mg of total RNA using Applied Biosystems Chemiluminescent RT-IVT Labelling Kit.

extract_protocol: After fresh tissues were homogenized by TissueLyser, total RNA was extracted by ISOGEN.

value: salivary gland


title: rt embryo heart_DMSO control_7d_rep1

source_name: rainbow trout embryo heart, 7d, DMSO, replicate 1


title: SG-5


title: A1_F_Fibroblasts_AML-Patient_1

value: Patient  1

tag: age

tag: gender

value: male

value: primary long-term bone marrow cultures (LTBMC)

tag: disease state

value: FAB:M0, karyotype:normal


title: rt embryo heart_DMSO control_3d_rep3

description: Gene expression in hearts of rainbow trout embryos exposed to DMSO (used as a carrier in the experiment) for 3d

source_name: rainbow trout embryo heart, 3d, DMSO, replicate 3


title: rt embryo heart_retene_3d_rep1

source_name: rainbow trout embryo heart, 3d, 32 µg/l retene, replicate 1


title: rt embryo heart_DMSO control_3d_rep1

source_name: rainbow trout embryo heart, 3d, DMSO, replicate 1


title: rt embryo heart_DMSO control_3d_rep2

source_name: rainbow trout embryo heart, 3d, DMSO, replicate 2


title: SG-3


title: rt embryo heart_retene_3d_rep3

source_name: rainbow trout embryo heart, 3d, 32 µg/l retene, replicate 3


title: TSTPHC-020

city: Berlin

first: Jeroen

last: Maertzdorf

address: Chariteplatz 1

institute: MPIIB

scan_protocol: Custom RT2 384 well Profiler Arrays (Qiagen) were run on an ABI 7900HT 384-well block machine according to manufacturers instructions

data_processing:
Genes with Ct values >32 in at least 40% samples in both groups, and more than 50% of the samples in either group were filtered out
Raw Ct values were normalized to the mean of 4 duplicate housekeeping genes.

label: SYBR Green

source_name: whole blood

label_protocol: cDNA was synthesized using RT2 SYBR® Green qPCR Mastermix (Qiagen) according to manufacturers instructions

extract_protocol: Total RNA was isolated from PAXgene tubes according to manufacturers protocol (Qiagen)

tag: neg or pos

value: TSTpos

value: healthy

tag: cell type

value: whole blood

tag: activation agent

tag: time


title: TSTPHC-022


title: TSTPHC-023


title: TSTPHC-024


title: TSTPHC-019


title: SG-2


title: TSTPHC-018


title: metaLN-5

source_name: Lymph node with metastasis of OSCC

value: lymph node with metastasis of oral squamous cell carcinoma (OSCC)


title: TSTPHC-016


title: TSTPHC-017


title: rt embryo heart_retene_1d_rep3

description: Gene expression in hearts of rainbow trout embryos exposed to 32 µg/l retene for 1d

source_name: rainbow trout embryo heart, 1d, 32 µg/l retene, replicate 3

value: embryo


title: metaLN-1


title: SG-1


title: rt embryo heart_retene_1d_rep2

source_name: rainbow trout embryo heart, 1d, 32 µg/l retene, replicate 2


title: metaLN-6


title: rt embryo heart_retene_1d_rep1

source_name: rainbow trout embryo heart, 1d, 32 µg/l retene, replicate 1


title: metaLN-2


title: metaLN-3


title: metaLN-7


title: metaLN-4


title: LN

source_name: Normal lymph node

value: normal lymph node


title: rt embryo heart_DMSO control_1d_rep3

description: Gene expression in hearts of rainbow trout embryos exposed to DMSO (used as a carrier in the experiment) for 1d

source_name: rainbow trout embryo heart, 1d, DMSO, replicate 3

value: DMSO


title: rt embryo heart_DMSO control_1d_rep2

source_name: rainbow trout embryo heart, 1d, DMSO, replicate 2


title: Low_glucose(5mM)_rep2

city: Seoul

first: Jung Min

last: Kim

address: Gangnam-gu Teheran-ro 216

department: Department of Health Genomics

country: South Korea

institute: NAR Center, Inc. & Genoplan, Inc.

description: Gene expression after 48hrs in low glucose (5mM)-treated human RNAKT-15 cells

hyb_protocol: Complementary RNA was hybridized using the Agilent`s Gene Expression Hybridization Kit.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for array slides.

data_processing: The scanned images were analyzed Agilent's GeneSpring Software.

source_name: RNAKT-15 cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions.

growth_protocol: RNAKT-15 cells were grown in DMEM supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin, 10 mM nicotinamide, 10 μM troglitazone, and 16.7 μM zinc sulfate. Cells were cultured in humidified incubator at 37℃ and 5% CO2.

extract_protocol: RNA was prepared using theTrizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: RNAKT-15 cells were treated with low- (5mM) or high-glucose (33mM) for 48 hours.

tag: agent

tag: replicate


title: Low_glucose(5mM)_rep1


title: High_glucose(33mM)_rep3

description: Gene expression after 48hrs in high glucose (33mM)-treated human RNAKT-15 cells


title: TSTPHC-014


title: High_glucose(33mM)_rep2


title: TSTPHC-013


title: Low_glucose(5mM)_rep3


title: rt embryo heart_DMSO control_1d_rep1

source_name: rainbow trout embryo heart, 1d, DMSO, replicate 1

tag: number of hearts pooled for the sample

tag: developmental stage


title: CD, biological rep1 (gene level)

city: Chongqing

first: Jin

last: Shang

address: No. 183, Xinqiao Main Street

country: China

institute: Third Military Medical University

description: Gene expression data from human CESCs

hyb_protocol: After fragmentation, 5 ug cDNA were hybridized for 16hr at 45C in 60rpm of spanning on Human Transcriptome Array 2.0. The microarray was washed and stained using Affymetrix GeneChip Command Console (AGCC) software.

scan_protocol: The microarray was scanned using AGCC software.

data_processing: We used Expression Console software to pre-treat .CEL files through Robust Multichip Analysis (RMA) algorithm (3), including background correction, probeset signal integration, quantile normalization. After pretreatment, the obtained chp files were analyzed by Transcriptome Analysis Console software to identify differentially expressed genes (DEGs) and alternatively spliced genes (ASGs).

source_name: Chondrogenic differentiation of CESCs

label_protocol: Fragmented single-stranded DNA was labeled using DNA labeling reagent according to standard Affymetrix protocol.

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

value: Chondrogenic differentiation of CESCs


title: OD, biological rep1 (gene level)

description: Gene expression data from human CESCs

source_name: Osteogenic differentiation

value: Osteogenic differentiation


title: High_glucose(33mM)_rep1


title: TSTPHC-005


title: TSTPHC-012


title: TSTPHC-003


title: H_6hr_3

city: Singapore

first: Michael

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

hyb_protocol: Fragmented samples were hybridized according to Affymetrix guidelines for 17hr in 45°C on GeneChip Mouse Gene 1.0 ST Array; The arrays were then washed and stained using the standard fluidics protocol (FS450_0007) for gene arrays on the GeneChip Fluidics Station 450.

scan_protocol: The mouse gene chips were scanned using GeneChip Scanner 3000. The images were analyzed using Expression Console and standard array quality controls analyses were carried out according to the instructions provided by Affymetrix.

data_processing: Data was RMA normalized using R v 2.15.2 in bioconductor using the AffyPLM package

organism: Mus musculus

source_name: Hyphae (Aspergillus fumigatus), 6hr

label_protocol: Single-stranded DNA were prepared according to the Ambion WT Expression Kit from 100ng of total RNA. 5.5ug of ssDNA were fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling Kit.

growth_protocol: D1 cells were grown in IMDM with 2mM L-glutamine, 100U/mL Penicillin/Streptomycin and 55μM β-mercaptoethanol (Gibco, Life Technologies, Carlsbad, California, USA), supplemented with 30% supernatant from NIH/3T3 cells transfected to produce GM-CSF. The final concentration of GM-CSF in the medium was 10ng/mL.

extract_protocol: Total RNA was extracted following the double extraction protocol using Trizol and Qiagen RNeasy Micro Extraction Kit. Total RNA integrity was assessed by Agilent Bioanalyzer.

treatment_protocol: For stimulation experiments, cells were harvested and seeded on suspension plate overnight.  For stimulation, the following were used:  whole glucan particle (Particulate B glucan, 10μg/ml) (Wellmune, Biothera, Minnesota, USA), poly-1-6-β-d-glucopyranosyl-1-3-β-d-glucopyranose (Soluble B glucan 10μg/m) (Wellmune, Biothera, Minnesota, USA), and Aspergillus fumigatus (AF293 ratio cells:con 1:1, cells:swollen/Hyphae 0.1:1) (MYA-4609, ATCC, Manassas, Virginia, USA).

