title: whole cerebellum postnatal day 21, replicate b, chip Mu11K_sub_A

description: human fetal lung 72 dpc


title: No Addition, Experiment 3, Time point 1

status: Public on Jan 23 2009

type: RNA

city: Santa Cruz

first: Aaron

middle: E

last: Cozen

state: CA

address: 1165 High St.

department: Ocean Sciences

country: USA

institute: University of California, Santa Cruz

hyb_protocol: Spotted microarray slides were hydrated for three minutes in a humidified chamber, snap-dried at 100˚C, covalently linked with 250mJoules in a UV crosslinker (Stratagene), and incubated at 42˚C in a solution of 5X SSC, 1% BSA and 0.1%SDS for 45 minutes prior to hybridization. For each hybridization Cy3-labeled cDNA derived from 5ug of experimental RNA and Cy5-labeled cDNA derived from 5µg reference pool RNA were combined with 1mg/ml herring sperm DNA, 0.38mg/ml yeast tRNA, 4X SSC and 0.5%SDS in a total volume of 55µl, and hybridized for 14 to 18 hours at 60˚C in sealed hybridization chambers. After hybridization slides were washed for two minutes in 0.05%SDS and 0.1X SSC followed by two minutes in 0.05X SSC and dried by room temperature centrifugation at 100X G for eight minutes.

scan_protocol: Slides were scanned at 5µm resolution immediately after washing using a Genepix 4000B microaray scanner (Molecular Devices).

data_processing: Microarray features were analyzed using Genepix 6 software, using median pixel intensities at each of the two channel wavelengths for each spotted feature (Molecular Devices). These values were normalized using the loess function of the open-source Bioconductor package “marray” for the statistical program R (Gentleman, Carey et al. 2004), so that the normalized global and print-tip median log2(Ch1/Ch2) ratio of each array was zero. For each individual array feature the median intensity values of four replicate spots were used for subsequent analyses.

molecule: total RNA

organism: Pyrobaculum aerophilum

source_name: Total RNA from P. aerophilum cultures

label_protocol: Aminoallyl-labeled cDNAs were prepared from 5µg of sample RNA using 5µg of random hexamers (3µg/µl) and the Superscript III labeling kit (Invitrogen). These were subsequently labeled with cy3-NHS ester or cy5-NHS ester (GE Healthcare) following the manufacturer’s instructions.

growth_protocol: Cultures of P. aerophilum were grown in media containing (per liter) 10g NaCl, 1.3g (NH4)2SO4, 0.28g KH2PO4, 0.25g MgSO4•7H2O, 1mg NaSeO4, 0.1mg Na2WO4•2H2O, 70mg CaCl2•2H2O, 0.5g yeast extract, 1mg (NH4)2Fe(SO4)2•6H2O, 0.5mg resazurin, and 10ml of a trace element solution. The trace element solution (DSM141) was prepared by combining the following components (per liter) in a 78.5µM solution of nitriloacetic acid adjusted to pH6.5: 3g MgSO4•7H2O, 0.5g MnSO4•H2O, 1g NaCl, 0.1g FeSO4•7H2O, 0.18g CoSO4•7H2O, 0.1g CaCl2•2H2O, 0.18g ZnSO4•7H2O, 0.01g CuSO4•5H2O, 0.02g KAl(SO4)2•12H2O, 0.01g H3BO3, 0.01g Na2MoO4•2H2O, 0.025g NiCl2•6H2O, and 0.0003g NaSeO3•5H2O. The complete media preparation was adjusted to pH 6.8 and sterilized by autoclaving.

extract_protocol: Total RNA was extracted from frozen cell pellets using a polytron tissue homogenizer and Tri reagent (Sigma-Aldrich), following the manufacturer’s instructions. RNA samples were treated with DNase I (Ambion) to remove any residual DNA, re-extracted with Tri-reagent, and normalized to 1µg/µl before proceeding with preparation of cDNA for microarray analysis.

treatment_protocol: Cultures of P. aerophilum were incubated at 96˚C, typically with 200ml of media in 0.5 liter wide mouth bottles under a gas headspace of N2, and shaking at 200rpm. For aerobic cultures, 5% (v/v) of atmospheric air was added to the headspace for a final concentration of approximately 1% O2. Three replicate respiratory induction experiments were performed in which cultures were grown with a 1% O2 gas headspace, followed by amendment with different respiratory substrates when the cultures became anoxic. No reducing agents were used. Depletion of O2 in cultures was monitored by recording changes in the redox-indicator dye resazurin from pink to clear. After depletion of O2 cultures were cooled to ambient temperature, diluted with a 25% volume of fresh growth media and dispensed in 200ml volumes to bottles in an anaerobic chamber. Separate bottles were prepared for collection at each of three time points. Bottles received either 1% (v/v) additions from 1M stocks of NaNO3, Na2HAsO4, or Fe(III)-citrate pH 6, 5% (v/v) of atmospheric air in the gas headspace, or no added electron acceptor in each induction experiment. These were re-equilibrated to growth temperature (96˚C), and after 2.5 hours (T1), 4.5 hours (T2) or 7.5 hours (T3) one bottle from each respiratory condition was collected for RNA preparation. Cells were collected for RNA analysis by centrifugation at 10,000g for 10 minutes. Cell pellets were frozen in liquid N2 and stored at -80˚C.

