title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP040_48H

city: Singapore

first: Sachel

last: Mok

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

hyb_protocol: Microarray hybridizations were carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, hybridizations were performed for 16 hours at 65°C using a Maui hybridization system (BioMicro Systems, Salt Lake City, Utah, USA).

scan_protocol: Scanning as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v6.0 software (Axon Instruments, Union City, California, USA).

data_processing: Data processing as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, Lowess normalization and subsequent filtering for quality control were carried out using Acuity 4.0 (Axon Instruments). Spots were considered of good quality when they were unflagged and had at least 95% of pixels median intensity greater than the local background plus 2 times the standard deviation of the background for either dye channel. The values presented in the sample data represent log2-transformed ratios of the measurement in the sample channel (Cy5) divided by the corresponding measurement in the reference channel (Cy3, P. falciparum RNA reference pool).

organism: Plasmodium falciparum

source_name: P. falciparum parasites (ex-vivo), CP040, 48H, ART-resistant, Pailin, Cambodia

label_protocol: Labeling  carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5.

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

tag: culture type

value: Ex-vivo culture

tag: time point

value: 48H post-sampling

tag: origin

value: patient ID CP040, Pailin, Cambodia

tag: response to artemsinin

value: artemisinin-resistant

source_name: P. falciparum 3d7 RNA reference pool

value: Lab Strain 3D7

tag: sample type

value: mix of several samples collected across the 48-hour intraerythrocytic life cycle


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP040_42H

status: Public on Dec 07 2010

type: RNA

molecule: total RNA

source_name: P. falciparum parasites (ex-vivo), CP040, 42H, ART-resistant, Pailin, Cambodia

value: 42H post-sampling

tag: strain


title: HRG_AFB1_0.05µM_n2_replicate 1

city: Rennes

first: rozenn

last: jossé

address: 2 av Prof Léon Bernard

country: France

institute: INSERM U991

description: Gene expression after 24h-treatment with 0.05µM AFB1 in HepaRG cells

hyb_protocol: 1650 ng of Cy3-RNAs were hybridized using the Hybridisation Kit Plus (Agilent) onto 4×44K Whole Human Genome Microarrays (G4112F, Agilent). After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014850_D_F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Homo sapiens

source_name: HRG_AFB1_0.05µM_n2_replicate 1

label_protocol: Five hundred ng of total RNA from each cell culture were reverse-transcribed into double-strand cDNAs and amplified for 2 h at 40°C using the Quick Amp Labeling Kit (Agilent). cDNAs were transcribed into antisense cRNA and labeled with CTP-Cy3 fluorescent dye for 2 h at 40°C following the manufacturer's protocol. Cyanine-labeled cRNAs were purified using RNeasy minikit (Qiagen, Inc., Valencia, CA).

growth_protocol: HepaRG cells were seeded at a density of 2.6x104 cells/cm2 in Williams’ E medium supplemented with 10% FCS, 100 units/mL penicillin, 100 μg/mL streptomycin, 5 μg/mL insulin, 2 mM glutamine and 5x10−5 M hydrocortisone hemisuccinate. After two weeks they were shifted to the same culture medium supplemented with 2% DMSO for two more weeks. At that time HepaRG cells were well differentiated and used for treatments by chemicals. Human hepatocytes undergoing resection for primary and secondary tumors were obtained by collagenase perfusion of histologically normal liver fragments and used for the preparation of RNA samples and primary cultures. Hepatocyte cultures were obtained by seeding 170,000 cells/cm² in 6-well plates in a Williams’ E medium supplemented with 10% FCS, 100 units/µl penicillin, 100 µg/ml streptomycin, 1 µg/ml insulin, 2 mM glutamine, and 1 µg/ml bovine serum albumin. The medium was discarded 12 h after seeding, and cells were thereafter maintained in serum-free medium supplemented with 5 x 10-5 M hydrocortisone hemisuccinate. HH were used 24 h after seeding.

extract_protocol: Cells were harvested in lysis buffer (RLT buffer and β-mercaptoethanol). Total RNA was isolated using the RNeasy mini kit (Qiagen). RNA quantity and purity were assessed with a Nanodrop ND-1000 spectrophotometer (Nyxor Biotech, Paris, France) and RNA integrity was checked with a Bioanalyzer 2100 (Agilent Technologies, Massy, France).

treatment_protocol: AFB1 was dissolved in DMSO and treatments were performed in a FCS-free medium. All control and treated cultures received 0.1% DMSO as the vehicle final concentration.

tag: cell line

value: HepaRG

tag: treatment

value: 0.05µM aflatoxin B1 (AFB1)


title: HRG_AFB1_0.05µM_n1_replicate 1

source_name: HRG_AFB1_0.05µM_n1_replicate 1


title: histologically normal breast epithelium from ER- breast cancer patient sample 14  (296H)

city: Boston

first: Kelly

last: Graham

state: MA

address: 650 Albany Street

department: Hematology/Oncology

country: USA

institute: Boston University School of Medicine

description: Gene Expression data from case 296H:Histologically Normal Epithelium from ER- Breast Cancer Patient

hyb_protocol: 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)

scan_protocol: The stained arrays were scanned using a G2500 Scanner (Agilent)

data_processing: The .CEL files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.

label: Biotin

label_protocol: T7-based RNA ampliﬁcation was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).

extract_protocol: RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).

treatment_protocol: Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most NlEpi samples (n=20) were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells). Some NlEpi samples (n=10) lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions.  Most NlEpi samples consisted only of TDLUs, but about 20% of samples (mainly from older patients) contained some ducts, as well.

tag: breast cancer patient id

tag: er status

value: ER-

tag: tissue

value: normal breast epithelium (laser capture microdissected)


title: RR2_wtdctDAAA_1_Cy3_ch1_rpoNdctDAAA_1_7DE1157

city: Irvine

first: Michael

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description: biological replicate, Date of Scan Fri Mar 28 06:59:21 2008

hyb_protocol: overnight hyb on Corning UltraGAPS slides at 42°C in 25% formamide / 5xSSC / 0.1% BSA

scan_protocol: Perkin Elmer ScanArray 5000 scanner, image acquisition with ScanArray Express 3.0.1 software, spot quantification using Quantarray 3.0 software, adaptive quantification, protocol STv5_SP040504_adapforsmallpins_040817

data_processing: normalized based on total signal for each channel, background subtracted VALUE data obtained from log of normalized background subtracted ch1/ch2 signal.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Transcription_profile from wt grown in presence of dctDAAA, replicate 1

label_protocol: Standard labeling using Cy3-dCTP with reverse transcriptase and random hexamers

extract_protocol: RNEasy kit (Qiagen)

tag: genotype/variation

value: wt

tag: growth phase

value: late log

tag: agent

value: dctDAAA

source_name: Transcription_profile from rpoN mutant grown in presence of dctDAAA, replicate 1

label_protocol: Standard labeling using Cy5-dCTP with reverse transcriptase and random hexamers

value: rpoN mutant


title: 252978410022_B7A_CY5_ETP98038_CY3.mev.refIsIB.out

type: genomic

city: Rockville

first: John

last: Braisted

state: MD

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

hyb_protocol: Equal concentrations of DNA probe from the appropriate Cy3 and Cy5 labeled probes were combined, dried and then resuspended in hybridization buffer as defined by the Agilent Oligonucleotide Array-Based CGH protocol.  Resuspended probes were denatured at 95 degree Celcius and held at 37 degree Celcius prior to hybridization.  The probe mixture then was added to the Agilent microarray slide and allowed to hybridize for 24 hours rotating at 20 rpm in a hybridization oven at 65 degree Celcius.   Hybridized slides were washed sequentially as defined by the Agilent Oligonucleotide Array-Based CGH protocol.

scan_protocol: Scanned on Axon GenePix 4000 scanner.  PMT values were optimized during scanning to balance channel intensities.

data_processing:
Procedures to calculate the value of log2 ratio:
1. Use Agilent software Feature Extraction to analyze spotted arrays.
2. Use TM4 suite software ExpressConverter to modify Agilent Feature Extraction file into *.mev.
3. Calculate the value of log2 ratio (Reference/Query) from the normalized .mev file:
    3a). If both channels (QUERY_MEDIAN_INTENSITY and REF_MEDIAN_INTENSITY) are zero, assign the value "null".
    3b). If one channel is zero and the other is not zero, substitute the zero with one (1) and then, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE
    3c). If neither channel is zero, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE.

molecule: genomic DNA

organism: Escherichia coli

source_name: Genomic DNA purified from wild type bacteria

label_protocol: 4ug of genomic DNA was labeled at 37 degree Celcius overnight using DNA polymerase I Klenow fragment (New England Biolabs), a 25X 2:1 amino allyl dUTP (Ambion) dNTP mix, and random hexamers (Invitrogen).  Labeled DNA was purified with Qiaquick PCR purification kit (QIAGEN).The purified labelled DNA was then dye coupled with the appropriate cye dye (CY3/CY5).

growth_protocol: cells were grown in LB overnight at 37 degrees celcius.

extract_protocol: Genomic DNA was isolated by lysozyme and proteinase K treatment.


title: 252978410022_B7A_CY5_BCE069_DS2_CY3.mev.refIsIB.out

value: BCE069, DS2


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP040_30H

source_name: P. falciparum parasites (ex-vivo), CP040, 30H, ART-resistant, Pailin, Cambodia

value: 30H post-sampling


title: histologically normal breast epithelium from ER- breast cancer patient sample 13  (413H)

description: Gene Expression data from case 413H:Histologically Normal Epithelium from ER- Breast Cancer Patient


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP040_36H

source_name: P. falciparum parasites (ex-vivo), CP040, 36H, ART-resistant, Pailin, Cambodia

value: Ex-vivo culture

value: 36H post-sampling


title: histologically normal breast epithelium from ER- breast cancer patient sample 11  (429H)

description: Gene Expression data from case 429H:Histologically Normal Epithelium from ER- Breast Cancer Patient


title: HRG_Control_n1_replicate 2

description: Gene expression after 24h-treatment with 0.1% DMSO in HepaRG cells

source_name: HRG_Control_n1_replicate 2

value: untreated


title: Rat treated with PBS 36hr, rep 2

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description:
Gene expression data from rat treated with PBS 36hr rep 2.
924_JEC_4_rat_02_PBS36h_01_1584

hyb_protocol: Five μg of the cRNA was fragmented and hybridized to a Rat 230 2.0 Affymetrix GeneChip (one chip per sample; 5-10 biological replicates per sample type). All samples were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus according to manufacturer protocols (Affymetrix; Santa Clara CA).