tag: cell line

value: D1 dendritic cells

tag: treatment

value: Hyphae (Aspergillus fumigatus) 6 hr


title: TSTPHC-002


title: TSTPHC-004


title: TSTPHC-015


title: TSTPHC-010


title: TSTPHC-001


title: TSTPHC-011


title: TSTNHC-104

value: TSTneg


title: TSTNHC-105


title: SW_6hr_2

source_name: swollen conidia (Aspergillus fumigatus), 6hr


title: C_6hr_2

source_name: Conidia (Aspergillus fumigatus), 6hr

value: Conidia (Aspergillus fumigatus) 6hr


title: C_6hr_3


title: C_6hr_1


title: H_6hr_1

source_name: Hyphae (Aspergillus fumigatus), 6 hr


title: TSTNHC-103


title: UD, biological rep1 (gene level)

description: Gene expression data from human CESCs

source_name: Undifferentiated CESCs

value: Undifferentiated CESCs


title: SW_6hr_3

value: swollen conidia (Aspergillus fumigatus), 6hr


title: TSTNHC-100

source_name: whole blood


title: H_6hr_2


title: TSTNHC-101


title: TSTNHC-102


title: TSTNHC-096


title: TSTNHC-098


title: TSTNHC-097


title: TSTNHC-099


title: SW_6hr_1


title: TSTMP-105


title: PB_6hr_1

source_name: Particluate B glucan, 6hr

value: Particluate B glucan 6hr


title: TSTMP-104


title: PB_6hr_3


title: PB_6hr_2


title: SB_6hr_1

source_name: soluble B glucan, 6hr

value: soluble B glucan 6hr


title: SB_6hr_2


title: U_6hr_1

source_name: untreated

value: untreated 6hr


title: SB_6hr_3


title: TSTMP-103

value: TSTpos

value: healthy


title: U_6hr_3


title: U_6hr_2


title: TSTMP-102

value: whole blood


title: TSTMP-091


title: TSTMP-090


title: TSTMP-100


title: TSTMP-088


title: TSTMP-089


title: TSTMP-087


title: TSTMP-086


title: TSTMP-084


title: TSTMP-085


title: TSTMP-080


title: TSTMP-081


title: C_4hr_2

source_name: Conidia (Aspergillus fumigatus), 4hr

value: Conidia (Aspergillus fumigatus) 4hr


title: H_4hr_3

source_name: Hyphae (Aspergillus fumigatus), 4hr

value: Hyphae (Aspergillus fumigatus) 4hr


title: TSTMP-083


title: H_4hr_1


title: H_4hr_2


title: SB_4hr_3

source_name: soluble B glucan, 4hr

value: soluble B glucan 4hr


title: SW_4hr_2

source_name: swollen conidia (Aspergillus fumigatus), 4hr

value: swollen conidia (Aspergillus fumigatus) 4hr


title: SW_4hr_1


title: PB_4hr_3

source_name: Particluate B glucan, 4hr

value: Particluate B glucan 4hr


title: C_4hr_3

value: D1 dendritic cells


title: C_4hr_1


title: SB_4hr_1


title: U_4hr_2

value: untreated 4hr


title: U_4hr_3


title: U_4hr_1


title: SW_4hr_3


title: PB_4hr_1


title: TSTMP-078


title: TSTMP-077


title: PB_4hr_2


title: TSTMP-076


title: SB_4hr_2


title: H_1hr_3

source_name: Hyphae (Aspergillus fumigatus), 1hr

value: Hyphae (Aspergillus fumigatus) 1hr


title: TSTMP-075


title: H_1hr_1


title: TSTMP-074


title: H_1hr_2


title: TSTAR-063


title: TSTAR-064


title: SW_1hr_2

source_name: swollen conidia (Aspergillus fumigatus), 1hr

value: swollen conidia (Aspergillus fumigatus) 1hr


title: TSTAR-048

value: TSTneg


title: TSTAR-047


title: SW_1hr_3


title: TSTAR-046


title: TSTAR-052


title: TSTAR-054


title: SW_1hr_1


title: TSTAR-067


title: TSTAR-068


title: TSTAR-045


title: C_1hr_2

source_name: Conidia (Aspergillus fumigatus), 1hr

value: Conidia (Aspergillus fumigatus) 1hr


title: PB_1hr_3

source_name: Particluate B glucan, 1hr

value: Particluate B glucan 1hr


title: C_1hr_3


title: PB_1hr_2


title: TSTAR-044


title: C_1hr_1


title: PB_1hr_1


title: SB_1hr_1

source_name: soluble B glucan, 1hr

value: soluble B glucan 1hr


title: SB_1hr_2


title: TSTAR-043


title: TSTAR-041


title: U_1hr_3_repeat1

value: untreated 1hr


title: TSTAR-039

value: TSTpos


title: TSTAR-038

value: healthy


title: SB_1hr_3


title: U_1hr_2_repeat2


title: TSTAR-042

value: whole blood


title: U_1hr_3_repeat2


title: U_1hr_2_repeat1


title: TSTAR-036


title: TSTAR-035


title: U_1hr_1_repeat2


title: TSTAR-013


title: TSTAR-040


title: TSTAR-002


title: TSTAR-037


title: TSTAR-021


title: SJRTB-310

value: GeneXpert-pos

value: TB


title: U_1hr_1_repeat1


title: TSTAR-001


title: SJRTB-309


title: TSTAR-016


title: SJRTB-303


title: SJRTB-302


title: Adipo diff ASC 25mM Glc D21 replicate 2

description:
Expression array, adipose derived mesenchymal stem cells, adipogenic differentiated, 25 mM glucose, day 21
21b D21 adipo diff

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalised using Illumina GenomeStudio v2011.1; Gene Expression Module 1.9.0.

source_name: Adipo diff ASC_25mM glucose_day 21

label_protocol: Biotinylated cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit

growth_protocol: The adipose stem cells were cultured  in DMEM/F12 Glutamax  containing 10% FCS and 1 % PenStrep. Cells were pretreated for 2 passages with KO DMEM with 10 ng/ml EGF and 20 ng/ml bFGF and B27 until D-1

extract_protocol: RNA was extracted using the GenElute™ Mammalian Total RNA Miniprep Kit (Sigma Aldrich)  in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were cultured in DMEM/F12 and trypsinized when reaching 70-80% confluency. Cell culture media was changed every 3 days

value: Adipose tissue

value: Mesenchymal stem cells


title: SJRTB-300


title: CAPAN2-PD2

city: Dallas

first: Erik

last: Knudsen

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description: PD replicate 2

hyb_protocol: Standard Illumina Human HT-12 V4.0 expression beadchip hybridization protocol

scan_protocol: Standard Ilumina scanning protocol using Illumina HiScan scanner.

data_processing: Data were background subtracted and quantile normalized among arrays and log2 transformed and analysis were preformed using R/Bioconductor packages

source_name: CAPAN2 PD

label_protocol: RNA was labeled with biotin using the Illumina Total PrepKit from Ambion.

growth_protocol: Cells were grown in DMEM+10%FBS

extract_protocol: RNA was extracted using the QIAGEN kit and manufacturer's protocol was followed. Experion RNA analysis System (Bio-Rad)were used for quality control

treatment_protocol: CAPAN2 Cells were treated with DMSO/ PD-0332991


title: CAPAN2-PD3

description: PD replicate 3


title: CAPAN2-PD1

description: PD replicate 1


title: Adipo diff ASC 15mM Glc D21 replicate 1

description:
Expression array, adipose derived mesenchymal stem cells, adipogenic differentiated, 15 mM glucose, day 21
14 D21 adipo diff

source_name: Adipo diff ASC_15mM glucose_day 21


title: Adipo diff ASC 25mM Glc D21 replicate 1

description:
Expression array, adipose derived mesenchymal stem cells, adipogenic differentiated, 25 mM glucose, day 21
21 D21 adipo diff


title: Adipo diff ASC 15mM Glc D21 replicate 2

description:
Expression array, adipose derived mesenchymal stem cells, adipogenic differentiated, 15 mM glucose, day 21
14b D21 adipo diff


title: CAPAN2-ctrl3

description: control replicate 3

source_name: CAPAN2 control

value: DMSO


title: Adipo diff ASC 5mM Glc D21 replicate 2

description:
Expression array, adipose derived mesenchymal stem cells, adipogenic differentiated, 5 mM glucose, day 21
7b D21 adipo diff

source_name: Adipo diff ASC_5mM glucose_day 21


title: CAPAN2-ctrl2

description: control replicate 2


title: EZH2_KO_rep2

city: Los Angeles

first: Vasu

last: Punj

state: CA

address: Biggy Street

institute: USC

description:
SAMPLE 4
6260971027_E.AVG

scan_protocol: Standard Illumina scan protocol

data_processing: The data were processed and anlayzed by the Array Pipe software.

source_name: MCF7 cells

label_protocol: Biotinylated cRNA was prepared with the Ambion MessageAmp kit for Illumina array.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

value: Breast cancer cell line MCF7

tag: genotype/variation

value: EZH2 KO


title: H1.2_KO_rep1

description:
SAMPLE 5
6260971027_C.AVG

value: H1.2 KO


title: SJRTB-299

source_name: whole blood


title: SJRTB-298


title: CAPAN2-ctrl1

description: control replicate 1


title: SJRTB-295


title: SJRTB-294


title: SJRTB-292


title: H1.2_KO_rep2

description:
SAMPLE 6
6260971027_F.AVG


title: EZH2_KO_rep1

description:
SAMPLE 3
6260971027_B.AVG


title: Adipo diff ASC 5mM Glc D21 replicate 1

description:
Expression array, adipose derived mesenchymal stem cells, adipogenic differentiated, 5 mM glucose, day 21
7 D21 adipo diff


title: Control ShRNA_rep2

description:
SAMPLE 2
6260971027_D.AVG

value: Control


title: SJRTB-291


title: SJRTB-288


title: SJRTB-286


title: SJRTB-285


title: SJRTB-280


title: SJRTB-279


title: SJRTB-277


title: SJRTB-281


title: SJRTB-267


title: SJRTB-271


title: Control ShRNA_rep1

description:
SAMPLE 1
6260971027_A.AVG


title: SJRTB-266


title: ASC 15mM Glc D21

description:
Expression array, adipose derived mesenchymal stem cells, 15 mM glucose day 21
13 D21 undiff

source_name: ASC_15mM glucose_day 21

value: mesenchymal stem cells (MSCs)


title: RD_DMSO_5

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

hyb_protocol: The standard hybridization protocol was used as recommended by Affymetrix

