title: RA Synovial biopsy T12 post-adalimumab therapy, Poor Responder 1

status: Public on Apr 15 2009

city: Brussels

first: Bernard

middle: Robert

last: Lauwerys

address: Avenue Hippocrate 10

department: Institut de Recherches Expérimentales et Cliniques

country: Belgium

institute: Université catholique de Louvain

description: Patient has rheumatoid arthritis (RA), according to the American College of rheumatology criteria for the diagnosis of RA. All patients included in this study had active disease at the time of initiation of adalimumab therapy and were resistant to conventional therapy. They all had erosive changes imaged on conventional x-rays of the hands and/or feet. All patients were treated with disease-modifying antirheumatic drugs (DMARD’s), 23 with methotrexate (median dose 15 mg/week, range 7.5 – 20 mg/week), and 2 with leflunomide (20 mg/day); 18 of them were treated with low-dose steroids (prednisolone ≤ 7.5 mg/day). Six patients had been included in double-blind clinical trials before inclusion in the present study (1 in a Golimumab versus placebo trial, 3 in a MapKinase inhibitor versus placebo trial and 2 in a TACE-inhibitor versus placebo trial). These trials were stopped at least 3 months prior to initiation of TNF-blocking therapy. All drug dosages were stable from at least 3 months prior to initiation of TNF blocking therapy until completion of the study. No steroid injections were allowed during the duration of the study.

hyb_protocol: GeneChip® Human genome U133 Plus 2.0 Arrays (spotted with 1,300,000 oligonucleotides informative for 47,000 transcripts originated from 39,000 genes, Affymetrix UK Ltd, High Wycombe, UK) were hybridized overnight at 45°c in monoplicates with 10 μg cRNA. The slides were then washed and stained using the EukGE-WS2v5 Fluidics protocol on the Genechip® Fluidics Station (Affymetrix) before being scanned on a Genechip® Scanner 3000.

scan_protocol: The slides were scanned on a Genechip® Scanner 3000.

data_processing: For the initial normalization and analysis steps, data were retrieved on Affymetrix GCOS software. The frequency of positive genes (genes with a flag present) was between 45 and 55% on each slide. After scaling of all probe sets to a value of 100, the amplification scale was reported inferior to 3.0 for all slides. The signals yielded by the poly-A RNA, hybridization and housekeeping controls (GAPDH 3’/5’ ratio < 2) were indicative of the good quality of the amplification and hybridization procedures.

source_name: Synovial biopsy, RA patient, 12 weeks after adalimumab therapy, poor responder

label_protocol: Labeling of RNA (cRNA synthesis) was performed according to a standard Affymetrix® procedure (One-Cycle Target Labeling kit, Affymetrix UK Ltd., High Wycombe, UK); briefly total RNA was first reverse transcribed into single-stranded cDNA using a T7-Oligo(dT) Promoter Primer and Superscript II reverse transcriptase. Next, RNase H was added together with E. Coli DNA polymerase I and E. Coli DNA ligase, followed by a short incubation with T4 DNA polymerase in order to achieve synthesis of the second-strand cDNA. The purified double-stranded cDNA served as the template for the in vitro transcription reaction, which was carried out overnight in the presence of T7 RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix. At the end of this procedure, the biotinylated complementary RNA (cRNA) was cleaned, and fragmented by a 35-minute incubation at 95°c.

extract_protocol: Total RNA was extracted from the synovial biopsies using the Nucleospin® RNA II extraction kit (Macherey-Nagel), including DNase treatment of the samples. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips (Agilent Technologies Inc). All samples had a 28s/18s ratio > 1.8.

treatment_protocol:
Adalimumab therapy was initiated at a dosage of 40 mg subcutaneously every other week. Disease activity at baseline and 12 weeks after initiation of therapy (T12) was evaluated using DAS(28)-CRP (3- and 4-variables) scores, and response to therapy was assessed according to the EULAR response criteria that categorize patients in responders (good- or moderate-) and non- (or poor-) responders based on changes in DAS activity between T0 and T12 and absolute DAS values at T12.

Synovial biopsies were obtained by needle-arthroscopy of knee of the patients at T12. For each procedure, 4 to 8 synovial samples were snap-frozen in liquid nitrogen and stored at –80°C for later RNA extraction. The same amount of tissue was kept at -80°C for immunostaining experiments on frozen sections. The remaining material was fixed in 10% formalin and paraffin embedded for conventional optical evaluation and immunostaining of selected markers. All the experiments (RNA extraction, histology, immunohistochemistry) were performed on at least 4 biopsies harvested during every procedure in order to correct for variations related to the potential heterogeneous distribution of synovial inflammation.

value: synovial tissue from knee

tag: disease

value: rheumatoid arthritis


title: RA Synovial biopsy T12 post-adalimumab therapy, Good Responder 3

type: RNA

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Synovial biopsy, RA patient, 12 weeks after adalimumab therapy, good responder

tag: tissue


title: RA Synovial biopsy T12 post-adalimumab therapy, Poor Responder 2


title: RA Synovial biopsy T12 post-adalimumab therapy, Good Responder 1


title: Fibroblast-like Synovial Cells from RA patient C - TNFalpha

description: Patient C

data_processing: For the initial normalization and analysis steps, data were retrieved on Affymetrix GCOS software. The frequency of positive genes (genes with a flag present) was between 42% and 45% on each slide. After scaling of all probe sets to a value of 100, the amplification scale was reported inferior to 1.5 for all slides. The signals yielded by the poly-A RNA, hybridization and housekeeping controls (GAPDH 3’/5’ ratio < 1.3) were indicative of the good quality of the amplification and hybridization procedures.

source_name: Cultured FLS from RA individual, overnight incubation with TNFalpha

extract_protocol: After overnight incubation with the indicated cytokines, cells were harvested and total RNA was extracted using the Nucleospin® RNA II extraction kit (Macherey-Nagel, Düren, Germany).

treatment_protocol:
Fibroblast-like cells (FLS) were purified from synovial biopsies from RA patients. Briefly, minced synovial fragments were digested in 1 mg/ml hyaluronidase solution (Sigma Aldrich, St Louis, MO) for 15 minutes at 37°C and 6 mg/ml collagenase type IV (Invitrogen, Paisley, UK) for 2 hours at 37°C. Next, cells were washed, resuspended in high-glucose Dulbecco’s Modified Eagle Medium (Invitrogen) supplemented with 1% antibiotics-antimycotics (Invitrogen) and 1% MEM sodium pyruvate (Invitrogen), and seeded at 10,000 cells/cm2 in 6-well plates. When the cells reached confluence, adherent cells were detached using sterile 0.5% trypsin-EDTA (Invitrogen) and used as FLS between passages 3 and 9. For the cytokine stimulation experiments, cells were seeded in 24-well plates at 25,000/well.

The cells were incubated overnight with (or without) the indicated cytokine (cfr. title) at the following concentrations : TNF-α (R&D Systems, Minneapolis, MN) 10 ng/ml, IL-1β (R&D Systems) 10 ng/ml.

tag: cell type

value: cultured fibroblast-like synovial cells

tag: treatment

value: TNFalpha


title: Ler2DNA

status: Public on Apr 14 2009

type: genomic

city: St. Louis

first: Ivan

last: Baxter

state: MO

address: 975 North Warson Rd

department: PLant Genetics Research Unit

country: USA

institute: USDA-ARS

description: DNA sample for Bulk Segregant analysis from http://naturalsystems.uchicago.edu/naturalvariation/methods/ColLerCEL.zip Borevitz J. Array Genotyping and Mapping, Arabidopsis Protocols

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

label: biotin

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: leaves

label_protocol: Invitrogen Bioprime labelling kit

extract_protocol: Qiagen DNeasy kit

tag: age

value: ~6 weeks

value: Leaves


title: Fibroblast-like Synovial Cells from RA patient B - TNFalpha

description: Patient B


title: Fibroblast-like Synovial Cells from RA patient C - IL1beta

description: Patient C

source_name: Cultured FLS from RA individual, overnight incubation with IL1beta


title: Ler1DNA


title: Ler3DNA


title: RA Synovial biopsy T12 post-adalimumab therapy, Good Responder 2


title: RA Synovial biopsy T12 post-adalimumab therapy, Poor Responder 3


title: HighCa_seg_pool_Ler_col_F2

description: DNA sample for Bulk Segregant analysis


title: LowCa_seg_pool_Ler_col_F2

description: DNA sample for Bulk Segregant analysis. This is the mutant pool.


title: Fibroblast-like Synovial Cells from RA patient A - TNFalpha

description: Patient A


title: Fibroblast-like Synovial Cells from RA patient B - IL1beta

description: Patient B


title: RA Synovial biopsy T12 post-adalimumab therapy, Moderate Responder 3

source_name: Synovial biopsy, RA patient, 12 weeks after adalimumab therapy, moderate responder


title: RA Synovial biopsy T12 post-adalimumab therapy, Moderate Responder 1


title: hepatoma_mutant_DMSO_rep3

status: Public on Apr 17 2009

city: Ann Arbor

first: Maureen

middle: A

last: Sartor

state: MI

address: 2017 Palmer Commons-100 Washtenaw Ave.

institute: University of Michigan

hyb_protocol: Affymetrix GeneChip Mouse Genome Arrays were hybridized with 15 mg of fragmented aRNA for 16 hr at 45oC.  Hybridization, staining, and washing were carried out using the Affymetrix GeneChip Hybridization Wash and Stain Kit following the manufacturer’s protocols.

scan_protocol: Scanned according to Affymetrix protocols.

data_processing: Data was pre-processed with RMA.

organism: Mus musculus

source_name: hepatoma mutant cells, DMSO 8hr

label_protocol: Ambion Biotin-Enhanced Message Amp II kit (Austin, Texas), following the manufacturer’s protocols

growth_protocol: Grown in alpha MEM medium with 5% fetal bovine serum

extract_protocol: Total RNA was extracted using NucleoSpin RNA II columns (Macherey-Nagel) according to the manufacturer’s instructions.  RNA extracts were validated on preparation for quality and integrity using the Agilent 2100 Bioanalyzer.  All RNA samples had RNA Integrity Number greater than 7.0.

treatment_protocol: No treatment in DMSO for 8 hr.

tag: Strain

tag: Gender

value: Male

tag: Cell line

value: Hepa-1c1c7 derivative with AHR unable to bind DNA

tag: Tissue

value: Liver tumor


title: RA Synovial biopsy T12 post-adalimumab therapy, Moderate Responder 4


title: Null, 12 hours treatment, rep 3

city: Stockholm

first: Jeremy

last: Lambert

country: Sweden

institute: Karolinska Institutet

description: Microsoft Excel program was used to merge the overlapping significant genes from the settings. Annotations from Affymetrix for significant genes were checked in NCBI public database and pathway analysis were used by Ingenuity.

hyb_protocol: Fifteen micrograms of the resulting biotin-tagged cRNA was fragmented to strands of 35 to 200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 320) to probe sets on an Affymetrix Genechip Rice Genome Array.

scan_protocol: The chip was washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 400, followed by scanning on a GeneChip Scanner 3000 (Affymetrix, Inc.).

data_processing: The results were quantified, and normalized using MAS5.0. The genes with probe set signal lower than 50 on the repeated arrays were considered as non-expression and filtered out. The cutoff value of expression fold change was set as 2.0 that was commonly used for microarray analysis to further increase the stringency. GeneSpring software from Agilent was used for the filtration and pathway analysis.