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Yp genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

organism: Rattus norvegicus

source_name: lymph node, PBS, 36hr

label_protocol: One μg of total RNA was amplified and biotin-ddUTP-labeled using the Enzo BioArray™ Single-Round RNA Amplification and Biotin Labeling System (ENZO Life Sciences Inc; Farmingdale, NY).

growth_protocol: The fully virulent Y. pestis 195/P wild-type strain, originally isolated from a patient with pneumonic plague in India, and a pYV– variant of this strain were used in this study. Starter cultures were grown overnight in heart infusion broth (HIB) at 28°C. The bacteria were then subcultured in Luria broth (LB) for 18h at 21°C to mimic the temperature during passage though the flea. Bacteria were quantified by Petroff-Hausser direct count, and inocula were prepared that contained 5 x10^4 WT bacteria/ml or 5 x 10^9 pYV– bacteria/ml in sterile PBS, pH 7.4.

extract_protocol: Isolated right inguinal lymph nodes from groups of five to 10 rats were pressed through a 70 μm cell strainer into 10 ml of RNAprotect (Qiagen; Valencia, CA). One ml of each sample was removed for bacterial load analysis by quantitative RT- PCR. The remaining sample was centrifuged at 4000 x g for 10 min, the RNAprotect decanted, and the resulting pellet stored at -80º C. The RNA was prepared for microarray analysis. Briefly, the samples were homogenized using QIAshredder columns and total RNA was isolated using the RNeasy 96 kit (Qiagen). The RNA quality and quantity were measured on a Bioanalyzer 2100 using RNA LabChips (Agilent Technologies; Santa Clara, CA) and spectrophotometry.

treatment_protocol: Six- to eight-week-old female Brown Norway rats (Rattus norvegicus) were injected intradermally in the right lower lumbar region with 50 ul of PBS containing 10^3 CFU of WT or 10^8 CFU of pYV– Y. pestis 195/P. Additional groups of rats were injected with 50 ul of sterile PBS, 10^8 paraformaldehyde-killed WT Y. pestis 195/P, or co-infected with 10^3 CFU of WT and 10^8 CFU of the pYV– variant. At 36 or 60h after infection, the rats were euthanized and the right inguinal lymph node were collected.

value: Brown Norway

tag: gender

value: female

tag: age

value: 6-8 weeks

value: lymph node

value: PBS

tag: time


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP040_18H

source_name: P. falciparum parasites (ex-vivo), CP040, 18H, ART-resistant, Pailin, Cambodia

tag: culture type

value: 18H post-sampling

value: patient ID CP040, Pailin, Cambodia

value: artemisinin-resistant

value: Lab Strain 3D7

value: mix of several samples collected across the 48-hour intraerythrocytic life cycle


title: HRG_Control_n1_replicate 1

source_name: HRG_Control_n1_replicate 1

value: HepaRG


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP040_12H

source_name: P. falciparum parasites (ex-vivo), CP040, 12H, ART-resistant, Pailin, Cambodia

tag: time point

value: 12H post-sampling


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP040_6H

source_name: P. falciparum parasites (ex-vivo), CP040, 6H, ART-resistant, Pailin, Cambodia

value: 6H post-sampling

tag: origin


title: histologically normal breast epithelium from ER- breast cancer patient sample 15  (401H)

description: Gene Expression data from case 401H:Histologically Normal Epithelium from ER- Breast Cancer Patient

value: ER-

value: normal breast epithelium (laser capture microdissected)


title: 252978410022_B7A_CY5_BCE062_DS2_CY3.mev.refIsIB.out

value: BCE062, DS2


title: histologically normal breast epithelium from ER- breast cancer patient sample 9  (452H)

description: Gene Expression data from case 452H:Histologically Normal Epithelium from ER- Breast Cancer Patient


title: 252978410026_B7A_CY5_WS2068A_CY3.mev.refIsIB.out

data_processing:
1. Use Agilent software Feature Extraction to analyze spotted arrays.
2. Use TM4 suite software ExpressConverter to modify Agilent Feature Extraction file into *.mev.
3. Calculate the value of log2 ratio (Reference/Query) from the normalized .mev file:
    3a). If both channels (QUERY_MEDIAN_INTENSITY and REF_MEDIAN_INTENSITY) are zero, assign the value "null".
    3b). If one channel is zero and the other is not zero, substitute the zero with one (1) and then, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE
    3c). If neither channel is zero, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE.


title: HH_Control_pool2_replicate 1

description: Gene expression after 24h-treatment with 0.1% DMSO in human hepatocytes

source_name: HH_Control_pool2_replicate 1

value: pool n°2 of 3 donors of human hepatocytes

tag: cell type

value: human hepatocytes

value: untreated


title: HH_AFB1_0.05µM_pool2_replicate 1

description: Gene expression after 24h-treatment with 0.05µM AFB1 in human hepatocytes

source_name: HH_AFB1_0.05µM_pool2_replicate 1

tag: sample type

value: 0.05µM aflatoxin B1 (AFB1)


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP040_0H

source_name: P. falciparum parasites (ex-vivo), CP040, 0H, ART-resistant, Pailin, Cambodia

value: Ex-vivo culture

value: 0H post-sampling

tag: response to artemsinin

source_name: P. falciparum 3d7 RNA reference pool

tag: strain


title: HH_AFB1_0.25µM_pool1_replicate 1

description: Gene expression after 24h-treatment with 0.25µM AFB1 in human hepatocytes

source_name: HH_AFB1_0.25µM_pool1_replicate 1

value: pool n°1 of 3 donors of human hepatocytes

tag: treatment

value: 0.25µM aflatoxin B1 (AFB1)


title: HH_AFB1_0.25µM_pool2_replicate 2

source_name: HH_AFB1_0.25µM_pool2_replicate 2


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP040_24H

source_name: P. falciparum parasites (ex-vivo), CP040, 24H, ART-resistant, Pailin, Cambodia

value: 24H post-sampling

value: patient ID CP040, Pailin, Cambodia

value: artemisinin-resistant


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP037_42H

source_name: P. falciparum parasites (ex-vivo), CP037, 42H, ART-resistant, Pailin, Cambodia

value: 42H post-sampling

value: patient ID CP037, Pailin, Cambodia

value: Lab Strain 3D7

value: mix of several samples collected across the 48-hour intraerythrocytic life cycle


title: 252978410026_B7A_CY5_sPRH_418_CY3.mev.refIsIB.out

source_name: Genomic DNA purified from wild type bacteria


title: 252978410026_B7A_CY5_WS1896A_CY3.mev.refIsIB.out


title: histologically normal breast epithelium from ER- breast cancer patient sample 10  (298H)

description: Gene Expression data from case 298H:Histologically Normal Epithelium from ER- Breast Cancer Patient

tag: breast cancer patient id

value: ER-

value: normal breast epithelium (laser capture microdissected)


title: histologically normal breast epithelium from ER+ breast cancer patient sample 13  (394H)

description: Gene Expression data from case 394H:Histologically Normal Epithelium from ER+ Breast Cancer Patient

tag: er status

value: ER+


title: histologically normal breast epithelium from ER+ breast cancer patient sample 14  (275H)

description: Gene Expression data from case 275H:Histologically Normal Epithelium from ER+ Breast Cancer Patient

tag: tissue


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP037_24H

source_name: P. falciparum parasites (ex-vivo), CP037, 24H, ART-resistant, Pailin, Cambodia


title: HH_Control_pool2_replicate 2

source_name: HH_Control_pool2_replicate 2

value: pool n°2 of 3 donors of human hepatocytes

value: human hepatocytes


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP037_32H

source_name: P. falciparum parasites (ex-vivo), CP037, 32H, ART-resistant, Pailin, Cambodia

value: 32H post-sampling


title: HH_AFB1_0.05µM_pool1_replicate 1

source_name: HH_AFB1_0.05µM_pool1_replicate 1

value: 0.05µM aflatoxin B1 (AFB1)


title: histologically normal breast epithelium from ER+ breast cancer patient sample 15  (228H)

description: Gene Expression data from case 228H:Histologically Normal Epithelium from ER+ Breast Cancer Patient


title: 252978410021_B7A_CY5_ETP05_046_CY3.mev.refIsIB.out


title: 252978410071_B7A_CY5_292_1_CY3.mev.refIsIB.out


title: HH_Control_pool1_replicate 2

source_name: HH_Control_pool1_replicate 2

value: untreated


title: HH_Control_pool1_replicate 1

source_name: HH_Control_pool1_replicate 1

value: pool n°1 of 3 donors of human hepatocytes


title: histologically normal breast epithelium from ER+ breast cancer patient sample 10  (405H)

description: Gene Expression data from case 405H:Histologically Normal Epithelium from ER+ Breast Cancer Patient


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP037_4H

source_name: P. falciparum parasites (ex-vivo), CP037, 4H, ART-resistant, Pailin, Cambodia

value: Ex-vivo culture

value: 4H post-sampling


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP037_6H

source_name: P. falciparum parasites (ex-vivo), CP037, 6H, ART-resistant, Pailin, Cambodia

value: 6H post-sampling


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP037_8H

source_name: P. falciparum parasites (ex-vivo), CP037, 8H, ART-resistant, Pailin, Cambodia

value: 8H post-sampling

value: artemisinin-resistant


title: 252978410026_B7A_CY5_E24377A_CY3.mev.refIsIB.out


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP037_16H

source_name: P. falciparum parasites (ex-vivo), CP037, 16H, ART-resistant, Pailin, Cambodia

value: 16H post-sampling

value: patient ID CP037, Pailin, Cambodia


title: 252978410021_B7A_CY5_BCE054_MS24_CY3.mev.refIsIB.out


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP037_0H

source_name: P. falciparum parasites (ex-vivo), CP037, 0H, ART-resistant, Pailin, Cambodia

value: 0H post-sampling

value: Lab Strain 3D7

value: mix of several samples collected across the 48-hour intraerythrocytic life cycle


title: histologically normal breast epithelium from ER+ breast cancer patient sample 12  (453H)

description: Gene Expression data from case 453H:Histologically Normal Epithelium from ER+ Breast Cancer Patient

value: ER+

value: normal breast epithelium (laser capture microdissected)


title: histologically normal breast epithelium from ER+ breast cancer patient sample 6  (345H)

description: Gene Expression data from case 345H:Histologically Normal Epithelium from ER+ Breast Cancer Patient


title: histologically normal breast epithelium from ER+ breast cancer patient sample 5  (248H)

description: Gene Expression data from case 248H:Histologically Normal Epithelium from ER+ Breast Cancer Patient


title: 252978410021_B7A_CY5_BCE008_MS1_CY3.mev.refIsIB.out


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP025_48H

source_name: P. falciparum parasites (ex-vivo), CP025, 48H, ART-resistant, Pailin, Cambodia

value: 48H post-sampling

value: patient ID CP025, Pailin, Cambodia

source_name: P. falciparum 3d7 RNA reference pool


title: 252978410059_B7A_CY5_ETP98112_CY3.mev.refIsIB.out


title: histologically normal breast epithelium from ER+ breast cancer patient sample 11  (311H)

description: Gene Expression data from case 311H:Histologically Normal Epithelium from ER+ Breast Cancer Patient


title: 252978410059_B7A_CY5_ETP05_047_CY3.mev.refIsIB.out


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP037_2H

source_name: P. falciparum parasites (ex-vivo), CP037, 2H, ART-resistant, Pailin, Cambodia

value: 2H post-sampling


title: 252978410059_B7A_CY5_ETP98097_CY3.mev.refIsIB.out


title: histologically normal breast epithelium from ER+ breast cancer patient sample 9  (258H)

description: Gene Expression data from case 258H:Histologically Normal Epithelium from ER+ Breast Cancer Patient


title: 252978410025_B7A_CY5_ETP05_050_CY3.mev.refIsIB.out


title: Subcutaneous Adipose tissue_Lean_4

city: Toulouse

first: Nathalie

last: Viguerie

address: Avenue Poulhes

institute: INSERM

description: Labelling and hybridization qualities were verified with Agilent's spike in kit

hyb_protocol: Samples were hybridized to Agilent 44k whole human genome microarrays. Sample preparation and microarray washing were performed according to manufacturer’s recommendations (Agilent Technologies).

scan_protocol: Arrays were scanned using InnoScan®700 scanner (Innopsys, Carbonne, France, EU). Images were quantified using MAPIX®V3.02 software (Innopsys).

data_processing:
Intensity ratios between Cy5 and Cy3 were filtered using an average intensity of 1.5 times above the background signal and normalized with a global Loess procedure without background substraction with R package LIMMA (Bioconductor).
Value is the Log2 of normalized Cy5/Cy3 value ratio.

source_name: Reference RNA pool made of a mix of commercial human liver, adipose tissue and skeletal muscle

label_protocol:
RNA quantity and quality were checked with the Experion automated electrophoresis system (BioRad Laboratories).
Total RNA (250 ng) from each sample was amplified and transcribed into fluorescent cRNA using Low RNA Input Linear Amplification kit (Agilent Technologies).

extract_protocol: Total RNA was extracted with RNeasy Mini kit (Qiagen) according to manufacturer instructions.