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/ServiceCores/FC1/FC1.html).

data_processing: RMA normalization log2 at the transcript level using the oligo package (v.1.34.0) of Bioconductor (release 3.2)

label: Cy3 fluorescent label

source_name: RD cells_DMSO treated

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Human Gene 2.0 ST Array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: RNA was isolated from the cells using the Qiagen RNeasy Kit. The quality and quantity of the sample were assessed using Agilent 2100 Bioanalyzer and NanoDrop 1000 spectrophotometer.

value: RD

value: Embryonal rhabdomyosarcoma (ERMS) cell line

value: female

tag: origin

value: fibroblast

tag: treated with


title: SJRTB-265


title: RD_DMSO_3


title: ASC 5mM Glc D21

description:
Expression array, adipose derived mesenchymal stem cells, 5 mM glucose day 21
6 D21 undiff

source_name: ASC_5mM glucose_day 21

tag: tissue


title: ASC 25mM Glc D21

description:
Expression array, adipose derived mesenchymal stem cells, 25 mM glucose day 21
20 D21 undiff

source_name: ASC_25mM glucose_day 21


title: RD_TSA_1

source_name: RD cells_TSA treated

value: muscle

value: TSA


title: SJRTB-263

value: whole blood


title: RD_DMSO_1


title: SJRTB-282

value: GeneXpert-pos


title: RD_TSA_3


title: SJRTB-259

value: TB


title: 381T_TSA_3

source_name: 381T cells_TSA treated


title: SJRTB-262


title: 381T_DMSO_5

source_name: 381T cells_DMSO treated


title: RD_TSA_5


title: 381T_TSA_1


title: 381T_DMSO_1


title: SJRTB-257


title: SJRTB-255


title: 381T_DMSO_3


title: InVivoWhole_96hr_3.9µM Cu_rep1

city: Wuhan

first: Xin-ying

last: Zhou

state: Hubei

address: Luoshi South Road

institute: Huazhong Agriculture University

description:
Gene expression after 96hr in 3.9µM Cu-exposed zebrafish embryos
Cu-96h

hyb_protocol: The labeled cRNAs were hybridized onto the Whole Genome Oligo Array (4x44K, Agilent Technologies).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package.

organism: Danio rerio

source_name: Whole embryo, 96hr, 3.9µM Cu, replicate 1

label_protocol: 1µg RNA is used for labeling.The specific activity (pmol dyes per ug cRNA) of the labeled RNA can be obtained by calculation: Specific Activity=(pmol per ul dye)/(ug per ul cRNA)

growth_protocol: Zebrafish were maintained in a circulating filtration system (28±0.5℃, 14:10h light:dark), fed three times a day.

extract_protocol: Total RNA was extracted with TRIzol Reagent, chloroform and isopropanol.

treatment_protocol: After natural spawning, fertilized embryos were selected and staged by morphological features, then performed with 0 and 3.9µM Cu as dispositions.

value: Whole embryo

tag: age

value: Cu


title: SJRTB-254


title: SJRTB-249


title: SJRTB-253


title: SJRTB-251


title: SJRTB-246


title: 2_4-RA-resc-WT-4xOFT-pool 7

city: Marseille

first: Heather

middle: C

last: Etchevers

address: 27 boulevard Jean Moulin

department: INSERM U1251

country: France

institute: INSERM/Aix-Marseille Univ

hyb_protocol: Labeled cRNAs were hybridized on a single Agilent 8x60K SurePrint G3 Mouse GE 8x60K microarray for 40 hours at 65°C in an ozone-free environment.

scan_protocol: The slide was then scanned on Agilent DNA scanner G2505C at 3 µm using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%). Raw data were extracted using Feature Extraction software.

data_processing: Data were filtered and analyzed on GeneSpring using the standard analysis protocol GE1_107_Sep09.

source_name: 4x OFT, WT embryos at E10.5

label_protocol: 50 ng total RNA input labeled with Cy3 using the Agilent One-color Low Input Quick Amp labeling kit. Labeled and purified cRNA quantities were assessed on a Nanodrop spectrophotometer.

extract_protocol: Total RNA was extracted without DNase treatment using Macherey-Nagel Nucleospin RNA columns. After assessing quality with an Agilent Bioanalyzer 2100, samples with an RNA Integrity Number (RIN) over 8.0 were selected for each condition (mutant or wildtype littermates).

treatment_protocol: Four pooled samples of four microdissected outflow tracts from both conditions (1 and 2 - retinoic acid-rescued embryos of Raldh2 KO or WT genotype respectively) were collected.

value: E10.5 embryo

value: cardiac outflow tract

tag: genotype

value: WT, maternal RA supplementation


title: SJRTB-150

tag: disease state


title: SJRTB-151

tag: neg or pos


title: SJRTB-149

tag: cell type


title: InVivoWhole_24hr_3.9µM Cu_rep1

description:
Gene expression after 24hr in 3.9µM Cu-exposed zebrafish embryos
Cu-24h-1

source_name: Whole embryo, 24hr, 3.9µM Cu, replicate 1


title: SJRTB-145

tag: activation agent


title: SJRTB-146

tag: time


title: InVivoWhole_96hr_0Cu_rep1

description:
Gene expression after 96hr in 0Cu-exposed zebrafish embryos
Control-96h-1

source_name: Whole embryo, 96hr, 0Cu, replicate 1

tag: agent

value: control


title: InVivoWhole_24hr_0Cu_rep1

description:
Gene expression after 24hr in 0Cu-exposed zebrafish embryos
Control-24h-1

source_name: Whole embryo, 24hr, 0Cu, replicate 1


title: SJRTB-152


title: 2_2-RA-resc-WT-4xOFT-pool 2


title: SJRTB-144


title: 2_1-RA-resc-WT-4xOFT-pool1


title: SJRTB-143


title: 1_1-RA-resc-Raldh2KO-4xOFT-pool1

source_name: 4x OFT, RA-rescued Raldh2-/- embryos at E10.5

value: Raldh2-/-, maternal RA supplementation


title: 1_3-RA-resc-Raldh2KO-4xOFT-pool3


title: 1_2-RA-resc-Raldh2KO-4xOFT-pool2


title: SJRTB-142


title: 2_3-RA-resc-WT-4xOFT-pool 5


title: Hypoxia_Day0_4

city: Liverpool

first: Peter

last: Davidsen

state: Merseyside

address: Crown Street

country: United Kingdom

institute: University of Liverpool

hyb_protocol: Cy3-labelled cRNA (600 ng/sample) was hybridized at 65C for 16 hours

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um).

data_processing: The data were analyzed with R/Bioconductor (v3.0.1), quantile normalized values were obtained with the 'marray' package

label_protocol: One hundred nanograms of total RNA from each sample was amplified and converted into labelled cRNA using Agilent’s Low Input Quick Amp Labelling Kit according to the manufacturer’s recommendations

extract_protocol: Total RNA was extracted using the RNeasy Mini extraction kits (Qiagen, USA) according to the manufacturer’s recommendations

tag: gender

value: male

value: soleus

value: hypoxia

value: 0 d


title: Hypoxia_Day14_3


title: SJRTB-140


title: SJRTB-139


title: Hypoxia_Day14_4


title: Hypoxia_Day14_1


title: Hypoxia_Day0_1b


title: Hypoxia_Day14_2


title: SJRTB-138


title: 1_4-RA-resc-Raldh2KO-4xOFT-pool7


title: SJRTB-137


title: TSTAR-028

value: TSTpos

value: healthy


title: Hypoxia_Day0_3


title: SJRTB-136


title: SJRTB-135


title: SJRTB-133


title: SJRTB-130


title: SJRTB-128


title: Hypoxia_Day0_2b


title: Hypoxia_Day7_4

value: 7 d


title: Hypoxia_Day3_4

value: 3 d


title: Hypoxia_Day0_2


title: Hypoxia_Day7_2


title: Hypoxia_Day0_1a


title: Hypoxia_Day3_1


title: Hypoxia_Day7_1


title: SJRTB-118

value: GeneXpert-pos

value: whole blood


title: SJRTB-123

value: TB


title: Hypoxia_Day3_2a


title: SJRTB-124


title: SJRTB-127


title: SJRTB-126


title: SJRTB-110


title: SJRTB-117


title: SJRTB-114


title: SJRTB-106


title: VDC Kidney Normal Replicate 5

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from untreated kidney tissue.

hyb_protocol: 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files.

source_name: untreated kidney

label_protocol: One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol.

growth_protocol: Not applicable since the tissue samples were collected at the end of the necropsy from the National Toxicology Program's bioassay on Vinylidene chloride in the B6C3F1 mouse.

extract_protocol: Frozen normal liver tissue and hepatocellular carcinomas (both spontaneously arising or due to chemical exposure) samples were lysed and homogenized in TRIzol reagent (Invitrogen) using a rotor-stator homogenizer. Isolation of RNA was performed according to the mini kit protocol. RNA samples were purified by On-column deoxyribonuclease (DNase) treatment using the Invitrogen PureLink DNase kit. RNA concentration and 260/280 ratio was measured using a bioanalyzer (Agilent Technologies, Santa Clara, CA), and RNA quality was checked on Embi Tec Precast RNA gels (Embec cat# GE-6010). Samples were aliquoted and stored at -80ºC.