tag: Cultures of P. aerophilum grown under aerobic conditions, then shifted to growth with no added terminal electron acceptor (See "Channel 1 Treatment Protocol"). Time point 1 (T1) samples were collected 2.5 hours after this shift.

label_protocol: Same as Channel 1

growth_protocol: Same as Channel 1

extract_protocol: Same as Channel 1

treatment_protocol: Same as Channel 1, with differences described in "Channel 2 Characteristics"

tag: A reference pool of RNA prepared from 45 cultures of P. aerophilum grown under aerobic conditions, then shifted to anoxic growth with different terminal electron acceptors, and collected at three time points (See "Channel 1 Treatment Protocol" and "Channel 1 Growth Protocol"). RNA from each of the 45 different samples used individually for Channel 1 were combined in equal amounts to create the reference pool used in Channel 2.


title: No Addition, Experiment 3, Time point 2

tag: Cultures of P. aerophilum grown under aerobic conditions, then shifted to growth with no added terminal electron acceptor (See "Channel 1 Treatment Protocol"). Time point 2 (T2) samples were collected 4.5 hours after this shift.


title: O2, Experiment 3, Time point 3

tag: Cultures of P. aerophilum grown under aerobic conditions, then shifted to growth with additional O2 (See "Channel 1 Treatment Protocol"). Time point 3 (T3) samples were collected 7.5 hours after this shift.


title: whole cerebellum postnatal day 1, replicate b, chip Mu11K_sub_A

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

description: human fetal lung 103 dpc

hyb_protocol: 25 micrograms of each biotin-labeled cRNA was hybridized to an Affymetrix Mu11K sub A and B chip according to the manufacturer's protocol. Four biotinylated hybridization controls (BioB, BioC, BioD, and Cre) were included in each hybridization reaction to verify consistent hybridization efficiency. Hybridization is carried out according the Affymetrix GeneChip® Manual. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.

scan_protocol: Standard Affymetrix protocol.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

organism: Mus musculus

source_name: Whole cerebella pooled mouse

label_protocol: In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.

growth_protocol: Not applicable.

extract_protocol: 10 micrograms of total RNA was used to generate target cRNA for hybridization to Affymetrix Mu11K chipset subA and subB oligonucleotide microarrays. A single chip set was used for each time-point. Before target generation, individual RNA samples were pooled so that each target was derived from a minimum of 3 individual cerebella. This step was performed to minimize both biologic variability and the number of microarrays necessary to generate informative data. After pooling, RNA was re-purified using Qiagen purification kits (Valencia, CA). Target cRNA was synthesized according to manufacturer's protocol. Briefly, total RNA was reverse transcribed into a complete cDNA library (SuperScript Choice kit; Invitrogen) using a T7/T24 primer (Genset Corp., La Jolla, CA). This cDNA was subsequently in vitro transcribed into biotin-labeled cRNA (High Yield RNA Transcript Labeling kit; Enzo Diagnostics, Farmingdale, NY). The resulting cRNA was fragmented and assessed for quality by gel electrophoresis. Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols.

treatment_protocol: Not applicable.

tag: microarray hybridization date


title: whole cerebellum postnatal day 50, replicate b, chip Mu11K_sub_A

description: human fetal lung 134 dpc


title: No Addition, Experiment 2, Time point 3

tag: Cultures of P. aerophilum grown under aerobic conditions, then shifted to growth with no added terminal electron acceptor (See "Channel 1 Treatment Protocol"). Time point 3 (T3) samples were collected 7.5 hours after this shift.