value: mix of male and female

value: mix of liver, adipose tissue and skeletal muscle

source_name: Human subcutaneous adipose tissue, lean

value: lean

value: female

value: subcutaneous adipose tissue


title: Subcutaneous Adipose tissue_Lean_7


title: histologically normal breast epithelium from ER+ breast cancer patient sample 3  (359H)

description: Gene Expression data from case 359H:Histologically Normal Epithelium from ER+ Breast Cancer Patient


title: Subcutaneous Adipose tissue_Lean_3


title: Subcutaneous Adipose tissue_Lean_6


title: 252978410021_B7A_CY5_1080200_CY3.mev.refIsIB.out

source_name: Genomic DNA purified from wild type bacteria


title: Subcutaneous Adipose tissue_Lean_8


title: Subcutaneous Adipose tissue_Lean_5


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP025_42H

source_name: P. falciparum parasites (ex-vivo), CP025, 42H, ART-resistant, Pailin, Cambodia

value: Ex-vivo culture

value: 42H post-sampling


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP025_36H

source_name: P. falciparum parasites (ex-vivo), CP025, 36H, ART-resistant, Pailin, Cambodia

value: 36H post-sampling

value: artemisinin-resistant


title: histologically normal breast epithelium from ER+ breast cancer patient sample 1  (351H)

description: Gene Expression data from case 351H:Histologically Normal Epithelium from ER+ Breast Cancer Patient


title: histologically normal breast epithelium from ER+ breast cancer patient sample 2  (297BH)

description: Gene Expression data from case 297BH:Histologically Normal Epithelium from ER+ Breast Cancer Patient


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP025_24H

source_name: P. falciparum parasites (ex-vivo), CP025, 24H, ART-resistant, Pailin, Cambodia

value: 24H post-sampling


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP025_30H

source_name: P. falciparum parasites (ex-vivo), CP025, 30H, ART-resistant, Pailin, Cambodia

value: 30H post-sampling

value: Lab Strain 3D7


title: 252978410025_B7A_CY5_C35959_CY3.mev.refIsIB.out


title: 252978410025_B7A_CY5_BCE039_MS13_CY3.mev.refIsIB.out


title: Subcutaneous Adipose tissue_Lean_2


title: Visceral Adipose tissue_Lean_7

source_name: Human visceral adipose tissue, lean

value: visceral adipose tissue


title: 252978410024_B7A_CY5_BCE069_MS15_CY3.mev.refIsIB.out


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP025_18H

source_name: P. falciparum parasites (ex-vivo), CP025, 18H, ART-resistant, Pailin, Cambodia

value: 18H post-sampling

value: mix of several samples collected across the 48-hour intraerythrocytic life cycle


title: Visceral Adipose tissue_Lean_8


title: Visceral Adipose tissue_Lean_6


title: 252978410058_B7A_CY5_ETP05_009_CY3.mev.refIsIB.out


title: Subcutaneous Adipose tissue_Lean_1


title: 252978410058_B7A_CY5_ETP05_010_CY3.mev.refIsIB.out


title: 252978410059_B7A_CY5_532_WS6866B1_CY3.mev.refIsIB.out


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP025_6H

source_name: P. falciparum parasites (ex-vivo), CP025, 6H, ART-resistant, Pailin, Cambodia

value: 6H post-sampling

value: patient ID CP025, Pailin, Cambodia


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP025_0H

source_name: P. falciparum parasites (ex-vivo), CP025, 0H, ART-resistant, Pailin, Cambodia

value: 0H post-sampling


title: ex-vivo_ ART-sensitive_ Pailin Cambodia_CP022_42H

source_name: P. falciparum parasites (ex-vivo), CP022, 42H, ART-sensitive, Pailin, Cambodia

value: patient ID CP022, Pailin, Cambodia

value: artemisinin-sensitive


title: Visceral Adipose tissue_Lean_4

value: mix of male and female

value: mix of liver, adipose tissue and skeletal muscle

value: lean

value: female


title: ex-vivo_ ART-sensitive_ Pailin Cambodia_CP022_48H

source_name: P. falciparum parasites (ex-vivo), CP022, 48H, ART-sensitive, Pailin, Cambodia

value: Ex-vivo culture

value: 48H post-sampling


title: ex-vivo_ ART-resistant_ Pailin Cambodia_CP025_12H

source_name: P. falciparum parasites (ex-vivo), CP025, 12H, ART-resistant, Pailin, Cambodia

value: 12H post-sampling

value: artemisinin-resistant


title: Visceral Adipose tissue_Lean_5


title: ex-vivo_ ART-sensitive_ Pailin Cambodia_CP022_30H

source_name: P. falciparum parasites (ex-vivo), CP022, 30H, ART-sensitive, Pailin, Cambodia

value: 30H post-sampling

value: Lab Strain 3D7


title: ex-vivo_ ART-sensitive_ Pailin Cambodia_CP022_36H

source_name: P. falciparum parasites (ex-vivo), CP022, 36H, ART-sensitive, Pailin, Cambodia

value: 36H post-sampling

source_name: P. falciparum 3d7 RNA reference pool


title: 252978410025_B7A_CY5_BCE007_MS11_CY3.mev.refIsIB.out


title: 252978410058_B7A_CY5_179100_CY3.mev.refIsIB.out


title: Visceral Adipose tissue_Lean_3

source_name: Reference RNA pool made of a mix of commercial human liver, adipose tissue and skeletal muscle

value: visceral adipose tissue


title: 252978410024_B7A_CY5_BCE019_MS16_CY3.mev.refIsIB.out


title: 252978410058_B7A_CY5_178900_CY3.mev.refIsIB.out


title: 252978410024_B7A_CY5_BCE046_MS16_CY3.mev.refIsIB.out


title: ex-vivo_ ART-sensitive_ Pailin Cambodia_CP022_24H

source_name: P. falciparum parasites (ex-vivo), CP022, 24H, ART-sensitive, Pailin, Cambodia

value: 24H post-sampling

value: mix of several samples collected across the 48-hour intraerythrocytic life cycle


title: Visceral Adipose tissue_Lean_2


title: Visceral Adipose tissue_Lean_1


title: ex-vivo_ ART-sensitive_ Pailin Cambodia_CP022_12H

source_name: P. falciparum parasites (ex-vivo), CP022, 12H, ART-sensitive, Pailin, Cambodia


title: 252978410035_B7A_CY5_ETP05_039_CY3.mev.refIsIB.out

source_name: Genomic DNA purified from wild type bacteria


title: ex-vivo_ ART-sensitive_ Pailin Cambodia_CP022_18H

source_name: P. falciparum parasites (ex-vivo), CP022, 18H, ART-sensitive, Pailin, Cambodia

value: 18H post-sampling


title: 252978410024_B7A_CY5_BCE018_DS6_CY3.mev.refIsIB.out

value: BCE018, DS6


title: Subcutaneous Adipose tissue_Metabolic Syndrome_8

source_name: Reference RNA pool made of a mix of commercial human liver, AT and skeletal muscle

source_name: Human subcutaneous adipose tissue, metabolic syndrome

value: metabolic syndrome

value: subcutaneous adipose tissue


title: ex-vivo_ ART-sensitive_ Pailin Cambodia_CP022_6H

source_name: P. falciparum parasites (ex-vivo), CP022, 6H, ART-sensitive, Pailin, Cambodia

value: 6H post-sampling

value: patient ID CP022, Pailin, Cambodia

value: artemisinin-sensitive


title: Subcutaneous Adipose tissue_Metabolic Syndrome_6

value: mix of male and female

value: mix of liver, adipose tissue and skeletal muscle

value: female


title: Subcutaneous Adipose tissue_Metabolic Syndrome_7


title: 252978410023_B7A_CY5_ETP98115_CY3.mev.refIsIB.out


title: ex-vivo_ ART-sensitive_ Pailin Cambodia_CP022_0H

source_name: P. falciparum parasites (ex-vivo), CP022, 0H, ART-sensitive, Pailin, Cambodia

value: Ex-vivo culture

value: 0H post-sampling


title: Subcutaneous Adipose tissue_Metabolic Syndrome_5


title: ex-vivo_ ART-sensitive_ Mae Sot Thailand_NHP4460_40H

source_name: P. falciparum parasites (ex-vivo), NHP4460, 40H, ART-sensitive, Mae Sot, Thailand

value: 40H post-sampling

value: patient ID NHP4460, Mae Sot, Thailand

value: Lab Strain 3D7


title: Normal D07-6_sty

city: Essen

first: Rene

last: Scholtysik

address: Virchowstrasse 173

department: IFZ

country: Germany

institute: University Hospital Essen

description: Hybridized to 250K_Sty

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The CEL-Files were analyzed using the BRLMM-algorithm to produce genotype calls, stored in the corresponding CHP-Files.
CEL- and CHP-Format by Affymetrix

source_name: whole blood DNA extraction

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: QiaAmp DNA Blood Kit

value: normal reference

value: blood

tag: disease state

value: normal


title: 252978410035_B7A_CY5_ETP05_020_CY3.mev.refIsIB.out


title: 252978410020_B7A_CY5_ETP98114_CY3.mev.refIsIB.out


title: Subcutaneous Adipose tissue_Metabolic Syndrome_3


title: 252978410023_B7A_CY5_178850_CY3.mev.refIsIB.out


title: Normal RefDNAc

description: Hybridized to 250K_Sty

source_name: Reference DNA provided by Affymetrix


title: Normal B3_sty

description: Hybridized to 250K_Sty


title: ex-vivo_ ART-sensitive_ Mae Sot Thailand_NHP4460_32H

source_name: P. falciparum parasites (ex-vivo), NHP4460, 32H, ART-sensitive, Mae Sot, Thailand

value: 32H post-sampling

value: mix of several samples collected across the 48-hour intraerythrocytic life cycle


title: Normal D07-7_sty

description: Hybridized to 250K_Sty


title: Subcutaneous Adipose tissue_Metabolic Syndrome_1

value: metabolic syndrome

value: subcutaneous adipose tissue


title: 252978410020_B7A_CY5_BCE046_DS7_CY3.mev.refIsIB.out

value: BCE046, DS7


title: 252978410035_B7A_CY5_ETP05_016_CY3.mev.refIsIB.out


title: Normal B5_sty

description: Hybridized to 250K_Sty


title: Subcutaneous Adipose tissue_Metabolic Syndrome_2


title: Visceral Adipose tissue_Metabolic Syndrome_8

source_name: Human visceral adipose tissue, metabolic syndrome

value: visceral adipose tissue


title: ex-vivo_ ART-sensitive_ Mae Sot Thailand_NHP4460_24H

source_name: P. falciparum parasites (ex-vivo), NHP4460, 24H, ART-sensitive, Mae Sot, Thailand

value: 24H post-sampling

value: artemisinin-sensitive


title: ex-vivo_ ART-sensitive_ Mae Sot Thailand_NHP4460_16H

source_name: P. falciparum parasites (ex-vivo), NHP4460, 16H, ART-sensitive, Mae Sot, Thailand

value: 16H post-sampling


title: Normal D07-3_sty

description: Hybridized to 250K_Sty


title: 252978410023_B7A_CY5_174750_CY3.mev.refIsIB.out


title: Visceral Adipose tissue_Metabolic Syndrome_7

value: mix of male and female

value: mix of liver, adipose tissue and skeletal muscle

value: female


title: ex-vivo_ ART-sensitive_ Mae Sot Thailand_NHP4460_8H

source_name: P. falciparum parasites (ex-vivo), NHP4460, 8H, ART-sensitive, Mae Sot, Thailand

value: Ex-vivo culture

value: 8H post-sampling

value: patient ID NHP4460, Mae Sot, Thailand

source_name: P. falciparum 3d7 RNA reference pool


title: Normal D07-5_sty

description: Hybridized to 250K_Sty

value: normal reference

value: blood


title: ex-vivo_ ART-sensitive_ Mae Sot Thailand_NHP4460_0H

source_name: P. falciparum parasites (ex-vivo), NHP4460, 0H, ART-sensitive, Mae Sot, Thailand

value: 0H post-sampling

value: Lab Strain 3D7


title: Visceral Adipose tissue_Metabolic Syndrome_5

source_name: Reference RNA pool made of a mix of commercial human liver, adipose tissue and skeletal muscle

value: metabolic syndrome


title: Visceral Adipose tissue_Metabolic Syndrome_6


title: Normal N10_sty

description: Hybridized to 250K_Sty

value: normal


title: 252978410020_B7A_CY5_BCE046_DS2_CY3.mev.refIsIB.out

source_name: Genomic DNA purified from wild type bacteria

value: BCE046, DS2


title: 252978410035_B7A_CY5_BCE055_DS1_CY3.mev.refIsIB.out

value: BCE055, DS1


title: ex-vivo_ ART-sensitive_ Mae Sot Thailand_NHP4459_40H

source_name: P. falciparum parasites (ex-vivo), NHP4459, 40H, ART-sensitive, Mae Sot, Thailand