treatment_protocol: The kidney samples used in this study were collected from the National Toxicology Program's chronic bioassay on Vinylidene chloride (VDC). Male and female B6C3F1 mice were exposed to 0, 6.25, 12.5, and 25ppm VDC by inhalation, 5 days a week for 2 years. At the end of 2 years, there was a dose dependent increase in the incidence of renal cell carcinomas. Husbandry and experimental procedures were in compliance with requirements set forth by the Public Health Service’s Guide for the Care and Use of Laboratory Animals. At necropsy, tissue sections of non-tumor kidney from treated (hyperplasia) and non-treatd (vehicle control) animals, and RCC from VDC-exposed animals, were collected and flash-frozen in liquid nitrogen for RNA isolation and subsequent microarray analysis and RTPCR validation.

value: untreated kidney

tag: strain


title: VDC Kidney Normal Replicate 1


title: VDC Kidney Hyperplasia Replicate 6

description: Gene expression from treated kidney tissue.

source_name: treated kidney

value: treated kidney


title: VDC Kidney Normal Replicate 4


title: VDC Kidney Normal Replicate 6


title: VDC Kidney Hyperplasia Replicate 3


title: VDC Kidney Normal Replicate 3


title: VDC Kidney Hyperplasia Replicate 1


title: SJRTB-113


title: VDC Kidney Normal Replicate 2


title: SJRTB-108


title: VDC Kidney Carcinoma Replicate 5

description: Gene expression from kidney carcinoma tissue.

source_name: kidney carcinoma

value: kidney carcinoma


title: SJRTB-112

source_name: whole blood


title: SJRTB-107


title: 381T_TSA_5

city: Seattle

source_name: 381Tcells_TSA treated

value: Embryonal rhabdomyosarcoma (ERMS) cell line

value: female

value: muscle

value: TSA


title: VDC Kidney Hyperplasia Replicate 4


title: VDC Kidney Carcinoma Replicate 4


title: SJRTB-104


title: VDC Kidney Hyperplasia Replicate 5


title: SJRTB-096


title: SJRTB-099


title: VDC Kidney Carcinoma Replicate 6


title: VDC Kidney Hyperplasia Replicate 2


title: SJRTB-098


title: SJRTB-095


title: SJRTB-090


title: SJRTB-091


title: SJRTB-097


title: VDC Kidney Carcinoma Replicate 3


title: SJRTB-087


title: SJRTB-082


title: SJRTB-083


title: SJRTB-088


title: MR 4-25 3

description: Gene expression of MR 4-25 cells

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: MR 4-25 cells

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: The S49 (Neo) and MR 4-25 cells was maintained in RPMI-1640supplemented with 10% heat-inactivated FCS,4.8 mM glutamine and 100 IU of penicillin and 100mg/ml of streptomycin and were maintained in a humidified, 7% CO2 atmosphere.

extract_protocol: RNA was prepared using the Qiagen RNeasy midi kit (Qiagen Sciences, Germantown, MD) following the manufacturers instructions.  This included DNase treatment of all samples.

treatment_protocol: No Treatment

value: MR 4-25 cells


title: SJRTB-081


title: SJRTB-080


title: MR 4-25 1

description: Gene expression of MR 4-25 cells


title: VDC Kidney Carcinoma Replicate 1


title: SJRTB-079


title: MR 4-25 2

description: Gene expression of MR 4-25 cells


title: SJRTB-092


title: VDC Kidney Carcinoma Replicate 2


title: SJRTB-068


title: Neo 1

description: Gene expression of S49 Neo cells

source_name: S49 Neo cells

value: S49 Neo cells


title: SJRTB-075


title: SJRTB-067


title: SJRTB-058


title: SJRTB-089


title: SJRTB-050


title: SJRTB-053


title: Neo 3

description: Gene expression of S49 Neo cells


title: SJRTB-040


title: SJRTB-036


title: Neo 2

description: Gene expression of S49 Neo cells


title: SJRTB-047


title: Serum10%_CGGBP1 shmiR_rep1

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

country: India

institute: IIT Gandhinagar

description: Cells were cleared of medium, frozen on dry ice and maintained at -80C. All samples were used for RNA extraction simultaneously.

hyb_protocol: Proprietary  protocol of Affymetrix for GeneTitan arrays (HuGene-1_1-st-v1)

data_processing: Analyzed Data (Analysis Software = Expression Console, Method = plier (med-norm, target=0, doavg=false, calctarget=true, lowprecision=false,pm-gcbg))

source_name: Normal human foreskin (male) fibroblasts 1064Sk

growth_protocol: 37C, 5% CO2, humidity, 10%FCS, 0.5% Glutamine, MEM (All SIGMA)

extract_protocol: Total RNA extracted using Trizol

treatment_protocol: Normal human fibroblasts were serum-starved for 72 h. One set of cells were continued to be starved for additional 12h while another set was stimulated with 10% FBS for 12h.

tag: protocol

value: Serum10%_CGGBP1 shmiR

tag: passage

value: Passage between 18 and 20 used, normal cells that senesce after 50-60 passages, all checkpoints intact


title: SJRTB-033


title: SJRTB-032


title: SJRTB-028


title: SJRTB-027


title: SJRTB-030


title: SJRTB-026


title: SJRTB-025


title: SJRTB-024


title: Serum10%_CGGBP1 shmiR_rep3

scan_protocol: Proprietary  protocol of Affymetrix for GeneTitan arrays (HuGene-1_1-st-v1)


title: SJRTB-034


title: Serum10%_CGGBP1 shmiR_rep2

label_protocol: Proprietary  protocol of Affymetrix for GeneTitan arrays (HuGene-1_1-st-v1)


title: SJRTB-023


title: Starved_CGGBP1 shmiR_rep3

value: Starved_CGGBP1 shmiR


title: SJRTB-022


title: Starved_CGGBP1 shmiR_rep1


title: Serum10%_Control shmiR_rep2

value: Serum10%_Control shmiR


title: Serum10%_Control shmiR_rep3


title: SJRTB-020


title: Starved_Control shmiR_rep3

value: Starved_Control shmiR


title: Serum10%_Control shmiR_rep1


title: Starved_CGGBP1 shmiR_rep2


title: SJRTB-019

value: GeneXpert-pos


title: SJRTB-018

value: whole blood


title: SJRTB-015

value: TB


title: Starved_Control shmiR_rep2


title: rib mutant embryos replicate 1

city: Baltimore

first: Deborah

middle: J

last: Andrew

state: MD

address: 725 N. Wolfe St., Hunterian G-1

department: Cell Biology

institute: Johns Hopkins University School of Medicine

description: Gene expression data from rib1/ribP7 mutant embryos

hyb_protocol: Following fragmentation cRNAs were hybridized 16hes at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix' GeneChip Scanner 3000 7G and default parameters described by the manufacturer.

data_processing: Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform. RMA normalization was used to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.

label: Biotin

organism: Drosophila melanogaster

source_name: Multiple Drosophila embryos stages 11-16

label_protocol: Biotinylated cRNAs were prepared with the GeneChip HT 3' IVT Express Kit per manufacturer's instructions.

growth_protocol: Embryos (WT and rib1/ribP7) were collected for 8h at RT and allowed to age for 11 hours prior to their isloation using a COPAS Select embro sorter (Union Biometrica).

extract_protocol: Total RNA was isolated by Trizol (Invitrogen) extraction and cleaned up with the Qiagen RNeasy kit (Qiagen). Total RNA (100ng) was labeled and amplified using standard Affymetrix protocols.

tag: embryonic stages

value: stages 11-16


title: Starved_Control shmiR_rep1


title: rib mutant embryos replicate 2


title: wild-type embryos replicate 2

description: Gene expression data from WT embryos

value: WT


title: SJRTB-011


title: SJRTB-017


title: SJRTB-010


title: SJRTB-007


title: SJRTB-009


title: wild-type embryos replicate 3

description: Gene expression data from WT embryos


title: SJRTB-006


title: SJRTB-002


title: SJRTB-004


title: wild-type embryos replicate 1

description: Gene expression data from WT embryos


title: SAFs Normal Diet, biological replicate 3

city: Beaverton

first: Cecily

middle: Vauna

last: Bishop

state: OR

address: 505 NW 185th Ave

department: Division of Reproductive & Developmental Sciences

institute: Oregon National Primate Research Center

hyb_protocol: Purified SAF RNA was hybridized to individual Affymetrix™ GeneChip Rhesus Macaque Genome Arrays by the OHSU Gene Profiling Shared Resource (GPSR), similar to previous macaque microarray studies (PMCID: PMC3925330). Hybridization protocols were performed as previously reported by the OHSU GPSR (PMCID:PMC2649161).

scan_protocol: Image processing and expression analysis were performed using Affymetrix GeneChip Command Console (AGCC) v. 3.1.1 and Affymetrix Expression Console v. 1.1 software, respectively.

data_processing:
An absolute expression analysis was performed using the Affymetrix analysis algorithm, MAS 5.0 (Microarray Suite 5.0) for each GeneChip genome array hybridization. Following the initial analysis, the absolute analyses were rerun using global scaling to an average target intensity of 200. For each analysis, scaled or unscaled, the parameters α1 andα2 are set to 0.05 and 0.065, respectively.
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0

organism: Macaca mulatta

source_name: ovary SAF_Normal Diet female collected at/near menses

label_protocol: Samples were amplified and labeled using NuGEN Ovation RNA Amplification System v.2 protocol (3’IVT assay).

extract_protocol: Presumptive healthy SAFs were chosen for transcriptome evaluation based on criteria similar to previous studies: the presence of a clear antrum lacking dark oocytes or granulosa cells. Isolated SAFs were pooled by female/ovary (3.7±0.3 SAFs/ovary, n=3 ovaries/group), cleaned of extraneous stroma using 30-gauge needles, ruptured, and entire cellular contents (follicle wall/granulosa cells and cumulous-oocyte complex) placed into lysis buffer for RNA isolation (Absolutely RNA Nanoprep Kit, Agilent Technologies, Inc. USA).