source_name: Saos-2 osteosarcoma, p53-null, 12 hours treatment

label_protocol: Biotin labeled cRNA was produced according to Affymetrix protocol

extract_protocol: RNA was extracted using RNeasy Mini Kit (Qiagen, Sweden) according to manufacturer’s instructions

tag: mutation

value: p53 null

value: 12 hours treatment with Prima

tag: cell line

value: osteosarcoma


title: Null, 6 hours treatment, rep 1

source_name: Saos-2 osteosarcoma, p53-null, 6 hours treatment

value: 6 hours treatment with Prima


title: Null, Untreated, rep 3

source_name: Saos-2 osteosarcoma, p53-null, untreated

value: untreated


title: Null, Untreated, rep 1


title: RA Synovial biopsy T12 post-adalimumab therapy, Moderate Responder 5


title: Null, 6 hours treatment, rep 2


title: Null, 6 hours treatment, rep 3


title: Arabidopsis per1 in Pi deficiency medium biological rep2

city: Taipei

first: Wolfgang

last: Schmidt

address: No. 128, Sec 2, Academia Rd, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

description: gene expression data from arabidopsis roots under iron efficiency medium

hyb_protocol: Ten microgram labeled samples were hybridized to the ATH1 Genome Array at 45℃ for 16.5 h. Washing and staining involved Fluidic Station-450 and the ATH1 Genome.

scan_protocol: Array was scanned with use of the Affymetrix GeneChip Scanner 7G.

data_processing: The results were quantified and analyzed by use of MicroArray Suite 5.0 software (Affymetrix Inc.).

source_name: per1 plants in Pi deficiency medium

label_protocol: Ten microgram of total RNA was used for cDNA synthesis, labeled by in vitro transcription, followed by fragmentation according to the manufacturer's suggestion (GeneChip Expression Analysis Technical Manual rev5, Affymetrix)

growth_protocol: Plants were grown on agar medium

extract_protocol: Total RNA was extracted with Qiagen RNeasy mini kit.

treatment_protocol: Plats were grown for on control media for 10 days and then transferred to either control or phosphate-free media for 10 h.

value: root

tag: ecotype

tag: genotype


title: Arabidopsis per1 in control medium biological rep1

source_name: per1 plants in control medium


title: Arabidopsis Columbia in control medium biological rep2

description: gene expression data from arabidopsis roots under iron deficiency medium

source_name: columbia plants in control medium

value: wild type


title: Arabidopsis per1 in Pi deficiency medium biological rep1


title: RA Synovial biopsy T12 post-adalimumab therapy, Moderate Responder 2


title: Fibroblast-like Synovial Cells from RA patient A - No treatment

description: Patient A

source_name: Cultured FLS from RA individual, no cytokine treatment

value: no cytokine


title: Arabidopsis per1 in control medium biological rep2


title: Arabidopsis Columbia in Pi deficiency medium biological rep2

source_name: columbia plants in Pi deficiency medium


title: Arabidopsis Columbia in Pi deficiency medium biological rep1


title: Synovial Sarcoma-like tumor from R-CreER/SSM2 mouse (RCS9)

first: MALAY

last: HALDAR

address: 7751 charing square lane

department: Pathology and Immunology

institute: Washington University in St. Louis

description: Gene expression data from murine synovial sarcoma-like tumors

hyb_protocol: Following fragmentation, 15ug of cRNA were hybridized for 16 hrs. at 45oC on GeneChip Mouse Genome 430 2.0 Array.  The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Array data was normalized using the RMA method in the GeneSifter software.

source_name: Tumors generated in a female mouse exposed to one pulse of 0.1mg/gm Tamoxifen at 3 months of age.

label_protocol: Biotinylated cRNA was prepared using the One Cycle Target Labeling Control Reagent Kit according to the manufacturer’s specifications (Affymetrix, 900493).

growth_protocol: Tumors were generated in R-CreER/SSM2 mice by random and sporadic expression of the synovial sarcoma associated SYT-SSX2 fusion oncogene in various tissues.

extract_protocol: Trizol (Invitrogen) extraction of Total RNA was performed and the RNA was purified using the RNeasy kit (Qiagen) using manufacturers' instructions.

treatment_protocol: Mice were humanely sacrificed and the tumors were dissected out. Expression of SYT-SSX2 was further confirmed by EGFP mediated fluorosocence of the Tumors detected under a dissecting scope with a GFP filter. Tumors were minced and put it Trizol (invitrogen).

tag: Genotype

value: R-CreER/SSM2. Age 10 months.


title: Synovial Sarcoma-like tumor from R-CreER/SSM2 mouse (RCS10)

source_name: Tumors generated in a male mouse not exposed  Tamoxifen.

value: R-CreER/SSM2. Age:10 month.


title: Null, 12 hours treatment, rep 1


title: Null, Untreated, rep 2


title: Synovial Sarcoma-like tumor from R-CreER/SSM2 mouse (RCS8)


title: Synovial Sarcoma-like tumor from R-CreER/SSM2 mouse (RCS5)

value: R-CreER/SSM2. Age:13 month.


title: Synovial Sarcoma-like tumor from R-CreER/SSM2 mouse (RCS6)

value: R-CreER/SSM2. Age:9 month.


title: Salivary glands at 16 weeks, biological rep1

status: Public on Apr 11 2009

city: Gainesville

first: Ammon

middle: B

last: Peck

state: FL

address: 1945 SW 16th Avenue

department: Department of Infectious Diseases & Pathology

institute: University of Florida

description: Gene expression profiles within the salivary glands of C57BL/6.NOD-Aec1Aec2 mice at 16 weeks of age (representing the early clinical phase of autoimmunity).

hyb_protocol: Fragmented cRNA was hybridized for 16 h at 45°C to the array chips (Affymetrix). Genechips were washed ans stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Microarray data were processed and normalized using RMA.

source_name: Salivary glands of C57BL/6.NOD-Aec1Aec2 mice at 16 weeks of age

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using the RNeasy Mini-Kit (Qiagen, Valencia, CA), as per the manufacturer’s protocol.

value: salivary glands

value: 16 week

tag: gender


title: Salivary glands at 20 weeks, biological rep2

description: Gene expression profiles within the salivary glands of C57BL/6.NOD-Aec1Aec2 mice at 20 weeks of age (representing the early onset of clinical SjSlike disease characterized by secretory dysfunction).

source_name: Salivary glands of C57BL/6.NOD-Aec1Aec2 mice at 20 weeks of age

value: 20 week

value: Male


title: Arabidopsis Columbia in control medium biological rep1


title: Salivary glands at 20 weeks, biological rep4


title: Salivary glands at 12 weeks, biological rep1

description: Gene expression profiles within the salivary glands of C57BL/6.NOD-Aec1Aec2 mice at 12 weeks of age (representing the initial influx of leukocytes into the salivary glands).

source_name: Salivary glands of C57BL/6.NOD-Aec1Aec2 mice at 12 weeks of age

value: 12 week


title: Salivary glands at 8 weeks, biological rep3

description: Gene expression profiles within the salivary glands of C57BL/6.NOD-Aec1Aec2 mice at 8 weeks of age (representing the early pre-clinical stage).

source_name: Salivary glands of C57BL/6.NOD-Aec1Aec2 mice at 8 weeks of age

value: 08 week


title: Salivary glands at 16 weeks, biological rep2


title: Inflorescence_ngaquad_2

city: Rehovot

first: Idan

middle: D.

last: Efroni

address: Weizmann

country: Israel

institute: Weizmann Institute

description:
30 DAS Ler ecotype inflorescence of flowers stages 12 and younger.
Inf_Ler_Ngaquad_2

hyb_protocol: Standard affymetrix protocol

scan_protocol: Standard affymetrix protocol

data_processing: Values obtained using using the GC-RMA protocol, using R 2.7.2 (www.r-project.org) and Bioconductor 2.2 (www.bioconductor.org/).

label: Standard affymetrix protocol

label_protocol: Standard affymetrix protocol

extract_protocol: Using qiagen RNAEasy kit, according to manufacturer protocol

value: nga1-1 nga2-1 nga3-1 nga4-1

value: Ler

value: 30 DAS


title: Inflorescence_miR-NGA_2

description:
30 DAS Ler ecotype inflorescence of flowers stages 12 and younger.
Inf_Ler_mirNGA_2

value: 35S:miR-NGA, targeting the nga1-4


title: Salivary glands at 20 weeks, biological rep3


title: Salivary glands at 8 weeks, biological rep4


title: Salivary glands at 16 weeks, biological rep4


title: Salivary glands at 12 weeks, biological rep4


title: Inflorescence_wt_5

description:
30 DAS Ler ecotype inflorescence of flowers stages 12 and younger.
Inf_Ler_WT_5


title: Inflorescence_ngaquad_1

description:
30 DAS Ler ecotype inflorescence of flowers stages 12 and younger.
Inf_Ler_Ngaquad_1


title: Salivary glands at 20 weeks, biological rep5


title: Salivary glands at 8 weeks, biological rep5


title: Salivary glands at 16 weeks, biological rep3


title: Salivary glands at 8 weeks, biological rep2


title: Salivary glands at 12 weeks, biological rep2


title: Salivary glands at 12 weeks, biological rep5


title: Salivary glands at 12 weeks, biological rep3


title: Inflorescence_miR-NGA_1

description:
30 DAS Ler ecotype inflorescence of flowers stages 12 and younger.
Inf_Ler_mirNGA_1


title: Salivary glands at 20 weeks, biological rep1


title: Salivary glands at 16 weeks, biological rep5


title: Salivary glands at 8 weeks, biological rep1


title: Inflorescence_wt_6

description:
30 DAS Ler ecotype inflorescence of flowers stages 12 and younger.
Inf_Ler_WT_6


title: Inflorescence_wt_7

description:
30 DAS Ler ecotype inflorescence of flowers stages 12 and younger.
Inf_Ler_WT_7


title: Salivary glands at 4 weeks, biological rep5

description: Gene expression profiles within the salivary glands of C57BL/6.NOD-Aec1Aec2 mice at 4 weeks of age (representing the pre-disease stage).

source_name: Salivary glands of C57BL/6.NOD-Aec1Aec2 mice at 4 weeks of age

value: 04 week


title: Inflorescence_wt_1

description:
30 DAS Ler ecotype inflorescence of flowers stages 12 and younger.
Inf_Ler_WT_1

value: wild type


title: Inflorescence_wt_4

description:
30 DAS Ler ecotype inflorescence of flowers stages 12 and younger. Long days
Inf_Ler_WT_4


title: Salivary glands at 4 weeks, biological rep2


title: Salivary glands at 4 weeks, biological rep3


title: Inflorescence_wt_3

description:
30 DAS Ler ecotype inflorescence of flowers stages 12 and younger. Long days
Inf_Ler_WT_3


title: Salivary glands at 4 weeks, biological rep4


title: Salivary glands at 4 weeks, biological rep1


title: T cells+10nM MAZ1310 for 6 hours-biological replicate 1

status: Public on Apr 10 2009

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description:
Gene expression data from T cells treated with 10nM MAZ1310 in Th17 cytokine conditions for 6 hours
C57B/6J from Jackson labs

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: RMA

source_name: T cells activated in Th17 polarizing cytokines for 6 hours

label_protocol: BioArray High Yield RNA transcript labeling T7 kit (Enzo Life Sciences)

growth_protocol: T cells were stimulation using anti-CD3/ anti-CD28 antibodies. Further cultured with TGFb plus IL-6 and treated with 10 nM Halofuginone (HF) or its inactive derivative, MAZ1310

extract_protocol: Total RNA was extracted with Trizol. Total RNA was purified using RNeasy columns (Quiagen) according to manufacturer's instructions

treatment_protocol: T cells were scraped from antibody-coated wells, pelleted by centrifugation and cell pellets were flash frozen prior to RNA extraction.

