title: AML_19

value: f

value: BM

tag: karyotype

value: MUT

tag: cebpa

tag: bv6 response

value: untreated


title: AML_39

status: Public on Dec 31 2014

type: RNA

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

country: Germany

institute: Charité

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: mononuclear cells from bone marrow

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.

extract_protocol: The total RNA was purified with a TRIzol-based protocol.

treatment_protocol: Primary AML samples were cultivated using RPMI 1640 (Biochrom AG, Berlin, Germany), supplemented with 20% FCS (Sigma-Aldrich, St. Louis, MO, USA), 2 mM L-Glutamin (Biochrom AG), and Penicillin/Streptomycin (GIBCO, Invitrogen Corporation, Grand Island, NY, USA). Prior to treatment, cells were stained with trypan blue (Sigma-Aldrich), counted, and diluted to a density of 1.0x106 cells/ml. Thawing of viably frozen samples followed the DSMZ (German Collection of microorganisms and cell lines, Braunschweig) guideline. Agents used to treat primary AML sample for 24 hours in vitro were DMSO (control/carrier; dimethyl sulfoxide; Sigma-Aldrich) and BV6 was synthesized at Genentech, Inc. (South San Francisco, CA, USA).

tag: age (years)

tag: gender

value: m

tag: sample source

value: WT

value: resistant

tag: treatment


title: AML_56

value: sensitive


title: T4.SEA#2

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

country: USA

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

organism: Mus musculus

source_name: Spleen

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

tag: age

value: 6 weeks

tag: exclusion markers

tag: genetic background

value: SEA/GnJ

tag: phenotype markers

tag: separation method

value: FACs Aria

tag: Sex

value: Male


title: P6_Rep2

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

description: Replicate 2 of 3. Differentiating neuroblastoma #2.

hyb_protocol: Hybridization was performed according to the Agilent 60-mer oligo microarray processing protocol v2.1 with the following modifications: 2 microgram labeled DNA per channel were mixed; no fractionation; probes were denatured for 3 min at 98 degree celcius; hybridization at 65 degree celcius; SSPE washes as recommended; slides were dipped in acetonitril (10 s) then dried.

scan_protocol: Scanned with a G2505B Microarray Scanner (Agilent Technologies). Quantification software: Feature Extraction 9 (Agilent Technologies).

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOESS normalization.

source_name: neuroblastoma, patient 6

label_protocol: The samples for hybridization were prepared from total RNA according to the Atlas SMART Fluorescent Probe Amplification Kit protocol (Clontech-Takara Bio Europe), with minor modifications: The RNA template was hydrolyzed under alkaline conditions before cDNA purification, and the PCR amplification process was monitored and stopped in the exponential phase. Quantity and Cy-dye incorporation rates of the generated target material were assessed using a NanoDrop ND-100 spectrophotometer.

growth_protocol: NB cell line SH-EP was cultured at 37C, 5% CO2 and grown in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum (FBS). A total of six NB samples (P1-P6) were obtained prior to cytotoxic therapy from patients participating in the NB97 German Neuroblastoma Study Group following informed consent. Selected tumors were localized in the adrenal glands and contained at least 60% tumor cells.

extract_protocol: Total RNA was isolated from 30 to 60 mg of snap-frozen tissue or cell cultures using Qiagen’s RNeasy MiniKit.

treatment_protocol: Treatment with helminthosporium carbonum (HC)-toxin (15 nM) and valproic acid (VPA; 1 mM) was carried out as indicated. Dulbecco’s phosphate-buffered saline (DPBS) served as solvent for VPA, methanol for HC-toxin.

tag: tissue

value: neuroblastoma

tag: nb differentiation degree

value: differentiating neuroblastoma #2

source_name: Total RNA from pooled NB cells

tag: sample type

value: reference


title: AML_51


title: P5_Rep2

description: Replicate 2 of 3. Ganglioneuroblastoma #2.

source_name: neuroblastoma, patient 5

value: ganglioneuroblastoma #2


title: sample775

city: Homburg

first: Andreas

last: Keller

address: Building 60

institute: Saarland University

hyb_protocol: according to manufacturers instruction (febit biomed)

scan_protocol: Wizard software on standard Microsoft Windows Workstation PC

data_processing: Summarizing of technical replica by median and quantile normalization. Following BG correction, negative values were corrected to 1. R Version 3.0.2

label: biotin

source_name: RNA from blood

label_protocol: MPEA, microfluidic primer extension assay Biotin labeling

extract_protocol: Blood of controls and patients was extracted in PAXgene Blood RNA tubes (BD, Franklin Lakes, New Jersey USA). The content of blood sampling tubes of each patient and healthy donor was used for RNAe extraction. The total RNA including the miRNA was isolated using the miRNeasy kit (Qiagen GmbH, Hilden) according to manufacturers instructions..

treatment_protocol: stored at -20 degree

tag: disease

value: Wilms Tumor


title: P5_Rep3

description: Replicate 3 of 3. Ganglioneuroblastoma #2.


title: sample772

value: others


title: P6_Rep1

description: Replicate 1 of 3. Differentiating neuroblastoma #2.


title: AML_67

source_name: mononuclear cells from peripheral blood

value: f

value: PB

tag: karyotype


title: AML_2

value: MUT

tag: cebpa

value: untreated


title: AML_28

value: WT

tag: bv6 response


title: T4.SEA#1


title: AML_16

tag: age (years)

value: m

value: BM

value: resistant


title: P4_Rep3

description: Replicate 3 of 3. Ganglioneuroblastoma #1.

source_name: neuroblastoma, patient 4

value: ganglioneuroblastoma #1


title: T4.RIII#1

value: 6 weeks

value: RIIIS/J

value: FACs Aria


title: P4_Rep2

description: Replicate 2 of 3. Ganglioneuroblastoma #1.

value: neuroblastoma


title: P4_Rep1

description: Replicate 1 of 3. Ganglioneuroblastoma #1.

value: reference


title: sample771


title: P3_Rep3

description: Replicate 3 of 3. Differentiating neuroblastoma #1.

source_name: neuroblastoma, patient 3

value: differentiating neuroblastoma #1


title: sample770


title: P5_Rep1

description: Replicate 1 of 3. Ganglioneuroblastoma #2.

value: ganglioneuroblastoma #2


title: sample769

value: benign prostate hyperplasia


title: P3_Rep2

description: Replicate 2 of 3. Differentiating neuroblastoma #1.


title: sample768


title: sample773

value: Wilms Tumor


title: sample767

value: chronic obstructive pulmonary disease (COPD)


title: T4.RIII#2

value: Male


title: sample766

value: lung cancer


title: T4.P#2

value: P/J


title: T4.PL#2

value: PL/J


title: hDC_EBVdUT_4h-rep2

city: Columbus

first: Maria-Eugenia

last: ariza

state: OH

address: 460 Medical Center Drive, Room 365

department: Department of Molecular Virology, Immunology and Medical Genetics

institute: Institute for Behavioral Medicine Research

description:
hDC_EBV-dUTPase_T4-2
Gene expression data in hDC treated with EBV-dUTPase protein for 4 h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 h at 45C on human genome U133 Plus 2.0 GeneChip. GeneChips were washed using the automated Affymetrix fluidics station and the bound biotin-labeled cRNA detected using a Streptavidin-Phycoerythrin conjugate. Subsequent signal amplification was performed using a biotinylated anti-streptavidin antibody.

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

data_processing: Affymetrix GeneChip hybridization data were normalized using Model-Based Expression Indexes (MBEI) in dChip. Differentially expressed genes between control and treated samples were then identified for each normalized data set using the criteria fold change >2 and p<0.05. GO and KEGG annotations were retrieved for these genes using the Affymetrix NetAffx analysis tool and gene expression patterns were clustered using dChip unsupervised clustering algorithm with centroid linkage.

source_name: dendritic cells_EBV-dUTPase treated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA using a one-cycle reaction  (Affymetrix GeneChip Expression Analysis Manual).

growth_protocol: human dendritic Langerhan cells (hDCs) were obtained from MatTek Corporation (Ashland MD). These cells were generated from CD34+ progenitor cells derived from human umbilical cord blood (HUCB) cells and cultured using specially formulated medium, DC-100-MM, (MatTek) containing a cytokine cocktail designed to induce differentiation of the CD34+ into DCs. These DCs express surface markers CD1a, HLA-DR, co-stimulatory molecules, Birbeck granules and surface markers characteristic of both plasmacytoid and myeloid DC.

extract_protocol: Total RNA was isolated using the RNAqueous-4PCR kit (Ambion, Grand Island, NY), following the procedure supplied by the manufacturer. Trace amounts of DNA were removed by treatment with DNase 1 and the RNA quantity and integrity was analyzed using the EnGenCore 2100 Bioanalyzer (Agilent, Santa Clara, CA).

treatment_protocol: hDC (1x106) were seeded at a density of 300,000 cells/ml. The next day, cells were treated with purified EBV-encoded dUTPase protein (10 mg/ml) or left untreated for 4 h. After treatment, cells were harvested for total RNA isolation.

tag: cell type

value: human dendritic Langerhan cells (hDCs), derived from human umbilical cord blood (HUCB) cells

tag: treated with

value: purified EBV-encoded dUTPase (10 µg/ml) for 4 h


title: hDC_EBVdUT_4h-rep1

description:
hDC_EBV-dUTPase_T4-1
Gene expression data in hDC treated with EBV-dUTPase protein for 4 h


title: T4.PL#1


title: sample765


title: T4.PWD#2

value: PWD/PHJ


title: P2_Rep3

description: Replicate 3 of 3. Poorly differentiated neuroblastoma #2.

source_name: neuroblastoma, patient 2

value: poorly differentiated neuroblastoma #2


title: hDC_EBVdUT_4h-rep3

description:
hDC_EBV-dUTPase_T4-3
Gene expression data in hDC treated with EBV-dUTPase protein for 4 h


title: sample764


title: P3_Rep1

description: Replicate 1 of 3. Differentiating neuroblastoma #1.


title: hDC_control_4h_rep1

description:
hDC_Control_T4-1
Gene expression data in control hDC at 4 h

source_name: dendritic cells_control

value: none (untreated control)


title: P2_Rep2

description: Replicate 2 of 3. Poorly differentiated neuroblastoma #2.


title: hDC_control_4h_rep2

description:
hDC_Control_T4-2
Gene expression data in control hDC at 4 h


title: P1_Rep3

description: Replicate 3 of 3. Poorly differentiated neuroblastoma #1.

source_name: neuroblastoma, patient 1

value: poorly differentiated neuroblastoma #1


title: T4.PWD#1

value: 6 weeks

value: FACs Aria


title: T4.P#1


title: P1_Rep2

description: Replicate 2 of 3. Poorly differentiated neuroblastoma #1.

value: neuroblastoma

value: reference


title: sample762


title: sample763


title: T4.NZW#2

value: NZW/LacJ


title: P2_Rep1

description: Replicate 1 of 3. Poorly differentiated neuroblastoma #2.


title: T4.NZB#1

value: NZB/BINJ


title: AdrenalMedulla_Rep3

description: Replicate 1 of 3. Adrenal Medulla.

source_name: adrenal medulla

value: adrenal medulla


title: T4.NOR#1

value: NOR/LtJ

value: Male


title: spheroid culture at day 15

city: Taipei

first: chia-chi

last: chang

address: No.201, Sec 2, Shih-Pai Road

country: Taiwan

institute: Medical research & education of VGHT

description: Gene expression data from human primary colon cancer cells at spheroid culture for 15 days.

hyb_protocol: 15 µg of complimentary RNA from each sample was hybridized to Affymetrix Human U133 plus 2.0 Array. Hybridization and scanning were performed according to manufacturer instructions (Affymetrix).

scan_protocol: GeneChips were scanned using the Genechip scanner 3000 (GCOS1.1).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Human primary colon cancer cells were kept in spheroid culture for 0, 5, and 15 days.