value: young adult

tag: diet

value: normal, standard diet

value: Ovary

tag: tissue subtype

value: Small Antral Follicle (SAF)

tag: Stage

value: early follicular phase


title: SAFs Western-style Diet, biological replicate 3

source_name: ovary SAF_WSD female collected at/near menses

value: female

value: western-style diet (WSD)

tag: tissue


title: SAFs Western-style Diet+Chronic T, biological replicate 2

source_name: ovary SAF_WSD+T female collected at/near menses

tag: age

value: western-style diet with chronically elevated androgen levels (WSD+T)


title: SAFs Western-style Diet+Chronic T, biological replicate 3


title: SAFs Western-style Diet, biological replicate 2


title: rib mutant embryos replicate 3

tag: genotype


title: 21°C - Hemocytes from diseased FL clams - replicate 3

status: Public on Dec 20 2015

city: Stony Brook

first: Kailai

last: Wang

address: Stony Brook University

institute: Stony Brook University

description: raw data file: p30c168.gpr

hyb_protocol: All arrays were hybridized with the same amount of cRNA (300 ng of each Cy3- and Cy5-labeled cRNA).

scan_protocol: Arrays were scanned with a GenePix 4000B scanner using the suggested Agilent scan settings.

data_processing:
Generated fluorescence intensities were normalized to remove within-array and between-array variations using the LIMMA package in R software.
After normalization, probes with intensities less than two-fold background intensities (in all biological replicates) were eliminated from further analysis.

organism: Mercenaria mercenaria

source_name: 21°C - FL - Hemocytes - Diseased

label_protocol: Labeled (Cy3 or Cy5) complementary RNA (cRNA) was synthesized from 150 ng of RNA purified from different tissues of healthy and diseased clams using the Two-Color Microarray-Based Gene Expression Analysis Protocol (Quick Amp Labeling) following manufacturer’s protocol

growth_protocol: Adult clams were collected from an aquaculture plot.

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

treatment_protocol: Healthy, QPX chellenged, and naturally infected clams were kept at 13°C and 21°C for 2 months until sampling and RNA extraction.

value: hemocytes

value: Adult

tag: clam origin

value: FL

tag: condition

value: Diseased

tag: temperature


title: 21°C - Hemocytes from diseased FL clams - replicate 1

description: raw data file: p28c162.gpr


title: 21°C -Mantle from diseased MA clams - replicate 3

description: raw data file: p45n59.gpr

source_name: 21°C - MA - Mantle - Diseased

value: mantle

value: MA


title: 21°C -Mantle from diseased FL clams - replicate 2

description: raw data file: p29c165.gpr

source_name: 21°C - FL - Mantle - Diseased


title: 21°C -Mantle from diseased FL clams - replicate 1

description: raw data file: p28c162.gpr


title: SAFs Normal Diet, biological replicate 2


title: 21°C - Hemocytes from diseased FL clams - replicate 2

description: raw data file: p29c165.gpr


title: 21°C -Mantle from healthy FL clams - replicate 2

description: raw data file: p32c267.gpr

source_name: 21°C - FL - Mantle - Healthy

value: Healthy


title: SAFs Normal Diet, biological replicate 1


title: 13°C - Hemocytes from diseased FL clams - replicate 3

description: raw data file: p39c240.gpr

source_name: 13°C - FL - Hemocytes - Diseased


title: 21°C -Mantle from diseased FL clams - replicate 3

description: raw data file: p30c168.gpr


title: 21°C -Mantle from diseased MA clams - replicate 1

description: raw data file: p43n56.gpr


title: 21°C - Hemocytes from healthy FL clams - replicate 2

description: raw data file: p36c216.gpr

source_name: 21°C - FL - Hemocytes - Healthy


title: 21°C - Hemocytes from healthy FL clams - replicate 3

description: raw data file: p38c213.gpr


title: 21°C -Mantle from healthy FL clams - replicate 3

description: raw data file: p33c261.gpr


title: 21°C - Hemocytes from healthy FL clams - replicate 1

description: raw data file: p35c210.gpr


title: 21°C - Mantle from healthy FL clams - replicate 1

description: raw data file: p31c264.gpr


title: 21°C -Mantle from diseased MA clams - replicate 2

description: raw data file: p44n55.gpr


title: SAFs Western-style Diet, biological replicate 1


title: 13°C - Hemocytes from healthy FL clams - replicate 3

description: raw data file: p31c243.gpr

source_name: 13°C - FL - Hemocytes - Healthy


title: 13°C - Hemocytes from diseased FL clams - replicate 1

description: raw data file: p34c264.gpr


title: 13°C - Hemocytes from healthy FL clams - replicate 2

description: raw data file: p33c261.gpr


title: 13°C -Mantle from diseased MA clams - replicate 3

description: raw data file: p42n57.gpr

source_name: 13°C - MA - Mantle - Diseased


title: 13°C - Hemocytes from diseased FL clams - replicate 2

description: raw data file: p37c246.gpr


title: SAFs Western-style Diet+Chronic T, biological replicate 1


title: 13°C - Hemocytes from healthy FL clams - replicate 1

description: raw data file: p32c267.gpr


title: 13°C -Mantle from diseased MA clams - replicate 2

description: raw data file: p41n58.gpr


title: 13°C -Mantle from diseased MA clams - replicate 1

description: raw data file: p40n67.gpr


title: 13°C -Mantle from diseased FL clams - replicate 3

description: raw data file: p35c210.gpr

source_name: 13°C - FL - Mantle - Diseased


title: Duodenum_on gluten-containing diet 25

status: Public on Dec 19 2015

city: Madrid

first: Concepción

last: Núñez

address: C/Profesor Martín Lagos

department: Inmunología Clínica

country: Spain

institute: Instituto de Investigación Sanitaria Hospital Clínico San Carlos

data_processing:
PUS10 and GLB1 genes showed high stability and were used as endogenous reference genes.
Fold Change worksheet reports celiac disease/control ratios.

label: FAM, VIC

source_name: Intestinal biopsy

label_protocol: cDNA was obtained by RT-PCR reaction (High Capacity RNA-to-cDNA Master Mix, Applied Biosystems, Foster City, CA, USA)

extract_protocol: Total RNA was extracted with RNeasy Mini Kit (Qiagen, Westburg, Leuden, The Netherlands).

tag: disease state

value: Pediatric control

value: Duodenum


title: Duodenum_on gluten-containing diet 31


title: Duodenum_on gluten-containing diet 30


title: Duodenum_on gluten-containing diet 29


title: Duodenum_on gluten-containing diet 28


title: Duodenum_on gluten-containing diet 24

value: Adult control


title: Duodenum_on gluten-containing diet 27


title: Duodenum_on gluten-containing diet 26


title: 13°C -Mantle from diseased FL clams - replicate 2

description: raw data file: p36c216.gpr


title: 13°C -Mantle from diseased FL clams - replicate 1

description: raw data file: p34c264.gpr


title: Duodenum_on gluten-containing diet 23


title: Duodenum_on gluten-containing diet 21


title: Duodenum_on gluten-containing diet 19

value: Pediatric celiac patient


title: Duodenum_on gluten-containing diet 14


title: Duodenum_on gluten-containing diet 20


title: Duodenum_on gluten-containing diet 16


title: Duodenum_on gluten-containing diet 13


title: 13°C - Mantle from healthy FL clams - replicate 3

description: raw data file: p38c213.gpr

source_name: 13°C - FL - Mantle - Healthy


title: Duodenum_on gluten-containing diet 12


title: Duodenum_on gluten-containing diet 17


title: Duodenum_on gluten-containing diet 11


title: 13°C - Mantle from healthy FL clams - replicate 1

description: raw data file: p39c240.gpr


title: Duodenum_on gluten-containing diet 22


title: Duodenum_on gluten-containing diet 10


title: 13°C - Mantle from healthy FL clams - replicate 2

description: raw data file: p37c246.gpr


title: Duodenum_on gluten-containing diet 9


title: Duodenum_on gluten-containing diet 8


title: Duodenum_on gluten-containing diet 18


title: Duodenum_on gluten-containing diet 7


title: Duodenum_on gluten-containing diet 15


title: Duodenum_on gluten-containing diet 4

value: Adult celiac patient


title: Duodenum_on gluten-containing diet 3


title: Duodenum_on gluten-containing diet 5


title: Duodenum_on gluten-containing diet 6


title: Duodenum_on gluten-containing diet 2


title: Duodenum_on gluten-containing diet 1


title: Intact_rep2

city: Moscow

first: Evgeniy

last: Riabenko

address: 9 Institutskiy per.

department: Department of Control and Applied Mathematics

country: Russia

institute: Moscow Institute of Physics and Technology

description: Intact skin samples, biological rep2

hyb_protocol: Samples for whole genome expression analysis using Affymetrix microarrays were prepared according to the manufacturer’s recommendation (Affymetrix Manual P/N 701880 Rev. 4).  Sample labeling was performed in according with and GeneChip® WT Terminal Labeling and Hybridization User Manual (Affymetrix Manual P/N 702880 Rev. 4).

scan_protocol: Wash, Stain and Scan of arrays were performed in according with GeneChip® Expression Wash, Stain and Scan User Manual (Affymetrix Manual P/N 702731 Rev. 3).

data_processing: Arrays were preprocessed in GeneChip Command Console Software (AGCC, Affymetrix, version 1.4.1.46) and Affymetrix Transriptome Analysis Console (version 3.0.0.466) using RMA-sketch option.