title: whole cerebellum postnatal day 30, replicate b, chip Mu11K_sub_A

description: human fetal lung 108 dpc biological replicate 2


title: No Addition, Experiment 2, Time point 1

source_name: total RNA from P. aerophilum cultures


title: whole cerebellum postnatal day 1, replicate a, chip Mu11K_sub_A

description: human fetal lung 108 dpc biological replicate 1


title: whole cerebellum postnatal day 15, replicate b, chip Mu11K_sub_A

description: human fetal lung 63 dpc biological replicate 2


title: whole cerebellum postnatal day 60, replicate a, chip Mu11K_sub_B

description: human fetal lung 91 dpc


title: No Addition, Experiment 2, Time point 2


title: whole cerebellum postnatal day 7, replicate b, chip Mu11K_sub_B

description: human fetal lung 53 dpc


title: No Addition, Experiment 1, Time point 1


title: No Addition, Experiment 1, Time point 3


title: whole cerebellum postnatal day 60, replicate b, chip Mu11K_sub_B

description: human fetal lung 94 dpc


title: whole cerebellum postnatal day 5, replicate a, chip Mu11K_sub_B

description: human fetal lung 108 dpc biological replicate 3


title: whole cerebellum postnatal day 15, replicate a, chip Mu11K_sub_A

description: human fetal lung 63 dpc biological replicate 1


title: whole cerebellum postnatal day 7, replicate a, chip Mu11K_sub_B

description: human fetal lung 82 dpc


title: whole cerebellum postnatal day 10, replicate a, chip Mu11K_sub_A

description: human fetal lung 76 dpc biological replicate 1


title: whole cerebellum postnatal day 5, replicate b, chip Mu11K_sub_B

description: human fetal lung 117 dpc


title: No Addition, Experiment 1, Time point 2


title: whole cerebellum postnatal day 10, replicate b, chip Mu11K_sub_A

description: human fetal lung 110 dpc biological replicate 1


title: whole cerebellum postnatal day 50, replicate b, chip Mu11K_sub_B

description: human fetal lung 101 dpc


title: yw289-1_21_normal_FFPE

type: genomic

city: Santa Clara

first: Yuker

last: Wang

address: 3380 Central Expressway

institute: Affymetrix

hyb_protocol: George Karlin-Neumann, Marina Sedova, Ronald Sapolsky, Jonathan Forman, Yuker Wang, Martin Moorhead, and Malek Faham Molecular Inversion Probes and Universal Tag Arrays: Application to Highplex Targeted SNP Genotyping p. 199 – 211; Cold Spring Harbor Lab’s “Genetic Variation: A Laboratory Manual”, edited by M.P. Weiner, S.B. Gabriel & J.C. Stephens (2007).

data_processing:
George Karlin-Neumann, Marina Sedova, Ronald Sapolsky, Steven Lin,
Yuker Wang, Martin Moorhead, and Malek Faham
Molecular Inversion Probe Targeted Genotyping: Application to Copy Number Determination
p. 249 – 252; Cold Spring Harbor Lab’s “Genetic Variation: A Laboratory Manual”, edited by M.P. Weiner, S.B. Gabriel & J.C. Stephens (2007).

Briefly, we used two chips per sample. For SNP A/B, one (xxxA.CEL) chip give signal / copy number of A allele, the other chip (xxxC.CEL) give that of B allele.  Copy number assessment of a given SNP is the sum of allele A and B.  We use normals as the reference for the test samples.  The copy number is a relative value between the test and normal references.

For more details, see Wang Y, Moorhead M, Karlin-Neumann G, Wang NJ, Ireland J, Lin S, Chen C, Heiser LM, Chin K, Esserman L, Gray JW, Spellman PT, Faham M.:    Analysis of molecular inversion probe performance for allele copy number determination.  Genome Biol. 2007;8(11):R246
Wang YK, Moorhead M, Karlin-Neumann G, Falkowski M, Chen C, Siddiqui F, Davis RW, Willis TD, Faham M.: Allele quantification using Molecular Inversion Probes (MIP). Nucleic Acids Res. 21:2528, 2005.

label: naked genomic DNA

molecule: genomic DNA

organism: Homo sapiens

source_name: normal liver adjacent tissue

extract_protocol: genomic DNA extracted from a FFPE block. It's a customer sample

tag: normal liver adjacent tissue


title: yw289-1_25_normal_FFPE

description:
George Karlin-Neumann, Marina Sedova, Ronald Sapolsky, Steven Lin,
Yuker Wang, Martin Moorhead, and Malek Faham
Molecular Inversion Probe Targeted Genotyping: Application to Copy Number Determination
p. 249 – 252; Cold Spring Harbor Lab’s “Genetic Variation: A Laboratory Manual”, edited by M.P. Weiner, S.B. Gabriel & J.C. Stephens (2007).

scan_protocol: George Karlin-Neumann, Marina Sedova, Ronald Sapolsky, Jonathan Forman, Yuker Wang, Martin Moorhead, and Malek Faham Molecular Inversion Probes and Universal Tag Arrays: Application to Highplex Targeted SNP Genotyping p. 199 – 211; Cold Spring Harbor Lab’s “Genetic Variation: A Laboratory Manual”, edited by M.P. Weiner, S.B. Gabriel & J.C. Stephens (2007).