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

value: colon


title: sample759

value: colon cancer


title: UB_PXD101_10122009_07PB8200

growth_protocol: not applicable

treatment_protocol: Samples are from untreated patients (de novo AML)

tag: gender

value: female

tag: group

value: PD [non-responder (progressive disease)]


title: T4.NZW#1

tag: age

tag: exclusion markers


title: UB_PXD101_09092009_09KM1171

value: other

value: CRorPR [responder (complete remission or partial remission)]


title: T4.NZB#2

tag: genetic background

tag: phenotype markers


title: spheroid culture at day 5

description: Gene expression data from human primary colon cancer cells at spheroid culture for 5 days.


title: UB_PXD101_09092009_08KM2827

value: male

value: CN-AML


title: UB_PXD101_10122009_08KM6125


title: normal  culture

description: Gene expression data from human primary colon cancer cells at normal culture.


title: T4.NON#2

value: 6 weeks

value: NON/ShiLtJ

tag: separation method

tag: Sex


title: UB_PXD101_09092009_09KM0284


title: AdrenalMedulla_Rep2

description: Replicate 1 of 3. Adrenal Medulla.

tag: tissue


title: T4.NON#1

value: FACs Aria


title: P1_Rep1

description: Replicate 1 of 3. Poorly differentiated neuroblastoma #1.

value: neuroblastoma

tag: nb differentiation degree

value: poorly differentiated neuroblastoma #1

tag: sample type

value: reference


title: sample761

tag: disease

value: lung cancer


title: UB_PXD101_09092009_07PB8054

tag: karyotype

value: complex karyotype


title: AdrenalMedulla_Rep1

description: Replicate 1 of 3. Adrenal Medulla.

value: adrenal medulla


title: sample760


title: sample758


title: T4.NOR#2

value: NOR/LtJ

value: Male


title: HC-toxin_128h_Rep3

description: Replicate 3 of 3. Helminthosporium carbonum toxin treatment (15 nM), 128 h.

source_name: SH-EP, HC toxin, 128h

tag: cell line

value: SH-EP

tag: treatment

value: helminthosporium carbonum toxin

tag: treatment time


title: T4.NOD#2

value: NOD/ShiLtJ


title: HC-toxin_128h_Rep1

description: Replicate 1 of 3. Helminthosporium carbonum toxin treatment (15 nM), 128 h.


title: HC-toxin_72h_Rep3

description: Replicate 3 of 3. Helminthosporium carbonum toxin treatment (15 nM), 72 h.

source_name: SH-EP, HC toxin, 72h


title: HC-toxin_72h_Rep2

description: Replicate 2 of 3. Helminthosporium carbonum toxin treatment (15 nM), 72 h.


title: T4.NOD#1


title: HC-toxin_72h_Rep1

description: Replicate 1 of 3. Helminthosporium carbonum toxin treatment (15 nM), 72 h.


title: UB_PXD101_07102009_08PB6087

tag: age (years)

value: PD [non-responder (progressive disease)]


title: HC-toxin_6h_Rep3

description: Replicate 3 of 3. Helminthosporium carbonum toxin treatment (15 nM), 6 h.

source_name: SH-EP, HC toxin, 6h

value: 6 h


title: UB_PXD101_07102009_08PB6226

source_name: mononuclear cells from bone marrow

tag: gender

value: male

value: CN-AML


title: T4.MSM#2

source_name: Spleen

value: 6 weeks

value: MSM/Ms


title: HC-toxin_6h_Rep1

description: Replicate 1 of 3. Helminthosporium carbonum toxin treatment (15 nM), 6 h.


title: HC-toxin_128h_Rep2

description: Replicate 2 of 3. Helminthosporium carbonum toxin treatment (15 nM), 128 h.


title: HC-toxin_6h_Rep2

description: Replicate 2 of 3. Helminthosporium carbonum toxin treatment (15 nM), 6 h.


title: HC-toxin_1h_Rep3

description: Replicate 3 of 3. Helminthosporium carbonum toxin treatment (15 nM), 1 h.

source_name: SH-EP, HC toxin, 1h

value: 1 h


title: UB_PXD101_01102009_08PB5841

value: other

tag: group


title: T4.MRL#2

tag: age

value: MRL/MpJ

value: FACs Aria


title: T4.MSM#1

tag: exclusion markers


title: HC-toxin_1h_Rep2

description: Replicate 2 of 3. Helminthosporium carbonum toxin treatment (15 nM), 1 h.

source_name: Total RNA from pooled NB cells

value: reference


title: T4.MRL#1

tag: genetic background


title: T4.MA#1

value: MA/MyJ

tag: phenotype markers


title: UB_PXD101_01102009_07PB8219

value: female

value: CRorPR [responder (complete remission or partial remission)]


title: UB_PXD101_01102009_08KM5216


title: HC-toxin_1h_Rep1

description: Replicate 1 of 3. Helminthosporium carbonum toxin treatment (15 nM), 1 h.

value: SH-EP


title: UB_PXD101_07102009_08KM7177


title: T4.LP#2

value: LP/J

tag: separation method

value: Male


title: T4.LP#1

tag: Sex


title: VPA_128h_Rep3

description: Replicate 3 of 3. Valproic acid treatment (1 mM), 128 h.

source_name: SH-EP, VPA, 128h

value: valproic acid


title: T4.MA#2


title: VPA_128h_Rep2

description: Replicate 2 of 3. Valproic acid treatment (1 mM), 128 h.


title: UB_PXD101_01102009_07PB8683

value: PD [non-responder (progressive disease)]


title: T4.LG#1

value: LGJ


title: T4.LG#2


title: VPA_128h_Rep1

description: Replicate 1 of 3. Valproic acid treatment (1 mM), 128 h.


title: VPA_72h_Rep3

description: Replicate 3 of 3. Valproic acid treatment (1 mM), 72 h.

source_name: SH-EP, VPA, 72h


title: VPA_72h_Rep2

description: Replicate 2 of 3. Valproic acid treatment (1 mM), 72 h.


title: MDA_MB_231-not_transfected-3

city: Piscataway

first: Jessica

middle: Corban Wos

last: Graham

state: NJ

address: 170 Frelinghuysen Road

department: Toxicology

institute: The University of Medicine and Dentistry of New Jersey

description: MDA-MB-231 breast tumor epithelial cells

hyb_protocol: SPIA product and fragmented cDNA are analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization. 3.75ug of amplified and labeled cDNA was used in the hybridization cocktail for GeneChip analysis. Detailed protocols for sample preparation suing the NuGEN Ovation amplification and labeling kits can be found at http://www.nugeninc.com.

scan_protocol: All samples were subjected to gene expression analysis via the Affymetrix Human Genome U133 Plus 2.0 high-density oligonucleotide array which currently queries over 47,000 transcripts.  Hybridization, staining and washing of all arrays were performed in the Affymetrix fluidics module as per the manufacturer’s protocol.  Streptavidin phycroerythrin stain (SAPE, Molecular Probes) was the fluorescent conjugate used to detect hybridized target sequences. The detection and quantitation of target hybridization was performed with a GeneArray Scanner 3000 (Affymetrix) All arrays referred to in this study were assessed for “array performance” prior to data analysis.

data_processing: The data were generated using the Affymetrix Scanner according to Affymetrix protocol. The intensities are from MAS5.0

source_name: MDA-MB-231 cells in monolayer culture

label_protocol: Microarray experiments (GEO Accession numbers pending paper acceptance) were performed by the Bionomics Research and Technology Center at EOHSI (UMDNJ, Piscataway, NJ). Forty nanograms of total RNA from each sample were used to generate a high fidelity cDNA for array hybridization.  The cDNA were amplified, fragmented and labeled with biotin using NuGEN Ovation Amplification and Labeling kit V2 (NuGEN, San Diago, CA).

growth_protocol: Cell cultures were maintained at 37°C in a humidified atmosphere of 5% CO2 and 95% air. MDA-MB-231 and 231wCFry cells were cultured in Advanced DMEM with 10% heat inactivated FBS, 100 μg/ml penicillin-streptomycin solution.

extract_protocol: Total RNA was extracted from 70% confluent cell cultures using the RNeasy (QIAGEN) kit.

treatment_protocol: The 10,791 base pair COP rat Fry cDNA (GenBank accession number EU563851.1) was cloned in four sections and then reconstructed in the expression vector which was inserted into the pEGFP-N1 plasmid. The cells were transfected and subject to puromycin selection. A stable clone was selected which expressed Fry at levels comparable to the non-transformed normal mammary epithelial cell line, MCF10A. We termed the selected clone, 231wCFry.


title: MDA_MB_231-transfected_with_wtCopFry-3

description: MDA-MB-231 breast tumor epithelial cells stably transfected with the wild-type Cop Fry allele

source_name: 231wCFry cells in monolayer culture


title: MDA_MB_231-transfected_with_wtCopFry-2

value: transfected with the wild-type Cop Fry allele


title: MDA_MB_231-not_transfected-2


title: MDA_MB_231-transfected_with_wtCopFry-1


title: VPA_72h_Rep1

description: Replicate 1 of 3. Valproic acid treatment (1 mM), 72 h.


title: T4.JF1Ms#2

value: 6 weeks


title: MDA_MB_231-not_transfected-1


title: T4.JF1Ms#1


title: T4.FVB#2

value: FVB/NJ


title: MCF10A-shFRY transfected with FRY-targetting shRNA-1

description: MCF10A mammary epithelial cells stably transfected with FRY-targeting shRNA

data_processing: The data were generated using the Affymetrix Scanner according to Affymetrix protocol. GeneMaths.XT (Applied Maths) was utilized for primary analysis of array data and the RMA processing algorithm was utilized.

source_name: 10A-shFRY cells in monolayer culture

growth_protocol: Cell cultures were maintained at 37°C in a humidified atmosphere of 5% CO2 and 95% air. MCF10A and 10AshFRY cells were cultured in Mammary Epithelium Basal Medium (MEBM), supplemented with MEGM SingleQuots (Lonza) (gentamicin sulfate amphotericin-B, 20 ng/ml human epidermal growth factor, 10 μg/ml insulin, 5 μg/ml hydrocortisone and bovine pituitary extract).

treatment_protocol: The FRY-targetting shRNA (Mission shRNA, Sigma) or nontargetting shRNA (Mission shRNA, Sigma) was stably transfected into MCF10A cells.  The cells were transfected and subject to puromycin selection. A stable clone was selected which expressed FRY at levels ~60% below levels expressed normallin in the MCF10A cells and a stable clone was selected which expressed the non-targetting shRNA.  We termed the clone expressing FRY-targeting shRNA, 10A-shFRY and the cell line expressing the control vector, 10A-CV.

tag: expression

value: transfected with FRY-targetting shRNA


title: VPA_6h_Rep3

description: Replicate 3 of 3. Valproic acid treatment (1 mM), 6 h.

source_name: SH-EP, VPA, 6h

value: 6 h


title: MCF10A-shFRY transfected with FRY-targetting shRNA-3


title: T4.DDY#2

value: DDY/JclSidSeyFrkJ


title: T4.KK#1

value: FACs Aria


title: MCF10A-shFRY transfected with FRY-targetting shRNA-2


title: VPA_6h_Rep2

description: Replicate 2 of 3. Valproic acid treatment (1 mM), 6 h.