label: streptavidin-phycoerythrin

source_name: Intact murine skin

growth_protocol: Inbred BALB/c male mice were used in this study. All mice were between 5 and 6 weeks of age and were purchased from the Stolbovaya nursery of the Russian Academy of Medical Sciences. The mice were fed a completely pelleted laboratory chow and had access to food and tap water ad libitum.

extract_protocol: Tissue samples were crushed in liquid nitrogen. QIAzol lysis reagent (Qiagen, Germany) was added and the homogenate was centrifuged through a QIAshredder column (Qiagen, Germany). Total RNA was extracted from the eluate by the miRNeasy mini kit (Qiagen, Germany) according to the manufacturer’s instructions. Genomic DNA contamination was removed by performing DNaseI digestion on the RNA binding column for 15 min. Total RNA was eluted in 50 μl of RNase-free H2O and stored at −80°C. RNA yield and purity was assessed spectrophotometrically by measuring OD260 and OD260/280 ratio respectively in RNase-free H2O using NanoDrop ND-1000 (NanoDrop Technologies, USA). For all samples  OD260/280 ratio was between 2.0 and 2.2.  RNA integrity was determined using the Agilent Bioanalyser 2100 System (Agilent Technologies, USA). Values of RNA quality indicator (RIN) generated by Bioanalyser system’s software ranged from 7.7 to 9.1.

treatment_protocol: The mice were anesthetized, the backs of the mice were shaved with an animal clipper and after disinfection with 70% ethanol, two full-thickness dermal wounds were made on the opposite sides of the midline of each mouse using a 4 mm punch biopsy instrument. Wounds were made through the epidermis, dermis, and subcutaneous tissue layers while leaving the fascia intact. The animals were individually caged after wounding. At a specified time point after the wounding (1 and 4 days), mice were sacrificed by carbon dioxide inhalation. The wounds and surrounding tissues or intact skin samples were removed with an 8 mm biopsy punch.

value: skin

tag: time point

value: Intact (uninjured)


title: Wounded_4days_rep2

description: Wouded skin samples, day 4 after injury, biological rep2

source_name: Wounded murine skin, day 4 after injury

label_protocol: Samples for whole genome expression analysis using Affymetrix microarrays were prepared according to the manufacturer’s recommendation (Affymetrix Manual P/N 701880 Rev. 4).  Sample labeling was performed in according with and GeneChip® WT Terminal Labeling and Hybridization User Manual (Affymetrix Manual P/N 702880 Rev. 4).

value: Day 4 post injury


title: Wounded_1day_rep1

description: Wouded skin samples, day 1 after injury, biological rep1

source_name: Wounded murine skin, day 1 after injury

value: Day 1 post injury


title: Wounded_1day_rep2

description: Wouded skin samples, day 1 after injury, biological rep2


title: Intact_rep1

description: Intact skin samples, biological rep1


title: PP, biological replicate 1

city: Durham

first: Karyn

last: Mcfadden

address: 213 Research Drive

department: MGM

institute: Duke

description:
Donor TX217, PP
Gene expression data from EBV infected B cells that proliferate early afer infection
Due to a miscommunication error, the Duke Genomics facility labeled the CEL file names in reverse. We identified the issue immediately and retrieved the RNA to generate cDNA and validate a number of microarray targets by qRT-PCR. The microarray was validated using original stock samples and freshly isolated samples. We also probed for genes that would exhibit known changes based on the biology of the system and validated pathways that were predicted to change based on the microarray. In all cases, we confirmed that the CEL file names were mislabeled.  Finally, we repeated the microarray analysis using 2 additional donors in which we confirmed that the samples were labeled in reverse. We have now confirmed this microarray data by qRT-PCR, immunoblot analysis, pathway interrogation and independent repeats.  We did not feel that it would be appropriate to alter the original CEL file names so we provided the original file names and corrected the sample description.

hyb_protocol: Targets were hybridized to the Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).  Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array in the Affymetrix Hybridization Oven.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G System.

data_processing: The data were analyzed with Partek Genomics Suite  using Affymetrix default analysis settings and RMA normalization.

source_name: Human B cells, 7.5 days post infection with EBV, proliferating

label_protocol: 200 ng of total RNA was processed using the MessageAmp™ Premier RNA Amplification Kit (Part Number 4385821, AM1792, 4383452). Affymetrix GeneChip analysis was performed according to the manufacturer’s instructions,

growth_protocol: Buffy coats were obtained from normal donors through the Gulf Coast Regional Blood Center and peripheral blood mononuclear cells (PBMC) were isolated by Ficoll Histopaque gradient. Primary cells were cultured in RPMI 1640 plus 15% fetal calf serum (FCS), 2 mM L-glutamine, penicillin/streptomycin and Cyclosporine A (0.5 µg/ml) at37C with 5% CO2.

extract_protocol: Total mRNA was isolated from sorted PA and PP cells using an RNeasy kit (Qiagen, #74106) according to the manufacturer’s protocol.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from human blood and stained with CellTrace Violet followed by infection with the B95-8 strain of EBV. The cells were then stained with a second proliferation tracking dye, CFSE, at 4 days post infection to coincide with the initial burst of hyper-proliferation. The cells were then monitored over time with those that are low for the Violet stain but high for the CFSE stain termed proliferated-arrested (PA) and those that are low for both stains designated proliferated-proliferated (PP).

tag: cell type

value: B cell

value: Proliferating

value: Day 7.5 post-infection with EBV


title: PA, biological replicate 3

description:
Donor TX224, PA
Gene expression data from EBV infected B cells that proliferate then arrest early after infection
Due to a miscommunication error, the Duke Genomics facility labeled the CEL file names in reverse. We identified the issue immediately and retrieved the RNA to generate cDNA and validate a number of microarray targets by qRT-PCR. The microarray was validated using original stock samples and freshly isolated samples. We also probed for genes that would exhibit known changes based on the biology of the system and validated pathways that were predicted to change based on the microarray. In all cases, we confirmed that the CEL file names were mislabeled.  Finally, we repeated the microarray analysis using 2 additional donors in which we confirmed that the samples were labeled in reverse. We have now confirmed this microarray data by qRT-PCR, immunoblot analysis, pathway interrogation and independent repeats.  We did not feel that it would be appropriate to alter the original CEL file names so we provided the original file names and corrected the sample description.

source_name: Human B cells, 7.5 days post infection with EBV, arrested

value: Arrested


title: PA, biological replicate 2

description:
Donor TX218, PA
Gene expression data from EBV infected B cells that proliferate then arrest early after infection
Due to a miscommunication error, the Duke Genomics facility labeled the CEL file names in reverse. We identified the issue immediately and retrieved the RNA to generate cDNA and validate a number of microarray targets by qRT-PCR. The microarray was validated using original stock samples and freshly isolated samples. We also probed for genes that would exhibit known changes based on the biology of the system and validated pathways that were predicted to change based on the microarray. In all cases, we confirmed that the CEL file names were mislabeled.  Finally, we repeated the microarray analysis using 2 additional donors in which we confirmed that the samples were labeled in reverse. We have now confirmed this microarray data by qRT-PCR, immunoblot analysis, pathway interrogation and independent repeats.  We did not feel that it would be appropriate to alter the original CEL file names so we provided the original file names and corrected the sample description.


title: Wounded_4days_rep1

description: Wouded skin sampes, day 4 after injury, biological rep1


title: FGF2

city: Jupiter

first: Siddaraju

middle: Valagerehalli

last: Boregowda

state: Florida

address: 130 Scripps Way

department: Molecular Medicine

institute: Scripps Florida

description: Gene expression data from MSCs at subconfluence cultured in FGF2 supplemented growth media.

hyb_protocol: Biotin labeled cDNA was fragmented and hybridized to the Human Gene ST 1.0 microarray (901086,  Affymetrix) according to Affymetrix protocol.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G with an attached autoloader.

data_processing: Data analysis was performed using Expression Console analysis software (Affymetrix). Functional profiling of microarray data was performed using g:Profiler based on hierarchical sorting using the best parent fit (Reimand et al., 2011). Unbiased gene annotation enrichment analysis for the top five functional clusters of Twist1 targets was performed by DAVID analysis using automated functional annotation clustering based on GO Terms of biological processes (GO_BP_FAT). Gene lists were annotated using the gene accession conversion tool to ensure accuracy. The individual genes of these five categories were then curated for enhanced accuracy by systematic search of the GeneCards compendium (http://www.genecards.org), which validated almost all of the initial genes.

source_name: Human MSCs at subconfluence cultured in growth media supplemented with 20 ng/ml FGF2 for 24h.

label_protocol: cDNA were labelled with biotin according to Affymetrix protocol

growth_protocol: Human MSCs were obtained from bone marrow as previously described (Russell et al., Stem Cells 2010; 28:788)  2010) and seeded at 500-1000 cells/cm2 in complete culture media (CCM) consisting of α-MEM  with 2 mM L-glutamine (GIBCO), 17% FBS (HyClone), 100 U/ml penicillin and 100 μg/ml  streptomycin.

extract_protocol: Total RNA was extracted using Trizol reagent according to manufacturer's protocol.

treatment_protocol: All cultures were at subconfluence during RNA extraction to guarantee log phage of growth.