value: CD4+ CD25- T cells

tag: agent

tag: time

value: 6 hrs


title: T cells+10nM MAZ1310 for 3 hours-biological replicate 1

description:
Gene expression data from T cells treated with 10nM MAZ1310 in Th17 cytokine conditions for 3 hours
C57B/6J from Jackson labs

source_name: T cells activated in Th17 polarizing cytokines for 3 hours

value: 3 hrs


title: Inflorescence_wt_2

description:
30 DAS Ler ecotype inflorescence of flowers stages 12 and younger. Long days
Inf_Ler_WT_2


title: T cells+10nM HF for 3 hours-biological replicate 1

description:
Gene expression data from T cells treated with 10nM HF in Th17 cytokine conditions for 3 hours
C57B/6J from Jackson labs

value: halofuginone


title: T cells+10nM HF for 6 hours-biological replicate 1

description:
Gene expression data from T cells treated with 10nM HF in Th17 cytokine conditions for 6 hours
C57B/6J from Jackson labs


title: T cells+10nM HF for 6 hours-biological replicate 2


title: T cells+10nM MAZ1310 for 3 hours-biological replicate 3


title: T cells+10nM HF for 3 hours-biological replicate 2


title: T cells+10nM MAZ1310 for 3 hours-biological replicate 2


title: T cells+10nM MAZ1310 for 6 hours-biological replicate 3


title: T cells+10nM HF for 3 hours-biological replicate 3


title: T cells+10nM HF for 6 hours-biological replicate 3


title: T cells+10nM MAZ1310 for 6 hours-biological replicate 2


title: Immortalized MEFs WB, v-src expression retroviral vector infected, rep2

city: Singapore

first: Seiichi

last: Mori

state: Singapore

address: Centre for Life Sciences #02-07, 28 Medical Drive

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: v-src retroviral vector-infected immortalized mouse embryonic fibroblasts

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

extract_protocol: Cells were lysed directly in the culture dish and the lysates were used for extraction.  Total RNA was extracted by Qiagen RNEasy kit according to the manufacturer's instructions.

tag: parental cell line

value: WB

tag: vector

value: pBabe-human v-src (v-src vector)

tag: replicate


title: 5_seedling_Red_rep1

first: Melanie

last: Correll

address: 142 Frazier Rogers Hall

department: Agricultural and Biological Engineering

description: Gene expression from 5, 7-day-old dark-grown seedlings plus 1 hour red light

hyb_protocol: Samples (3.75 μg) were hybridized to the Arabidopsis ATH1 Genome Affymetrix® GeneChip® following the Affymetrix® standard protocol (Affymetrix Inc., CA)

scan_protocol: arrays were washed and stained with streptavidin-phycoerythrin (SAPE) on an Affymetrix® GeneChip® Fluidics Station 450, and scanned on a GeneChip® Scanner 3000 (Affymetrix Inc., CA)

data_processing: Microarray Suite Version 5 software (Affymetrix, Santa Clara, CA) was used to convert intensity data into quantitative estimates of gene expression. All expression values were globally scaled to 500. A probability statistic associated with each gene's presence or absence was also generated. Genes not expressed in either of the samples were considered absent. Absent genes were removed from the data set and not included in further analyses.  The array elements were designated using The Arabidopsis Information Resource (ver. 7.0, April 2007).

source_name: 7-day-old Arabidopsis Seedlings

label_protocol: RNA amplification and labeling was performed by the Ovation® biotin system protocol (NuGEN CA).20 ng of total RNA was reverse transcribed using a chimeric cDNA/mRNA primer, and a second complimentary cDNA strand was synthesized. cDNA then was amplified with ribo-SPIA™ enzyme and SPIA DNA/RNA primers (NuGEN, CA). Amplified DNA was purified with Zymo Research DNA Clean and Concentrator-25™ (Zymo Research), cleaved to produce 50- to 100-bp fragments, and biotinylated.

growth_protocol: Arabidopsis ecotype Landsberg erecta (Ler) seeds were sterilized in 70% (v/v) ethanol for 5 min, two rinses of 90% (v/v) ethanol and four rinses in sterile ddH2O. Seeds were sown onto pre-sterilized cellophane that was placed on top of an agar growth medium  consisting of half-strength MS medium with 1% (w/v) sucrose, 1.2% (w/v) agar in square (100 mm X 315 mm) Petri dishes. Seeds were stratified for 2 d at 4 °C in the dark and then exposed to white light for 2 h at room temperature to synchronize germination. Seedlings were grown for 7 d in the dark at 23 °C before being transferred to either red light (1 h) or continued darkness. Seedlings were immersed in 100 uL RNAlater® (Ambion, TX) in pre-sterilized tubes and stored at -80˚C until RNA extraction.

extract_protocol: Samples were removed from the -80 °C freezer and warmed to room temperature (25 °C) until all of the RNAlater® had thawed (~5 min).  Thawed samples were ground directly in the microcentrifuge tube using a sterilized pestle tip and the Pellet Pestle® Motor (Kontes, NJ).  Grinding was continued until there were no remaining visible particulates (~4 min).  Lysis buffer (450 uL; RLT buffer, Qiagen, CA) was added to each sample, and the tubes were vortexed for 5 seconds. RNA was further isolated from the disrupted plant seedling using the RNeasy® Plant Mini Kit (Qiagen Inc, Valencia, CA) and residual DNA was removed by performing an on-column digestion using an RNAse-free DNAse kit (Ambion, TX).

treatment_protocol: Red light treatments were for 1h at fluence rate, through the red filter of ~10 μmol m-2 s-1 with a transmission maximum of 630 nm.  Dark treatment were continued in the dark

tag: Ecotype

value: Landsber erecta, Age:7 days, Tissue:whole seedling


title: 5_seedlings _dark_rep1

description: Gene expression from 5, 7-day-old dark-grown seedlings plus 1 hour dark


title: Immortalized MEFs WC, v-src expression retroviral vector infected, rep2

value: WC


title: Immortalized MEFs WC, v-src expression retroviral vector infected, rep3


title: Immortalized MEFs WA, v-src expression retroviral vector infected, rep3

value: WA


title: Immortalized MEFs WA, v-src expression retroviral vector infected, rep2


title: Immortalized MEFs WB, v-src expression retroviral vector infected, rep3


title: Immortalized MEFs WC, v-src expression retroviral vector infected, rep1


title: Immortalized MEFs WC, human c-myc expression retroviral vector infected, rep3

source_name: human c-myc retroviral vector-infected immortalized mouse embryonic fibroblasts

value: pBabe-human c-myc (c-myc vector)


title: Immortalized MEFs WB, human c-myc expression retroviral vector infected, rep3


title: Immortalized MEFs WB, human c-myc expression retroviral vector infected, rep1


title: Immortalized MEFs WC, human c-myc expression retroviral vector infected, rep1


title: Immortalized MEFs WA, v-src expression retroviral vector infected, rep1


title: Immortalized MEFs WA, empty retroviral vector infected, rep2

source_name: empty retroviral vector-infected immortalized mouse embryonic fibroblasts

value: pBabe-puro (empty vector)


title: Immortalized MEFs WB, empty retroviral vector infected, rep1


title: Immortalized MEFs WB, empty retroviral vector infected, rep2


title: Immortalized MEFs WA, empty retroviral vector infected, rep3


title: Immortalized MEFs WB, human c-myc expression retroviral vector infected, rep2


title: Immortalized MEFs WC, human c-myc expression retroviral vector infected, rep2


title: Immortalized MEFs WA, human c-myc expression retroviral vector infected, rep1


title: Immortalized MEFs WA, empty retroviral vector infected, rep1


title: Immortalized MEFs WA, human c-myc expression retroviral vector infected, rep3


title: Immortalized MEFs WB, empty retroviral vector infected, rep3


title: Immortalized MEFs WC, empty retroviral vector infected, rep2


title: Immortalized MEFs WC, empty retroviral vector infected, rep3


title: NUP98-HOXD13+MEIS1-WT_rep3

status: Public on Apr 09 2009

city: Gothenburg

first: Lars

last: Palmqvist

address: Sahlgrenska University Hospital

department: Institute of Biomedicine

institute: University of Gothenburg

description: Retroviral vector coding for wildtype MEIS1 was introduced in cultured bone marrow cells transformed by NUP98-HOXD13

hyb_protocol: Chip Type	Mouse430_2 Chip Lot	AKE Operator	administrator Sample Type	total RNA Project	p0531 Protocol	EukGE-WS2v5 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	30 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	6 Mixes per Wash B Cycle	15 Stain Temperature (C)	35 First Stain Time (seconds)	300 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	30 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	300 Third Stain Time (seconds)	300 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	35 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	2 Module	3 Hybridize Date	Nov 1 2005

scan_protocol: Pixel Size	1.56 Filter	570 Scan Temperature Scan Date	Nov 1 2005 Scanner ID	50206370 Number of Scans	1 Scanner Type	M10

data_processing: GCOS 1.2

source_name: Cultured bone marrow, MEIS1-WT

label_protocol: The labeling was done according to the manufacturer instructions and performed at the Swegene MARC, Department of Immunotechnology, Lund University, Sweden

growth_protocol: Mice were bred and maintained at the British Columbia Cancer Research Center Animal Facility (Vancouver, BC). All experimental protocols were approved by the University of British Columbia Animal Care Committee. Establishment and characterization of pre-leukemic BM cell lines following transduction of BM cells with ND13 have been previously described (Pineault, Abramovich et al. 2005; Palmqvist, Argiropoulos et al. 2006). In brief, lines were established from BM cells previously treated with 5-fluorouracil (5-FU) from (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) (Ly5.1+/Ly5.2+) mice freshly transduced with the ND13-GFP or ND13pac virus and maintained for a period of 4 weeks in liquid culture [Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/ml of human interleukin-6 (hIL-6), 6 ng/ml of murine interleukin-3 (mIL3), and 100 ng/ml of murine stem cell factor (mSCF)]. All culture media and growth factors were obtained from StemCell Technologies Inc. (Vancouver, BC, Canada). Cells were maintained at a cell density below 1 x 106/ml. Cells were counted with the Vi-Cell XR Cell Viability Analyzer (Beckman Coulter Inc., Fullerton, California). To generate ND13+Meis1 or ND13+Meis1 mutant BM cell lines, the ND13 BM cells were transduced by co-cultivation on irradiated (4,000 cGy) E86 producers for Meis1-YFP (or Meis1 mutant forms), respectively, for a period of 2 days in the presence of 5 µg/ml of protamine sulfate (Sigma, Oakville, ON, Canada).

extract_protocol: Sorted cells were lyzed in Trizol™ (Invitrogen) and total RNA was extracted according to the manufacturer instructions.

tag: cell type


title: NUP98-HOXD13+MEIS1-WT_rep1

hyb_protocol: Chip Type	Mouse430_2 Chip Lot	AKE Operator	administrator Sample Type	total RNA Project	p0531 Protocol	EukGE-WS2v5 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	30 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	6 Mixes per Wash B Cycle	15 Stain Temperature (C)	35 First Stain Time (seconds)	300 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	30 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	300 Third Stain Time (seconds)	300 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	35 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	2 Module	3 Hybridize Date	Oct 26 2005

scan_protocol: Pixel Size	1.56 Filter	570 Scan Temperature Scan Date	Oct 26 2005 Scanner ID	50206370 Number of Scans	1 Scanner Type	M10

value: cultured bone marrow cells transformed by NUP98-HOXD13


title: NUP98-HOXD13+MIY-ctrl_rep3

description: Retroviral vector coding for YFP (MIY) was introduced as negative control in cultured bone marrow cells transformed by NUP98-HOXD13

hyb_protocol: Protocol	EukGE-WS2v5 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	30 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	6 Mixes per Wash B Cycle	15 Stain Temperature (C)	35 First Stain Time (seconds)	300 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	30 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	300 Third Stain Time (seconds)	300 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	35 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module	1

scan_protocol: Pixel Size	1.56 Filter	570 Scan Temperature Scan Date	Nov 01 2005 Scanner ID	50206370 Number of Scans	1 Scanner Type	M10

source_name: Cultured bone marrow, MIY-ctrl


title: Immortalized MEFs WA, human c-myc expression retroviral vector infected, rep2


title: NUP98-HOXD13+M33-MEIS1_rep1

description: Retroviral vector coding for M33-MEIS1 was introduced in cultured bone marrow cells transformed by NUP98-HOXD13

source_name: Cultured bone marrow, M33-MEIS1


title: NUP98-HOXD13+MEIS1-deltaHD_rep3

description: Retroviral vector coding for MEIS1, with deleted homeodomain, was introduced in cultured bone marrow cells transformed by NUP98-HOXD13

source_name: Cultured bone marrow, MEIS1-deltaHD


title: NUP98-HOXD13+M33-MEIS1_rep3

hyb_protocol: Chip Type	Mouse430_2 Chip Lot	AKE Operator	administrator Sample Type	total RNA Project	p0531 Protocol	EukGE-WS2v5 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	30 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	6 Mixes per Wash B Cycle	15 Stain Temperature (C)	35 First Stain Time (seconds)	300 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	30 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	300 Third Stain Time (seconds)	300 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	35 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	2 Module	3 Hybridize Date	Nov 29 2005

scan_protocol: Pixel Size	1.56 Filter	570 Scan Temperature Scan Date	Nov 29 2005 Scanner ID	50206370 Number of Scans	1 Scanner Type	M10


title: NUP98-HOXD13+M33-MEIS1_rep2


title: NUP98-HOXD13+MEIS1-deltaHD_rep2


title: NUP98-HOXD13+MEIS1-WT_rep2


title: Immortalized MEFs WC, empty retroviral vector infected, rep1


title: NUP98-HOXD13+MEIS1-deltaHD_rep1


title: NUP98-HOXD13_MIY-ctrl_rep2

scan_protocol: Pixel Size	1.56 Filter	570 Scan Temperature Scan Date	Nov 01 2005 12:46PM Scanner ID	50206370 Number of Scans	1 Scanner Type	M10

label_protocol: The labeling was done according to the manufacturer instructions and performed at the Swegene MARC, Department of Immunotechnology, Lund University


title: Liver, exposed isolation stress for 30 days #3

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

country: Japan

institute: Hirosaki University

description: No additional information

hyb_protocol: Following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000. Description