value: 40H post-sampling

value: patient ID NHP4459, Mae Sot, Thailand

value: mix of several samples collected across the 48-hour intraerythrocytic life cycle


title: Normal B2_sty

description: Hybridized to 250K_Sty


title: ex-vivo_ ART-sensitive_ Mae Sot Thailand_NHP4459_32H

source_name: P. falciparum parasites (ex-vivo), NHP4459, 32H, ART-sensitive, Mae Sot, Thailand

value: 32H post-sampling

value: artemisinin-sensitive


title: Normal B1_sty

description: Hybridized to 250K_Sty


title: 252978410023_B7A_CY5_173150_CY3.mev.refIsIB.out


title: 252978410019_B7A_CY5_WS0115A_CY3.mev.refIsIB.out


title: Normal N9_sty

description: Hybridized to 250K_Sty


title: Normal N8_sty

description: Hybridized to 250K_Sty


title: 252978410020_B7A_CY5_179550_CY3.mev.refIsIB.out


title: Visceral Adipose tissue_Metabolic Syndrome_2

value: mix of male and female

value: mix of liver, adipose tissue and skeletal muscle

value: female

value: visceral adipose tissue


title: Visceral Adipose tissue_Metabolic Syndrome_3


title: Normal N5_sty

description: Hybridized to 250K_Sty

value: normal reference


title: Visceral Adipose tissue_Metabolic Syndrome_4


title: ex-vivo_ ART-sensitive_ Mae Sot Thailand_NHP4459_24H

source_name: P. falciparum parasites (ex-vivo), NHP4459, 24H, ART-sensitive, Mae Sot, Thailand

value: Ex-vivo culture

value: 24H post-sampling


title: ex-vivo_ ART-sensitive_ Mae Sot Thailand_NHP4459_8H

source_name: P. falciparum parasites (ex-vivo), NHP4459, 8H, ART-sensitive, Mae Sot, Thailand

value: 8H post-sampling

value: Lab Strain 3D7


title: 252978410034_B7A_CY5_ETP98053_CY3.mev.refIsIB.out


title: ex-vivo_ ART-sensitive_ Mae Sot Thailand_NHP4459_16H

source_name: P. falciparum parasites (ex-vivo), NHP4459, 16H, ART-sensitive, Mae Sot, Thailand

value: 16H post-sampling


title: Normal N3_sty

description: Hybridized to 250K_Sty

value: blood

value: normal


title: 252978410006_B7A_CY5_ETP05_044_CY3.mev.refIsIB.out


title: Subcutaneous Adipose tissue_Obese_8

source_name: Human subcutaneous adipose tissue, obese

value: obese

value: subcutaneous adipose tissue


title: ex-vivo_ ART-sensitive_ Mae Sot Thailand_NHP4459_0H

source_name: P. falciparum parasites (ex-vivo), NHP4459, 0H, ART-sensitive, Mae Sot, Thailand

value: 0H post-sampling

value: patient ID NHP4459, Mae Sot, Thailand

value: mix of several samples collected across the 48-hour intraerythrocytic life cycle


title: Normal N6_sty

description: Hybridized to 250K_Sty

source_name: whole blood DNA extraction


title: Normal N7_sty

description: Hybridized to 250K_Sty


title: Normal N1_sty

description: Hybridized to 250K_Sty


title: Visceral Adipose tissue_Metabolic Syndrome_1

value: mix of male and female

value: metabolic syndrome


title: Subcutaneous Adipose tissue_Obese_7

value: mix of liver, adipose tissue and skeletal muscle

value: female


title: 252978410006_B7A_CY5_ETP05_026_CY3.mev.refIsIB.out


title: ex-vivo_ ART-sensitive_ Mae Sot Thailand_NHP2094_32H

source_name: P. falciparum parasites (ex-vivo), NHP2094, 32H, ART-sensitive, Mae Sot, Thailand

value: 32H post-sampling

value: patient ID NHP2094, Mae Sot, Thailand

value: artemisinin-sensitive


title: ex-vivo_ ART-sensitive_ Mae Sot Thailand_NHP2094_40H

source_name: P. falciparum parasites (ex-vivo), NHP2094, 40H, ART-sensitive, Mae Sot, Thailand

value: Ex-vivo culture

value: 40H post-sampling


title: Subcutaneous Adipose tissue_Metabolic Syndrome_4

source_name: Reference RNA pool made of a mix of commercial human liver, AT and skeletal muscle

source_name: Human subcutaneous adipose tissue, metabolic syndrome


title: Normal N2_sty

description: Hybridized to 250K_Sty

value: normal reference


title: ex-vivo_ ART-sensitive_ Mae Sot Thailand_NHP2094_24H

source_name: P. falciparum parasites (ex-vivo), NHP2094, 24H, ART-sensitive, Mae Sot, Thailand

value: 24H post-sampling

value: Lab Strain 3D7


title: 252978410034_B7A_CY5_ETP05_038_CY3.mev.refIsIB.out


title: ex-vivo_ ART-sensitive_ Mae Sot Thailand_NHP2094_16H

source_name: P. falciparum parasites (ex-vivo), NHP2094, 16H, ART-sensitive, Mae Sot, Thailand

value: 16H post-sampling

source_name: P. falciparum 3d7 RNA reference pool


title: 252978410006_B7A_CY5_ETP05_019_CY3.mev.refIsIB.out


title: Subcutaneous Adipose tissue_Obese_5

source_name: Reference RNA pool made of a mix of commercial human liver, adipose tissue and skeletal muscle

value: obese

value: subcutaneous adipose tissue


title: 252978410034_B7A_CY5_BCE061_DS1_CY3.mev.refIsIB.out

source_name: Genomic DNA purified from wild type bacteria

value: BCE061, DS1


title: 252978410019_B7A_CY5_E1786_CY3.mev.refIsIB.out


title: Subcutaneous Adipose tissue_Obese_4


title: Subcutaneous Adipose tissue_Obese_6


title: Subcutaneous Adipose tissue_Obese_3


title: Normal N4_sty

description: Hybridized to 250K_Sty

value: blood

value: normal


title: ex-vivo_ ART-sensitive_ Mae Sot Thailand_NHP2094_0H

source_name: P. falciparum parasites (ex-vivo), NHP2094, 0H, ART-sensitive, Mae Sot, Thailand

value: 0H post-sampling

value: mix of several samples collected across the 48-hour intraerythrocytic life cycle


title: Burkitt MPI-529_sty

description: Hybridized to 250K_Sty

source_name: Whole tissue of tumor biopsy

value: tumor

value: Burkitt lymphoma


title: ex-vivo_ ART-sensitive_ Mae Sot Thailand_NHP2094_8H

source_name: P. falciparum parasites (ex-vivo), NHP2094, 8H, ART-sensitive, Mae Sot, Thailand

value: 8H post-sampling

value: patient ID NHP2094, Mae Sot, Thailand


title: Burkitt MPI-532_sty

description: Hybridized to 250K_Sty


title: 252978410006_B7A_CY5_ETP05_012_CY3.mev.refIsIB.out


title: 252978410009_B7A_CY5_WS3572A1.mev.refIsIB.out


title: ex-vivo_ ART-sensitive_ Xepon Laos_XPN003_42H

source_name: P. falciparum parasites (ex-vivo), XPN003, 42H, ART-sensitive, Xepon, Laos

value: Ex-vivo culture

value: 42H post-sampling

value: patient ID XPN003, Xepon, Laos

value: artemisinin-sensitive


title: ex-vivo_ ART-sensitive_ Xepon Laos_XPN003_48H

source_name: P. falciparum parasites (ex-vivo), XPN003, 48H, ART-sensitive, Xepon, Laos

value: 48H post-sampling

value: Lab Strain 3D7


title: Subcutaneous Adipose tissue_Obese_2

value: mix of male and female

value: mix of liver, adipose tissue and skeletal muscle

source_name: Human subcutaneous adipose tissue, obese

value: obese

value: female


title: Burkitt MPI-527_sty

description: Hybridized to 250K_Sty


title: Visceral Adipose tissue_Obese_8

source_name: Human visceral adipose tissue, obese

value: visceral adipose tissue


title: Subcutaneous Adipose tissue_Obese_1

value: subcutaneous adipose tissue


title: Visceral Adipose tissue_Obese_7


title: 252978410009_B7A_CY5_F595C_CY3.mev.refIsIB.out


title: Burkitt MPI-323_sty

description: Hybridized to 250K_Sty


title: ex-vivo_ ART-sensitive_ Xepon Laos_XPN003_36H

source_name: P. falciparum parasites (ex-vivo), XPN003, 36H, ART-sensitive, Xepon, Laos

value: 36H post-sampling

value: mix of several samples collected across the 48-hour intraerythrocytic life cycle


title: Visceral Adipose tissue_Obese_6


title: Burkitt MPI-139_sty

description: Hybridized to 250K_Sty

value: tumor

value: Burkitt lymphoma


title: ex-vivo_ ART-sensitive_ Xepon Laos_XPN003_30H

source_name: P. falciparum parasites (ex-vivo), XPN003, 30H, ART-sensitive, Xepon, Laos

value: 30H post-sampling


title: 252978410034_B7A_CY5_BCE005_MS23_CY3.mev.refIsIB.out


title: ex-vivo_ ART-sensitive_ Xepon Laos_XPN003_24H

source_name: P. falciparum parasites (ex-vivo), XPN003, 24H, ART-sensitive, Xepon, Laos

value: Ex-vivo culture

value: 24H post-sampling


title: 252978410033_B7A_CY5_ETP_98004_CY3.mev.refIsIB.out


title: 252978410005_B7A_CY5_BCE039_DS2_CY3.mev.refIsIB.out

value: BCE039, DS2


title: 252978410018_B7A_CY5_sPRH21_CY3.mev.refIsIB.out


title: Burkitt MPI-528_sty

description: Hybridized to 250K_Sty


title: Visceral Adipose tissue_Obese_5


title: ex-vivo_ ART-sensitive_ Xepon Laos_XPN003_18H

source_name: P. falciparum parasites (ex-vivo), XPN003, 18H, ART-sensitive, Xepon, Laos

value: 18H post-sampling

value: patient ID XPN003, Xepon, Laos

value: artemisinin-sensitive


title: 252978410018_B7A_CY5_MG1655_CY3.mev.refIsIB.out


title: Visceral Adipose tissue_Obese_4

value: mix of male and female


title: Burkitt MPI-171_sty

description: Hybridized to 250K_Sty


title: ex-vivo_ ART-sensitive_ Xepon Laos_XPN003_12H

source_name: P. falciparum parasites (ex-vivo), XPN003, 12H, ART-sensitive, Xepon, Laos

value: 12H post-sampling

value: Lab Strain 3D7


title: Normal B4_sty

description: Hybridized to 250K_Sty

source_name: whole blood DNA extraction

value: normal reference

value: blood

value: normal


title: Burkitt MPI-138_sty

description: Hybridized to 250K_Sty


title: Visceral Adipose tissue_Obese_3

value: mix of liver, adipose tissue and skeletal muscle

value: obese

value: female

value: visceral adipose tissue


title: ex-vivo_ ART-sensitive_ Xepon Laos_XPN003_6H

source_name: P. falciparum parasites (ex-vivo), XPN003, 6H, ART-sensitive, Xepon, Laos

value: 6H post-sampling

value: mix of several samples collected across the 48-hour intraerythrocytic life cycle


title: ex-vivo_ ART-sensitive_ Xepon Laos_XPN003_0H

source_name: P. falciparum parasites (ex-vivo), XPN003, 0H, ART-sensitive, Xepon, Laos

value: Ex-vivo culture

value: 0H post-sampling

source_name: P. falciparum 3d7 RNA reference pool


title: Visceral Adipose tissue_Obese_2

source_name: Reference RNA pool made of a mix of commercial human liver, adipose tissue and skeletal muscle


title: Burkitt MPI-101_sty

description: Hybridized to 250K_Sty

value: tumor

value: Burkitt lymphoma


title: 252978410033_B7A_CY5_ETP98056_CY3.mev.refIsIB.out

source_name: Genomic DNA purified from wild type bacteria


title: 252978410009_B7A_CY5_E1787_CY3.mev.refIsIB.out


title: 252978410018_B7A_CY5_E1792_CY3.mev.refIsIB.out


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT077_48H

source_name: P. falciparum parasites (ex-vivo), BMT077, 48H, ART-sensitive, Xepon, Laos