source_name: primary normal adjacent tissue in FFPE form


title: yw289-1_13_normal_FFPE

label_protocol:
George Karlin-Neumann, Marina Sedova, Ronald Sapolsky, Jonathan
Forman, Yuker Wang, Martin Moorhead, and Malek Faham
Molecular Inversion Probes and Universal Tag Arrays: Application to Highplex Targeted SNP Genotyping
p. 199 – 211; Cold Spring Harbor Lab’s “Genetic Variation: A Laboratory Manual”, edited by M.P. Weiner, S.B. Gabriel & J.C. Stephens (2007).


title: yw289-1_29_normal_FFPE

tag: primary normal adjacent tissue in FFPE form


title: yw289-1_17_normal_FFPE


title: yw289-1_09_normal_FFPE


title: whole cerebellum postnatal day 30, replicate a, chip Mu11K_sub_B

description: human fetal lung 96 dpc


title: whole cerebellum postnatal day 3, replicate b, chip Mu11K_sub_B

description: human fetal lung 110 dpc biological replicate 2


title: whole cerebellum postnatal day 1, replicate b, chip Mu11K_sub_B

description: human fetal lung 98 dpc


title: yw289-1_02_normal_FFPE


title: whole cerebellum postnatal day 21, replicate b, chip Mu11K_sub_B

description: human fetal lung 59 dpc


title: whole cerebellum postnatal day 15, replicate b, chip Mu11K_sub_B

description: human fetal lung 113 dpc


title: whole cerebellum postnatal day 1, replicate a, chip Mu11K_sub_B

description: human fetal lung 83 dpc


title: yw289-1_36_normal_FFPE


title: whole cerebellum postnatal day 21, replicate a, chip Mu11K_sub_B

description: human fetal lung 74 dpc


title: yw289-1_35_tumor_FFPE

data_processing:
George Karlin-Neumann, Marina Sedova, Ronald Sapolsky, Steven Lin,
Yuker Wang, Martin Moorhead, and Malek Faham
Molecular Inversion Probe Targeted Genotyping: Application to Copy Number Determination
p. 249 – 252; Cold Spring Harbor Lab’s “Genetic Variation: A Laboratory Manual”, edited by M.P. Weiner, S.B. Gabriel & J.C. Stephens (2007).

Briefly, we used two chips per sample. For SNP A/B, one (xxxA.CEL) chip give signal / copy number of A allele, the other chip (xxxC.CEL) give that of B allele.  Copy number assessment of a given SNP is the sum of allele A and B.  We use normals as the reference for the test samples.  The copy number is a relative value between the test and normal references.

For more details, see Wang Y, Moorhead M, Karlin-Neumann G, Wang NJ, Ireland J, Lin S, Chen C, Heiser LM, Chin K, Esserman L, Gray JW, Spellman PT, Faham M.:    Analysis of molecular inversion probe performance for allele copy number determination.  Genome Biol. 2007;8(11):R246
Wang YK, Moorhead M, Karlin-Neumann G, Falkowski M, Chen C, Siddiqui F, Davis RW, Willis TD, Faham M.: Allele quantification using Molecular Inversion Probes (MIP). Nucleic Acids Res. 21:2528, 2005.

Briefly, we used two chips per sample. For SNP A/B, one (xxxA.CEL) chip give signal / copy number of A allele, the other chip (xxxC.CEL) give that of B allele.  Copy number assessment of a given SNP is the sum of allele A and B.  We use normals as the reference for the test samples.  The copy number is a relative value between the test and normal references.

For more details, see Wang Y, Moorhead M, Karlin-Neumann G, Wang NJ, Ireland J, Lin S, Chen C, Heiser LM, Chin K, Esserman L, Gray JW, Spellman PT, Faham M.:    Analysis of molecular inversion probe performance for allele copy number determination.  Genome Biol. 2007;8(11):R246
Wang YK, Moorhead M, Karlin-Neumann G, Falkowski M, Chen C, Siddiqui F, Davis RW, Willis TD, Faham M.: Allele quantification using Molecular Inversion Probes (MIP). Nucleic Acids Res. 21:2528, 2005.

source_name: primary tumor in FFPE form

tag: liver tumor


title: yw289-1_28_tumor_FFPE


title: yw289-1_24_tumor_FFPE


title: yw289-1_32_tumor_FFPE


title: yw289-1_16_tumor_FFPE


title: whole cerebellum postnatal day 3, replicate a, chip Mu11K_sub_B

description: human fetal lung 85 dpc


title: whole cerebellum postnatal day 10, replicate b, chip Mu11K_sub_B

description: human fetal lung 89 dpc


title: whole cerebellum postnatal day 10, replicate a, chip Mu11K_sub_B

description: human fetal lung 78 dpc


title: GBS_CiaR_THB_rep2

status: Public on Jan 22 2009

city: Shreveport

first: Daniel

middle: Wilson

last: Shelver

state: LA

address: 1501 Kings Highway

department: Microbiology and Immunology

institute: LSU Health Sciences Center in Shreveport

description:
Biological replicate 2 of 2.
Scanned microarray images were analyzed using GeneChip Operating Software (GCOS) 1.4 (Affymetrix).