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.

source_name: Liver

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 2 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen Life Technologies, Carlsbad, CA, USA), then purified with an RNeasy mini kit (Qiagen, Valencia, CA, USA).

tag: Characteristics

tag: Strain

value: BALB/c

value: male

tag: Age

value: 10 weeks

value: liver


title: Liver, exposed isolation stress for 30 days #1

description: No additional information

tag: Gender

tag: Tissue


title: Liver, Control #1

description: No additional information


title: Liver, Control #3

description: No additional information


title: DC Vaccinated Wild Type 11_wt_GL26_vac_R2

city: Los Angeles

first: Gretchen

last: Duvall

state: CA

address: 8700 Beverly BLVD

institute: Cedars Sinai Medical Center

description: RNA from tumor grown in mice brain injected with GL26 cell line

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: Mas5 Normalized

source_name: DC Vaccinated Wild Type

label_protocol: Standard Affymetrix

extract_protocol: Trizol extraction of total RNA was performed according to the Qiagen kit instructions.


title: Liver, exposed isolation stress for 30 days #2

description: No additional information


title: NUP98-HOXD13+MIY-ctrl_rep1

growth_protocol: Mice were bred and maintained at the British Columbia Cancer Research Center Animal Facility (Vancouver, BC). All experimental protocols were approved by the University of British Columbia Animal Care Committee. Establishment and characterization of pre-leukemic BM cell lines following transduction of BM cells with ND13 have been previously described (Pineault, Abramovich et al. 2005; Palmqvist, Argiropoulos et al. 2006). In brief, lines were established from BM cells previously treated with 5-fluorouracil (5-FU) from (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) (Ly5.1+/Ly5.2+) mice freshly transduced with the ND13-GFP or ND13pac virus and maintained for a period of 4 weeks in liquid culture [Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/ml of human interleukin-6 (hIL-6), 6 ng/ml of murine interleukin-3 (mIL3), and 100 ng/ml of murine stem cell factor (mSCF)]. All culture media and growth factors were obtained from StemCell Technologies Inc. (Vancouver, BC, Canada). Cells were maintained at a cell density below 1 x 106/ml. Cells were counted with the Vi-Cell XR Cell Viability Analyzer (Beckman Coulter Inc., Fullerton, California). To generate ND13+Meis1 or ND13+Meis1 mutant BM cell lines, the ND13 BM cells were transduced by co-cultivation on irradiated (4,000 cGy) E86 producers for Meis1-YFP (or Meis1 mutant forms), respectively, for a period of 2 days in the presence of 5 ug/ml of protamine sulfate (Sigma, Oakville, ON, Canada).


title: Untreated Nude 13_nude_GL26_R5

source_name: Untreated Nude

tag: RNA from tumor grown in mice brain injected with GL26 cell line


title: Untreated Nude 5_nude_GL26_R3


title: Ctrl MEF(-/-), 3hrs 643-EJ-6

city: Nashville

first: Josh

middle: T

last: Beckham

state: TN

address: 5824 Stevenson Center

department: Biomedical Engineering

institute: Vanderbilt University

description: Ctrl MEF(-/-), 3hrs 643-EJ-6

hyb_protocol: The biotinylated cRNA (20 µg) was fragmented and hybridized to an Affymetrix GeneChip Mouse Genome 430 2.0 Array containing 45,000 sets of 11 to 25-mer oligomers, representing 39,000 mouse transcripts (34,000 are annotated as well-defined genes). Hybridized cRNA was detected using streptavidin coupled to phycoerythrin.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G Plus 2 and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files.

data_processing: CEL files (raw Affymetrix data) were imported in GeneSpring 7.3 (Agilent Technologies) and transformed by Mas5. The "Value" column shows this normalized signal intensity value.

source_name: MEF(-/-) cells, unheated control

label_protocol: Following quality control, the RNA was prepared for microarray analysis using the GeneChip® One-Cycle Target Labeling and Control Reagents kit (Affymetrix Inc, Santa Clara, CA). Briefly, 1.5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter. In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.

growth_protocol: Maintained in DMEM with 10% Fetal Bovine Serum, and 2ul/ml of Normocin(Invivogen). Wells were covered with a gas permeable membrane to prevent water influx during thermal treatment.

extract_protocol: Cell lysates from 144 individual wells were pooled and total RNA was harvested to make each sample. Approximately 4-6 ug of RNA was isolated with the RNeasy Micro Kit (Qiagen, Valencia, CA) along with on column DNAse treatment (Qiagen). RLT buffer in the RNeasy Kit was used without adding β- mercaptoethanol in order to reduce background noise on the microarrays. Agilent’s Bioanalyzer microfluidic assay (Agilent Technologies, Palo Alto CA) was used to assay RNA integrity. Spectrophotometric and fluorometric methods were combined to quantitate protein and nucleic acids present in the sample, and to ensure quality control of each sample.

treatment_protocol: Cells were plate in 96 well plates at 3k/well, incubated 23 hrs before harvesting RNA

tag: Murine Embryo Fibroblast hsp70 knockout cells of both isoforms:hsp70.1 and hsp70.3


title: Untreated Wild Type 1_wt_GL26_R1

source_name: Untreated Wild Type


title: Untreated Nude 4_nude_GL26_R2


title: Untreated Wild Type 2_wt_GL26_R2


title: Liver, Control #2

description: No additional information

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


title: Untreated Wild Type 15_wt_GL26_R4


title: DC Vaccinated Wild Type 10_wt_GL26_vac_R1


title: Untreated Nude 3_nude_GL26_R1


title: Untreated Nude 12_nude_GL26_R4


title: Old Untreated Wild Type 9_wt_GL26_10m_R2

source_name: Old Untreated Wild Type


title: DC Vaccinated Wild Type 19_wt_GL26_vac_R4


title: Ctrl MEF(-/-), 3hrs 643-EJ-14

description: Ctrl MEF(-/-), 3hrs 643-EJ-14


title: Old Untreated Wild Type 8_wt_GL26_10m_R1


title: DC Vaccinated Wild Type 18_wt_GL26_vac_R3


title: Sample 18: normal ovarian surface epithelium

status: Public on Apr 07 2009

city: Portland

first: Solange

last: Mongoue

state: OR

address: 3181 SW Sam Jackson Park Road, CR-145

department: Cancer Institute

institute: Oregon Health & Science University

description: Gene expression data from ovarian surface kinome

hyb_protocol: DNA pre-processing and array hybridization were performed according to the manufacturer’s directions.  The detailed protocol is available at the following url: http://www.affymetrix.com/support/technical/manuals.affx.

scan_protocol: Array were scanned using GeneArray Laser Scanner (Affymetrix).

data_processing: The data were normalized using RMA.

source_name: normal ovarian surface epithelium

label_protocol: Each RNA sample was labeled using a two-step labeling process. In the first step, mRNA was converted to double-stranded cDNA using Reverse Transcriptase (Invitrogen, Carlsbad, CA) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (IDT). In vitro transcription was performed in the second step where the c-DNA was converted to labeled complementary RNA (the target) using T7 RNA polymerase in the presence of biotinylated UTP (Affymetrix) polymerase binding site sequence (IDT). In vitro transcription was performed in the second step where the c-DNA was converted to labeled complementary RNA (the target) using T7 RNA polymerase in the presence of biotinylated UTP (Affymetrix).

growth_protocol: The samples were obtained fresh in the operating room

extract_protocol: Approximately 3X106 OSE cells were used for the extraction of total RNA by homogenization in a guanidinium isothiocyanate based buffer (RNeasy Micro kit ,Qiagen, Valencia, CA) according to manufacturer’s instructions.

value: Ovarian Epithelium

tag: risk group

value: Normal


title: PS43_30,MEF(-/-), 3hrs 643-EJ-13

description: PS43_30,MEF(-/-), 3hrs 643-EJ-13

source_name: MEF(-/-) cells, pretreated

extract_protocol: At 3 hours after thermal treatment, cell lysates from 144 individual wells were pooled and total RNA was harvested to make each sample. Approximately 4-6 ug of RNA was isolated with the RNeasy Micro Kit (Qiagen, Valencia, CA) along with on column DNAse treatment (Qiagen). RLT buffer in the RNeasy Kit was used without adding β- mercaptoethanol in order to reduce background noise on the microarrays. Agilent’s Bioanalyzer microfluidic assay (Agilent Technologies, Palo Alto CA) was used to assay RNA integrity. Spectrophotometric and fluorometric methods were combined to quantitate protein and nucleic acids present in the sample, and to ensure quality control of each sample.

treatment_protocol: Cells were plate in 96 well plates at 3k/well, incubated 20hrs, Preshocked in a constant temperature water bath for 30 minutes, then returned to incubator for 3 hours before harvesting RNA


title: Sample 17: epithelial ovarian cancer

source_name: epithelial ovarian cancer

value: Cancer


title: Untreated Wild Type 14_wt_GL26_R3


title: PS43_30,MEF(-/-), 3hrs 643-EJ-5

description: PS43_30,MEF(-/-), 3hrs 643-EJ-5

hyb_protocol: The biotinylated cRNA (20 µg) was fragmented and hybridized to an Affymetrix GeneChip Mouse Genome 430 2.0 Array  containing 45,000 sets of 11 to 25-mer oligomers, representing 39,000 mouse transcripts (34,000 are annotated as well-defined genes). Hybridized cRNA was detected using streptavidin coupled to phycoerythrin.

label_protocol: Following quality control, the RNA was prepared for microarray analysis using the GeneChip® One-Cycle Target Labeling and Control Reagents kit (Affymetrix Inc, Santa Clara, CA).  Briefly, 1.5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter.  In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.