value: 48H post-sampling

value: patient ID BMT077, Xepon, Laos

value: artemisinin-sensitive


title: 252978410005_B7A_CY5_BCE035_MS8_CY3.mev.refIsIB.out

value: BCE035, MS8


title: Visceral Adipose tissue_Obese_1

value: mix of male and female


title: Burkitt MPI-123_sty

description: Hybridized to 250K_Sty

source_name: Whole tissue of tumor biopsy


title: Burkitt MPI-089_sty

description: Hybridized to 250K_Sty


title: Burkitt MPI-087_sty

description: Hybridized to 250K_Sty


title: Burkitt MPI-114_sty

description: Hybridized to 250K_Sty


title: Burkitt MPI-095_sty

description: Hybridized to 250K_Sty


title: Subcutaneous Adipose tissue_Overweight_7

source_name: Human subcutaneous adipose tissue, overweight

value: overweight

value: subcutaneous adipose tissue


title: Subcutaneous Adipose tissue_Overweight_8

value: mix of liver, adipose tissue and skeletal muscle


title: 252978410009_B7A_CY5_E747_0_CY3.mev.refIsIB.out


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT077_36H

source_name: P. falciparum parasites (ex-vivo), BMT077, 36H, ART-sensitive, Xepon, Laos

value: 36H post-sampling

value: Lab Strain 3D7


title: 252978410018_B7A_CY5_ARG3_CY3.mev.refIsIB.out


title: Subcutaneous Adipose tissue_Overweight_6

value: female


title: Burkitt MPI-084_sty

description: Hybridized to 250K_Sty


title: Subcutaneous Adipose tissue_Overweight_5


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT077_30H

source_name: P. falciparum parasites (ex-vivo), BMT077, 30H, ART-sensitive, Xepon, Laos

value: 30H post-sampling


title: Burkitt MPI-086_sty

description: Hybridized to 250K_Sty


title: 252978410005_B7A_CY5_BCE013_DS1_CY3.mev.refIsIB.out

value: BCE013, DS1


title: Subcutaneous Adipose tissue_Overweight_4


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT077_24H

source_name: P. falciparum parasites (ex-vivo), BMT077, 24H, ART-sensitive, Xepon, Laos

value: Ex-vivo culture

value: 24H post-sampling

value: mix of several samples collected across the 48-hour intraerythrocytic life cycle


title: 252978410033_B7A_CY5_C35209_CY3.mev.refIsIB.out


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT077_18H

source_name: P. falciparum parasites (ex-vivo), BMT077, 18H, ART-sensitive, Xepon, Laos

value: 18H post-sampling


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT077_12H

source_name: P. falciparum parasites (ex-vivo), BMT077, 12H, ART-sensitive, Xepon, Laos

value: 12H post-sampling


title: 252978410005_B7A_CY5_BCE008_MS13_CY3.mev.refIsIB.out


title: 252978410017_B7A_CY5_ICDDR_B_p9_CY3.mev.refIsIB.out


title: Subcutaneous Adipose tissue_Overweight_3


title: Burkitt MPI-079_sty

description: Hybridized to 250K_Sty

value: tumor

value: Burkitt lymphoma


title: Subcutaneous Adipose tissue_Overweight_1


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT077_0H

source_name: P. falciparum parasites (ex-vivo), BMT077, 0H, ART-sensitive, Xepon, Laos

value: 0H post-sampling

value: patient ID BMT077, Xepon, Laos

value: artemisinin-sensitive


title: Burkitt MPI-081_sty

description: Hybridized to 250K_Sty


title: Visceral Adipose tissue_Overweight_8

value: mix of male and female

source_name: Human visceral adipose tissue, overweight

value: overweight

value: visceral adipose tissue


title: 252978410033_B7A_CY5_BCE035_DS6_CY3.mev.refIsIB.out

value: BCE035, DS6


title: Subcutaneous Adipose tissue_Overweight_2

value: mix of liver, adipose tissue and skeletal muscle

value: female

value: subcutaneous adipose tissue


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT077_42H

source_name: P. falciparum parasites (ex-vivo), BMT077, 42H, ART-sensitive, Xepon, Laos

value: Ex-vivo culture

value: 42H post-sampling

value: Lab Strain 3D7


title: Burkitt MPI-080_sty

description: Hybridized to 250K_Sty


title: Burkitt MPI-077_sty

description: Hybridized to 250K_Sty


title: Visceral Adipose tissue_Overweight_7


title: 252978410004_B7A_CY5_BCE129_DS2_CY3.mev.refIsIB.out

value: BCE129, DS2


title: Burkitt MPI-078_sty

description: Hybridized to 250K_Sty


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT076_48H

source_name: P. falciparum parasites (ex-vivo), BMT076, 48H, ART-sensitive, Xepon, Laos

value: 48H post-sampling

value: patient ID BMT076, Xepon, Laos

value: mix of several samples collected across the 48-hour intraerythrocytic life cycle


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT077_6H

source_name: P. falciparum parasites (ex-vivo), BMT077, 6H, ART-sensitive, Xepon, Laos

value: 6H post-sampling


title: 252978410017_B7A_CY5_ETEC_JURUA_18_11_CY3.mev.refIsIB.out

value: ETEC Jurua


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT076_36H

source_name: P. falciparum parasites (ex-vivo), BMT076, 36H, ART-sensitive, Xepon, Laos

value: 36H post-sampling

value: artemisinin-sensitive


title: 252978410008_B7A_CY5_TW03741_CY3.mev.refIsIB.out


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT076_30H

source_name: P. falciparum parasites (ex-vivo), BMT076, 30H, ART-sensitive, Xepon, Laos

value: 30H post-sampling

source_name: P. falciparum 3d7 RNA reference pool


title: Burkitt MPI-082_sty

description: Hybridized to 250K_Sty

value: tumor

value: Burkitt lymphoma


title: Burkitt MPI-085_sty

description: Hybridized to 250K_Sty


title: Visceral Adipose tissue_Overweight_6

source_name: Reference RNA pool made of a mix of commercial human liver, adipose tissue and skeletal muscle

value: mix of male and female

value: mix of liver, adipose tissue and skeletal muscle

value: overweight

value: visceral adipose tissue


title: Visceral Adipose tissue_Overweight_4

value: female


title: Visceral Adipose tissue_Overweight_5


title: Visceral Adipose tissue_Overweight_3


title: Burkitt MPI-048_sty

description: Hybridized to 250K_Sty


title: Burkitt MPI-075_sty

description: Hybridized to 250K_Sty


title: 252978410016_B7A_CY5_ETP98068_CY3.mev.refIsIB.out

source_name: Genomic DNA purified from wild type bacteria


title: Burkitt MPI-044_sty

description: Hybridized to 250K_Sty

source_name: Whole tissue of tumor biopsy


title: 252978410016_B7A_CY5_ICDDR_B_p11_CY3.mev.refIsIB.out


title: Visceral Adipose tissue_Overweight_2


title: Burkitt MPI-034_sty

description: Hybridized to 250K_Sty


title: Burkitt MPI-055_sty

description: Hybridized to 250K_Sty


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT076_24H

source_name: P. falciparum parasites (ex-vivo), BMT076, 24H, ART-sensitive, Xepon, Laos

value: Ex-vivo culture

value: 24H post-sampling

value: Lab Strain 3D7


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT076_18H

source_name: P. falciparum parasites (ex-vivo), BMT076, 18H, ART-sensitive, Xepon, Laos

value: 18H post-sampling

value: patient ID BMT076, Xepon, Laos


title: Burkitt MPI-071_sty

description: Hybridized to 250K_Sty


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT076_6H

source_name: P. falciparum parasites (ex-vivo), BMT076, 6H, ART-sensitive, Xepon, Laos

value: 6H post-sampling

value: mix of several samples collected across the 48-hour intraerythrocytic life cycle


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT076_12H

source_name: P. falciparum parasites (ex-vivo), BMT076, 12H, ART-sensitive, Xepon, Laos

value: 12H post-sampling


title: Burkitt MPI-033_sty

description: Hybridized to 250K_Sty


title: 252978410016_B7A_CY5_E1785_CY3.mev.refIsIB.out


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT076_42H

source_name: P. falciparum parasites (ex-vivo), BMT076, 42H, ART-sensitive, Xepon, Laos

value: 42H post-sampling

value: artemisinin-sensitive


title: 252978410016_B7A_CY5_D02_2_CY3.mev.refIsIB.out


title: Visceral Adipose tissue_Overweight_1


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT076_0H

source_name: P. falciparum parasites (ex-vivo), BMT076, 0H, ART-sensitive, Xepon, Laos

value: 0H post-sampling


title: Burkitt MPI-043_sty

description: Hybridized to 250K_Sty

value: tumor

value: Burkitt lymphoma


title: 252978410017_B7A_CY5_E1788_CY3.mev.refIsIB.out


title: 252978410008_B7A_CY5_ETP98103_CY3.mev.refIsIB.ou


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT061_42H

source_name: P. falciparum parasites (ex-vivo), BMT061, 42H, ART-sensitive, Xepon, Laos

value: patient ID BMT061, Xepon, Laos


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT061_24H

source_name: P. falciparum parasites (ex-vivo), BMT061, 24H, ART-sensitive, Xepon, Laos


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT061_16H

source_name: P. falciparum parasites (ex-vivo), BMT061, 16H, ART-sensitive, Xepon, Laos

value: 16H post-sampling


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT061_12H

source_name: P. falciparum parasites (ex-vivo), BMT061, 12H, ART-sensitive, Xepon, Laos


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT061_32H

source_name: P. falciparum parasites (ex-vivo), BMT061, 32H, ART-sensitive, Xepon, Laos

value: 32H post-sampling


title: Burkitt MPI-018_sty

description: Hybridized to 250K_Sty


title: 252978410008_B7A_CY5_180050_CY3.mev.refIsIB.out


title: 252978410015_B7A_CY5_sPRH613_CY3.mev.refIsIB.out


title: 252978410017_B7A_CY5_C35776_CY3.mev.refIsIB.out


title: 252978410015_B7A_CY5_ICDDR_B_p8_CY3.mev.refIsIB.out


title: 252978410007_B7A_CY5_ETP98061_CY3.mev.refIsIB.out


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT061_8H

source_name: P. falciparum parasites (ex-vivo), BMT061, 8H, ART-sensitive, Xepon, Laos

value: 8H post-sampling


title: 252978410008_B7A_CY5_ETP98111_CY3.mev.refIsIB.out


title: 252978410015_B7A_CY5_ICDDR_B_p5_CY3.mev.refIsIB.out


title: Burkitt MPI-016_sty

description: Hybridized to 250K_Sty


title: FDB1_F_F_72_0_Sample_1_1_AMC_002933

city: Adelaide

first: Chung

middle: H

last: Kok

state: South Australia

address: North Terrace

country: Australia

institute: South Australia Health and Medical Research Institute

description: This sample comes from a single series of print runs by the Adelaide Microarray Facility. This is related to GSE3333 and layout corresponds to print run 2 of that experiment. We have included the index and orig index for reference

scan_protocol: Slides were scanned with a GenePix 3000B Scanner (Axon Instruments)

data_processing:
Images were visually inspected for artefacts and boxplots and image plots of Red and Green channels examined. Arrays with poor hybridisation efficiency,  or gross artefacts were excluded and repeated. Image analysis and spot identification and intensity extraction was performed using the Spot software package (http://experimental.act.cmis.csiro.au/Spot/index.php, CSIRO, Australia). Spot uses a seeded region growing algorithm to identify spots and is able to identify non-uniform shaped spots. Each estimated grid was visually inspected to ensure accurate spot identification. Morphological opening background correction was applied to mean spot signal intensities. Spot weights were assigned based on spot size. Full weight (1) were given to all spots except those which were maxed out. Spots with a channel maxed out were set to weights of 0.1. These weights were used during normalisation. Arrays were normalised using intensity-dependent print-tip loess normalization followed by within slide scale normalisation (as implemented in the LIMMA and MARRAY packages of BioConductors using the normaliseWithinArrays function ). Linear modelling was performed using array based weights as described in M. Ritchie PhD Thesis, University of Melbourne and using the estimate.gamma function.