value: Bone marrow

value: Mesenchymal stem cells


title: DP_Ets1_KO_3

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

hyb_protocol: RNA samples were amplified, labelled using Affymetrix's IVT labeling kit and hybridized according to the manufacturer's recommendations

data_processing: Expression data was obtained as Affymetrix CEL files, which were processed, background subtracted and normalized in R via the quantile normalization featured in the affy package for all microarray datasets, using the Mouse Gene 2.1 ST chip definition file (CDF) in the case of the microarrays described in this work, whereby probeset to gene annotation was carried out using the Affymetrix provided gene annotation

source_name: primary CD4+ CD8+ DP thymocytes

growth_protocol: Thymuses were extracted from 5-6-week-old C57BL/6 wild type and Ets1-/- mice and stored in RPMI medium. Cohorts of litter mates were used as biological replicates. To recover thymocytes, thymuses were subsequently passed twice through a 70m Falcon cell strainer and stored in PBS. Cells were crosslinked 10 min in 10% formaldehyde followed by 5 min quenching in 250 mM glycine. DP cells were subsequently sorted via AutoMACS using, in turn, a-CD8-PE antibody conjugated to a-PE beads, and ?-CD4 beads (Miltenyi). FACS profiles and cell purities were obtained for DP thymocytes via CD8-PE, CD4-FITC staining, respectively

extract_protocol: Trizol

treatment_protocol: total RNA was extracted using TRIzol (Invitrogen, USA) according to the manufacturers instructions with some modifications to ensure higher recovery rates of small RNAs. In brief, DP thymocytes were divided into 1x107 aliquots and 1ml of TRIzol was added. Cells were lysed with vigorous vortexing and pipetting. Homogenized samples were incubated at room temperature for 5 minutes and 0.2ml of chloroform was added. Samples were vigorously shaken and incubated at room temperature for an additional 5 minutes. Phase separation was carried out by centrifugation at 4C and 12,000g in a tabletop centrifuge for 15 minutes. The aqueous phase was transferred to fresh tubes and 1.5 volumes (approximately 1ml) of isopropanol together with 10ug of linear acrylamide (Ambion, USA) were added. Samples were vortexed and incubated at room temperature for 15 minutes. The precipitated RNA was pelleted by centrifugation at 4C and 12,000g in a tabletop centrifuge for 20 minutes. Pellets were washed with 80% ethanol, vortexed and centrifuged at 4C and 7,500g in a tabletop centrifuge for 10 minutes. Pellets were allowed to air dry and resuspended in nuclease-free water (Ambion, USA). DNA was digested using the rigorous Turbo DNase (Ambion, USA) treatment as per manufacturers instructions. RNA quantity was measured on a Nanodrop 1000 and the quality was verified using RNA Nano chips on a 2100 Bioanalyzer (Agilent, USA).

value: primary CD4+ CD8+ DP thymocytes

value: 5-6 weeks


title: PP, biological replicate 3

description:
Donor TX224, PP
Gene expression data from EBV infected B cells that proliferate early afer infection
Due to a miscommunication error, the Duke Genomics facility labeled the CEL file names in reverse. We identified the issue immediately and retrieved the RNA to generate cDNA and validate a number of microarray targets by qRT-PCR. The microarray was validated using original stock samples and freshly isolated samples. We also probed for genes that would exhibit known changes based on the biology of the system and validated pathways that were predicted to change based on the microarray. In all cases, we confirmed that the CEL file names were mislabeled.  Finally, we repeated the microarray analysis using 2 additional donors in which we confirmed that the samples were labeled in reverse. We have now confirmed this microarray data by qRT-PCR, immunoblot analysis, pathway interrogation and independent repeats.  We did not feel that it would be appropriate to alter the original CEL file names so we provided the original file names and corrected the sample description.


title: siTWIST1

description: Gene expression data from TWIST1 siRNA trasfected MSCs at subconfluence cultured in growth media.

source_name: Human MSCs at subcomfluence cultured in growth media and transfected with TWIST1 siRNA for 3 days.


title: PA, biological replicate 1

description:
Donor TX217, PA
Gene expression data from EBV infected B cells that proliferate then arrest early after infection
Due to a miscommunication error, the Duke Genomics facility labeled the CEL file names in reverse. We identified the issue immediately and retrieved the RNA to generate cDNA and validate a number of microarray targets by qRT-PCR. The microarray was validated using original stock samples and freshly isolated samples. We also probed for genes that would exhibit known changes based on the biology of the system and validated pathways that were predicted to change based on the microarray. In all cases, we confirmed that the CEL file names were mislabeled.  Finally, we repeated the microarray analysis using 2 additional donors in which we confirmed that the samples were labeled in reverse. We have now confirmed this microarray data by qRT-PCR, immunoblot analysis, pathway interrogation and independent repeats.  We did not feel that it would be appropriate to alter the original CEL file names so we provided the original file names and corrected the sample description.


title: SCRAMBLED

description: Gene expression data from scrambled siRNA transfected MSCs at subconfluence cultured in growth media.

source_name: Human MSCs at subconfluence cultured in growth media and trasfected with scambled siRNA for 3 days.


title: CONTROL

description: Gene expression data from MSCs at subconfluence cultured in growth media.

source_name: Human MSCs at subconfluence cultured in growth media.


title: DP_Ets1_KO_2

scan_protocol: RNA samples were amplified, labelled using Affymetrix's IVT labeling kit and hybridized according to the manufacturer's recommendations


title: PP, biological replicate 2

description:
Donor TX218, PP
Gene expression data from EBV infected B cells that proliferate early afer infection
Due to a miscommunication error, the Duke Genomics facility labeled the CEL file names in reverse. We identified the issue immediately and retrieved the RNA to generate cDNA and validate a number of microarray targets by qRT-PCR. The microarray was validated using original stock samples and freshly isolated samples. We also probed for genes that would exhibit known changes based on the biology of the system and validated pathways that were predicted to change based on the microarray. In all cases, we confirmed that the CEL file names were mislabeled.  Finally, we repeated the microarray analysis using 2 additional donors in which we confirmed that the samples were labeled in reverse. We have now confirmed this microarray data by qRT-PCR, immunoblot analysis, pathway interrogation and independent repeats.  We did not feel that it would be appropriate to alter the original CEL file names so we provided the original file names and corrected the sample description.


title: DP_WT_2

label_protocol: RNA samples were amplified, labelled using Affymetrix's IVT labeling kit and hybridized according to the manufacturer's recommendations

value: WT


title: DP_WT_1


title: DP_WT_3


title: DP_Ets1_KO_1


title: S3-H227

status: Public on Dec 18 2015

city: Houston

first: Suzanne

last: Fuqua

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description: log2 gene expression data

hyb_protocol: Standard Affymetix protocol for 3' IVT design

scan_protocol: Scanner GCS3000 7G

data_processing:
The data were analyzed with  Affy package in R, RMA method
Expressions estimated using RMA signal method

source_name: Human breast cancer

label_protocol: 3' IVT express

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

treatment_protocol: breast tumor samples, flash frozen

value: Breast cancer

tag: age (years)

tag: gender

value: Female

tag: menopausal status

value: Post-Menopausal

tag: histology group

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: Discovery TN

tag: er

value: Negative

tag: pr

tag: triple-negative status

value: TN

tag: tumor grade

value: Moderately Differentiated

tag: tumor size

tag: positive nodes

tag: metastases

value: No mets

tag: tnbc subtype

value: Luminal-AR (LAR)


title: S3-H97C

description: log2 gene expression data

tag: tissue

tag: race

value: Caucasian

tag: body mass index

value: Pre-Menopausal

value: Validation TN

value: Poorly Differentiated

value: Basal-Like Immune-Suppressed (BLIS)


title: S3-H94C

description: log2 gene expression data

tag: age (years)

tag: gender

value: Menopausal

value: Basal-Like Immune-Activated (BLIA)


title: S3-H99C

description: log2 gene expression data

value: Breast cancer

tag: histology group

value: Adenocarcinoma/Carcinoma, NOS

value: Adenocarcinoma of the breast with some tubular carcinoma

value: Well Differentiated

value: any size with direct extension


title: S3-H229

description: log2 gene expression data

value: Female

tag: menopausal status

value: Infiltrating Ductal Carcinoma

tag: histology

value: Discovery TN

value: Negative


title: S3-H95C

description: log2 gene expression data

tag: ajcc stage (7th edition, 2010)

tag: set

value: TN

value: No mets


title: S3-H226

description: log2 gene expression data

value: Caucasian

value: Post-Menopausal

tag: er

tag: pr

value: Moderately Differentiated

value: Mesenchymal (MES)


title: S3-H215

description: log2 gene expression data

value: Pre-Menopausal

tag: triple-negative status

tag: tumor grade

value: Basal-Like Immune-Suppressed (BLIS)


title: S3-H216

description: log2 gene expression data

value: Breast cancer

tag: tumor size

tag: positive nodes


title: S3-H221

description: log2 gene expression data

value: Poorly Differentiated

tag: metastases

tag: tnbc subtype


title: S3-H93C

description: log2 gene expression data

tag: tissue

tag: race

value: Validation TN


title: S3-H98C

description: log2 gene expression data

tag: age (years)

tag: body mass index


title: S3-H96C

description: log2 gene expression data

tag: gender

tag: histology group


title: S3-H222

description: log2 gene expression data

tag: histology

value: Basal-Like Immune-Activated (BLIA)


title: S3-H211

description: log2 gene expression data

tag: menopausal status

tag: ajcc stage (7th edition, 2010)


title: S3-H214

description: log2 gene expression data

tag: set

tag: er

value: Luminal-AR (LAR)


title: S3-H220

description: log2 gene expression data

value: Female

value: Adenocarcinoma/Carcinoma, NOS

value: Carcinoma of the breast

tag: pr

tag: triple-negative status


title: S3-H219

description: log2 gene expression data

value: Infiltrating Ductal Carcinoma

value: Discovery TN

value: Negative

tag: tumor grade

tag: tumor size


title: S3-H228

description: log2 gene expression data

value: TN

tag: positive nodes

tag: metastases

value: No mets


title: S3-H225

description: log2 gene expression data

tag: tissue

value: Caucasian

value: Post-Menopausal

value: Moderately Differentiated

tag: tnbc subtype


title: S3-H218

description: log2 gene expression data

tag: age (years)