title: PS43_30,MEF(-/-), 3hrs 643-EJ-11

description: PS43_30,MEF(-/-), 3hrs 643-EJ-11


title: Ctrl MEF(-/-), 3hrs 643-EJ-12

description: Ctrl MEF(-/-), 3hrs 643-EJ-12


title: Sample 15: normal ovarian surface epithelium


title: Sample 16: high risk ovarian epithelium

source_name: high risk ovarian epithelium

value: High Risk


title: Sample 14: normal ovarian surface epithelium


title: Sample 8: epithelial ovarian cancer


title: Sample 10: epithelial ovarian cancer


title: Sample 4: high risk ovarian epithelium


title: Sample 13: normal ovarian surface epithelium


title: Sample 2: high risk ovarian epithelium


title: Sample 12: epithelial ovarian cancer


title: Sample 11: high risk ovarian epithelium


title: Sample 7: high risk ovarian epithelium


title: Sample 5: normal ovarian surface epithelium


title: Sample 3: high risk ovarian epithelium


title: CLV3p cells rep2

status: Public on Apr 06 2009

city: SAS Nagar

first: Ram

middle: Kishor

last: Yadav

state: Punjab

address: Sector 81

department: Biology

country: India

institute: Indian Institute of Science Education and Research Mohali

description: Gene expression

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5

source_name: CLV3p cells

label_protocol: standard Affymetrix protocol

growth_protocol: 24 days old plants used for cell sorting

extract_protocol: QIAGEN Rneasy Plant Mini Kit used for total RNA isolation

tag: CLV3p cells from ap1-1;cal1-1 shoot apical meristem


title: Protoplast Induced rep2

description: Gene expression

source_name: Protoplast Indcued

tag: ap1-1;cal1-1 meristem tissue treated with protoplasting enzymes


title: Protoplast Induced rep1

description: Gene expression


title: CLV3p cells rep1

description: Gene expression


title: Sample 6: normal ovarian surface epithelium


title: CLV3p cells rep3

description: Gene expression


title: Uninduced rep1

description: Gene expression

source_name: Uninduced

tag: ap1-1;cal1-1 meristem only


title: FILp cells rep1

description: Gene expression

source_name: FILp cells

tag: FILp cells from ap1-1;cal1-1 shoot apical meristem


title: Uninduced rep2

description: Gene expression


title: Sample 1: high risk ovarian epithelium


title: FILp cells rep2

description: Gene expression


title: CLV3n cells rep1

description: Gene expression

source_name: CLV3n cells

tag: CLV3n cells from ap1-1;cal1-1 shoot apical meristem, CLV3n cells types lacks the CLV3p cells


title: WUSp cells rep2

description: Gene expression

source_name: WUSp cells

tag: WUSp cells from ap1-1cal1-1 shoot apical meristem


title: WUSp cells rep1

description: Gene expression


title: CLV3n cells rep3

description: Gene expression


title: FILp cells rep3

description: Gene expression


title: CLV3n cells rep2

description: Gene expression


title: MDA shp53, TGFbeta treated, biological replicate C

status: Public on Apr 03 2009

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description: Gene expression data from TGFbeta-treated mutantp53-depleted MDA-MB-231 cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome HG-U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software

data_processing: RMA of .CEL files using Bioconductor affy library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization

source_name: human metastatic breast cell line MDA-MB-231, infected with a Retroviral construct expressing small-hairpin RNA against TP53 (shp53), treated with TGFbeta (5ug/ml) for 3 hrs, mutant-p53 depleted MDA-MB-231 cells

label_protocol: Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's intructions.

growth_protocol: MDA-MB-231 were maintained in a 1:1 mixture of DMEM and F12 (DMEM/F12) supplemented with 10% serum and 2 mM glutamine.

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

treatment_protocol: Cells were serum starved for 24 hours and then treated in DMEM/F12 without serum

tag: mutant-p53 depleted cells

tag: TGFbeta treated


title: MDA shp53, untreated, biological replicate B

description: Gene expression data from untreated mutantp53-depleted MDA-MB-231 cells

source_name: human metastatic breast cell line MDA-MB-231, infected with a Retroviral construct expressing small-hairpin RNA against TP53 (shp53), untreated, mutant-p53 depleted MDA-MB-231 cells

tag: untreated


title: MDA shp53, untreated, biological replicate C


title: MDA shp53, TGFbeta treated, biological replicate B


title: MDA shp53, TGFbeta treated, biological replicate A


title: MDA shGFP, TGFbeta treated, biological replicate C

description: Gene expression data from TGFbeta-treated control MDA-MB-231 cells

source_name: human metastatic breast cell line MDA-MB-231, infected with a Retroviral construct expressing small-hairpin RNA against GFP (shGFP), treated with TGFbeta (5ug/ml) for 3 hrs, control MDA-MB-231 cells

tag: control cells


title: MDA shGFP, TGFbeta treated, biological replicate A


title: MDA shGFP, untreated, biological replicate D

description: Gene expression data from untreated control MDA-MB-231 cells

source_name: human metastatic breast cell line MDA-MB-231, infected with a Retroviral construct expressing small-hairpin RNA against GFP (shGFP), untreated, control MDA-MB-231 cells


title: MDA shp53, TGFbeta treated, biological replicate D


title: MDA shGFP, TGFbeta treated, biological replicate D


title: MDA shp53, untreated, biological replicate D


title: MDA shp53, untreated, biological replicate A


title: MDA shGFP, TGFbeta treated, biological replicate B


title: MDA shGFP, untreated, biological replicate C


title: MDA shGFP, untreated, biological replicate B


title: Pre Ctrl 3

description: RNA from frozen Glioblastoma Multiforme tumor

data_processing: MAS5 Normalized

source_name: Pre Vaccination Control Non Vaccinated tumor


title: Post Vac Patient 2

source_name: Post Vaccination tumor

tag: Post Vaccination tumor


title: Pre Vac Patient 5

source_name: Pre Vaccination tumor

tag: Pre Vaccination tumor


title: Post Ctrl 4

source_name: Post Vaccination Control Non Vaccinated tumor


title: Post Ctrl 5

tag: Post Vaccination Control Non Vaccinated tumor


title: Post Vac Patient 3


title: Pre Vac Patient 3


title: Post Vac Patient 4


title: Pre Ctrl 2

tag: Pre Vaccination Control Non Vaccinated tumor


title: Pre Vac Patient 4


title: Post Vac Patient 6


title: Pre Vac Patient 2


title: Pre Vac Patient 6


title: Pre Ctrl 4


title: Pre Vac Patient 1


title: Post Ctrl 2


title: Pre Ctrl 5


title: Post Vac Patient 5


title: Post Ctrl 1


title: Post Vac Patient 1


title: Pre Ctrl 1


title: Post Ctrl 3


title: FHV RNA1 replicon expressing S2 cells, biological replicate 3

status: Public on Apr 01 2009

first: David

last: Miller

address: 3560B MSRB II, 1150 W. Medical Center Dr.

department: Internal Medicine

description: Miller S2 FHV replicon 3

hyb_protocol: Fragmented cRNAs were hybridized to Affymetrix Drosophila genome array chips for 16 h at 45C, washed, and stained using an Affymetrix microfluids station.

scan_protocol: Chips were scanned with an Affymetrix Scanner 3000.

data_processing: The data were analyzed using the Affymetrix package of Bioconductor - expression values were calculated using a robust multi-array average (RMA).

organism: Drosophila melanogaster

source_name: Drosophila S2 cells, FHV infected for 12 h

label_protocol: Biotinylated cRNAs were prepared from 5-10 ug total RNA using standard Affymetix protocol.

growth_protocol: Cells cultured at 25C in Schneider's Drosophila media supplemented with 10% heat-inactivated fetal bovine serum, 10 U/ml penicillin, and 10 ug/ml streptomycin.

extract_protocol: Trizol extraction of total RNA done per the manufacturer's instruction.  Total RNA digested with RQ1 DNAse and reisolated with RNAsy columns per the manufacturer's instructions.

treatment_protocol: Cells were induced with 1 mM copper sulfate for 18 h prior to RNA extraction.

tag: cell line

tag: virus

value: FHV RNA1 replicon

tag: infection

value: FHV infected for 12 h


title: etr1_1% sucrose_12-day-old_rep2

status: Public on Mar 31 2009

first: Wan-Hsing

last: Cheng

address: 128, Section 2, Academia Road, Nankang

hyb_protocol: standard Affymetrix expression array hybridization protocol

scan_protocol: standard Affymetrix expression array scanning protocol

source_name: etr1, 1% sucrose, 12-day-old

label_protocol: standard Affymetrix expression array protocol

extract_protocol: Qiagen RNeasy plant kit

tag: Genotype

tag: 12-day-old seedlings

tag: grown on 1% sucrose 1/2MS plate


title: FHV RNA1 replicon expressing S2 cells, biological replicate 1

description: Miller S2 FHV replicon 1


title: ein2_1% sucrose_14-day-old_rep2

source_name: ein2, 1% sucrose, 14-day-old

tag: 14-day-old seedlings

tag: grown on 1% sucrose 1/2 MS plate


title: FHV RNA1 replicon expressing S2 cells, biological replicate 2

description: Miller S2 FHV replicon 2

source_name: Drosophila S2 cells, mock infected

value: mock infected


title: aba2_1% sucrose_12-day-old_rep2

source_name: aba2, 1% sucrose, 12-day-old

tag: Genotyp


title: MDA shGFP, untreated, biological replicate A


title: Col-7_1% sucrose_12-day-old_rep1

source_name: Col-7, 1% sucrose, 12-day-old


title: Col-0_1% sucrose_14-day-old_rep2

source_name: Col-0, 1% sucrose, 14-day-old


title: etr1_1% sucrose_12-day-old_rep1


title: ein2_1% sucrose_14-day-old_rep1


title: Col-0_1% sucrose_14-day-old_rep1

hyb_protocol: Standard Affymetrix expression array hybridization protocol.

scan_protocol: Standard Affymetrix expression array scanning protocol.

label_protocol: Standard Affymetrix expression array protocol.


title: Col-0_1% sucrose_12-day-old_rep2

source_name: Col-0, 1% sucrose, 12-day-old


title: control replicon expressing S2 cells

description: Miller S2 FHV replicon control

value: control plasmid


title: aba2_1% sucrose_12-day-old_rep1


title: Ler_leaf_2

status: Public on Apr 02 2009

city: beer sheva

first: inbar

last: plaschkes

address: BGU univarsity

institute: NIBN-BGU

description: no additional information

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix 3000G

data_processing: Data analysis was performed using Partek®. Additional quality assessment and visualizations were done using SpotFire DecisionSite (Tibco). Microarray CEL files were read into Partek and preprocessed by Robust Multiarray Averaging (RMA, Irizarry et al 2003) using default parameters, followed by quantile normalization and probe summarization using median polish. Expression signals were generated and displayed on log 2 scale. Signals distribution plots, principal component analysis and hierarchical clustering of the normalized samples were examined, in order to assess the quality of the microarrays. Statistical hypothesis testing for identification of differentially expressed genes was done using 2-Way ANOVA in Partek, where the fixed effects were the “tissue” (leaf or protoplast) and “source plant” (Ler or kyp).  “Sources of variation analysis” in Partek showed a much higher average F-ratio of the tissue effect compared to the average F-ratio of the source plant effect (466 vs. 20.4, respectively). P-values were calculated for each effect as well as for the interaction between them, and further adjusted for multiple tesing by step-up FDR according to Benjamini and Hochberg (1995). Fold change values are represented on linear scale, where positive and negative values indicate up- and down-regulation, respectively. Differentially expressed genes were defined as those having absolute expression signal > 5 in at least one of the arrays, FDR adjusted p-value < 0.05 in any of the effects or interaction, and  fold change value either below -1.3 or above 1.3. Among the 1,499 differentially expressed genes, 1,484 genes showed significant tissue effect,  109 genes showed significant source plant effect and 37 genes showed significant interaction. 98 genes had both tissue and source plant significant effect. Hierarchical clustering applied to the differentially expressed genes using the Pearson correlation coefficient as a measure of similarity (data not shown), yielded two main clusters according to “tissue”. Together with the sources of variation analysis and the numbers of differentially expressed genes in each contrast, these data suggests a much more robust tissue effect compared to the source plant effect.

label_protocol: The probe Preparation, cDNA synthesis, cRNA reactions and hybridizationaccording to Affymetrix GeneChip®  Expression Analysis Technical Manual was carried out in the Weizmann Institute microarray unit.