value: reference


title: MCF10A-CV transfected with non-targetting shRNA-3

description: MCF10A mammary epithelial cells stably transfected with non-targeting shRNA

source_name: MCF10A-CV cells in monolayer culture

value: transfected with non-targetting shRNA


title: MCF10A-CV transfected with non-targetting shRNA-2


title: T4.KK#2


title: T4.DDY#1


title: MCF10A-CV transfected with non-targetting shRNA-1


title: VPA_1h_Rep3

description: Replicate 3 of 3. Valproic acid treatment (1 mM), 1 h.

source_name: SH-EP, VPA, 1h

value: 1 h


title: VPA_6h_Rep1

description: Replicate 1 of 3. Valproic acid treatment (1 mM), 6 h.


title: T4.DBA2#2


title: T4.FVB#1


title: VPA_1h_Rep2

description: Replicate 2 of 3. Valproic acid treatment (1 mM), 1 h.


title: VPA_1h_Rep1

description: Replicate 1 of 3. Valproic acid treatment (1 mM), 1 h.


title: Control_Rep3

description: Replicate 3 of 3. Control cells, untreated, 0 h.

source_name: SH-EP, control

value: untreated

value: 0 h


title: T4.DBA2#1


title: T4.CE#2

value: CE/J


title: T4.CE#1

value: Male


title: Control_Rep2

description: Replicate 2 of 3. Control cells, untreated, 0 h.

value: SH-EP


title: HMMME

city: Nishinomiya

first: Yoshie

last: Yoshikawa

state: Hyogo

address: 1-1 Mukogawa-cho

department: Genetics

country: Japan

institute: Hyogo College of Medicine

description: Riken BRC MM cell line HMMME

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G.

data_processing: The CEL files were produced with Affymetrix GeneChip Operating Software ver.1.4 or GeneChip Command Console for MM48, MM57, MM62, MM67, and MM80. These files were imported into the GeneSpring GX 11.5 (Agilent Technologies Inc.). The data were summarized using the Plier16 summarization algorithm with quantile normalization.

source_name: cultured malignant mesothelioma cells

label_protocol: Biotinylated cRNA were prepared using GeneChip IVT Labeling kit according to the standard Affymetrix protocol from 3 ug total RNA.

growth_protocol: Primary outgrowth cells from pleural effusions, ascites, or tumor tissues were cultured in α-MEM–10% FBS. Adherent cells were expanded by several passages for several weeks or months. These cells were used as primary cell cultures.

extract_protocol: Total RNA were isolated from cultured cells with AllPrep DNA/RNA mini kit (Qiagen) following the manufacturer's protocol.

tag: cell type

value: cultured malignant mesothelioma cells

value: HMMME

tag: mm histological type

value: Epithelioid

value: male

tag: specimen from which cells were isolated

value: Breast


title: T4.CBAJ#2

value: 6 weeks

value: CBA/J


title: MSTO-211H

description: ATCC MM cell line MSTO-211H

value: Biphasic

value: Lung


title: H2452

description: ATCC MM cell line H2452

value: unknown


title: H28

description: ATCC MM cell line H28

value: Sarcomatoid

value: Pleural effusion


title: T4.CBACA#1

value: CBA/CaJ

value: FACs Aria


title: T4.CBAJ#1


title: MM67-P

description: MM primary cell cultures MM67-P

source_name: cultured malignant mesothelioma primary cells

value: primary

value: female


title: Control_Rep1

description: Replicate 1 of 3. Control cells, untreated, 0 h.

value: SH-EP

value: untreated

value: 0 h

tag: sample type

value: reference


title: H2052

description: ATCC MM cell line H2052

value: cultured malignant mesothelioma cells

tag: cell line

value: male


title: MM57-P

description: MM primary cell cultures MM57-P

value: cultured malignant mesothelioma primary cells

value: Epithelioid


title: MM62-P

description: MM primary cell cultures MM62-P

value: Biphasic

value: Pleura


title: MM48-P

description: MM primary cell cultures MM48-P


title: MM45-P

description: MM primary cell cultures MM45-P


title: T4.CBACA#2

value: 6 weeks

value: Male


title: MM35-P

description: MM primary cell cultures MM35-P

value: Pleural effusion


title: MM46-P

description: MM primary cell cultures MM46-P

value: Sarcomatoid


title: T4.CAS#2

value: CAST/EiJ

value: FACs Aria


title: T4.CAS#3


title: MM34-P

description: MM primary cell cultures MM34-P

value: primary

value: Ascites


title: MM30-P

description: MM primary cell cultures MM30-P


title: MM80-P

description: MM primary cell cultures MM80-P


title: T4.C57L#1


title: T4.C57KS#1


title: T4.C3H#2


title: MM21-P

description: MM primary cell cultures MM21-P


title: T4.C57L#2


title: MM19-P

description: MM primary cell cultures MM19-P


title: T4.C57BR#2

value: CBA/CaJ


title: T4.C57BR#1


title: MM26-P

description: MM primary cell cultures MM26-P

value: female

value: Pleural


title: RM27-P

description: RM primary cell cultures RM27-P

source_name: cultured reactive mesothelial hyperplasia primary cells


title: T4.BPL#1


title: T4.C3H#1


title: T4.C57KS#2


title: MM16-P

description: MM primary cell cultures MM16-P


title: T4.BPL#2


title: T4.BTBR#1

value: BTBR T+ tf/J


title: Met5a

description: ATCC cell line Met5a

source_name: cultured normal pleura transformant

value: cultured normal pleura transformant

value: male

value: unknown

value: Pleural fluids


title: T4.B6#5


title: RM19-P

description: RM primary cell cultures RM19-P from the pleural effusion of the same patient with MM19-P

value: cultured reactive mesothelial hyperplasia primary cells


title: T4.Balb#2

value: 6 weeks

value: BALB/cByJ


title: T4.Balb#1

value: Male


title: T4.BTBR#2


title: T4.B6#4


title: CaOv_bulk_2

city: Atlanta

first: Nathan

middle: J.

last: Bowen

state: GA

address: 223 James P Brawley Drive

department: Center for Cancer Research and Therapeutic Development

institute: Clark Atlanta University

description: bulk ovarian cancer tissue sample 2 combined with GSE14407 for a comparison of an ovarian LCM/bulk analysis to the pancreatic LCM/bulk results

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Affymetrix .CEL files were processed using the Affymetrix Expression Console (EC) Software Version 5.0. Files were processed using the default MAS5 3' expression workflow.

label_protocol: Total RNA from each of the above extractions was amplified using the RiboAmp OA or HS kit (Arcturus) that maintain the original mRNA representation after two amplification rounds, enabling accurate gene expression profiles from ultra small samples. The amplified mRNA was subsequently labeled using the IVT Labeling Kit (Affymetrix), to produce biotin-labeled mRNA suitable for hybridizing to GeneChip Probe Arrays (Affymetrix U133 Plus 2.0).

extract_protocol: RNA was extracted from LCM cells on the MacroCaps in 25 μL of extraction buffer and isolated following PicoPure RNA Isolation Kit (Arcturus) protocols.

treatment_protocol: Laser Capture Microdissection : Tissue samples were individually embedded in cryo-matrix (Shandon) and seven micron frozen sections were cut and attached to uncharged microscope slides. Immediately after dehydration and staining (HistoGene, LCM Frozen Section Staining Kit, Arcturus), slideswere processed in an Autopix Laser Capture Microdissection instrument (Arcturus) and cells captured on CapSure MacroCaps. Approximately 30,000 cells were collected from each of the tissue samples.

tag: tissue

value: ovary

tag: disease state

value: ovarian adenocarcinoma

tag: tissue type

value: ovarian cancer


title: T4.B6#3

value: FACs Aria


title: CaPan_LCM_normal_2

description: laser capture microdissected adjacent healthy pancreatic tissue replicate 2

value: pancreas

value: pancreatic adenocarcinoma

value: adjacent healthy pancreatic


title: CaPan_LCM_cancer_2

description: laser capture microdissected pancreatic cancer replicate 2

value: pancreatic cancer


title: CaPan_LCM_cancer_1

description: laser capture microdissected pancreatic cancer replicate 1


title: CaPan_LCM_normal_1

description: laser capture microdissected adjacent healthy pancreatic tissue replicate 1


title: CaOv_bulk_1

description: bulk ovarian cancer tissue sample 1 combined with GSE14407 for a comparison of an ovarian LCM/bulk analysis to the pancreatic LCM/bulk results


title: T4.B6#2


title: T4.B6#1


title: T4.B10#1


title: T4.AKR#2

value: AKR/J


title: T4.B10#3


title: GN.WSB#2

source_name: Bone Marrow

value: WSB/EiJ

value: CD11b+ Ly6G+

value: Bone Marrow Extract


title: T4.129#2

source_name: Spleen


title: CaPan_brushing_healthy

description: ductal brushing of adjacent healthy pancreatic tissue


title: CaPan_bulk_normal

description: bulk adjacent healthy pancreatic tissue


title: T4.AJ#1

value: A/J


title: 8505c SOD3 plasmid sample A, long-term no medium change

city: Naples

first: Mikko

last: Laukkanen

address: Via E. Gianturco 111-113

country: Italy

institute: SDN Foundation

description:
2_A
Cells cultured for 5 days after medium change

hyb_protocol: Labelled cRNA was then hybridized into the Illumina Sentrix Human HT-12 v.3 Epression BeadChips at 58C overnight (17 h) following the standard Illumina hybridization protocol

scan_protocol: Arrays were scanned with Illumina’s Bead Array Scanner (Factor=1.0, PMT=520, Filter=100%) following the standard Illumina scanning protocol

data_processing:
Raw data: The numerical results were extracted with GenomeStudio Gene Expression Module v. 1.0.6 without any normalization or background subtraction.
The data set was normalized using quantile normalization with limma in R

source_name: 8505c anaplastic thyroid cancer cell line_SOD3_long-term incubation_no medium change

label_protocol: To synthesize the biotinylated cRNA, 300 ng of total RNA was amplified using Ambion’s Illumina TotalPrep RNA Amplification kit (cat # AMIL1791)

growth_protocol: Cells were grown in RPMI medium, 10% FBS.

extract_protocol: The mRNA was extracted using Qiagen RNAeasy minikit

treatment_protocol: Control and SOD3 plasmid were transfected into the cells using nucleofection protocol

value: 8505c SOD3, long-term no medium change

value: anaplastic thyroid cancer


title: 8505c Control plasmid sample A, long-term no medium change

description:
1_A
Cells cultured for 5 days after medium change

source_name: 8505c anaplastic thyroid cancer cell line_control_long-term incubation_no medium change

value: 8505c Control, long-term no medium change


title: T4.129#1

value: 6 weeks

value: Male


title: GN.WSB#1


title: 8505c Control plasmid sample B, long-term no medium change

description:
1_B
Cells cultured for 5 days after medium change


title: T4.AJ#2


title: 8505c Control plasmid sample C, long-term no medium change

description:
1_C
Cells cultured for 5 days after medium change


title: 8505c SOD3 plasmid sample B, short-term incubation

description:
4_B
Cells cultured for 24h after medium change

source_name: 8505c anaplastic thyroid cancer cell line_SOD3_short-term incubation

value: 8505c SOD3, short-term incubation


title: 8505c SOD3 plasmid sample B, long-term no medium change

description:
2_B
Cells cultured for 5 days after medium change


title: 8505c SOD3 plasmid sample C, long-term no medium change

description:
2_C
Cells cultured for 5 days after medium change


title: 6 Hr BRD8518 1 uM (D7)

city: Cambridge

first: Marek

middle: M

last: Nageic

address: 7 Cambridge Center

department: Center for the Development of Therapeutics

institute: Broad Institute

description:
6 Hr BRD8518 1 uM
Broad_D7_47

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix GeneChip Human Gene ST 2.0 Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Data were normalized using the Robust Multi-Array Average method as implemented in the R package oligo.