hyb_protocol: A hybridization cocktail containing 3.9 ug labelled cDNA was hybridized to the arrays. Hybridization was performed for 16 hours with a rotation of 60 rpm at a temperature of 45oC in a GeneChip Hybridization Oven 640 (Affymetrix). Arrays were washed and stained with a streptavidin-phycoerythrin conjugate using predefined protocols with a GeneChip Fluidics Station 450 (protocol ProkGE-WS2_450).

scan_protocol: Arrays were scanned with a GeneChip Scanner 300 7G (Affymetrix).

data_processing: Expression signals were calculated using the MAS5 statistical algorithm with the Affymetrix GCOS software version 1.4. Signal values were globally scaled to an intensity value of 500.

label: biotin

organism: Streptococcus agalactiae

source_name: Streptococcus agalactiae CiaR, grown in THB

label_protocol: cDNA was synthesized from 10 ug of total RNA using Superscript II reverse transcriptase (Invitrogen). Carryover RNA was degraded with 1 N NaOH followed by 1 N HCl. cDNA was purified and concentrated using a MinElute PCR Purification kit (Qiagen). Samples were fragmented with DNase I (Promega; Madison, WI) and biotin end-labelled with GeneChip DNA Labeling Reagent (Affymetrix).

growth_protocol: Group B Streptococcus (GBS) strains were cultured in Todd Hewitt broth (THB) to an O.D.600 = 0.3.

extract_protocol: 50 ml of cells (O.D.600 = 0.3) were harvested by centrifugation. GBS cells were then placed in a 950 ul suspension of QBio lysing matrix B, 50mM sodium acetate pH 4.0, 0.5% SDS, and 25% acidic phenol (Amresco; Solon, OH). Cells were mechanically disrupted with the lysing matrix using a FastPrep® 120 device (MP Biomedicals; Solon, OH) with a speed setting of 5 and pulse length of 22 s. The mixture was separated by centrifugation for 10 minutes. RNA was precipitated by adding sodium acetate (pH 5.2) to a final concentration of 0.3M and adding 2 volumes of 100% ethanol. One ml of Trizol reagent (Sigma-Aldrich) was added and incubated at room temperature for 5 min. 200 ul of chloroform was added, shaken vigorously, and allowed to remain at room temperature for 2 minutes. The mixture was centrifuged for ten minutes, the aqueous phase was recovered and RNA was precipitated with an equal volume of 100% isopropanol. The pellet was air-dried and resuspended in 50 ul DEPC-treated water. Residual DNA was removed using DNaseI (Promega) and subsequent clean-up with a RNEasy mini spin column (Qiagen).

tag: Strain CiaR, derivative of wild-type strain COH1 harboring ciaR::CAT mutation.


title: whole cerebellum postnatal day 15, replicate a, chip Mu11K_sub_B

description: human fetal lung 87 dpc


title: yw289-1_08_tumor_FFPE


title: GBS_CiaR_THB_rep1

description:
Biological replicate 1 of 2.
Scanned microarray images were analyzed using GeneChip Operating Software (GCOS) 1.4 (Affymetrix).


title: whole cerebellum postnatal day 30, replicate b, chip Mu11K_sub_B

description: human fetal lung 122 dpc


title: yw289-1_01_tumor_FFPE

label_protocol:
MIP technology
George Karlin-Neumann, Marina Sedova, Ronald Sapolsky, Jonathan
Forman, Yuker Wang, Martin Moorhead, and Malek Faham
Molecular Inversion Probes and Universal Tag Arrays: Application to Highplex Targeted SNP Genotyping
p. 199 – 211; Cold Spring Harbor Lab’s “Genetic Variation: A Laboratory Manual”, edited by M.P. Weiner, S.B. Gabriel & J.C. Stephens (2007).

extract_protocol: genomic DNA extracted from a FFPE block.  It's a customer sample.

tag: male liver tumor


title: GBS_COH1_THB_rep1

source_name: Streptococcus agalactiae COH1, grown in THB

tag: Strain COH1, wild-type clinical isolate.