For this array the weight was: 1.3428351.

organism: Mus musculus

source_name: FDB1_FI-Delta_72hrs Rep 1

label_protocol: Indirect labelling using Cy-Scribe post-labelling kit (Amersham) as per the instructions (protocol available at http://www.microarray.adelaide.edu.au/protocols/cdna/)

growth_protocol: FDB1 cells were grown in Iscove's modified Dulbecco's medium supplemented with 10% fetal calf serum and 500 U/mL mIL-3. See PMID: 10607694

extract_protocol: Trizol procedure

treatment_protocol: At 0h cells were washed 3 times in Iscove's modified Dulbecco's medium. Cells were then allowed to grow without factor for 72 hours

tag: cell line

value: FDB1_FI-Delta cells

source_name: FDB1_FI-Delta_0hrs Rep 1


title: 252978410007_B7A_CY5_BCE049_MS9_CY3.mev.refIsIB.out

value: BCE049, MS9


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT061_6H

source_name: P. falciparum parasites (ex-vivo), BMT061, 6H, ART-sensitive, Xepon, Laos

value: Ex-vivo culture

source_name: P. falciparum 3d7 RNA reference pool

value: Lab Strain 3D7


title: 252978410015_B7A_CY5_E1392_75_CY3.mev.refIsIB.out

source_name: Genomic DNA purified from wild type bacteria


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT061_4H

source_name: P. falciparum parasites (ex-vivo), BMT061, 4H, ART-sensitive, Xepon, Laos

value: 4H post-sampling


title: Burkitt MPI-006_sty

description: Hybridized to 250K_Sty

source_name: Whole tissue of tumor biopsy


title: Burkitt MPI-001_sty

description: Hybridized to 250K_Sty


title: FDB1_FY_FY_72_0_Sample_4_4_AMC_002938

data_processing:
Images were visually inspected for artefacts and boxplots and image plots of Red and Green channels examined. Arrays with poor hybridisation efficiency,  or gross artefacts were excluded and repeated. Image analysis and spot identification and intensity extraction was performed using the Spot software package (http://experimental.act.cmis.csiro.au/Spot/index.php, CSIRO, Australia). Spot uses a seeded region growing algorithm to identify spots and is able to identify non-uniform shaped spots. Each estimated grid was visually inspected to ensure accurate spot identification. Morphological opening background correction was applied to mean spot signal intensities. Spot weights were assigned based on spot size. Full weight (1) were given to all spots except those which were maxed out. Spots with a channel maxed out were set to weights of 0.1. These weights were used during normalisation. Arrays were normalised using intensity-dependent print-tip loess normalization followed by within slide scale normalisation (as implemented in the LIMMA and MARRAY packages of BioConductors using the normaliseWithinArrays function ). Linear modelling was performed using array based weights as described in M. Ritchie PhD Thesis, University of Melbourne and using the estimate.gamma function.

For this array the weight was: 0.8222124.

source_name: FDB1_FI-Delta-Y577F_72hrs Rep 4

value: FDB1_FI-Delta-Y577F cells

source_name: FDB1_FI-Delta-Y577F_0hrs Rep 4


title: FDB1_FY_F_0_0_Sample_2_4_AMC_002932

data_processing:
Images were visually inspected for artefacts and boxplots and image plots of Red and Green channels examined. Arrays with poor hybridisation efficiency,  or gross artefacts were excluded and repeated. Image analysis and spot identification and intensity extraction was performed using the Spot software package (http://experimental.act.cmis.csiro.au/Spot/index.php, CSIRO, Australia). Spot uses a seeded region growing algorithm to identify spots and is able to identify non-uniform shaped spots. Each estimated grid was visually inspected to ensure accurate spot identification. Morphological opening background correction was applied to mean spot signal intensities. Spot weights were assigned based on spot size. Full weight (1) were given to all spots except those which were maxed out. Spots with a channel maxed out were set to weights of 0.1. These weights were used during normalisation. Arrays were normalised using intensity-dependent print-tip loess normalization followed by within slide scale normalisation (as implemented in the LIMMA and MARRAY packages of BioConductors using the normaliseWithinArrays function ). Linear modelling was performed using array based weights as described in M. Ritchie PhD Thesis, University of Melbourne and using the estimate.gamma function.

For this array the weight was: 1.3641430.

source_name: FDB1_FI-Delta-Y577F_0hrs Rep 2

source_name: FDB1_FI-Delta_0hrs Rep 4


title: Burkitt MPI-017_sty

description: Hybridized to 250K_Sty


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT061_2H

source_name: P. falciparum parasites (ex-vivo), BMT061, 2H, ART-sensitive, Xepon, Laos

value: 2H post-sampling

value: mix of several samples collected across the 48-hour intraerythrocytic life cycle


title: 252978410014_B7A_CY5_sPRH450_CY3.mev.refIsIB.out


title: ex-vivo_ ART-sensitive_ Xepon Laos_BMT061_0H

source_name: P. falciparum parasites (ex-vivo), BMT061, 0H, ART-sensitive, Xepon, Laos


title: FDB1_FY_FY_0_72_Sample_3_3_AMC_002937

data_processing:
Images were visually inspected for artefacts and boxplots and image plots of Red and Green channels examined. Arrays with poor hybridisation efficiency,  or gross artefacts were excluded and repeated. Image analysis and spot identification and intensity extraction was performed using the Spot software package (http://experimental.act.cmis.csiro.au/Spot/index.php, CSIRO, Australia). Spot uses a seeded region growing algorithm to identify spots and is able to identify non-uniform shaped spots. Each estimated grid was visually inspected to ensure accurate spot identification. Morphological opening background correction was applied to mean spot signal intensities. Spot weights were assigned based on spot size. Full weight (1) were given to all spots except those which were maxed out. Spots with a channel maxed out were set to weights of 0.1. These weights were used during normalisation. Arrays were normalised using intensity-dependent print-tip loess normalization followed by within slide scale normalisation (as implemented in the LIMMA and MARRAY packages of BioConductors using the normaliseWithinArrays function ). Linear modelling was performed using array based weights as described in M. Ritchie PhD Thesis, University of Melbourne and using the estimate.gamma function.

For this array the weight was: 0.8238116.

source_name: FDB1_FI-Delta-Y577F_0hrs Rep 3

source_name: FDB1_FI-Delta-Y577F_72hrs Rep 3


title: Burkitt MPI-005_sty

description: Hybridized to 250K_Sty


title: 252978410014_B7A_CY5_PUTI_O26_UMN_O26_CY3.mev.refIsIB.out

value: PUTI O26 UMN O26


title: Normal N9_nsp

description: Hybridized to 250K_Nsp

source_name: whole blood DNA extraction

value: normal reference

value: blood

value: normal


title: Normal N8_nsp

description: Hybridized to 250K_Nsp


title: 252978410014_B7A_CY5_E20738A_CY3.mev.refIsIB.out


title: Burkitt MPI-003_sty

description: Hybridized to 250K_Sty

value: tumor

value: Burkitt lymphoma


title: Burkitt MPI-032_sty

description: Hybridized to 250K_Sty


title: FDB1_F_F_0_72_Sample_2_2_AMC_002934

data_processing:
Images were visually inspected for artefacts and boxplots and image plots of Red and Green channels examined. Arrays with poor hybridisation efficiency,  or gross artefacts were excluded and repeated. Image analysis and spot identification and intensity extraction was performed using the Spot software package (http://experimental.act.cmis.csiro.au/Spot/index.php, CSIRO, Australia). Spot uses a seeded region growing algorithm to identify spots and is able to identify non-uniform shaped spots. Each estimated grid was visually inspected to ensure accurate spot identification. Morphological opening background correction was applied to mean spot signal intensities. Spot weights were assigned based on spot size. Full weight (1) were given to all spots except those which were maxed out. Spots with a channel maxed out were set to weights of 0.1. These weights were used during normalisation. Arrays were normalised using intensity-dependent print-tip loess normalization followed by within slide scale normalisation (as implemented in the LIMMA and MARRAY packages of BioConductors using the normaliseWithinArrays function ). Linear modelling was performed using array based weights as described in M. Ritchie PhD Thesis, University of Melbourne and using the estimate.gamma function.

For this array the weight was: 0.9833072.

source_name: FDB1_FI-Delta_0hrs Rep 2

source_name: FDB1_FI-Delta_72hrs Rep 2


title: FDB1_FY_F_0_0_Sample_1_4_AMC_002939

data_processing:
Images were visually inspected for artefacts and boxplots and image plots of Red and Green channels examined. Arrays with poor hybridisation efficiency,  or gross artefacts were excluded and repeated. Image analysis and spot identification and intensity extraction was performed using the Spot software package (http://experimental.act.cmis.csiro.au/Spot/index.php, CSIRO, Australia). Spot uses a seeded region growing algorithm to identify spots and is able to identify non-uniform shaped spots. Each estimated grid was visually inspected to ensure accurate spot identification. Morphological opening background correction was applied to mean spot signal intensities. Spot weights were assigned based on spot size. Full weight (1) were given to all spots except those which were maxed out. Spots with a channel maxed out were set to weights of 0.1. These weights were used during normalisation. Arrays were normalised using intensity-dependent print-tip loess normalization followed by within slide scale normalisation (as implemented in the LIMMA and MARRAY packages of BioConductors using the normaliseWithinArrays function ). Linear modelling was performed using array based weights as described in M. Ritchie PhD Thesis, University of Melbourne and using the estimate.gamma function.

For this array the weight was: 1.4217789.

source_name: FDB1_FI-Delta-Y577F_0hrs Rep 1


title: gDNA_ART-resistant_ Pailin Cambodia_CP040_rep2

source_name: P. falciparum parasites, CP040, art_resistant, Pailin, Cambodia

extract_protocol: Total genomic DNA extracted using phenol-chlorofom method as previously described : Mackinnon, M.J. et al. Comparative transcriptional and genomic analysis of Plasmodium falciparum field isolates. PLoS Pathog 5, e1000644 (2009)

value: patient ID CP040, Pailin, Cambodia

value: artemisinin-resistant

source_name: P. falciparum 3d7 genomic DNA


title: 252978410004_B7A_CY5_BCE069_MS9_CY3.mev.refIsIB.out

source_name: Genomic DNA purified from wild type bacteria

value: BCE069, MS9


title: Normal N10_nsp

description: Hybridized to 250K_Nsp


title: gDNA_ART-resistant_ Pailin Cambodia_CP040_rep1


title: 252978410013_B7A_CY5_TW3574_CY3.mev.refIsIB.out


title: FDB1_F_FY_72_72_Sample_2_4_AMC_002936

data_processing:
Images were visually inspected for artefacts and boxplots and image plots of Red and Green channels examined. Arrays with poor hybridisation efficiency,  or gross artefacts were excluded and repeated. Image analysis and spot identification and intensity extraction was performed using the Spot software package (http://experimental.act.cmis.csiro.au/Spot/index.php, CSIRO, Australia). Spot uses a seeded region growing algorithm to identify spots and is able to identify non-uniform shaped spots. Each estimated grid was visually inspected to ensure accurate spot identification. Morphological opening background correction was applied to mean spot signal intensities. Spot weights were assigned based on spot size. Full weight (1) were given to all spots except those which were maxed out. Spots with a channel maxed out were set to weights of 0.1. These weights were used during normalisation. Arrays were normalised using intensity-dependent print-tip loess normalization followed by within slide scale normalisation (as implemented in the LIMMA and MARRAY packages of BioConductors using the normaliseWithinArrays function ). Linear modelling was performed using array based weights as described in M. Ritchie PhD Thesis, University of Melbourne and using the estimate.gamma function.