source_name: HEPG2 cells treated with 8518

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).

growth_protocol: 10000 HepG2 cells are plated in each well of a Corning, black 96-well, tissue culture plate (#3904) in 40μL of DMEM/10% FBS/1x Pen-Strep-Glutamine media. The cells are then incubated overnight in a tissue culture incubator at 37°C and 5% CO2.

extract_protocol: RNA was prepared using RNeasy Minipreps (Qiagen) following the manufacture’s protocol.

treatment_protocol: The cells (6-wells each treatment) were treated with BRD-8518 (0.005uM-3.33 uM, two-fold dilution) for 6 hr at 37C.   The cells were also treated with BRD-8518 (1 uM) or Oncostatin M (100 ng/mL) for 1 hr and 24 hr at 37C.  DMSO controls were set up for each timepoint.  Compounds were added to the cells to a final DMSO concentration of 0.25%.   Oncostatin M was dissolved in PBS and DMSO was added to the wells to bring the final concentration to 0.25%.

tag: compound

tag: dose

value: 1 uM

tag: timepoint (hours)


title: T4.AKR#1

tag: age

tag: exclusion markers

value: FACs Aria


title: GN.SWR#1

tag: genetic background

value: SWR/J

tag: phenotype markers


title: 6 Hr BRD8518 1 uM (D8)

description:
6 Hr BRD8518 1 uM
Broad_D8_48


title: CaPan_bulk_cancer

description: bulk pancreatic cancer tissue

value: pancreas

value: pancreatic adenocarcinoma


title: 8505c SOD3 plasmid sample A, short-term incubation

description:
4_A
Cells cultured for 24h after medium change

tag: group


title: 6 Hr DMSO (D6)

description:
6 Hr DMSO
Broad_D6_46

source_name: HEPG2 cells no treatment (control)

value: control (DMSO)


title: 8505c SOD3 plasmid sample C, short-term incubation

description:
4_C
Cells cultured for 24h after medium change


title: 8505c Control plasmid sample C, short-term incubation

description:
3_C
Cells cultured for 24h after medium change

source_name: 8505c anaplastic thyroid cancer cell line_control_short-term incubation

value: 8505c Control, short-term incubation


title: CaPan_brushing_cancer

description: ductal brushing of pancreatic cancer tissue

value: pancreatic cancer


title: GN.SM#2

value: SM/J

value: CD11b+ Ly6G+

tag: separation method

tag: Sex


title: 6 Hr DMSO (D5)

description:
6 Hr DMSO
Broad_D5_45


title: GN.SM#1

value: Bone Marrow Extract


title: 6 Hr DMSO (D4)

description:
6 Hr DMSO
Broad_D4_44


title: 8505c Control plasmid sample B, short-term incubation

description:
3_B
Cells cultured for 24h after medium change

tag: cell type


title: 1 Hr BRD8518 1 uM (B8)

description:
1 Hr BRD8518 1 uM
Broad_B8_16


title: GN.SEA#2

value: SEA/GnJ


title: GN.SJL#1

value: SJL/J


title: 1 Hr DMSO (B7)

description:
1 Hr DMSO
Broad_B7_15


title: 6 Hr DMSO (D3)

description:
6 Hr DMSO
Broad_D3_43


title: GN.SJL#2


title: 1 Hr BRD8518 1 uM (C1)

description:
1 Hr BRD8518 1 uM
Broad_C1_17


title: genomic DNA from CpGenome Universal Methylated DNA and lymphocytes

type: genomic

city: Durham

first: Susan

middle: K.

last: Murphy

state: NC

address: B226 LSRC B Wing, Research Drive, Box 91012

department: Obstetrics and Gynecology

institute: Duke University Medical Center

description:
control
CpGenome+43N2 (1:1)

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

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

data_processing: Illumina GenomeStudio v2010.3 software. The non_normalized.txt contains unmethylated and methylated signal intensities.

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

growth_protocol: Genomic DNA was extracted from cells cultured in a 10 cm dish at 70-90% confluence

extract_protocol: Genomic DNA was extracted and purified using the Qiagen QIAamp® DNA Kit according to the manufacturer's protocol

tag: gender

value: female

value: control


title: GN.SEA#1

value: 6 weeks

value: Male


title: 1 Hr BRD8518 1 uM (C2)

description:
1 Hr BRD8518 1 uM
Broad_C2_18

value: 1 uM


title: genomic DNA from CpGenome Universal Methylated DNA

description:
control
CpGenome

source_name: CpGenome Universal Methylated DNA

tag: sample type

value: CpGenome Universal Methylated DNA


title: GN.RIII#2

value: RIIIS/J


title: 8505c Control plasmid sample A , short-term incubation

description:
3_A
Cells cultured for 24h after medium change

tag: cell line

value: anaplastic thyroid cancer


title: genomic DNA from ovarian cancer cell line_TOV-21G

description:
ovarian cancer cell line
TOV-21G

source_name: ovarian cancer cell line

value: ovarian cancer

value: cancer


title: 1 Hr DMSO (B5)

description:
1 Hr DMSO
Broad_B5_13

value: control (DMSO)


title: genomic DNA from ovarian cancer cell line_UWB1.289

description:
ovarian cancer cell line
UWB1.289


title: GN.PWD#2

value: PWD/PHJ


title: GN.PWD#1


title: GN.RIII#1


title: 1 Hr DMSO (B6)

description:
1 Hr DMSO
Broad_B6_14


title: 1 Hr OSM 100 ng/mL (B4)

description:
1 Hr OSM 100 ng/mL
Broad_B4_12

source_name: HEPG2 cells treated with Oncostatin M

value: OSM

value: 100 ng/mL


title: genomic DNA from ovarian cancer cell line_RMG-V

description:
ovarian cancer cell line
RMG-V

value: RMG-V


title: genomic DNA from lymphocytes 5_43N2_CONTROL

description:
control
43N2_CONTROL_5

source_name: lymphocytes

value: lymphocytes


title: 24 Hr DMSO (B1)

description:
24 Hr DMSO
Broad_B1_9


title: 1 Hr OSM 100 ng/mL (B3)

description:
1 Hr OSM 100 ng/mL
Broad_B3_11


title: GN.P#1

value: P/J

value: CD11b+ Ly6G+

value: Bone Marrow Extract


title: 1 Hr OSM 100 ng/mL (B2)

description:
1 Hr OSM 100 ng/mL
Broad_B2_10


title: genomic DNA from ovarian cancer cell line_SK-OV-3

description:
ovarian cancer cell line
SK-OV-3

value: female


title: GN.PL#1

value: 6 weeks

value: PL/J

value: Male


title: genomic DNA from ovarian cancer cell line_SK-OV-8

description:
ovarian cancer cell line
SK-OV-8


title: 24 Hr DMSO (A8)

description:
24 Hr DMSO
Broad_A8_8


title: genomic DNA from ovarian cancer cell line_RMG-I

description:
ovarian cancer cell line
RMG-I

value: RMG-I


title: GN.NZW#2

value: NZW/LacJ


title: GN.NZW#1


title: 24 Hr DMSO (A7)

description:
24 Hr DMSO
Broad_A7_7


title: genomic DNA from ovarian cancer cell line_PEO1

description:
ovarian cancer cell line
PEO1

value: ovarian cancer


title: genomic DNA from ovarian cancer cell line_TAYA

description:
ovarian cancer cell line
TAYA

value: TAYA

value: cancer


title: genomic DNA from ovarian cancer cell line_TYK-nu

description:
ovarian cancer cell line
TYK-nu

value: TYK-nu


title: genomic DNA from lymphocytes 6_43N2_CONTROL

description:
control
43N2_CONTROL_6

value: control


title: 24 Hr BRD8518 1 uM (A6)

description:
24 Hr BRD8518 1 uM
Broad_A6_6

value: 1 uM


title: 24 Hr BRD8518 1 uM (A5)

description:
24 Hr BRD8518 1 uM
Broad_A5_5


title: genomic DNA from ovarian cancer cell line_RMG-II

description:
ovarian cancer cell line
RMG-II

value: RMG-II


title: GN.P#2


title: genomic DNA from ovarian cancer cell line_PA1

description:
ovarian cancer cell line
PA1


title: 24 Hr BRD8518 1 uM (A4)

description:
24 Hr BRD8518 1 uM
Broad_A4_4


title: GN.NZB#2

value: NZB/BINJ


title: GN.NON#2

value: NON/ShiLtJ


title: GN.NOR#1

value: NOR/LtJ

value: CD11b+ Ly6G+


title: GN.NON#1

value: Bone Marrow Extract


title: GN.NOD#2

value: 6 weeks

value: NOD/ShiLtJ


title: GN.NZB#1

value: Male


title: GN.PL#2

value: PL/J


title: genomic DNA from ovarian cancer cell line_OVCAR8

description:
ovarian cancer cell line
OVCAR8

value: female


title: genomic DNA from ovarian cancer cell line_OVTOKO

description:
ovarian cancer cell line
OVTOKO

value: OVTOKO

value: ovarian cancer


title: 24 Hr OSM 100 ng/mL (A3)

description:
24 Hr OSM 100 ng/mL
Broad_A3_3

value: OSM

value: 100 ng/mL


title: GN.NOR#2


title: genomic DNA from lymphocytes 4_43N2_CONTROL

description:
control
43N2_CONTROL_4

value: lymphocytes

value: control


title: 24 Hr OSM 100 ng/mL (A2)

description:
24 Hr OSM 100 ng/mL
Broad_A2_2


title: genomic DNA from endometriosis_Hs832.(C)T

description:
normal
Hs832.(C)T

source_name: endometriosis

value: endometriosis

value: normal


title: genomic DNA from ovarian cancer cell line_OVCAR2

description:
ovarian cancer cell line
OVCAR2

value: cancer


title: GN.MSM#2

value: MSM/Ms


title: genomic DNA from ovarian cancer cell line_NIH:OVCAR-3

description:
ovarian cancer cell line
NIH:OVCAR-3


title: genomic DNA from ovarian cancer cell line_OVISE

description:
ovarian cancer cell line
OVISE

value: OVISE


title: genomic DNA from ovarian cancer cell line_OVCAR4-NCI

description:
ovarian cancer cell line
OVCAR4-NCI


title: genomic DNA from ovarian cancer cell line_OVCAR5

description:
ovarian cancer cell line
OVCAR5


title: GN.NOD#1

value: CD11b+ Ly6G+

value: Bone Marrow Extract


title: GN.MRL#1

value: 6 weeks

value: MRL/MpJ


title: GN.MA#1

value: MA/MyJ

value: Male


title: GN.MRL#2


title: genomic DNA from ovarian cancer cell line_OVCA429

description:
ovarian cancer cell line
OVCA429

value: female


title: GN.MSM#1


title: 24 Hr OSM 100 ng/mL (A1)

description:
24 Hr OSM 100 ng/mL
Broad_A1_1


title: genomic DNA from lymphocytes 3_43N2_CONTROL

description:
control
43N2_CONTROL_3


title: GN.LP#2


title: genomic DNA from ovarian cancer cell line_OVCA432

description:
ovarian cancer cell line
OVCA432

value: ovarian cancer


title: GN.LG#2

value: LGJ


title: genomic DNA from ovarian surface epithelium_IOSE144

description:
normal
IOSE144

source_name: ovarian surface epithelium

value: ovarian surface epithelium


title: GN.LP#1


title: GN.LG#1


title: genomic DNA from ovarian cancer cell line_OMC-3

description:
ovarian cancer cell line
OMC-3


title: genomic DNA from ovarian cancer cell line_OVCA420

description:
ovarian cancer cell line
OVCA420


title: genomic DNA from ovarian cancer cell line_OV90

description:
ovarian cancer cell line
OV90


title: genomic DNA from ovarian cancer cell line_ovary1847 (A1847)