tag: race

value: Basal-Like Immune-Suppressed (BLIS)


title: S3-H212

description: log2 gene expression data

value: Breast cancer

tag: gender

tag: body mass index

value: Menopausal


title: S3-H217

description: log2 gene expression data

value: Asian

value: Pre-Menopausal

tag: histology group

tag: histology

value: Poorly Differentiated


title: S3-H213

description: log2 gene expression data

value: Female

tag: menopausal status

tag: ajcc stage (7th edition, 2010)


title: S3-H230

description: log2 gene expression data

tag: set

tag: er

value: Mesenchymal (MES)


title: S3-H198

description: log2 gene expression data

tag: pr

tag: triple-negative status


title: S3-H208

description: log2 gene expression data

tag: tumor grade

tag: tumor size

value: Luminal-AR (LAR)


title: S3-H205

description: log2 gene expression data

value: Infiltrating Ductal Carcinoma

tag: positive nodes

tag: metastases

value: Basal-Like Immune-Activated (BLIA)


title: S3-H206

description: log2 gene expression data

tag: tissue

value: Discovery TN

value: Negative

tag: tnbc subtype


title: S3-H203

description: log2 gene expression data

tag: age (years)

tag: race

value: TN


title: S3-H201

description: log2 gene expression data

tag: gender

value: Caucasian

tag: body mass index


title: L820_Control_24h_rep2

city: Gothenburg

first: Joydeep

last: Bhadury

address: Medicinaregatan 1G, plan 6

department: Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Cancer Center

country: Sweden

institute: Universirty of Gothenburg

description: B1; SAMPLE 5

hyb_protocol: As per Manufacturers protocol (Illumina). Experiments perfomed at the Genomics Core Facility, At Univeristy of Gothenburg, Sweden

data_processing: Data extracted using Genome Studio (illumina), with background substraction with or without normalization (Cubic Spline)

growth_protocol: Lambda820 cells were cultured in RPMI/10 % FBS

extract_protocol: RNA was prepared using Nucleospin RNA extraction kit (MN).

treatment_protocol: Lambda820 cells were cultured in the presence or absence of DMSO (1:1000), 10 µM RVX2135, 10 µM VE-821 or 10 µM RVX2135/10 µM VE-821 for 24 h. Cells were pelleted by centrifugation before RNA extraction

tag: cell line

tag: cell type

value: murine Myc-driven lymphpma cells

tag: treated with

value: vehicle (DMSO)

tag: time point

value: 24 h after treatment start


title: S3-H197

description: log2 gene expression data

value: Breast cancer

tag: menopausal status

tag: histology group

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

tag: er

value: No mets


title: S3-H204

description: log2 gene expression data

value: Post-Menopausal

tag: pr

tag: triple-negative status

tag: tumor grade

tag: tumor size

tag: positive nodes

tag: metastases

value: Basal-Like Immune-Suppressed (BLIS)


title: S3-H200

description: log2 gene expression data

tag: tissue

tag: age (years)

tag: gender

tag: race

tag: body mass index

value: Pre-Menopausal

value: Poorly Differentiated

tag: tnbc subtype


title: S3-H207

description: log2 gene expression data

value: Female

tag: menopausal status

tag: histology group

value: Moderately Differentiated

value: Mesenchymal (MES)


title: S3-H199

description: log2 gene expression data

value: Infiltrating Ductal Carcinoma

tag: histology

tag: ajcc stage (7th edition, 2010)


title: L820_VE821_RVX2135_24h_rep2

description: B4; SAMPLE 8

scan_protocol: As per Manufacturers protocol (Illumina). Experiments perfomed at the Genomics Core Facility, At Univeristy of Gothenburg, Sweden

tag: cell line

tag: cell type

tag: treated with

tag: time point


title: L820_RVX2135_24h_rep2

description: B3; SAMPLE 7

label_protocol: As per Manufacturers protocol (Illumina). Experiments perfomed at the Genomics Core Facility, At Univeristy of Gothenburg, Sweden


title: S3-H209

description: log2 gene expression data

tag: set

value: Discovery TN

tag: er

tag: pr

tag: triple-negative status

tag: tumor grade

tag: tumor size


title: S3-H224

description: log2 gene expression data

tag: tissue

tag: age (years)

tag: gender

tag: race

value: Negative

tag: positive nodes


title: L820_VE821_24h_rep1

description: A2; SAMPLE 2


title: L820_VE821_24h_rep2

description: B2; SAMPLE 6


title: S3-H193

description: log2 gene expression data

tag: body mass index

tag: menopausal status

tag: histology group

tag: histology

value: TN

tag: metastases

tag: tnbc subtype

value: Basal-Like Immune-Activated (BLIA)


title: S3-H196

description: log2 gene expression data

value: Caucasian

tag: ajcc stage (7th edition, 2010)

tag: set


title: L820_VE821_RVX2135_24h_rep1

description: A4; SAMPLE 4

tag: cell line

tag: cell type

value: murine Myc-driven lymphpma cells

tag: treated with

tag: time point


title: S3-H202

description: log2 gene expression data

tag: tissue

tag: er

tag: pr

tag: triple-negative status

tag: tumor grade

tag: tumor size

value: Luminal-AR (LAR)


title: S3-H191

description: log2 gene expression data

value: Breast cancer

tag: age (years)

tag: gender

tag: race

tag: body mass index

tag: menopausal status

tag: positive nodes


title: S3-H210

description: log2 gene expression data

value: Menopausal

tag: histology group

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

tag: metastases

value: No mets

tag: tnbc subtype


title: S3-H194

description: log2 gene expression data

tag: tissue

value: Post-Menopausal

tag: er

value: Basal-Like Immune-Suppressed (BLIS)


title: left ventricle_caffeine_A1AR-/-

city: Gainesville

first: Xiefan

last: Fang

address: 1200 Newell Drive, ARB R1-148

department: Pediatrics

institute: University of Florida

hyb_protocol: NimbleGen Hybridization kit

scan_protocol: Two-color array scanning with MS 200 Microarray Scanner and MS 200 Data Collection Software

data_processing: The DNA methylation array data were analyzed using methods developed by Palmke et al. (Comprehensive analysis of DNA-methylation in mammalian tissues using MeDIP-chip. Methods 53: 175-184.2011) and by Tobias Straub (http://www.protocol-online.org/cgi-bin/prot/view_cache.cgi?ID=3973). Data were normalized within (Lowess-based) and between (quantile-based) arrays and probe level log2 ratio of Cy5/Cy3 (M-value) was used as a measure of MeDIP enrichment. The data processing was done with R.

source_name: MeDIP DNA

label_protocol: NimbleGen Dual-Color DNA Labeling Kit

extract_protocol: DNeasy Blood & Tissue Kit (Qiagen)

tag: strain

value: mixed background (129/OlaHsd/C57BL)

tag: genotype

tag: Sex

value: male

tag: age

value: 8-10 weeks

value: heart left ventricle

source_name: Input DNA


title: S3-H190

description: log2 gene expression data

tag: age (years)

tag: gender

value: Female

value: Infiltrating Ductal Carcinoma

tag: pr

tag: triple-negative status

tag: tumor grade

value: Poorly Differentiated

tag: tumor size

value: Mesenchymal (MES)


title: L820_RVX2135_24h_rep1

description: A3; SAMPLE 3

tag: cell line

tag: cell type

tag: treated with

tag: time point

value: 24 h after treatment start


title: left ventricle_caffeine_A1AR+/+


title: left ventricle_normal saline_A1AR-/-


title: left ventricle_normal saline_A1AR+/+


title: L820_Control_24h_rep1

description: A1; SAMPLE 1

value: vehicle (DMSO)


title: S3-H188

description: log2 gene expression data

tag: race

value: Asian/Pacific Islander

tag: menopausal status

tag: histology group

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

value: Discovery TN

value: Negative

value: TN

tag: positive nodes

tag: metastases

tag: tnbc subtype


title: BE2C_tetoff_KDM4C_D-2

city: Augusta

first: Justin

last: Choi

state: GA

address: 1410 Laney Walker Blvd.

department: Cancer Center

institute: Georgia Regents University

description: RNA expression value

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Data were normalized, significance determined by ANOVA, and fold change calculated with the Partek Genomics Suite (Partek Inc., St. Louis, MO).

source_name: BE2C_tetoff_KDM4C_D-6 days

label_protocol: TdT-labled cRNA were prepared with an Affymetrix GeneChip WT Terminal labeling kit

growth_protocol: BE(2)-C_tetoff_KDM4C cells were cultured in DME/F-12 1:1 (HyClone SH30023, Thermo Scientific) supplemented with 10% dialyzed FBS (Gibco 26400-036).

extract_protocol: Total RNA was isolated from the cell samples using Trizol (Invitrogen), and RNA quality and quantity was assessed using a Agilent BioAnalyzer and a Nanodrop Spectrophotometer.

treatment_protocol: BE(2)-C_tetoff_KDM4C cells were cultured in the presence or absence of doxycycline for 6 days.

tag: tumor cell line

value: Neuroblastoma

tag: treatment


title: BE2C_tetoff_KDM4C_D+3

description: RNA expression value

source_name: BE2C_tetoff_KDM4C_D+6 days

value: doxycycline


title: BE2C_tetoff_KDM4C_D-1

description: RNA expression value