title: GBS_COH1_THB_rep2


title: yw289-1_20_tumor_FFPE


title: hsp5_without_aphids_1

city: Huddinge

first: Gabriele

last: Delp

address: Alfred Nobels allé 7

department: Life Sciences

country: Sweden

institute: Södertörns University College

description: Analysis of changes in transcript accumulation in four different barley genotypes in response to aphid infestation. To avoid allelobiotic effects between different barley genotypes, the experiment was performed with only one line at a time and to avoid induction of defence responses in control plants by volatiles emitted from aphid-infested plants, control and infested plants were kept in separate growth chambers. The experiment was performed twice, separately with each plant genotype, and chambers were swapped between experiments. Three plants from each experiment were combined in each replicate.

hyb_protocol: We used the Affymetrix Hybridization Oven 640 and GeneChip® Fluidics Station 450 according to the manufacturer's recommended protocols.

scan_protocol: We used the Affymetrix GeneChip® Scanner 3000 according to the manufacturer's recommended protocols.

data_processing: The data was analyzed using Gene Chip Operating Software (Affymetrix). GCOS was also applied for target intensity scaling of each array to an identical value (100) and quantification of the signal log ratio.

organism: Hordeum vulgare subsp. spontaneum

source_name: Barley variety Hsp5 leaves without aphids

label_protocol: We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.

growth_protocol: Barley seeds were germinated in Petri dishes on filter paper moistened with 0.75 % hydrogen peroxide in water. After 3 days at 4° C in darkness, seeds were kept at room temperature for 2 days. Seedlings were then planted individually in pots with commercial potting mix. Seedlings were grown in a growth chamber at a 16/8 hr photoperiod, 160 µmol/m2s and a temperature of 20° C.

extract_protocol: RNA was extracted from 0.6 to 0.8 g (fresh weight) leaf tissue per sample using the Concert™ Plant RNA Reagent (Invitrogen) according to the large-scale protocol. This extraction was immediately followed by an additional purification step using the Qiagen RNeasy kit (Qiagen) following the RNA clean up protocol, including an on-column DNase treatment, according to the manufacturer’s instructions.

treatment_protocol: Seven days after seedlings were planted into soil, empty cages were put on their first leaf (no-aphid control). Plants were kept at a 16/8 hr photoperiod, 160 µmol/m2s and a temperature of 20° C. After 48 hr cages were removed from the plants and the piece of leaf in the cage was cut out and snap-frozen in liquid nitrogen. Each biological replicate consisted of 6 leaf pieces (the part of the leaf that was enclosed in the tube).

tag: Strain

tag: Partially resistant to R. padi

tag: First leaf

tag: Control

tag: Biological replicate 1


title: yw289-1_12_tumor_FFPE


title: kara_without_aphids_3

organism: Hordeum vulgare

source_name: Barley variety Kara leaves without aphids

value: Kara

tag: Susceptible to R. padi

tag: Biological replicate 3


title: hsp5_with_aphids_3

source_name: Barley variety Hsp5 leaves with aphids

treatment_protocol: Seven days after seedlings were planted into soil, 20 aphids (mixed instars) per plant were put in a cage on the first leaf. Plants were kept at a 16/8 hr photoperiod, 160 µmol/m2s and a temperature of 20° C. After 48 hr aphids were removed from the plants and the piece of leaf in the cage was cut out and snap-frozen in liquid nitrogen.  Each biological replicate consisted of 6 leaf pieces (the part of the leaf that was enclosed in the tube).


title: kara_with_aphids_1

source_name: Barley variety Kara leaves with aphids


title: kara_without_aphids_1


title: hsp5_without_aphids_2

tag: Biological replicate 2


title: hsp5_with_aphids_2


title: kara_with_aphids_3


title: kara_with_aphids_2


title: kara_without_aphids_2


title: CHD7_ENCODE_ChIPchip_SHSY5Y_2

city: Cleveland

first: Mike

middle: Paul

last: Schnetz

state: OH

address: 10900 Eulid Ave

department: Genetics

institute: Case Western Reserve University

hyb_protocol: Samples were hybridized according to Nimblegen established protocol

scan_protocol: Samples were scanned according to Nimblegen established protocol

data_processing: Ratios computed and biweight mean normalized using NimbleScan software package

source_name: CHD7 ChIP in SH-SY5Y

label_protocol: Sample was labeled using Enzo Life Sciences labeling kit according to manufacturer's instructions

extract_protocol: Refer to Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis Scacheri PC et al, PLoS Genet. 2006 Apr;2(4):e51. Epub 2006 Apr 7.