For this array the weight was: 0.8213316.

value: FDB1_FI-Delta cells


title: FDB1_FY_F_72_72_Sample_1_3_AMC_002935

data_processing:
Images were visually inspected for artefacts and boxplots and image plots of Red and Green channels examined. Arrays with poor hybridisation efficiency,  or gross artefacts were excluded and repeated. Image analysis and spot identification and intensity extraction was performed using the Spot software package (http://experimental.act.cmis.csiro.au/Spot/index.php, CSIRO, Australia). Spot uses a seeded region growing algorithm to identify spots and is able to identify non-uniform shaped spots. Each estimated grid was visually inspected to ensure accurate spot identification. Morphological opening background correction was applied to mean spot signal intensities. Spot weights were assigned based on spot size. Full weight (1) were given to all spots except those which were maxed out. Spots with a channel maxed out were set to weights of 0.1. These weights were used during normalisation. Arrays were normalised using intensity-dependent print-tip loess normalization followed by within slide scale normalisation (as implemented in the LIMMA and MARRAY packages of BioConductors using the normaliseWithinArrays function ). Linear modelling was performed using array based weights as described in M. Ritchie PhD Thesis, University of Melbourne and using the estimate.gamma function.

For this array the weight was: 0.8026397.

source_name: FDB1_FI-Delta-Y577F_72hrs Rep 1

source_name: FDB1_FI-Delta_72hrs Rep 3


title: Normal N6_nsp

description: Hybridized to 250K_Nsp


title: gDNA_ART-sensitive_ Xepon Laos_XPN003_rep1

data_processing: Data processing as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, Lowess normalization and subsequent filtering for quality control were carried out using Acuity 4.0 (Axon Instruments). Spots were considered of good quality when they were unflagged and had at least 95% of pixels median intensity greater than the local background plus 2 times the standard deviation of the background for either dye channel. The values presented in the sample data represent log2-transformed ratios of the measurement in the sample channel (Cy5) divided by the corresponding measurement in the reference channel (Cy3, P. falciparum RNA reference pool).

source_name: P. falciparum parasites, XPN003, ART-sensitive, Xepon, Laos

value: patient ID XPN003, Xepon, Laos

value: artemisinin-sensitive


title: Normal N7_nsp

description: Hybridized to 250K_Nsp


title: FDB1_F_F_72_0_Sample_2_2_AMC_002940

data_processing:
Images were visually inspected for artefacts and boxplots and image plots of Red and Green channels examined. Arrays with poor hybridisation efficiency,  or gross artefacts were excluded and repeated. Image analysis and spot identification and intensity extraction was performed using the Spot software package (http://experimental.act.cmis.csiro.au/Spot/index.php, CSIRO, Australia). Spot uses a seeded region growing algorithm to identify spots and is able to identify non-uniform shaped spots. Each estimated grid was visually inspected to ensure accurate spot identification. Morphological opening background correction was applied to mean spot signal intensities. Spot weights were assigned based on spot size. Full weight (1) were given to all spots except those which were maxed out. Spots with a channel maxed out were set to weights of 0.1. These weights were used during normalisation. Arrays were normalised using intensity-dependent print-tip loess normalization followed by within slide scale normalisation (as implemented in the LIMMA and MARRAY packages of BioConductors using the normaliseWithinArrays function ). Linear modelling was performed using array based weights as described in M. Ritchie PhD Thesis, University of Melbourne and using the estimate.gamma function.

For this array the weight was: 1.3509069.


title: gDNA_ART-resistant_ Pailin Cambodia_CP037_rep2

source_name: P. falciparum parasites, CP037, art_resistant, Pailin, Cambodia

value: Ex-vivo culture

value: patient ID CP037, Pailin, Cambodia

value: Lab Strain 3D7


title: 252978410013_B7A_CY5_TW3585_CY3.mev.refIsIB.out


title: 252978410004_B7A_CY5_BCE058_MS13_CY3.mev.refIsIB.out


title: Normal N3_nsp

description: Hybridized to 250K_Nsp


title: Normal N5_nsp

description: Hybridized to 250K_Nsp


title: gDNA_ART-resistant_ Pailin Cambodia_CP025_rep2

source_name: P. falciparum parasites, CP025, art_resistant, Pailin, Cambodia

value: patient ID CP025, Pailin, Cambodia


title: gDNA_ART-resistant_ Pailin Cambodia_CP037_rep1


title: Normal N2_nsp

description: Hybridized to 250K_Nsp


title: WT H202 vs. OxyR mutant H20 Rep2

city: Dallas

first: Todd

middle: C.

last: Hoopman

state: TX

address: 5323 Harry Hines Blvd.

department: Microbiology

institute: University of Texas Southwestern Medical Center

hyb_protocol: Equivalent amounts of the Cy3- and Cy5-labeled cDNA samples were mixed, lyophilized, and then dissolved in 21 microliters of H2O. After denaturation for 3 minutes at 94 degrees Celsius these samples were kept on ice until they were used for DNA hybridization. The hybridization mixture containing 15 microliters of 4X hybridization buffer (GE Healthcare), 24 microliters of formamide (40% volume/volume), and 21 microliters of the Cy3- and Cy5-labeled cDNA. The mixture was added to a DNA microarray slide and incubated at 50 degrees Celsius overnight (~ 16 hours). After hybridization the slides were washed twice in 6X SSPE containing 0.01% Tween 20 at 50 degrees Celsius for 5 min, twice in 0.8X SSPE containing 0.001% Tween 20 at 50 degrees Celsius for 5 min, and twice in 0.8X SSPE at room temperature.

scan_protocol: The slides were dried by centrifugation at 900 x g in loosely capped 50-ml conical tubes for 3 minutes. Microarray slides were scanned with a GenePix 4100A microarray reader (Molecular Devices, Sunnyvale, CA) and analyzed with GenePix 4.0 software (Molecular Devices).

data_processing: The Acuity 4.0 software package (Molecular Devices) was utilized to analyze the microarray data. Raw data were first normalized using a ratio-based normalization method to equalize the means and medians of the features to 1 and exclude ratios that were less than 0.1 or greater than 10. Features that were flagged by the software as bad, absent, or not found were also excluded from further analysis. Secondly, a Lowess-based normalization was applied to the microarray data prior to final analysis. The RNA isolated from the in vitro broth-grown O35E wild-type cells exposed to hydrogen peroxide was utilized as the baseline gene expression template. To identify those genes in the wild-type strain that exhibited an altered expression profile upon exposure to hydrogen peroxide relative to the in vitro broth-grown oxyR mutant cells exposed to hydrogen peroxide, a threshold of twofold-increased or decreased expression over the baseline was utilized.

organism: Moraxella catarrhalis

source_name: Moraxella catarrhalis strain O35E, 19 hours growth, 50 mM hydrogen peroxide

label_protocol: Five micrograms of total RNA from the O35E cells exposed to 50 mM hydrogen peroxide were mixed with 3.0 micrograms of M. catarrhalis genome directed primers and dried in the Speed-Vac. Once lyophilized the sample was reconstituted with 11 microliters of H2O and heated at 70 degrees Celsius for 5 minutes. The mixture was then cooled to room temperature for 10 minutes. cDNA synthesis was then performed with the Ambion Amino Allyl cDNA synthesis kit per the manufacturer's instructions RNA hydrolysis was accomplished with the addition of 15 microliters of sodium hydroxide (0.1M) and the sample was maintained at 70 degrees Celsius for 15 minutes. 15 microliters of hydrochloric acid (0.1M) was then added and the amino allyl-labeled cDNA was purified with a QIAGEN QIAquick gel extraction kit. After purification, Cy3 dye (GE Heathcare) was added and labelling occured per the manufacturers instructions. The CyDye-labeled cDNA sample was purified by using Microcon YM30 columns. A NanoDrop spectrophotometer was used to measure the concentration of the CyDye-labeled cDNA sample.

growth_protocol: Bacterial cells were grown in BHI to mid-logarithmic phase and utilized to inoculate tissue culture plates.

extract_protocol: The contents of each well underwent total RNA extraction with the Ambion Ribopure Bacteria kit as per manufacturer's instructions and then were treated with DNase I from a MessageClean kit as per manufacturer's instructions.

treatment_protocol: Hydogen peroxide (50 mM final concentration) was added to in vitro grown M. catarrhalis strain O35E for a 15 minute exposure period.

value: Moraxella catarrhalis strain O35E grown for 19 hours in BHI broth and then exposed to 50 mM hydrogen peroxide for 15 minutes.

tag: genetic background

value: hydrogen peroxide

tag: genotype

value: wild type

source_name: Moraxella catarrhalis strain O35E oxyR mutant, 19 hours growth, water control

label_protocol: Five micrograms of total RNA from the O35E cells exposed to 50 mM hydrogen peroxide were mixed with 3.0 micrograms of M. catarrhalis genome directed primers and dried in the Speed-Vac. Once lyophilized the sample was reconstituted with 11 microliters of H2O and heated at 70 degrees Celsius for 5 minutes. The mixture was then cooled to room temperature for 10 minutes. cDNA synthesis was then performed with the Ambion Amino Allyl cDNA synthesis kit per the manufacturer's instructions RNA hydrolysis was accomplished with the addition of 15 microliters of sodium hydroxide (0.1M) and the sample was maintained at 70 degrees Celsius for 15 minutes. 15 microliters of hydrochloric acid (0.1M) was then added and the amino allyl-labeled cDNA was purified with a QIAGEN QIAquick gel extraction kit. After purification, Cy5 dye (GE Heathcare) was added and labelling occured per the manufacturers instructions. The CyDye-labeled cDNA sample was purified by using Microcon YM30 columns. A NanoDrop spectrophotometer was used to measure the concentration of the CyDye-labeled cDNA sample.

treatment_protocol: Hydogen peroxide (50 mM final concentration) was added to in vitro grown M. catarrhalis strain O35E oxyR mutant for a 15 minute exposure period.

value: Moraxella catarrhalis strain O35E oxyR mutant grown for 19 hours in BHI broth and then exposed to water only for 15 minutes.

value: water

tag: oxyR mutant


title: Burkitt MPI-532_nsp

description: Hybridized to 250K_Nsp

source_name: Whole tissue of tumor biopsy

value: tumor


title: Normal N4_nsp

description: Hybridized to 250K_Nsp

value: normal reference

value: blood

value: normal


title: gDNA_ART-resistant_ Pailin Cambodia_CP025_rep1

value: artemisinin-resistant


title: WT H202 vs. OxyR mutant H202 Rep2

source_name: Moraxella catarrhalis strain O35E oxyR mutant, 19 hours growth, 50 mM hydrogen peroxide

value: Moraxella catarrhalis strain O35E oxyR mutant grown for 19 hours in BHI broth and then exposed to 50 mM hydrogen peroxide for 15 minutes.


title: WT H202 vs. OxyR mutant H20 Rep1

source_name: Moraxella catarrhalis strain O35E, 19 hours growth, water control


title: 252978410004_B7A_CY5_BCE003_DS5_CY3.mev.refIsIB.out

value: BCE003, DS5


title: FDB1_F_FY_0_0_Sample_1_3_AMC_002931

data_processing:
Images were visually inspected for artefacts and boxplots and image plots of Red and Green channels examined. Arrays with poor hybridisation efficiency,  or gross artefacts were excluded and repeated. Image analysis and spot identification and intensity extraction was performed using the Spot software package (http://experimental.act.cmis.csiro.au/Spot/index.php, CSIRO, Australia). Spot uses a seeded region growing algorithm to identify spots and is able to identify non-uniform shaped spots. Each estimated grid was visually inspected to ensure accurate spot identification. Morphological opening background correction was applied to mean spot signal intensities. Spot weights were assigned based on spot size. Full weight (1) were given to all spots except those which were maxed out. Spots with a channel maxed out were set to weights of 0.1. These weights were used during normalisation. Arrays were normalised using intensity-dependent print-tip loess normalization followed by within slide scale normalisation (as implemented in the LIMMA and MARRAY packages of BioConductors using the normaliseWithinArrays function ). Linear modelling was performed using array based weights as described in M. Ritchie PhD Thesis, University of Melbourne and using the estimate.gamma function.