description:
ovarian cancer cell line
ovary1847 (A1847)


title: GN.JF1Ms#1


title: GN.JF1Ms#2


title: GN.MA#2


title: GN.KK#1


title: genomic DNA from ovarian cancer cell line_KOC-5c

description:
ovarian cancer cell line
KOC-5c


title: genomic DNA from ovarian cancer cell line_TOV-112D

description:
ovarian cancer cell line
TOV-112D


title: GN.KK#2


title: GN.DDY#1

value: DDY/JclSidSeyFrkJ


title: genomic DNA from ovarian cancer cell line_MCAS

description:
ovarian cancer cell line
MCAS

value: MCAS


title: genomic DNA from ovarian cancer cell line_Hey

description:
ovarian cancer cell line
Hey

value: Hey


title: genomic DNA from ovarian cancer cell line_KOC-7c

description:
ovarian cancer cell line
KOC-7c


title: genomic DNA from ovarian surface epithelium_IOSE80

description:
normal
IOSE80

value: normal


title: GN.DBA2#2


title: GN.DBA2#1


title: genomic DNA from ovarian cancer cell line_OVK-18

description:
ovarian cancer cell line
OVK-18

value: cancer


title: GN.DDY#2


title: GN.FVB#2

value: FVB/NJ


title: genomic DNA from ovarian cancer cell line_JHOS-4

description:
ovarian cancer cell line
JHOS-4


title: GN.CE#2

value: CE/J


title: GN.CE#1

value: CD11b+ Ly6G+


title: genomic DNA from lymphocytes 2_43N2_CONTROL

description:
control
43N2_CONTROL_2

value: lymphocytes

value: control


title: GN.CBAJ#1

value: 6 weeks

value: CBA/J

value: Bone Marrow Extract


title: GN.CBACA#2

value: CBA/CaJ

value: Male


title: genomic DNA from ovarian cancer cell line_JHOM-2B

description:
ovarian cancer cell line
JHOM-2B

value: female

value: ovarian cancer


title: genomic DNA from ovarian cancer cell line_JHOC-9

description:
ovarian cancer cell line
JHOC-9


title: GN.CBACA#1


title: GN.CAS#3

value: CAST/EiJ


title: genomic DNA from ovarian cancer cell line_JHOS-2

description:
ovarian cancer cell line
JHOS-2


title: genomic DNA from ovarian cancer cell line_JHOS-3

description:
ovarian cancer cell line
JHOS-3


title: genomic DNA from ovarian surface epithelium_HOSE/E7/hTERT

description:
normal
HOSE/E7/hTERT

value: ovarian surface epithelium


title: genomic DNA from lymphocytes 1_43N2_CONTROL

description:
control
43N2_CONTROL_1


title: Leaf vs. Seedling [sl24]

city: Lucknow

first: Ajit

last: Shasany

state: Uttar Pradesh

address: P.O. CIMAP

department: Biotechnology Division

country: India

institute: CSIR-Central Institute of Medicinal and Aromatic Plants

hyb_protocol: 10.0 µg of the labeled aRNA in 75 µl of Ocimum's Hyb buffer was used for hybridization with the CA028 custom array chip for Artemisia annua designed and printed at Ocimum Biosolutions, Hyderabad. Hybridized chips were scanned using Affymetrix 428TMarray scanner at three different PMT gains and the data was analyzed using Genowiz software from Ocimum Biosolutions.

scan_protocol: Arrays were scanned using an Affymetrix 428 scanner at three PMT settings 40,50 and 60.

data_processing: Image analysis was carried out using Imagene, version 5.6.1. The signal values obtained at three PMT settings 40,50 and 60 were averaged, to get the signal mean for further analysis. Replicate genes were also averaged before normalization. Thus obtained signal values from each channel were log2 transformed and normalized using LOWESS algorithm and MAD scaling. For each sample, Cy3 and Cy5 intensities related to that sample were averaged, and were further used to compare the samples.

organism: Artemisia annua

source_name: Leaf

label_protocol: Five microgram of total RNA was used for amplification using Amino Allyl MessageAmp™ II aRNA Amplification Kit from Ambion by linear transcription based RNA amplification system to produce cRNA. Briefly, mRNA was reverse transcribed with a oligo (dT) primer bearing T7 promoter at 42°C for 2 hrs and second strand cDNA synthesis was carried out at 16°C for 2 hrs. The resulting cDNA was then purified and was then transcribed with T7 RNA polymerase to generate multiple copies of aminoallyl antisense RNA (aRNA) at 37°C for 16 hrs. aRNA was then labelled with Cy3TM/Cy5TM post-labelling reactive dye pack (GE Healthcare, UK) at room temperature and unincorporated Cy3/Cy5  molecules were removed by purification process. Samples were purified using QIAGEN PCR purification kit before hybridization.

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. RNA concentration was determined by measuring its absorbance at 260 and 280 nm using a NanoDrop (NanoDrop, USA) and RNA quality was evaluated by electrophoretic analysis with Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Total RNA that met the quality standards was released for probe generation.

tag: tissue

value: Leaf

source_name: Seedling

value: Seedling


title: Seedling vs. Leaf [sl25]


title: GN.C57L#1


title: GN.CBAJ#2


title: genomic DNA from ovarian cancer cell line_JHOM-1

description:
ovarian cancer cell line
JHOM-1

tag: disease state

value: cancer


title: GN.C57BR#1


title: genomic DNA from ovarian cancer cell line_JHOC-8

description:
ovarian cancer cell line
JHOC-8


title: GN.C57KS#2


title: genomic DNA from ovarian cancer cell line_JHOC-7

description:
ovarian cancer cell line
JHOC-7


title: genomic DNA from ovarian cancer cell line_JHOC-5

description:
ovarian cancer cell line
JHOC-5


title: GN.C57KS#1


title: genomic DNA from ovarian cancer cell line_A2780-NCI

description:
ovarian cancer cell line
A2780-NCI


title: genomic DNA from ovarian cancer cell line_ES-2

description:
ovarian cancer cell line
ES-2


title: GN.C57BR#2


title: GN.CAS#2


title: GN.C57L#2


title: genomic DNA from ovarian cancer cell line_IGROV1-NCI

description:
ovarian cancer cell line
IGROV1-NCI


title: GN.C3H#2


title: genomic DNA from ovarian cancer cell line_Caov-3

description:
ovarian cancer cell line
Caov-3


title: genomic DNA from ovarian cancer cell line_DOV13

description:
ovarian cancer cell line
DOV13


title: GN.C3H#1


title: genomic DNA from ovarian cancer cell line_FUOV1

description:
ovarian cancer cell line
FUOV1


title: GN.Balb#2

value: BTBR T+ tf/J


title: PCB153_8P3_treated_54706502

city: Bergen

first: Fekadu

last: Yadetie

address: Thormøhlensgt. 53A/B

department: Biology

country: Norway

institute: University of Bergen

description:
About 1.5 years old juvenile Atlantic Cod (220–530 g body weight) injected (i.p.) with 8 mg PCB 153/kg BW, and sample collected after 14 days.
The second of 4 biological replicates treated with 8 mg PCB 153/kg BW.

hyb_protocol: Hybridization was performed by Roche NimbleGen, following their standard protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Roche NimbleGen, following their standard protocol. See www.nimblegen.com.

data_processing: Expression values were generated using quantile normalization (Bolstad et al., 2003, Bioinformatics, 19:185), and the Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, Nucleic Acids Res. 31: e15 and Irizarry et al., 2003, Biostatistics 4:249), as performed by NimbleGen. See www.nimblegen.com.

organism: Gadus morhua

source_name: Gadus morhua liver, treated with 8 mg PCB 153/kg BW

label_protocol: Labeling was performed by Roche NimbleGen (Roche NimbleGen , Madison, WI), following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Fish were maintained in 500 l tanks with continuously flowing seawater at 10 °C, 34‰ salinity and a 12h light/dark cycle and fed daily with commercial pellets (EWOS, Bergen, Norway).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit according to the manufacturer's protocol (Qiagen, Inc., Hilden, Germany).

treatment_protocol: After acclimation for 6 days, the fish were injected (i.p.) with vehicle, 0.5, 2 or 8 mg/kg BW PCB 153. The doses were given in two aliquots with 1 week interval. After 14 days of first injection, the fish were sacrificed and tissue sampled.

value: 1.5 years

value: liver

tag: treatment

value: polychlorinated biphenyl 153 (PCB 153)

tag: treatment dosage

value: 8 mg per kg body weight


title: PCB153_8P5_treated_54636702

description:
About 1.5 years old juvenile Atlantic Cod (220–530 g body weight) injected (i.p.) with 8 mg PCB 153/kg BW, and sample collected after 14 days.
The fourth of 4 biological replicates treated with 8 mg PCB 153/kg BW.


title: GN.B6#4

source_name: Bone Marrow

value: 6 weeks

value: CD11b+ Ly6G+


title: GN.BTBR#1

value: Bone Marrow Extract


title: GN.Balb#1


title: genomic DNA from ovarian cancer cell line_41M

description:
ovarian cancer cell line
41M


title: CD56 fraction healthy person H5

city: Saarbrücken

first: Christina

last: Backes

address: Campus, Building E 2.1

department: Chair for Clinical Bioinformatics

description: CD56 fraction healthy person H5

hyb_protocol: Hybridisations were performed in Agilent SureHyb chambers for 20 hours at 55C and washed according to manufacturer's instructions.

scan_protocol: Array-chips were scanned in a high resolution microarray scanner from Agilent Technologies using Scan Control 8.5.1 software, 3 microns resolution in double path mode.

data_processing: Signal intensity values were extracted from the raw data file using feature extraction software (Agilent Technologies). The gTotalProbeSignals were summed up to calculate the total expression value for each miRNA per sample. Quantile normalization was applied to normalize expression values across the arrays using the preprocessCore package of the programming language R. After that we log2-transformed the expression values.

source_name: CD56 cells

label_protocol: Total RNA samples were labelled using the Agilent miRNA Complete Labelling and Hybridisation Kit

extract_protocol: Total RNA including small RNAs was isolated using miRNeasy Micro Kit (Qiagen)  according to manufacturer’s instructions.

value: healthy

value: male

value: CD56 cells


title: CD56 fraction healthy person H6

description: CD56 fraction healthy person H6

value: female


title: GN.BTBR#2

value: Male


title: GN.B6#2


title: GN.B6#3


title: GN.B6#1


title: PCB153_8P4_treated_54706202

description:
About 1.5 years old juvenile Atlantic Cod (220–530 g body weight) injected (i.p.) with 8 mg PCB 153/kg BW, and sample collected after 14 days.
The third of 4 biological replicates treated with 8 mg PCB 153/kg BW.


title: GN.BPL#1

value: BALB/cByJ


title: CD56 fraction healthy person H4

description: CD56 fraction healthy person H4


title: GN.B6#5


title: PCB153_2P4_treated_54706802

description:
About 1.5 years old juvenile Atlantic Cod (220–530 g body weight) injected (i.p.) with 2 mg PCB 153/kg BW, and sample collected after 14 days.
The third of 3 biological replicates treated with 2 mg PCB 153/kg BW.

source_name: Gadus morhua liver, treated with 2 mg PCB 153/kg BW

value: 2 mg per kg body weight


title: GN.B10#1


title: PCB153_2P3_treated_57660802

description:
About 1.5 years old juvenile Atlantic Cod (220–530 g body weight) injected (i.p.) with 2 mg PCB 153/kg BW, and sample collected after 14 days.
The second of 3 biological replicates treated with 2 mg PCB 153/kg BW.