growth_protocol: Seeds of Arabidopsis thaliana Landsberg erecta (Ler) ecotype and kyp-2 mutant were sown and incubated at 4oC for 4 days and then grown under long-day conditions (14 h light) at 21oC

extract_protocol: Total RNAs were prepared from leaves and protoplasts using RNeasy Plant Mini Kit according to the manufacturer’s protocol (Qiagen)

treatment_protocol: Protoplasts were isolated from 5-6 week-old plants by incubating rosette leaves for 12-14 hours in N&M medium containing 1% cellulase “onozuka” R-10 and 0.25% macerozyme R10 (Yakult Honsha Co., Ltd., Japan). Protoplasts were separated by centrifugation, washed once with CPW medium and precipitated by centrifugation at low speed for 5 min.

tag: ecotype

value: Ler

tag: tissue

value: leaf


title: Col-7_1% sucrose_12-day-old_rep2


title: Col-0_1% sucrose_12-day-old_rep1

scan_protocol: Standard Affymetrix expression array scanning protocol

tag: 1% sucrose 1/2 MS plate


title: Ler_protoplast_2

description: no additional information

value: protoplast


title: E_C_Gad_sample5

city: Duarte

first: Paul

middle: M.

last: Salvaterra

address: 1500 E. Duarte Rd

department: Neuroscience

institute: Beckman Research Institute. City of Hope National Medical Center

description:
embryo culture 5-7 days, 2.1 kb Gad1(s)-RFP
E_C_Gad_sample5 (K+)

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: The data presented here have been processed using the R-Project Bioconductor statistical tools package using the affy library. The following were applied: RMA background correction, pmonly probe-level correction, quantile normalization, median-polish summary method. Raw data is provided in the form of .CEL files.

label_protocol: Standard Affymetrix protocol.

growth_protocol: Cultures were incubated at 25 C for 5-8 days prior to dissociation and harvesting for Fluorescent Active Cell Sorting (FACS). After this time the cells were fully differentiated into a variety of neuronal. We plated approximately 7.0 x 10E7 cells.

extract_protocol: Total RNA was extracted from FACS sorted fractions using the RNA-STAT 60 kit (Iso Tex Diagnostic, Friendswood TX, USA). The RNA yield was measured by the absorbance at 260 nm and a rough estimate of RNA quality was obtained from the A260/280 ratio. Samples were treated with DNAse I (Ambion, Austin TX, USA) to remove contaminating.  RNA clean of any contaminants was monitored by microcapillary electrophoresis (Bioanalyzer 2100, Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Embryo collection and culture were performed as previously described (Salvaterra, P.M., Hayashi, I., Perez-Magallanes, M., & Ikeda, K.  (2006) Primary culture of Drosophila embryo cells. in: Cell and Tissue Culture: Assorted Techniques, Elsevier Science USA,  pp. 151-155). Cultures were initiated by dissociating early gastrula stage embryos prior to the differentiation of any neurons.

tag: Strain

value: 2.1 kb Gad1(s)-RFP

tag: Age

value: Adults for collection were 2 weeks old

tag: Tissue

value: Embryo culture


title: kyp_protoplast_1

description: no additional information

tag: mutant

value: kyp


title: Ler_protoplast_1

description: no additional information


title: kyp_leaf_1

description: no additional information


title: kyp_protoplast_2

description: no additional information


title: E_C_Cha_sample5

description:
embryo culture 5-7 days, 7.4 kb Cha-Gal:UAS-GFP
E_C_Cha_sample5 (P+)

value: 7.4 kb Cha-Gal:UAS-GFP


title: Ler_leaf_1

description: no additional information


title: E_C_Gad_sample4

description:
embryo culture 5-7 days, 2.1 kb Gad1(s)-RFP
E_C_Gad_sample4 (J+)


title: E_C_Gad_sample3

description:
embryo culture 5-7 days, 2.1 kb Gad1(s)-RFP
E_C_Gad_sample3 (H+)


title: E_C_Cha_sample4

description:
embryo culture 5-7 days, 7.4 kb Cha-Gal:UAS-GFP
E_C_Cha_sample4 (N+)


title: E_C_Cha_sample3

description:
embryo culture 5-7 days, 7.4 kb Cha-Gal:UAS-GFP
E_C_Cha_sample3 (L+)


title: E_C_Gad_sample1

description:
embryo culture 5-7 days, 2.1 kb Gad1(s)-RFP
E_C_Gad_sample1 (I+)


title: E_C_Gad_sample2

description:
embryo culture 5-7 days, 2.1 kb Gad1(s)-RFP
E_C_Gad_sample2 (F+)


title: E_C_Cha_sample2

description:
embryo culture 5-7 days, 7.4 kb Cha-Gal:UAS-GFP
E_C_Cha_sample2 (K+)


title: Adult_female_haplo_4th_biological_replicate_1

status: Public on Mar 30 2009

city: Umea

first: Jan

last: Larsson

address: Umea University

department: Molecular Biology

institute: Umea University

description:
Gene expression data from adult females
h4_1

data_processing: Raw data was normalized using RMA (R and Bioconductor).

source_name: Adult female, haplo 4th, biological replicate 1

growth_protocol: Flies were cultivated and crossed in vials with potato-yeast-agar medium at 25 ̊ C.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) followed by a purification using RNeasy kit (Qiagen) according to the instruction by the suppliers.

treatment_protocol: Three replicates, each containing 10 adult female flies, were collected and frozen in -70 ̊ C prior to RNA extraction

tag: Adult female, 0-24h


title: Adult_female_haplo_4th_biological_replicate_2

description:
Gene expression data from adult females
h4_2

source_name: Adult female, haplo 4th, biological replicate 2


title: E_C_Cha_sample1

description:
embryo culture 5-7 days, 7.4 kb Cha-Gal:UAS-GFP
E_C_Cha_sample1 (G+)


title: Adult_female_haplo_4th_biological_replicate_3

description:
Gene expression data from adult females
h4_3

source_name: Adult female, haplo 4th, biological replicate 3


title: Adult_female_Df(2L)J-H/+_biological_replicate_3

description:
Gene expression data from adult females
JH-3

source_name: Adult female, Df(2L)J-H/+, biological replicate 3


title: Adult_female_Df(2L)J-H/+_haplo_4th_biological_replicate_2

description:
Gene expression data from adult females
JH_h4-2

source_name: Adult female, Df(2L)J-H/+, haplo 4th, biological replicate 2


title: Adult_female_Df(2L)J-H/+_haplo_4th_biological_replicate_1

description:
Gene expression data from adult females
JH_h4-1

source_name: Adult female, Df(2L)J-H/+, haplo 4th, biological replicate 1


title: Adult_female_Df(2L)J-H/+_haplo_4th_biological_replicate_3

description:
Gene expression data from adult females
JH_h4-3

source_name: Adult female, Df(2L)J-H/+, haplo 4th, biological replicate 3


title: Adult_female_Df(3L)4470/+_biological_replicate_3

description:
Gene expression data from adult females
ED4470-3

source_name: Adult female, Df(3L)4470/+, biological replicate 3


title: Adult_female_Df(2L)J-H/+_biological_replicate_2

description:
Gene expression data from adult females
JH-2

source_name: Adult female, Df(2L)J-H/+, biological replicate 2


title: Adult_female_Df(2L)ED4651/+_biological_replicate_2

description:
Gene expression data from adult females
ED4651-2

source_name: Adult female, Df(2L)ED4651/+, biological replicate 2


title: Adult_female_wild_type_biological_replicate_3

description:
Gene expression data from adult females
WT-3

source_name: Adult female, wild type, biological replicate 3


title: Adult_female_Df(2L)ED4651/+_biological_replicate_1

description:
Gene expression data from adult females
ED4651-1

source_name: Adult female, Df(2L)ED4651/+, biological replicate 1


title: Adult_female_wild_type_biological_replicate_1

description:
Gene expression data from adult females
WT-1

source_name: Adult female, wild type, biological replicate 1


title: Adult_female_Df(2L)J-H/+_biological_replicate_1

description:
Gene expression data from adult females
JH-1

source_name: Adult female, Df(2L)J-H/+, biological replicate 1


title: Adult_female_Df(2L)ED4651/+_biological_replicate_3

description:
Gene expression data from adult females
ED4651-3

source_name: Adult female, Df(2L)ED4651/+, biological replicate 3


title: Adult_female_Dp(2;2)Cam3/+_triplo_4th_biological_replicate_1

description:
Gene expression data from adult females
DpC_t4-1

source_name: Adult female, Dp(2;2)Cam3/+, triplo 4th, biological replicate 1


title: Adult_female_wild_type_biological_replicate_2

description:
Gene expression data from adult females
WT-2

source_name: Adult female, wild type, biological replicate 2


title: Adult_female_Dp(2;2)Cam3/+_triplo_4th_biological_replicate_2

description:
Gene expression data from adult females
DpC_t4-2

source_name: Adult female, Dp(2;2)Cam3/+, triplo 4th, biological replicate 2


title: Adult_female_pof-mutant_triplo_4th_biological_replicate_2

description:
Gene expression data from adult females
D119_t4-2

source_name: Adult female, pof-mutant, triplo 4th, biological replicate 2


title: Adult_female_pof-mutant_triplo_4th_biological_replicate_3

description:
Gene expression data from adult females
D119_t4-3

source_name: Adult female, pof-mutant, triplo 4th, biological replicate 3


title: Adult_female_Dp(2;2)Cam3/+_triplo_4th_biological_replicate_3

description:
Gene expression data from adult females
DpC_t4-3

source_name: Adult female, Dp(2;2)Cam3/+, triplo 4th, biological replicate 3


title: Adult_female_pof-mutant_biological_replicate_1

description:
Gene expression data from adult females
D119_d4-1

source_name: Adult female, pof-mutant, biological replicate 1


title: Adult_female_Df(3L)4470/+_biological_replicate_1

description:
Gene expression data from adult females
ED4470-1

source_name: Adult female, Df(3L)4470/+, biological replicate 1


title: Adult_female_pof-mutant_triplo_4th_biological_replicate_1

description:
Gene expression data from adult females
D119_t4-1

source_name: Adult female, pof-mutant, triplo 4th, biological replicate 1


title: Adult_female_Df(3L)4470/+_biological_replicate_2

description:
Gene expression data from adult females
ED4470-2

source_name: Adult female, Df(3L)4470/+, biological replicate 2


title: Adult_female_pof-mutant_biological_replicate_2

description:
Gene expression data from adult females
D119_d4-2

source_name: Adult female, pof-mutant, biological replicate 2


title: testis_wildtype_biological_replicate_1

description:
Gene expression data from male testes
WTA

source_name: testis, wildtype, biological replicate 1

treatment_protocol: Three replicates, each of 60 testes from 0-24h old males, were dissected in PBS and frozen in -70 ̊ C prior to RNA extraction.

tag: Testes from 0-24h old males


title: Adult_female_pof-mutant_biological_replicate_3

description:
Gene expression data from adult females
D119_d4-3

source_name: Adult female, pof-mutant, biological replicate 3


title: testis_pof-mutant_biological_replicate_2

description:
Gene expression data from male testes
MB

source_name: testis, pof-mutant, biological replicate 2


title: testis_pof-mutant_biological_replicate_3

description:
Gene expression data from male testes
MC

source_name: testis, pof-mutant, biological replicate 3


title: testis_wildtype_biological_replicate_2

description:
Gene expression data from male testes
WTB

source_name: testis, wildtype, biological replicate 2


title: testis_pof-mutant_biological_replicate_1

description:
Gene expression data from male testes
MA

source_name: testis, pof-mutant, biological replicate 1


title: HCT116 cells treated with vehicle (DMSO) for 6 hours, replicate f

status: Public on Mar 26 2009

city: Nutley

first: James

last: Rosinski

state: NJ

address: 340 Kingsland St

department: In Silico Sciences

institute: Roche

hyb_protocol: Hybridization Mix contained, in addition to cRNA, reagents from the Hybridization Control Kit and Control Oligo B2.  Staining and washing steps were performed as suggested by the manufacturer (Affymetrix, Santa Clara, CA).

scan_protocol: Each hybridized Affymetrix GeneChip array was scanned with a GeneChip Scanner 3000 7G (Agilent/Affymetrix).