For this array the weight was: 1.0099539.

source_name: FDB1_FI-Delta_0hrs Rep 1

value: FDB1_FI-Delta cells

source_name: FDB1_FI-Delta-Y577F_0hrs Rep 3

value: FDB1_FI-Delta-Y577F cells


title: gDNA_ART-sensitive_ Pailin Cambodia_CP022_rep1

source_name: P. falciparum parasites, CP022, ART-sensitive, Pailin, Cambodia

value: Ex-vivo culture

value: patient ID CP022, Pailin, Cambodia

value: artemisinin-sensitive


title: gDNA_ART-sensitive_ Pailin Cambodia_CP022_rep2

value: Lab Strain 3D7


title: Normal N1_nsp

description: Hybridized to 250K_Nsp

source_name: whole blood DNA extraction


title: 252978410013_B7A_CY5_180600_CY3.mev.refIsIB.out


title: 252978410003_B7A_CY5_ETP98062_CY3.mev.refIsIB.out


title: WT H202 vs. OxyR mutant H202 Rep1

value: hydrogen peroxide

value: Moraxella catarrhalis strain O35E grown for 19 hours in BHI broth and then exposed to 50 mM hydrogen peroxide for 15 minutes.

label_protocol: Five micrograms of total RNA from the O35E oxyR mutant cells exposed to hydrogen peroxide were mixed with 3.0 micrograms of M. catarrhalis genome directed primers and dried in the Speed-Vac. Once lyophilized the sample was reconstituted with 11 microliters of H2O and heated at 70 degrees Celsius for 5 minutes. The mixture was then cooled to room temperature for 10 minutes. cDNA synthesis was then performed with the Ambion Amino Allyl cDNA synthesis kit per the manufacturer's instructions RNA hydrolysis was accomplished with the addition of 15 microliters of sodium hydroxide (0.1M) and the sample was maintained at 70 degrees Celsius for 15 minutes. 15 microliters of hydrochloric acid (0.1M) was then added and the amino allyl-labeled cDNA was purified with a QIAGEN QIAquick gel extraction kit. After purification, Cy3 dye (GE Heathcare) was added and labelling occured per the manufacturers instructions. The CyDye-labeled cDNA sample was purified by using Microcon YM30 columns. A NanoDrop spectrophotometer was used to measure the concentration of the CyDye-labeled cDNA sample.

treatment_protocol: Hydrogen peroxide (50 mM final concentration) was added to in vitro grown M. catarrhalis strain O35E oxyR mutant for a 15 minute exposure period.


title: Burkitt MPI-528_nsp

description: Hybridized to 250K_Nsp

value: Burkitt lymphoma


title: 252978410013_B7A_CY5_ETEC_10_1_CY3.mev.refIsIB.out

value: ETEC 10/1


title: Identification of Gene Products Involved in the Oxidative Stress Response of Moraxella catarrhalis Rep 4

data_processing: The Acuity 4.0 software package (Molecular Devices) was utilized to analyze the microarray data. Raw data were first normalized using a ratio-based normalization method to equalize the means and medians of the features to 1 and exclude ratios that were less than 0.1 or greater than 10. Features that were flagged by the software as bad, absent, or not found were also excluded from further analysis. Secondly, a Lowess-based normalization was applied to the microarray data prior to final analysis. The RNA isolated from the in vitro broth-grown O35E.rpsl was utilized as the baseline gene expression template. To identify those genes that exhibited an altered expression profile in the chinchilla nasopharynx relative to the in vitro broth-grown cells, a threshold of twofold-increased or decreased expression over the baseline was utilized.

label_protocol: Five micrograms of total RNA from the O35E cells exposed to water were mixed with 3.0 micrograms of M. catarrhalis genome directed primers and dried in the Speed-Vac. Once lyophilized the sample was reconstituted with 11 microliters of H2O and heated at 70 degrees Celsius for 5 minutes. The mixture was then cooled to room temperature for 10 minutes. cDNA synthesis was then performed with the Ambion Amino Allyl cDNA synthesis kit per the manufacturer's instructions RNA hydrolysis was accomplished with the addition of 15 microliters of sodium hydroxide (0.1M) and the sample was maintained at 70 degrees Celsius for 15 minutes. 15 microliters of hydrochloric acid (0.1M) was then added and the amino allyl-labeled cDNA was purified with a QIAGEN QIAquick gel extraction kit. After purification, Cy5 dye (GE Heathcare) was added and labelling occured per the manufacturers instructions. The CyDye-labeled cDNA sample was purified by using Microcon YM30 columns. A NanoDrop spectrophotometer was used to measure the concentration of the CyDye-labeled cDNA sample.

treatment_protocol: Water was added to in vitro grown M. catarrhalis strain O35E for a 15 minute exposure period.

tag: growth protocol

value: 19 hours in BHI broth

tag: stress

value: water

tag: time

value: 15 minutes

tag: dose

value: 50 mM


title: gDNA_ ART-sensitive_ Xepon Laos_BMT077_rep1

source_name: P. falciparum parasites, BMT061, ART-sensitive, Xepon, Laos gDNA

tag: origin

value: patient ID BMT061, Xepon, Laos


title: Burkitt MPI-527_nsp

description: Hybridized to 250K_Nsp

tag: sample type

value: tumor


title: Identification of Gene Products Involved in the Oxidative Stress Response of Moraxella catarrhalis Rep3

data_processing: The Acuity 4.0 software package (Molecular Devices) was utilized to analyze the microarray data. Raw data were first normalized using a ratio-based normalization method to equalize the means and medians of the features to 1 and exclude ratios that were less than 0.1 or greater than 10. Features that were flagged by the software as bad, absent, or not found were also excluded from further analysis. Secondly, a Lowess-based normalization was applied to the microarray data prior to final analysis. The RNA isolated from the in vitro broth-grown O35E exposed to water only was utilized as the baseline gene expression template. To identify those genes that exhibited an altered expression profile upon exposure to hydrogen peroxide relative to the in vitro broth-grown cells exposed to water only control, a threshold of twofold-increased or decreased expression over the baseline was utilized.


title: Burkitt MPI-171_nsp

description: Hybridized to 250K_Nsp


title: Indentification of Gene Products Involved in the Oxidative Stress Response of Moraxella catarrhalis Rep 1


title: Burkitt MPI-529_nsp

description: Hybridized to 250K_Nsp


title: 252978410012_B7A_CY5_LSN02_012560_A_CY3.mev.refIsIB.out

data_processing:
1. Use Agilent software Feature Extraction to analyze spotted arrays.
2. Use TM4 suite software ExpressConverter to modify Agilent Feature Extraction file into *.mev.
3. Calculate the value of log2 ratio (Reference/Query) from the normalized .mev file:
    3a). If both channels (QUERY_MEDIAN_INTENSITY and REF_MEDIAN_INTENSITY) are zero, assign the value "null".
    3b). If one channel is zero and the other is not zero, substitute the zero with one (1) and then, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE
    3c). If neither channel is zero, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE.


title: 252978410012_B7A_CY5_ICDDR_B_p12_CY3.mev.refIsIB.out


title: 252978410003_B7A_CY5_C35662_CY3.mev.refIsIB.out


title: 252978410003_B7A_CY5_ETP05_007_CY3.mev.refIsIB.out


title: 252978410012_B7A_CY5_ETEC_18_2_CY3.mev.refIsIB.out

value: ETEC 18/2


title: CL_Spdef_HET1 Mice

first: Manoj

last: Bhasin

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

description: Colon sample from Spdef heterzygous  mice

hyb_protocol: All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays. The HT_MG-430A Array plate consists of 24 single MG-430A arrays arranged into standard SBS 24 well plate format. All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.

scan_protocol: HT Plate Scanner

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

source_name: Colon

label_protocol: For transcriptional profiling, total RNA was converted into cRNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA) and hybridized to Affymetrix HT Mouse Genome 430 microarrays.

growth_protocol: 16 week old mice

extract_protocol: Flash frozen samples (–80°C) were  homogenized. RNA was isolated using TRIzol Reagent (Invitrogen).

value: Colon


title: Identification of Gene Products Involved in the Oxidative Stress Response of Moraxella catarrhalis Rep 2


title: Burkitt MPI-139_nsp

description: Hybridized to 250K_Nsp

data_processing:
The CEL-Files were analyzed using the BRLMM-algorithm to produce genotype calls, stored in the corresponding CHP-Files.
CEL- and CHP-Format by Affymetrix


title: CL_Spdef_KN2 Mice

description: Colon sample from Spdef knockout  mice


title: CL_Spdef_KN1 Mice

description: Colon sample from Spdef knockout  mice


title: 252978410002_B7A_CY5_ETP98028_CY3.mev.refIsIB.out

source_name: Genomic DNA purified from wild type bacteria


title: Burkitt MPI-089_nsp

description: Hybridized to 250K_Nsp


title: CL_Spdef_HET2 Mice


title: Burkitt MPI-138_nsp

description: Hybridized to 250K_Nsp


title: Burkitt MPI-114_nsp

description: Hybridized to 250K_Nsp


title: 252978410012_B7A_CY5_42_1_C1_CY3.mev.refIsIB.out


title: 252978410002_B7A_CY5_BCE063_DS4_CY3.mev.refIsIB.out

value: BCE063, DS4


title: CL_WT1 Mice

description: Colon sample from wild Type of Mice

data_processing: The image data was processed using the  the Robust Multiarray method (RMA) to determine the specific hybridizing signal for eachprobe.


title: 252978410002_B7A_CY5_BCE041_MS11_CY3.mev.refIsIB.out


title: 252978410002_B7A_CY5_BCE007_CY3.mev.refIsIB.out


title: ST_Spdef_KN2 Mice

description: Stomach sample from Spdef knockout  mice

source_name: Stomach

value: Stomach


title: Burkitt MPI-101_nsp

description: Hybridized to 250K_Nsp


title: ST_Spdef_KN1 Mice


title: Burkitt MPI-084_nsp

description: Hybridized to 250K_Nsp


title: 252978410001_B7A_CY5_ETP98015_CY3.mev.refIsIB.out

source_name: mev data obtained from the feature extraction file used, no further normalization needed


title: ST_Spdef_HET2 Mice

description: Stomach sample from Spdef heterzygous  mice


title: 252978410007_B7A_CY5_BCE021_DS7_CY3.mev.refIsIB.out

value: BCE021, DS7


title: ST_Spdef_HET1 Mice


title: Burkitt MPI-085_nsp

description: Hybridized to 250K_Nsp


title: 252978410001_B7A_CY5_BCE063MS14_CY3.mev.refIsIB.out


title: Burkitt MPI-087_nsp

description: Hybridized to 250K_Nsp


title: ST_WT2 Mice

description: Stomach sample from wild Type of Mice


title: Burkitt MPI-081_nsp

description: Hybridized to 250K_Nsp


title: CL_WT2 Mice

description: Colon sample from wild Type of Mice


title: 252978410001_B7A_CY5_BCE001MS16_CY3.mev.refIsIB.out


title: Uncoated cellulose implant, 3 days, rat 7

city: Turku

first: Miretta

last: Tommila

address: Kiinamyllynkatu 10

department: Lääketieteellisen biokemian ja genetiikan laitos

country: Finland

institute: Turun yliopisto

description: no additional information

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalisation with limma in R

source_name: subcutaneous implantation of uncoated cellulose, 3 days, rat 7

label_protocol: For the Illumina gene expression analysis, 100 ng of purified total RNA was amplified and biotinylated in an overnight in vitro transcription reaction using the Illumina RNA TotalPrepTM amplification kit (Ambion, Applied Biosystems).

growth_protocol: Subcutaneous implantation into rat

extract_protocol: Total RNA from implants was isolated with RNeasy midi kit according to manufacturer´s instructions, followed by the Dnase I treatment (Promega) as recommended by manufacturer.

value: Sprague-Dawley

tag: age

value: 10 weeks

value: Granulation tissue

value: 3 days


title: ST_WT1 Mice

description: Stomach sample from wild Type of Mice

tag: strain


title: 252978410001_B7A_CY5_BCE022DS6_CY3.mev.refIsIB.out


title: Uncoated cellulose implant, 3 days, rat 6

description: no additional information

source_name: subcutaneous implantation of uncoated cellulose, 3 days, rat 6


title: Uncoated cellulose implant, 3 days, rat 4

description: no additional information

source_name: subcutaneous implantation of uncoated cellulose, 3 days, rat 4


title: Burkitt MPI-055_nsp

description: Hybridized to 250K_Nsp

value: Burkitt lymphoma


title: Burkitt MPI-075_nsp

description: Hybridized to 250K_Nsp


title: Uncoated cellulose implant, 1 day, rat 3

description: no additional information

source_name: subcutaneous implantation of uncoated cellulose, 1 day, rat 3

value: 1 day