title: CD56 fraction healthy person H3

description: CD56 fraction healthy person H3


title: GN.B10#3


title: GN.AKR#2

value: AKR/J


title: CD56 fraction healthy person H2

description: CD56 fraction healthy person H2


title: CD56 fraction healthy person H1

description: CD56 fraction healthy person H1


title: GN.AKR#1


title: PCB153_0.5P6_treated_54560202

description:
About 1.5 years old juvenile Atlantic Cod (220–530 g body weight) injected (i.p.) with 0.5 mg PCB 153/kg BW, and sample collected after 14 days.
The fourth of 4 biological replicates treated with 0.5 mg PCB 153/kg BW.

source_name: Gadus morhua liver, treated with 0.5 mg PCB 153/kg BW

value: 0.5 mg per kg body weight


title: GN.AJ#2

value: A/J


title: PCB153_8P2_treated_57660402

description:
About 1.5 years old juvenile Atlantic Cod (220–530 g body weight) injected (i.p.) with 8 mg PCB 153/kg BW, and sample collected after 14 days.
The first of 4 biological replicates treated with 8 mg PCB 153/kg BW.

value: 1.5 years


title: PCB153K3_control_54706402

description:
About 1.5 years old juvenile Atlantic Cod (220–530 g body weight) injected (i.p.) with vehicle (20% acetone and 80% soybean), and sample collected after 14 days.
The second of 4 biological replicate controls.

source_name: Gadus morhua liver, control

value: liver

value: vehicle control


title: PCB153_0.5P5_treated_57661102

description:
About 1.5 years old juvenile Atlantic Cod (220–530 g body weight) injected (i.p.) with 0.5 mg PCB 153/kg BW, and sample collected after 14 days.
The third of 4 biological replicates treated with 0.5 mg PCB 153/kg BW.

value: polychlorinated biphenyl 153 (PCB 153)


title: PCB153_2P2_treated_54560702

description:
About 1.5 years old juvenile Atlantic Cod (220–530 g body weight) injected (i.p.) with 2 mg PCB 153/kg BW, and sample collected after 14 days.
The first of 3 biological replicates treated with 2 mg PCB 153/kg BW.


title: CD56 fraction lung cancer patient L5

description: CD56 fraction lung cancer patient L5

value: small cell lung carcinoma


title: PCB153K5_control_54706102

description:
About 1.5 years old juvenile Atlantic Cod (220–530 g body weight) injected (i.p.) with vehicle (20% acetone and 80% soybean), and sample collected after 14 days.
The fourth of 4 biological replicate controls.


title: CD56 fraction lung cancer patient L6

description: CD56 fraction lung cancer patient L6

value: Lung adenocarcinoma


title: CD56 fraction lung cancer patient L10

description: CD56 fraction lung cancer patient L10


title: CD56 fraction lung cancer patient L4

description: CD56 fraction lung cancer patient L4


title: GN.AJ#1

value: 6 weeks

value: CD11b+ Ly6G+

value: Bone Marrow Extract


title: PCB153K4_control_57660702

description:
About 1.5 years old juvenile Atlantic Cod (220–530 g body weight) injected (i.p.) with vehicle (20% acetone and 80% soybean), and sample collected after 14 days.
The third of 4 biological replicate controls.


title: Cortex_cKO_P0_rep2

city: Ottawa

first: David

last: Picketts

state: Ontario

address: 501 Smyth Road

country: Canada

institute: University of Ottawa

hyb_protocol: streptavidin phycoerythrin.

scan_protocol: GeneArray Scanner at 488nm wavelength.

data_processing: The data were analyzed with FlexMicroarray and Affymetrix Power Tools using RMA as normalization method. Gene level was used as summary level and log transformed.

source_name: Cortex from cKO-Emx1 mice at P0

label_protocol: Biotinylated cRNA.

growth_protocol: P0 mouse cortex.

extract_protocol: Trizol RNA extraction, followed by RNA-Easy column purification.

treatment_protocol: 3 cortices pooled per sample, n=2 per genotype.

value: cortex

tag: strain

tag: genotype

tag: developmental stage


title: CD3 fraction healthy person H6

description: CD3 fraction healthy person H6

source_name: CD3 cells

value: healthy

value: female

tag: age

value: CD3 cells


title: GN.129#2

tag: genetic background

value: Male


title: PCB153K2_control_54706702

description:
About 1.5 years old juvenile Atlantic Cod (220–530 g body weight) injected (i.p.) with vehicle (20% acetone and 80% soybean), and sample collected after 14 days.
The first of 4 biological replicate controls.


title: CD56 fraction lung cancer patient L2

description: CD56 fraction lung cancer patient L2

value: CD56 cells


title: CD56 fraction lung cancer patient L3

description: CD56 fraction lung cancer patient L3

value: squamous cell carcinoma

value: male


title: PCB153_0.5P2_treated_54560902

description:
About 1.5 years old juvenile Atlantic Cod (220–530 g body weight) injected (i.p.) with 0.5 mg PCB 153/kg BW, and sample collected after 14 days.
The first of 4 biological replicates treated with 0.5 mg PCB 153/kg BW.

value: 1.5 years

value: 0.5 mg per kg body weight


title: CD3 fraction healthy person H5

description: CD3 fraction healthy person H5


title: Cortex_cKO_P0_rep1


title: GN.129#1

tag: phenotype markers


title: CD3 fraction healthy person H4

description: CD3 fraction healthy person H4


title: Cortex_control_P0_rep2

source_name: Cortex from control mice at P0


title: CD3 fraction healthy person H3

description: CD3 fraction healthy person H3


title: GN.BPL#2

value: BALB/cByJ


title: PCB153_0.5P3_treated_54560602

description:
About 1.5 years old juvenile Atlantic Cod (220–530 g body weight) injected (i.p.) with 0.5 mg PCB 153/kg BW, and sample collected after 14 days.
The second of 4 biological replicates treated with 0.5 mg PCB 153/kg BW.

value: liver

value: polychlorinated biphenyl 153 (PCB 153)


title: Cortex_control_P0_rep1


title: CTRL.24H 22175

city: New York

first: Bin

last: Ye

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

scan_protocol: Affymetrix Gene Chip 3000 7G scanner, software AGCC v2.0

data_processing:
Probe intensities were extracted from Affymetrix CEL files and normalized using RMA and summarized at the transcript cluster level using the R/Bioconductor (http://bioconductor.org) oligo package.  Array quality control was performed to remove arrays that significantly differed in performance.  Significance testing was performed by fitting gene-wise linear models using the limma Bioconductor package.  Significance testing was performed using a moderated t-test.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

source_name: control, 24 hours

label_protocol: standard Affymetrix protocol

growth_protocol: Macrophages were plated to achieve a density of 8 x 106 cells at the time of infection on 10 cm2 dishes.

extract_protocol: RNA was extracted using a RNeasy Mini Kit (Qiagen, Valencia, CA, USA) and stored at -80C until analysis.

treatment_protocol: Cn was heat-killed (HK Cn) by incubating at 60°C for 60 min. Cn were added at a Multiplicity of Infection (MOI) of 1:2 (unless otherwise noted) along with capsular monoclonal antibody (mAb) 18B7 {Casadevall:1998uk} at 5 µg/mL as an opsonin. Phagocytosis was allowed to proceed for 2 or 24 hours at 37°C under 5% CO2 atmosphere.

value: Macrophage

tag: infection

value: control

tag: time

value: 24 hours

value: J774.16 derived from J774 cell line from Balb/C ascites


title: CCRF-CEM cells treated with A-769662 (gene), replicate 3

city: Esch-sur-Alzette

first: Ines

last: Thiele

address: 7, avenue des Hauts-Fourneaux

department: Luxembourg Centre for Systems Biomedicine

country: Luxembourg

institute: University of Luxembourg

description: CCRF-CEM cells treated with A-769662

hyb_protocol: standard Affymetrix protocol by Aros (Aarhus, Denmark)

data_processing:
We generated DABG calls using ROOT (version 22) and XPS package for R (version 11.1). Calls for data mapping were assigned based on p<0.05 as cutoff probability distinguishing presence versus absence of genes. All 18 data sets were summarized for this analysis, using RMA.    Analysis for differential gene expression and alternative splicing were performed using AltAnalyse software (v2.02beta) using default options from raw data (CEL) files and Homo sapiens Ensemble release 65 database, probe set filtering was kept as DABG p-value < 0.05 and non-log expression < 70 for constitutive probe sets to determine gene expression levels. AltAnalyse relies on RMA for normalization.  For the comparison, CCRF-CEM was the experimental and Molt-4 the baseline group, and only CEL files of CCRF-CEM cells control replicate 1-3, and Mot-4 cells control replicate 1-3 were introduced into the analysis. The set of differentially expressed genes among cell lines was identified based on a p<0.05 FDR cutoff. Alternative splicing analysis was performed on core probe sets with a minimum alternative exon score of 2 and a maximum absolute gene expression change of 3.
AltAnalyze & XPS: HuEx-1_0-st-v2.r2.pgf
Bioconductor XPS package was used to generate Detection above background (DABG) calls after RMA normalisation for the entire data set of 18 CEL files (MixRMAMetacore and MixDABGMetacore_pval). Additionally, higher-level analysis of Differential gene expression (DATASET-CompareCelllines(geneLevel)) and Alternative splicing (Hs_Exon_C_vs_M.p5_average-splicing-index-exon-inclusion-GENE-results) were carried out for a subset of 6 CEL files (A834_01-A834_03 and A834_10-A834_12) using Altanalyse software after pre-processing of the  Affymetrix CEL files by AltAnalyze (using APT and RMA). Expression values for the RMA normalization for the subset of 6 CEL files (exp.CompareCellines(probesetLevel)).

source_name: CCRF-CEM cells

extract_protocol: Molt-4 and CCRF-CEM growing in RPMI advanced, 2 mM glutamax were resuspended in medium containing DMSO (0.67%) or 0.5 mM AICAR or 0.1 mM A-769662 at a cell concentration of 5 x 105 cells/ml. 2 ml cell suspensions were seeded in 12 well plates in triplicates. After 48 hrs of growth the cells were collected by centrifugation at 201 x g for 5 min. Cell pellets were snap frozen in liquid N2 and kept frozen until RNA extraction and analysis by Aros (Aarhus, Denmark).

value: CCRF-CEM cells


title: HK.2H 22174

source_name: heat killed Cn infection, 2 hours

value: heat killed Cn infection

value: 2 hours


title: GOS Versus Ribose

city: Cork

first: Mary

last: O'Connell Motherway

address: Western Road

department: Department of Microbiology and Alimentary Pharmabiotic Centre

country: Ireland

institute: University College Cork

description: Biological replicate 1

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing:
Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).
DNA-microarray data were processed as previously described (Garcia De La Nava, J., D. F. Santaella, J. C. Alba, J. M. Carazo, O. Trelles & A. Pascual-Montano, (2003) Engene: the processing and exploratory analysis of gene expression data. Bioinformatics 19: 657-658., van Hijum, S. A. F. T., J. Garcia De La Nava, O. Trelles, J. Kok & O. P. Kuipers, (2003) MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics. 2: 241-244., van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77). Data were Lowess normalized. The VALUE column contains normalized log10 potato galactan/ribose ratios from a single array experiment.