treatment_protocol: Immunoprecipitated chromatin

tag: ChIP from SH-SY5Y extract

source_name: Genomic DNA in SH-SY5Y

treatment_protocol: No immunoprecipitation

tag: Isolated SH-SY5Y genomic DNA


title: H3K4me3_ENCODE_ChIPchip_SHSY5Y_1

source_name: H3K4 trimethyl ChIP in SH-SY5Y

treatment_protocol: No Immunoprecipitation


title: H3K4me2_ENCODE_ChIPchip_SHSY5Y_1

source_name: H3K4 dimethyl ChIP in SH-SY5Y


title: 28-4_without_aphids_3

source_name: Barley variety 28:4 leaves without aphids

value: breeding line 28:4


title: hsp5_with_aphids_1


title: 28-4_without_aphids_2


title: 28-4_without_aphids_1


title: H3K4me1_ENCODE_ChIPchip_SHSY5Y_1

source_name: H3K4 monomethyl ChIP in SH-SY5Y


title: hsp5_without_aphids_3


title: 28-4_with_aphids_2

source_name: Barley variety 28:4 leaves with aphids


title: PBMC_Common_ref_vs_N'Dama190_T._congolense_infected_34_dpi

city: Dublin

first: David

last: MacHugh

address: University College Dublin, Belfield

department: College of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

description: No additional information.

hyb_protocol: Labelled samples were purified using the purification module included with the SuperScript™ Plus Direct cDNA labelling System, combined and supplemented with approximately 60-70 µl SlideHyb Glass Hybridization Buffer #3 (Ambion Inc., www.ambion.com) to a final probe volume of 100 µl. Probes were hybridized to bovine long oligonucleotide (BLO) microarrays, using an automated HS400 hybridization station (Tecan UK Ltd., www.tecan.com) with the following optimized protocol; WASH: 75°C, Runs 1, Wash 10 s, Soak 20 s; PROBE INJECTION: 85°C; Denaturation: 95°C, 2 mins; HYBRIDISATION: 42°C – 4 hrs; 35°C – 4 hrs; 30°C – 4 hrs; agitation frequency medium, WASH: 37°C, Runs 2, Wash 10 s, Soak 20 s; 25°C, Runs 2, Wash 15 s, Soak 30 s; 25°C, Runs 2, Wash 20 s, Soak 40 s and SLIDE DRYING: 25°C for 2 mins.

scan_protocol: Microarrays were scanned using a GenePix® 4000B scanner (Molecular Devices Corp., www.moleculardevices.com). Scans were performed at medium and high photomultipler tube (PMT) gain settings.

data_processing: Where appropriate, data from medium and high PMT gain scans were combined and corrected for saturation using the method described by Lyng et al., BMC Genomics. 2004 Feb 3;5(1):10. Spots classed by Genepix software as 'bad', 'absent' or 'not found' were flagged and downweighted in subsequent analysis. The Robust Multichip Average (RMA) expression measure (Irizarry et al., Biostatistics 2003, 4(2):249-264) was calculated. An intensity-based normalization method was employed: within microarray print-tip dependent locally weighted scatterplot smoothing (LOWESS) normalization, followed by quantile normalization between microarrays. Normalised data submitted here was combined across duplicate spots using the limma package of Bioconductor.

organism:
Bos taurus
Bos indicus

source_name: African Bos taurus and Bos indicus pooled PBMC from a Trypanosoma congolense infection time course.

label_protocol: Labelled cDNA was generated using the SuperScript™ Plus Direct cDNA labelling System (Invitrogen Corp., www.invitrogen.com) according to the manufacturers’ instructions. 10 µg of common reference RNA (CRR) was labelled with Alexa Fluor® 647.

extract_protocol: PBMC were isolated using Percoll™ gradients (GE Healthcare, www.gehealthcare.com) and as described in Ulmer et al., Immunobiology 1984, 166(3):238-250. The isolated PBMC were washed with sterile PBS and stored immediately at -80°C in Tri-reagent (Molecular Research Center, Inc, www.mrcgene.com) for further processing. Total RNA was extracted with chloroform and precipitated with isopropanol. Each sample was further DNase-treated with RQ1 RNase-free DNase (Promega Corp., www.promega.com) and purified using the RNeasy® mini kit (Qiagen, www.qiagen.com). A common reference RNA pool was generated by combining equal quantities of all samples in the study.

treatment_protocol: Peripheral blood (200 ml) was collected in heparanized syringes

tag: Source

value: Pooled peripheral blood mononuclear cells from eight Boran (B. indicus, trypanosusceptible) and eight N’Dama (B. taurus, trypanotolerant) female cattle aged between 19-28 months, raised together at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The cattle were each experimentally infected with the T. congolense clone IL1180, which was delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected before infection and at 14, 21, 25, 29 and 34 days post infection.

organism: Bos taurus

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama190, 34dpi

label_protocol: Labelled cDNA was generated using the SuperScript™ Plus Direct cDNA labelling System (Invitrogen Corp., www.invitrogen.com) according to the manufacturers’ instructions. 8 µg of sample RNA was labelled with Alexa Fluor® 555.

extract_protocol: PBMC were isolated using Percoll™ gradients (GE Healthcare, www.gehealthcare.com) and as described in Ulmer et al. Immunobiology 1984, 166(3):238-250. The isolated PBMC were washed with sterile PBS and stored immediately at -80°C in Tri-reagent (Molecular Research Center, Inc, www.mrcgene.com) for further processing. Total RNA was extracted with chloroform and precipitated with isopropanol. Each sample was further DNase-treated with RQ1 RNase-free DNase (Promega Corp., www.promega.com) and purified using the RNeasy® mini kit (Qiagen, www.qiagen.com).