data_processing: Affymetrix gene expression microarray data was first background corrected and normalized via the RMA procedure followed by QQ normalization (R/Bioconductor)

label_protocol: RNA was converted into cDNA and cRNA according to the manufacturer’s recommendation and using manufacturer’s kits (Affymetrix, Santa Clara, CA).  15 ug of total RNA was converted to cDNA with the One-cycle cDNA Synthesis Kit with the addition of reagents from the Poly-A RNA Control Kit.  cRNA was produced with the IVT Labeling Kit

growth_protocol: Cell lines were maintained in the recommended medium and supplemented with 10% heat-inactivated fetal bovine serum (Life Technologies, Gaithersburg, MD) and 2 mmol/L L-glutamine (Life Technologies)

extract_protocol: Total RNA was extracted from cells using the Qiagen RNeasy Mini Kit

treatment_protocol: HCT116 cells were grown in vehicle (DMSO), IC50, IC90 or the 3xIC90 dose of R547 for 0,1, 2, 4, 6, and 24 hours

tag: cell line


title: testis_wildtype_biological_replicate_3

description:
Gene expression data from male testes
WTC

source_name: testis, wildtype, biological replicate 3


title: HCT116 cells treated with vehicle (DMSO) for 6 hours, replicate a


title: HCT116 cells treated with vehicle (DMSO) for 4 hours, replicate f


title: HCT116 cells treated with vehicle (DMSO) for 2 hours, replicate a


title: HCT116 cells treated with vehicle (DMSO) for 4 hours, replicate e


title: HCT116 cells treated with vehicle (DMSO) for 6 hours, replicate e


title: HCT116 cells treated with vehicle (DMSO) for 2 hours, replicate d


title: HCT116 cells treated with vehicle (DMSO) for 4 hours, replicate c


title: HCT116 cells treated with vehicle (DMSO) for 24 hours, replicate c


title: HCT116 cells treated with vehicle (DMSO) for 2 hours, replicate b


title: HCT116 cells treated with vehicle (DMSO) for 4 hours, replicate a


title: HCT116 cells treated with vehicle (DMSO) for 6 hours, replicate c


title: HCT116 cells treated with vehicle (DMSO) for 24 hours, replicate b


title: HCT116 cells treated with vehicle (DMSO) for 1 hours, replicate e


title: HCT116 cells treated with vehicle (DMSO) for 24 hours, replicate f


title: HCT116 cells treated with vehicle (DMSO) for 2 hours, replicate e


title: HCT116 cells treated with vehicle (DMSO) for 24 hours, replicate d


title: HCT116 cells treated with vehicle (DMSO) for 1 hours, replicate b


title: Untreated HCT116 cells, replicate d

source_name: Untreated HCT116 cells, replicate d


title: Untreated HCT116 cells, replicate e

source_name: Untreated HCT116 cells, replicate e


title: Untreated HCT116 cells, replicate a

source_name: Untreated HCT116 cells, replicate a


title: HCT116 cells treated at the IC90 for 6 hours, replicate d


title: HCT116 cells treated with vehicle (DMSO) for 1 hours, replicate f


title: HCT116 cells treated with vehicle (DMSO) for 1 hours, replicate d


title: Untreated HCT116 cells, replicate b

source_name: Untreated HCT116 cells, replicate b


title: HCT116 cells treated at the IC90 for 4 hours, replicate e


title: HCT116 cells treated at the IC90 for 6 hours, replicate b


title: HCT116 cells treated at the IC90 for 4 hours, replicate d


title: HCT116 cells treated at the IC90 for 4 hours, replicate b


title: HCT116 cells treated at the IC90 for 2 hours, replicate b


title: HCT116 cells treated at the IC90 for 2 hours, replicate f


title: HCT116 cells treated at the IC90 for 1 hours, replicate d


title: HCT116 cells treated at the IC90 for 1 hours, replicate f


title: HCT116 cells treated at the IC90 for 4 hours, replicate a


title: HCT116 cells treated at the IC90 for 24 hours, replicate a


title: HCT116 cells treated at the IC90 for 2 hours, replicate c


title: HCT116 cells treated at the IC90 for 24 hours, replicate d


title: HCT116 cells treated at the IC90 for 24 hours, replicate e


title: HCT116 cells treated at the IC50 for 4 hours, replicate f


title: HCT116 cells treated at the IC90 for 24 hours, replicate f


title: HCT116 cells treated at the IC50 for 6 hours, replicate c


title: HCT116 cells treated at the IC50 for 6 hours, replicate e


title: HCT116 cells treated at the IC50 for 6 hours, replicate b


title: HCT116 cells treated at the IC50 for 4 hours, replicate e


title: HCT116 cells treated at the IC50 for 4 hours, replicate b


title: HCT116 cells treated at the IC90 for 1 hours, replicate e


title: HCT116 cells treated at the IC50 for 24 hours, replicate e


title: HCT116 cells treated at the IC50 for 2 hours, replicate d


title: HCT116 cells treated at the IC50 for 6 hours, replicate d


title: HCT116 cells treated at the IC50 for 24 hours, replicate f


title: HCT116 cells treated at the IC50 for 2 hours, replicate c


title: HCT116 cells treated at the IC50 for 2 hours, replicate e


title: HCT116 cells treated at the IC50 for 24 hours, replicate d


title: HCT116 cells treated at the IC90 for 1 hours, replicate b


title: HCT116 cells treated at the IC50 for 1 hours, replicate f


title: HCT116 cells treated at the IC50 for 24 hours, replicate c


title: HCT116 cells treated at the IC50 for 2 hours, replicate f


title: HCT116 cells treated at the IC50 for 4 hours, replicate a


title: HCT116 cells treated at 3xIC90 for 6 hours, replicate c


title: HCT116 cells treated at 3xIC90 for 2 hours, replicate b


title: HCT116 cells treated at 3xIC90 for 4 hours, replicate f


title: HCT116 cells treated at 3xIC90 for 6 hours, replicate d


title: HCT116 cells treated at 3xIC90 for 24 hours, replicate e


title: HCT116 cells treated at the IC50 for 1 hours, replicate c


title: HCT116 cells treated at 3xIC90 for 4 hours, replicate b


title: HCT116 cells treated at 3xIC90 for 1 hours, replicate c


title: HCT116 cells treated at the IC50 for 1 hours, replicate d


title: HCT116 cells treated at 3xIC90 for 1 hours, replicate f


title: HCT116 cells treated at 3xIC90 for 4 hours, replicate c


title: HCT116 cells treated at the IC50 for 1 hours, replicate b


title: HCT116 cells treated at 3xIC90 for 2 hours, replicate e


title: HCT116 cells treated at 3xIC90 for 24 hours, replicate f


title: HCT116 cells treated at 3xIC90 for 24 hours, replicate b


title: DU145 cells treated at 3xIC90 for 6 hours, replicate a

treatment_protocol: DU145 cells were grown in vehicle (DMSO), IC50, IC90 or the 3xIC90 dose of R547 for 0, 2, 6, and 24 hours


title: HCT116 cells treated at 3xIC90 for 1 hours, replicate a


title: DU145 cells treated with vehicle (DMSO) for 6 hours, replicate d


title: DU145 cells treated with vehicle (DMSO) for 6 hours, replicate c


title: DU145 cells treated with vehicle (DMSO) for 6 hours, replicate a


title: DU145 cells treated with vehicle (DMSO) for 6 hours, replicate b


title: DU145 cells treated with vehicle (DMSO) for 2 hours, replicate d


title: DU145 cells treated with vehicle (DMSO) for 24 hours, replicate c


title: DU145 cells treated with vehicle (DMSO) for 2 hours, replicate b


title: DU145 cells treated with vehicle (DMSO) for 2 hours, replicate a


title: DU145 cells treated with vehicle (DMSO) for 24 hours, replicate d


title: DU145 cells treated with vehicle (DMSO) for 2 hours, replicate c


title: Untreated DU145 cells, replicate 3

source_name: Untreated DU145 cells, replicate 3


title: DU145 cells treated with vehicle (DMSO) for 24 hours, replicate b


title: Untreated DU145 cells, replicate 4

source_name: Untreated DU145 cells, replicate 4


title: Untreated DU145 cells, replicate 2

source_name: Untreated DU145 cells, replicate 2


title: DU145 cells treated with vehicle (DMSO) for 24 hours, replicate a


title: DU145 cells treated at the IC90 for 6 hours, replicate d


title: DU145 cells treated at the IC90 for 2 hours, replicate c


title: DU145 cells treated at the IC90 for 6 hours, replicate c


title: DU145 cells treated at the IC90 for 24 hours, replicate b


title: DU145 cells treated at the IC90 for 6 hours, replicate a


title: DU145 cells treated at the IC90 for 2 hours, replicate f


title: DU145 cells treated at the IC90 for 2 hours, replicate e


title: DU145 cells treated at the IC50 for 6 hours, replicate c


title: DU145 cells treated at the IC50 for 2 hours, replicate a


title: DU145 cells treated at the IC90 for 2 hours, replicate d


title: DU145 cells treated at the IC90 for 24 hours, replicate c


title: DU145 cells treated at the IC90 for 6 hours, replicate b


title: DU145 cells treated at the IC50 for 6 hours, replicate b


title: DU145 cells treated at the IC50 for 24 hours, replicate b


title: DU145 cells treated at the IC50 for 2 hours, replicate d


title: DU145 cells treated at the IC50 for 2 hours, replicate c


title: DU145 cells treated at the IC50 for 2 hours, replicate b


title: DU145 cells treated at the IC50 for 24 hours, replicate d


title: DU145 cells treated at 3xIC90 for 6 hours, replicate c


title: DU145 cells treated at 3xIC90 for 6 hours, replicate d


title: DU145 cells treated at the IC50 for 24 hours, replicate a


title: DU145 cells treated at 3xIC90 for 6 hours, replicate b


title: DU145 cells treated at 3xIC90 for 2 hours, replicate d


title: DU145 cells treated at 3xIC90 for 2 hours, replicate c


title: DU145 cells treated at the IC90 for 24 hours, replicate a


title: DU145 cells treated at 3xIC90 for 24 hours, replicate c


title: DU145 cells treated at 3xIC90 for 2 hours, replicate b


title: PBMCs vehicle treated for 24 hours,replicate 3

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) were separated from whole blood of seven healthy donors and cultured in six T75 flasks per donor at 10^7 cells per flask in 10% heat-inactivated FBS in RPMI medium

treatment_protocol: Cells from donors 1-6 were grown in vehicle, the IC90 (0.2 uM R547) and 3xIC90 (0.6 uM R547) dose of R547 for 2 or 24 hours. Donor 7 was used as the untreated zero hour time-point