organism: Bifidobacterium breve UCC2003

source_name: Bifidobacterium breve UCC2003

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

growth_protocol:
Bifidobacterium breve UCC2003 was grown in modified de Man, Rogosa and Sharpe (mMRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), made from first principles, supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and 1% (w/v) of PGOS  or Ribose as the sole carbon source. Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) untill OD600 was 0.5.
Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

extract_protocol: RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

tag: growth protocol

value: GOS

value: Ribose


title: HK.24H 22177

source_name: heat killed Cn infection, 24 hours

tag: cell type


title: CD56 fraction lung cancer patient L11

description: CD56 fraction lung cancer patient L11

value: Lung adenocarcinoma

tag: gender

value: CD56 cells


title: GOS Versus Ribose dye swap

description: Biological replicate 2


title: CD3 fraction healthy person H1

description: CD3 fraction healthy person H1

value: healthy

value: female

value: CD3 cells


title: CD3 fraction healthy person H2

description: CD3 fraction healthy person H2


title: CD3 fraction lung cancer patient L10

description: CD3 fraction lung cancer patient L10


title: LIVE.24H 22176

source_name: live Cn infection, 24 hours

value: live Cn infection


title: CTRL.2H 22172

source_name: control, 2 hours


title: CD3 fraction lung cancer patient L6

description: CD3 fraction lung cancer patient L6

value: male


title: CCRF-CEM cells treated with A-769662 (gene), replicate 2

description: CCRF-CEM cells treated with A-769662

scan_protocol: standard Affymetrix protocol by Aros (Aarhus, Denmark)


title: CCRF-CEM cells treated with A-769662 (gene), replicate 1

description: CCRF-CEM cells treated with A-769662

label_protocol: standard Affymetrix protocol by Aros (Aarhus, Denmark)


title: CCRF-CEM cells treated with AICAR (gene), replicate 3

description: CCRF-CEM cells treated with AICAR

value: AICAR


title: CCRF-CEM cells treated with AICAR (gene), replicate 2

description: CCRF-CEM cells treated with AICAR


title: CCRF-CEM cells treated with AICAR (gene), replicate 1

description: CCRF-CEM cells treated with AICAR


title: LIVE.2H 22173

source_name: live Cn infection, 2 hours

value: Macrophage


title: CCRF-CEM cells control (gene), replicate 3

description: CCRF-CEM cells control

value: control


title: HK.24H 21828

value: 24 hours


title: CTRL.24H 21826

value: J774.16 derived from J774 cell line from Balb/C ascites


title: LIVE.24H 21827


title: HK.2H 21822


title: CD3 fraction lung cancer patient L11

description: CD3 fraction lung cancer patient L11


title: CTRL.2H 21820


title: CD3 fraction lung cancer patient L5

description: CD3 fraction lung cancer patient L5

value: small cell lung carcinoma


title: CD3 fraction lung cancer patient L3

description: CD3 fraction lung cancer patient L3

value: squamous cell carcinoma


title: CD3 fraction lung cancer patient L4

description: CD3 fraction lung cancer patient L4


title: CD3 fraction lung cancer patient L2

description: CD3 fraction lung cancer patient L2


title: LIVE.2H 21821

value: 2 hours


title: CD19 fraction healthy person H6

description: CD19 fraction healthy person H6

source_name: CD19 cells

value: CD19 cells


title: CD19 fraction healthy person H5

description: CD19 fraction healthy person H5


title: CD19 fraction healthy person H4

description: CD19 fraction healthy person H4


title: HK.24H 21689

value: heat killed Cn infection


title: CCRF-CEM cells control (gene), replicate 1

description: CCRF-CEM cells control

value: CCRF-CEM cells


title: CCRF-CEM cells control (gene), replicate 2

description: CCRF-CEM cells control


title: HK.2H 21687


title: Molt-4 cells treated with A-769662 (gene), replicate 1

description: Molt-4 cells treated with A-769662

source_name: Molt-4 cells

value: Molt-4 cells


title: CD19 fraction healthy person H3

description: CD19 fraction healthy person H3

value: healthy


title: CD19 fraction healthy person H2

description: CD19 fraction healthy person H2

value: female


title: Molt-4 cells treated with A-769662 (gene), replicate 2

description: Molt-4 cells treated with A-769662


title: LIVE.24H 21686


title: LIVE.2H 21684


title: Molt-4 cells treated with AICAR (gene), replicate 3

description: Molt-4 cells treated with AICAR


title: CD19 fraction healthy person H1

description: CD19 fraction healthy person H1


title: CTRL.2H 21683


title: Molt-4 cells treated with AICAR (gene), replicate 2

description: Molt-4 cells treated with AICAR


title: CTRL.24H 21682


title: Molt-4 cells treated with AICAR (gene), replicate 1

description: Molt-4 cells treated with AICAR


title: HK.2H 21492


title: HK.24H 21494


title: Molt cells control (gene), replicate 3

description: Molt-4 cells control


title: Molt cells control (gene), replicate 2

description: Molt-4 cells control


title: LIVE.24H 21491


title: CD19 fraction lung cancer patient L6

description: CD19 fraction lung cancer patient L6

value: Lung adenocarcinoma


title: CD19 fraction lung cancer patient L10

description: CD19 fraction lung cancer patient L10


title: CD19 fraction lung cancer patient L11

description: CD19 fraction lung cancer patient L11


title: CD19 fraction lung cancer patient L5

description: CD19 fraction lung cancer patient L5


title: CD19 fraction lung cancer patient L4

description: CD19 fraction lung cancer patient L4


title: KKAyLiver_11week_rep1

city: Sapporo

first: Hayashi

last: Yasuhiro

address: Kita-12, Nishi-6, Kita-ku

department: Faculty of Pharmaceutical Sciences

institute: Hokkaido University

description: 11w KKAy liver_1

hyb_protocol: 1.65 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 10x Blocking Agent and 25x Fragmentation Buffer following the manufacturer's instructions. On completion of the fragmentation reaction, 55 μl of 2x GE Hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 μm, Dye channel is set to Green and Green PMT is set to both XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014868_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The 75th percentile, baseline to median of all samples was used as the normalization method (GeneSpring).

source_name: KKAy liver, 11 weeks

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling kit, One-Color (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: All mice used in this study were maintained on a 12-hour light-dark cycle and fed a standard rodent chow. Mice were fasted overnight for 13.5 hours.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (QIAGEN Inc.) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: KKAy

value: 11 weeks

value: liver

value: diabetes


title: Molt cells control (gene), replicate 1

description: Molt-4 cells control

value: control


title: LIVE.2H 21489

value: Macrophage

value: live Cn infection


title: CTRL.24H 21488

value: 24 hours

value: J774.16 derived from J774 cell line from Balb/C ascites


title: Molt-4 cells treated with A-769662 (gene), replicate 3

description: Molt-4 cells treated with A-769662


title: KKAyLiver_4week_rep1

description: 4w KKAy liver_1

source_name: KKAy liver, 4 weeks

value: 4 weeks


title: KKAyLiver_4week_rep2

description: 4w KKAy liver_2


title: CD19 fraction lung cancer patient L3

description: CD19 fraction lung cancer patient L3

value: squamous cell carcinoma

value: male

value: CD19 cells


title: CD19 fraction lung cancer patient L2

description: CD19 fraction lung cancer patient L2


title: C57BLLiver_11week_rep1

description: 11w C57 liver_1

source_name: C57BL/6J liver, 11 weeks

value: normal


title: CTRL.2H 21486

value: 2 hours


title: C57BLLiver_11week_rep2

description: 11w C57 liver_2


title: KKAyLiver_11week_rep2

description: 11w KKAy liver_2


title: CD15 fraction healthy person H7

description: CD15 fraction healthy person H7

source_name: CD15 cells

value: healthy

value: female

value: CD15 cells


title: kdm5 mutant, biological rep3

city: Bronx

first: Julie

last: Secombe

state: United states

address: 1300 Morris park ave. Ullmann 809

institute: Albert einstein college of medicne

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45oC on GeneChip Drosophila Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000 (Affymetrix).

data_processing: CEL files were generated from DAT files using GCOS software (Affymetrix). Data were processed with Expression Console (Affymetrix) using the PLIER algorithm and Array Assist Lite software was used to generate GC-RMA files (log2 transformed) for each chip.

organism: Drosophila melanogaster

source_name: wing discs, third larva stage, kdm5 mutant

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Fly stocks were grown at 25oC on standard media, 60% humidity and a 12 hour light/dark cycle.

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

treatment_protocol: Wing imaginal discs were dissected from 3rd instar larvae (96hr AED) in PBS before being placed in Trizol for RNA extraction.

tag: strain/background

tag: genotype/variation

value: kdm5 mutant

value: wing imaginal discs

value: third instar larva


title: kdm5 mutant, biological rep2

tag: tissue


title: oocyte_Brwd1_mutant_rep3

city: Bar Harbor

first: Timothy

middle: Michael

last: Stearns

state: ME

address: 600 Main Street

department: Computational Sciences

institute: The Jackson Laboratory

description: GC_Gene1-0ST_GES12_38556_430-CNX-120323-24-39295_1.CEL

hyb_protocol: Following fragmentation and labeling , 2ug of cDNA were hybridized for 18 hr at 45C on GeneChip Mouse Gene ST 1.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Average signal intensities for each probe set within arrays were calculated by and exported from Affymetrix’s Expression Console (Version 1.1) software using the RMA method which incorporates convolution background correction, sketch-quantile normalization, and summarization based on a multi-array model fit robustly using the median polish algorithm.

source_name: Brwd1 mutant_GV-stage_oocytes

label_protocol: Fragmented biotinylated cDNA were produced from 1ng total RNA according to the standard protocol using the Ovation Pico WTA System V2 from Nugen for amplification and the Encore Biotin Module from Nugen for fragmentation and labeling.

growth_protocol: Oocytes were isolated from 2-6 month old female mice

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Micro kit according to the manufacturers instructions.

treatment_protocol: The mice were injected with 5 IU equine chorionic gonadotropin 44 h before oocyte isolation

tag: strain background

value: Brwd1 mutant

value: germinal vesicle (GV) stage

value: oocytes (100 cells)


title: kdm5 mutant, biological rep1


title: CD15 fraction healthy person H6

institute: Saarland University

description: CD15 fraction healthy person H6

tag: disease state


title: C57BLLiver_4week_rep2

description: 4w C57 liver_2

source_name: C57BL/6J liver, 4 weeks

value: liver


title: oocyte_Brwd1_mutant_rep2

description: GC_Gene1-0ST_GES12_38555_430-CNX-120323-24-39295_1.CEL


title: wt, biological rep2

source_name: wing discs, third larva stage, WT

value: WT


title: CD15 fraction healthy person H5

description: CD15 fraction healthy person H5


title: C57BLLiver_4week_rep1

description: 4w C57 liver_1

value: 4 weeks


title: wt, biological rep3


title: oocyte_wildtype_rep3

description: GC_Gene1-0ST_GES12_38553_430-CNX-120323-24-39295_1.CEL

value: wildtype


title: wt, biological rep1


title: CD15 fraction healthy person H3

description: CD15 fraction healthy person H3

value: male


title: CD15 fraction healthy person H2

description: CD15 fraction healthy person H2


title: Gfi1b wild type Ter119 positive cells 2

city: Essen

first: Cyrus

last: Khandanpour

state: NRW

address: Hufelandstr. 55

department: Department of Hematology

institute: University Hospital Of Essen

description: Gene expression data from fetal liver derived Gfi1b wild type erythroid cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized with Affymetrix Mouse Gene 1.0 ST Arrays and Scanned