tag: cell type

value: peripheral blood mononuclear cells


title: PBMCs vehicle treated for 2 hours,replicate 5


title: PBMCs vehicle treated for 2 hours,replicate 4


title: DU145 cells treated at 3xIC90 for 24 hours, replicate d


title: PBMCs vehicle treated for 2 hours,replicate 6


title: PBMCs vehicle treated for 24 hours,replicate 5


title: PBMCs vehicle treated for 24 hours,replicate 6


title: Untreated PBMCs, replicate 2

source_name: Untreated PBMCs, replicate 2


title: PBMCs vehicle treated for 2 hours,replicate 3


title: PBMCs vehicle treated for 2 hours,replicate 2


title: Untreated PBMCs, replicate 3

source_name: Untreated PBMCs, replicate 3


title: PBMCs treated at the IC90 for 2 hours,replicate 6


title: PBMCs vehicle treated for 24 hours,replicate 1


title: PBMCs vehicle treated for 2 hours,replicate 1


title: PBMCs vehicle treated for 24 hours,replicate 2


title: PBMCs vehicle treated for 24 hours,replicate 4


title: Untreated PBMCs, replicate 1

source_name: Untreated PBMCs, replicate 1


title: PBMCs treated at the IC90 for 2 hours,replicate 4


title: PBMCs treated at the IC90 for 2 hours,replicate 5


title: DU145 cells treated at the IC50 for 24 hours, replicate c


title: PBMCs treated at the IC90 for 2 hours,replicate 2


title: PBMCs treated at the IC90 for 2 hours,replicate 3


title: PBMCs treated at the IC90 for 2 hours,replicate 1


title: PBMCs treated at the IC90 for 24 hours,replicate 6


title: PBMCs treated at the IC90 for 24 hours,replicate 4


title: PBMCs treated at the IC90 for 24 hours,replicate 3


title: PBMCs treated at the IC90 for 24 hours,replicate 2


title: PBMCs treated at the IC90 for 24 hours,replicate 1


title: PBMCs treated at 3xIC90 for 2 hours,replicate 4


title: PBMCs treated at 3xIC90 for 2 hours,replicate 6


title: PBMCs treated at 3xIC90 for 24 hours,replicate 2


title: PBMCs treated at 3xIC90 for 24 hours,replicate 3


title: PBMCs treated at 3xIC90 for 24 hours,replicate 5


title: PBMCs treated at the IC90 for 24 hours,replicate 5


title: PBMCs treated at 3xIC90 for 2 hours,replicate 3


title: PBMCs treated at 3xIC90 for 24 hours,replicate 6


title: PBMCs treated at 3xIC90 for 2 hours,replicate 2


title: PBMCs treated at 3xIC90 for 2 hours,replicate 5


title: PBMCs treated at 3xIC90 for 24 hours,replicate 1


title: Neutrophil JIA 12 of 14

status: Public on Mar 25 2009

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

description: Affymetrix

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: GCOS 5.0

source_name: neutrophil

label_protocol: Affymetrix

extract_protocol: Trizol + RNEasy

tag: neutrophil


title: PBMC JIA 11 of 14

description: Affymetrix

source_name: PBMC

tag: PBMC


title: Neutrophil JIA 13 of 14

description: Affymetrix


title: Neutrophil JIA 7 of 14

description: Affymetrix


title: Neutrophil JIA 11 of 14

description: Affymetrix


title: Neutrophil JIA 3 of 14

description: Affymetrix


title: Neutrophil JIA 10 of 14

description: Affymetrix


title: PBMC JIA 13 of 14

description: Affymetrix


title: Neutrophil JIA 6 of 14

description: Affymetrix


title: Neutrophil JIA 9 of 14

description: Affymetrix


title: Neutrophil JIA 8 of 14

description: Affymetrix


title: PBMC JIA 7 of 14

description: Affymetrix


title: PBMC JIA 8 of 14

description: Affymetrix


title: Neutrophil JIA 14 of 14

description: Affymetrix


title: PBMC JIA 10 of 14

description: Affymetrix


title: PBMC JIA 9 of 14

description: Affymetrix


title: PBMC JIA 12 of 14

description: Affymetrix


title: PBMC JIA 6 of 14

description: Affymetrix


title: PBMC JIA 1 of 14

description: Affymetrix


title: PBMC JIA 14 of 14

description: Affymetrix


title: PBMC JIA 3 of 14

description: Affymetrix


title: PBMC JIA 4 of 14

description: Affymetrix


title: PBMC JIA 2 of 14

description: Affymetrix


title: PBMC JIA 5 of 14

description: Affymetrix


title: Neutrophil JIA 5 of 14

description: Affymetrix


title: Neutrophil JDM 2 of 14

description: Affymetrix

source_name: Neutrophil

tag: Neutrophil


title: Neutrophil JDM 12 of 14

description: Affymetrix


title: Neutrophil JIA 4 of 14

description: Affymetrix


title: Neutrophil JIA 2 of 14

description: Affymetrix


title: Neutrophil JDM 4 of 14

description: Affymetrix


title: Neutrophil JDM 8 of 14

description: Affymetrix


title: Neutrophil JDM 3 of 14

description: Affymetrix


title: PBMC Control 13 of 15

description: Affymetrix


title: Neutrophil JIA 1 of 14

description: Affymetrix


title: Neutrophil JDM 6 of 14

description: Affymetrix


title: PBMC Control 15 of 15

description: Affymetrix


title: PBMC Control 11 of 15

description: Affymetrix


title: PBMC Control 12 of 15

description: Affymetrix


title: PBMC Control 8 of 15

description: Affymetrix


title: PBMC Control 14 of 15

description: Affymetrix


title: PBMC Control 7 of 15

description: Affymetrix


title: Neutrophil JDM 1 of 14

description: Affymetrix


title: Neutrophil JDM 5 of 14

description: Affymetrix


title: PBMC Control 10 of 15

description: Affymetrix


title: Neutrophil JDM 10 of 14

description: Affymetrix


title: Neutrophil JDM 7 of 14

description: Affymetrix


title: Neutrophil JDM 11 of 14

description: Affymetrix


title: PBMC Control 9 of 15

description: Affymetrix


title: PBMC Control 6 of 15

description: Affymetrix


title: Neutrophil JDM 14 of 14

description: Affymetrix


title: Neutrophil JDM 13 of 14

description: Affymetrix


title: PBMC Control 4 of 15

description: Affymetrix


title: Neutrophil JDM 9 of 14

description: Affymetrix


title: PBMC Control 3 of 15

description: Affymetrix


title: Neutrophil Control 10 of 13

description: Affymetrix


title: Neutrophil Control 9 of 13

description: Affymetrix


title: Neutrophil Control 12 of 13

description: Affymetrix


title: Neutrophil Control 8 of 13

description: Affymetrix


title: PBMC Control 1 of 15

description: Affymetrix


title: PBMC Control 2 of 15

description: Affymetrix


title: Neutrophil Control 11 of 13

description: Affymetrix


title: Neutrophil Control 7 of 13

description: Affymetrix


title: Neutrophil Control 13 of 13

description: Affymetrix


title: Neutrophil Control 4 of 13

description: Affymetrix


title: Neutrophil control 1 of 13

description: Affymetrix


title: PBMC Control 5 of 15

description: Affymetrix


title: Neutrophil Control 3 of 13

description: Affymetrix


title: Floxed_Mstn_2

status: Public on Mar 24 2009

city: Rochester

first: Stephen

last: Welle

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

description: male, 7.5 months old, floxed myostatin genes, CAGG-CreER transgene, C57BL/6 background

hyb_protocol: Hybridization, washes, and staining with phycoerythrin-streptavidin (including antibody enhancement step) were carried out as recommended by Affymetrix for eukaryotic expression arrays, using hybridization oven and fluidics station purchased from Affymetrix.

scan_protocol: Scans were done with Affymetrix scanner exactly as recommended by Affymetrix.

data_processing: background subtraction and normalization were done with the GCRMA method.

source_name: gastrocnemius muscle

label_protocol: Biotinylated cDNA was prepared with kits from NuGEN as recommended by supplier.

growth_protocol: Mice were reared under normal conditions with food and water ad libitum.

extract_protocol: Total RNA was extracted into Trizol as recommended by supplier (Invitrogen).

treatment_protocol: All mice received a series of 8 injections of tamoxifen starting at 4 months of age to activate Cre recombinase to knock out myostatin in mice with floxed myostatin genes.

tag: gender

value: male

value: gastrocnemius muscle

tag: age

value: 7.5 months

tag: genotype

value: Mstn ko


title: Neutrophil Control 6 of 13

description: Affymetrix


title: Floxed_Mstn_3


title: Floxed_Mstn_4


title: Floxed_Mstn_1


title: Neutrophil Control 2 of 13

description: Affymetrix


title: WT_Mstn_4

description: male, 7.5 months old, normal myostatin genes, CAGG-CreER transgene, C57BL/6 background

value: wild-type


title: Floxed_Mstn_5


title: WT_Mstn_5


title: WT_Mstn_1


title: WT_Mstn_3


title: Ovarian cancer, untreated non-Side Population, rep2

first: Alberto

last: Corradin

state: PD

address: via Tiepolo

department: Dipertimento di Ingegneria dell'Informazione

institute: Università degli Studi di Padova

description: Human ovarian cancer cells obtained from ascitic fluid developed in mice injected i.p. with tumor cells were labeled with Hoechst dye and sorted as Hoechst high cells (non-SP, non-Side Population).  The cells were seeded for 5 h immediately after sorting.  Pellets of sorted cells obtained from 4 different sorting were pooled and analysed by micro-arrays analysis.

hyb_protocol: Affymetrix's manufacturer's protocol: hybridization onto Affymetrix Human Genome U133 Plus 2.0 array

scan_protocol: Affymetrix GCOS

data_processing: RMA normalization

source_name: ascitic fluid, ovarian cancer, untreated non-side population, rep2

label_protocol: GeneChip IVT Labeling Kit (Affymetrix, Santa Clara, CA)

growth_protocol: Sorted non-Side Population subset cells were immediately seeded in P24 plate at the concentration of 100,000 cells/well in a volume of 1 ml of RPMI medium, with or without interferon-alpha (IFN-alpha2b; 1000 IU/ml; IntronA, Schering-Ploug Europe, Bruxelles, Belgium). After 5h the cells were collected and centrifuged. The pellet was store at -80°C for the extraction of RNA. Pellets of sorted cells obtained from 4 different sorting were pooled and analysed by micro-arrays analysis.

extract_protocol: Qiagen RNeasy Mini Kit (Qiagen, Hilden, Germany)

treatment_protocol:
Ovarian cancer cells were derived from the malignant effusion developed in mice injected with cells obtained from ascitic fluid of ovarian cancer bearing-patient. Ascites cells were centrifuged at 1200 rpm for 5 min; red blood cells were lysed by ammonium chloride and the tumor cells were resuspended in RPMI 1640 medium (Euroclone, Pero, Italy) supplemented with 10% FCS (Life Technologies, Gaithersburg, MD), 1% hepes (10 mM, Cambrex Bioscience, Verviers, Belgium), 1% L-glutamine 2 mM, and 1% antibiotics-antimycotic mix (Life Technologies). One day later, the cells were harvested cells (106 cells/ml) were and incubated in DMEM containing 2% FCS, 10 mM hepes and 5 ug/ml Hoechst 33342 dye (Sigma-Aldrich, St. Louis, MO) for 90 min at 37°C, either alone or in the presence of 50 uM verapamil (Sigma). At the end of incubation, cells were washed and then incubated in PBS supplemented with 2% FCS, 10 mM HEPES and 1 ug/ml propidium iodide (PI) (Sigma) at 4°C for 10 min, to discriminate dead cells. The cells were then analysed in a FACSVantage fluorescence-activated cell sorter (Becton Dickinson, San Diego, CA) by using a dual wavelength analysis (blue: 424-444 nm; red: 675 nm) after excitation with 350 nm UV light.
To dissociate multi-cellular aggregates obtained from ascitic fluid, before staining with Hoechst buffer cells were incubated with Accumax solution (Chemicon International, Temecula, CA) for approximately 45 minutes at 37°C with intermittent mixing, until a single cell suspension was obtained.
The labeled cells were sorted for the collection of Hoechst high cells, named non-Side Population subset.


title: Ovarian cancer, untreated non-Side Population, rep1

source_name: ascitic fluid, ovarian cancer, untreated non-side population, rep1


title: Ovarian cancer, IFN-alpha treated non-Side Population, rep2

description: Human ovarian cancer cells obtained from ascitic fluid developed in mice injected i.p. with tumor cells were labeled with Hoechst dye and sorted as Hoechst high cells (non-SP, non-Side Population).  The cells were seeded in medium with interferon-alpha (IFN-alpha2b; 1000 IU/ml; IntronA, Schering-Ploug Europe, Bruxelles, Belgium) for 5 h immediately after sorting.  Pellets of sorted cells obtained from 4 different sorting were pooled and analysed by micro-arrays analysis.

source_name: ascitic fluid, ovarian cancer, IFN-alpha treated non-side population, rep2


title: Ovarian cancer, IFN-alpha treated non-Side Population, rep1

source_name: ascitic fluid, ovarian cancer, IFN-alpha treated non-side population, rep1


title: WT_Mstn_2


title: Neutrophil Control 5 of 13

description: Affymetrix