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

data_processing:
Data was processed using the AltAnalyze software V 2.08 (www.altanalyze.org) using the default parameters.
Cel Layout File: MoGene-1_0-st-v1.r4.clf
BackGround Probe File:  MoGene-1_0-st-v1.r4.bgp
Probe Group File: MoGene-1_0-st-v1.r4.pgf
The MoGene-1_0-st arrays used allow for a limited splicing analysis, or for a gene level analysis. Here we provide the gene-level analysis calculated by AltAnalyze using exclusively default parameters. During the gene level analysis process, AltAnalyze automatically remaps the transcript cluster IDs to Ensemble gene IDs if not chosen differently in the parameter settings.
We used the following (default) Expression Dataset Parameters:
-Remove probesets with DABG p-value above: 0.05
-Remove probesets expressed below (non-log): 1
-Perform alternative exon analysis: yes (calculated, but not provided here)
-Organize samples in groups: yes
-Determine gene expression levels using: constitutive probesets
-Include replicate experiment values in export: yes
-Comparison group test statistic: moderate t-test
-Remove batch effects (Combat): no
-Predict condition specific biomarkers: yes
-Perform expression clustering and visual QC: yes
-Perform cell profiling with LineageProfiler: yes
-Analyze ontologies and pathways with GO-Elite: yes
-Select the primary relational gene database used: Ensembl
Probesets were remapped to Ensembl genes by AltAnalyze internally using the matrix file "Mm_Ensembl_probesets" as a part of the "Gene level Analysis" process.

source_name: Mouse fetal liver 14.5 dpc

label_protocol: Target RNA was reverse transcried into cDNA and in-vitro transcription was performed according to the standard Affymetrix protocol from 10 ug total RNA to generate biotin-labeled cRNA.

growth_protocol: Mice were housed under Specific Pathogen Free (SPF) conditions

extract_protocol: TRIzol (Invitrogen) was used to isolate total RNA following the manufacturers instructions.

treatment_protocol: untreated

value: Ter119 positive erythroid cells

value: Gfi1b wild type


title: oocyte_Brwd1_mutant_rep1

description: GC_Gene1-0ST_GES12_38554_430-CNX-120323-24-39295_1.CEL


title: CD15 fraction healthy person H1

description: CD15 fraction healthy person H1


title: oocyte_wildtype_rep1

description: GC_Gene1-0ST_GES12_38551_430-CNX-120323-24-39295_1.CEL


title: oocyte_wildtype_rep2

description: GC_Gene1-0ST_GES12_38552_430-CNX-120323-24-39295_1.CEL


title: Gfi1b wild type Ter119 positive cells 1


title: CD15 fraction lung cancer patient L11

description: CD15 fraction lung cancer patient L11

value: Lung adenocarcinoma


title: CD15 fraction lung cancer patient L10

description: CD15 fraction lung cancer patient L10


title: CD15 fraction lung cancer patient L6

description: CD15 fraction lung cancer patient L6


title: CD15 fraction healthy person H4

description: CD15 fraction healthy person H4

value: healthy


title: Gfi1b knock-out Ter119 positive cells 1

description: Gene expression data from fetal liver derived Gfi1b conditional knockout erythroid cells

value: Gfi1b knock-out


title: CD15 fraction lung cancer patient L5

description: CD15 fraction lung cancer patient L5

value: small cell lung carcinoma

value: female

value: CD15 cells


title: Low-PMI-2

city: Wuhan

first: Yi

last: Huang

state: Hubei

address: No. 2 Xudong Second Road, Wuchang District

department: Rapeseed Genetics and Breeding

country: China

institute: Oil Crops Research Institute, Chinese Academy of Agricultural Sciences

description: A Brassica genomics resource was developed at the Plant Biotechnology Institute, National Research Council Canada (PBI-NRC) and Agriculture and Agri-Food Canada (AAFC) in collaboration with other institutes. About 95,418 unique sequences were assembled using 781,826 EST sequences mainly from three species: B. napus, B. rapa, and B. oleracea. These unique sequences were submitted to CombiMatrix for the development of a 35-40mer oligonucleotide microarray, for which probes were synthesized in situ onto electrodes on a microchip. The customized Combimatrix Brassica array comprised 90,500 probes and was called as 90K array.

hyb_protocol: 1. The pre-hybridization and hybridization procedures were performed precisely according to the protocol of CombiMatrix (www.combimatrix.com).   2. Cy5 dye-labeled RNA populations from individual tissue samples were hybridized to the 90K array and three biological replicates were performed.

scan_protocol: 1. Hybridized arrays were scanned using a LuxScan 10K Scanner (CapitalBio Corporation, Beijing, China) at 5 μm resolution, 100% laser power, and different PMT values to obtain a similar overall intensity between slides.   2. The scans were saved as TIF files.

data_processing: 1. Raw spot fluorescence intensities were collected using LuxScan version 2.0 (CapitalBio Corporation, Beijing, China) and saved as .txt file.   2. Samples that were originally negative after background subtraction and those with an overall signal intensity of less than 100 were filtered out.   3. Array features annotated as “Empty”, “Blank”, and internal controls were flagged and excluded from the analysis.  4. Twelve LSR files containing the raw probe intensity values were imported into R and the signal intensities were quantile normalization was performed to normalize between arrays using the R-package LIMMA [24] with a 5% false discovery rate (FDR<=0.05).   5. Probes with at least one missing value within triplicates were removed from subsequent analysis.   6. The background-corrected signal intensity of each probe on the array was combined by averaging three biological replicates.   7. A gene was considered to be differentially expressed when its fold-change in expression between two samples was larger than 1.5- or less than 0.67-fold.

organism: Brassica napus

source_name: main inflorescence

label_protocol: 1. About 3.0 µg of total RNA for each sample was reverse transcribed into amino allyl-modified aRNA using a Message™ II aRNA Amplification Kit (Cat: 1753, Ambion, Austin, TX, USA), according to the manufacturer's protocol.   2. The quality of amplification was identified using agarose gel electrophoresis, and the aRNA yield was quantified using a NanoDrop® 1000 spectrophotometer.   3. The aRNA was selected as the template for fluorescent target preparation for microarray experiments.  4. About 5.0 µg of aRNA was labeled with mono-reactive NHS esters of Cy5 in the dark for 30 min at room temperature, and the samples were then purified and used as targets for hybridization.

growth_protocol: 1. Two elite Brassica napus L. lines, cv. Zhongshuang 11 (ZS11), which was used for genome sequencing, and 73290, which was used for re-sequencing, developed by the Rapeseed Biotechnology Breeding Unit, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences (Wuhan, China), were used to generate an F2:3 population harboring 183 offspring for QTL mapping of yield traits.    2. Subsequently, an F6 inbred line (RIL) population was obtained from the F2:3 population by single-seed-descendant. Nine lines with an extremely high number of PMIs and Nine with an extreme number were selected from the above F6 RIL population. Afterwards, ZS11, 73290, and the 18 extreme RIL lines were used for gene expression profiling analysis in the main inflorescence.

extract_protocol: 1. Using an RNeasy Mini Kit (Cat. 74124, Qiagen, Mississauga, ON) according to the manufacturer’s recommendations, total RNA of inflorescence primordia was extracted in biological triplicate, each consisting of three main inflorescence sections taken from three independent plants.   2. Trace amounts of DNA were removed using DNase I (Cat. 18068-015, Invitrogen, USA).   3. The RNA yield and purity were determined spectrophotometrically with a NanoDrop®1000 spectrophotometer (Thermo Fisher Scientific, USA), and the intactness of RNA was verified by electrophoresis on a 1% agarose gel with 1×TBE running buffer at 70 V for 40 min.   4. Purified total RNA was precipitated and re-suspended in DEPC-treated water to a final concentration of about 500 ng/µL.   5. For the extreme PMI lines, the total RNA of inflorescence primordia was extracted individually and pooled at equal concentrations within each extreme-PMI group. Nine lines were used for each biological replicate in the reverse transcription analysis.

treatment_protocol: 1. Seeds were sown on May 17, 2011 in the experimental station of Qinghai University (Xining, Qinghai Province, China).   2. Individual plants of each accession, which did not exhibit any obvious phenotypic differences, were reserved by eliminating potential false types at several developmental stages.  3. The development of the main inflorescence (MI) was observed under an anatomical microscope (OLympus, Japan). The inflorescence primordia of three to five plants for each accession was examined every three days under the microscope, beginning at the eighth leaf stage.   4. The main inflorescence primordia of five plants per line that were at the pistil-stamen primordia initiation stage of the first floral on the main inflorescence, were harvested in the morning, immediately frozen in nitrogen, and then kept at -80⁰С for total RNA isolation.

tag: pmi line

value: Low-PMI


title: Low-PMI-3


title: High-PMI-3

value: High-PMI


title: CD15 fraction lung cancer patient L4

description: CD15 fraction lung cancer patient L4


title: DSNs, biological rep1

city: Dalian

first: Ying

last: Ge

address: 9 Western Section, Lvshun South Street

institute: Dalian Medical University

description:
DSNs_r1
tumor bearing mice were treated with 10 mg/kg of docetaxel-loaded solid lipid nanoparticles (DSNs) by tail vein injection with the frequency of every 4 days. Mice were sacrificed on day 12 (D12) and tumor tissues were isolated.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized with Genechip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned with Genechip Scanner 3000

data_processing: The expression raw data was preprocessed using Robust Multichip Analysis (RMA) with quantile normalization and custom CDF file hgu133plus2hsentrezgcdf, v17.1.0

source_name: tumor treated by DSNs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Tumor suppression effects of DSNs and TAX were investigated with tumor-bearing female BALB/c nude mice in JOINN Laboratories (Beijing, China). BALB/c nude mice were purchased from Vital River Laboratories (Beijing, China). Mice were subcutaneous injected with MCF-7 cells. After three weeks, the tumor bearing mice were sacrificed for further experiments. The tumor tissues were isolated and cut into pieces at about 2 mm3 under aseptic conditions. Around 4-5 weeks old mice were subcutaneously inoculated with tumor tissues on the right flank. Tumors were allowed to grow to about 50-100 mm3.

treatment_protocol: Mice bearing similar volume of tumors were chosen and divided into four groups randomly with 6 mice in each group. Mice from different groups were treated with 10 mg/kg of TAX, DSNs, equivalent BSNs or glucose (GLU) separately by tail vein injection with the frequency of every 4 days. Body weight and tumor size were measured every 3 days. Mice were sacrificed on day 12 (D12) and tumor tissues were isolated and frozen in liquid nitrogen immediately for RNA isolation

tag: treatment (of tumor-bearing female balb/c nude mice)

value: tumor


title: DSNs, biological rep2

description:
DSNs_r2
tumor bearing mice were treated with 10 mg/kg of docetaxel-loaded solid lipid nanoparticles (DSNs) by tail vein injection with the frequency of every 4 days. Mice were sacrificed on day 12 (D12) and tumor tissues were isolated.


title: TAX, biological rep2

description:
TAX_r2
tumor bearing mice were treated with 10 mg/kg of Taxotere (TAX) by tail vein injection with the frequency of every 4 days. Mice were sacrificed on day 12 (D12) and tumor tissues were isolated.

source_name: tumor treated by TAX

value: Taxotere


title: TAX, biological rep1

description:
TAX_r1
tumor bearing mice were treated with 10 mg/kg of Taxotere (TAX) by tail vein injection with the frequency of every 4 days. Mice were sacrificed on day 12 (D12) and tumor tissues were isolated.


title: High-PMI-1


title: High-PMI-2


title: Low-PMI-1


title: BSNs, biological rep1

description:
BSNs_r1
tumor bearing mice were treated with 10 mg/kg of blank solid lipid nanoparticles (BSNs) by tail vein injection with the frequency of every 4 days. Mice were sacrificed on day 12 (D12) and tumor tissues were isolated.

source_name: tumor treated by BSNs

value: blank solid lipid nanoparticles


title: 73290-3

tag: parental line


title: 73290-2


title: Gfi1b knock-out Ter119 positive cells 2


title: CD15 fraction lung cancer patient L3

description: CD15 fraction lung cancer patient L3

value: squamous cell carcinoma


title: CD15 fraction lung cancer patient L2

description: CD15 fraction lung cancer patient L2