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama190) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 34 days post-infection


title: lina_without_aphids_3

source_name: Barley variety Lina leaves without aphids

extract_protocol: RNA was extracted from 0.6 to 0.8 g (fresh weight) leaf tissue per sample using the Concert™ Plant RNA Reagent (Invitrogen) according to the large-scale protocol. This extraction was immediately followed by an additional purification step using the Qiagen RNeasy kit (Qiagen) following the  RNA clean up protocol, including an on-column DNase treatment, according to the manufacturer’s instructions.

value: Lina


title: PBMC_Common_ref_vs_N'Dama190_T._congolense_infected_29_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama190, 29dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama190) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 29 days post-infection


title: lina_without_aphids_2


title: lina_without_aphids_1


title: PBMC_Common_ref_vs_N'Dama190_T._congolense_infected_21_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama190, 21dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama190) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 21 days post-infection


title: PBMC_Common_ref_vs_N'Dama190_T._congolense_infected_14_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama190, 14dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama190) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 14 days post-infection


title: lina_with_aphids_3

source_name: Barley variety Lina leaves with aphids


title: PBMC_Common_ref_vs_N'Dama189_T._congolense_infected_25_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama189, 25dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama189) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 25 days post-infection


title: 28-4_with_aphids_1


title: PBMC_Common_ref_vs_N'Dama189_T._congolense_infected_34_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama189, 34dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama189) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 34 days post-infection


title: lina_with_aphids_2

extract_protocol: RNA was extracted using the Concert™ Plant RNA Reagent (Invitrogen) according to the large-scale protocol, immediately followed by a purification step using the Qiagen RNeasy kit (Qiagen), including an on-column DNase treatment.


title: 28-4_with_aphids_3


title: CHD7_ENCODE_ChIPchip_SHSY5Y_1


title: lina_with_aphids_1


title: PBMC_Common_ref_vs_N'Dama190_T._congolense_infected_25_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama190, 25dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama190) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 25 days post-infection


title: PBMC_Common_ref_vs_N'Dama189_T._congolense_infected_21_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama189, 21dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama189) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 21 days post-infection


title: PBMC_Common_ref_vs_N'Dama184_T._congolense_infected_34_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama184, 34dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama184) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 34 days post-infection


title: PBMC_Common_ref_vs_N'Dama184_T._congolense_infected_14_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama184, 14dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama184) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 14 days post-infection


title: PBMC_Common_ref_vs_N'Dama184_T._congolense_infected_25_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama184, 25dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama184) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 25 days post-infection


title: PBMC_Common_ref_vs_N'Dama184_T._congolense_infected_21_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama184, 21dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama184) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 21 days post-infection


title: PBMC_Common_ref_vs_N'Dama189_T._congolense_infected_14_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama189, 14dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama189) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 14 days post-infection


title: PBMC_Common_ref_vs_N'Dama184_T._congolense_infected_29_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama184, 29dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama184) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 29 days post-infection


title: PBMC_Common_ref_vs_N'Dama179_T._congolense_infected_29_dpi

description: No additional information.

source_name: African Bos taurus and Bos indicus pooled PBMC from a Trypanosoma congolense infection time course.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama179, 29dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama179) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 29 days post-infection


title: CHD7_ENCODE_ChIPchip_DLD1_1

source_name: CHD7 ChIP in DLD1

tag: ChIP from DLD1 extract

source_name: Genomic DNA in DLD1

tag: Isolated DLD1 genomic DNA


title: PBMC_Common_ref_vs_N'Dama178_T._congolense_infected_34_dpi

description: No additional information.

value: Pooled peripheral blood mononuclear cells from eight Boran (B. indicus, trypanosusceptible) and eight N’Dama (B. taurus, trypanotolerant) female cattle aged between 19-28 months, raised together at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The cattle were each experimentally infected with the T. congolense clone IL1180, which was delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected before infection and at 14, 21, 25, 29 and 34 days post infection.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama178, 34dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama178) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 34 days post-infection


title: PBMC_Common_ref_vs_N'Dama179_T._congolense_infected_14_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama179, 14dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama179) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 14 days post-infection


title: PBMC_Common_ref_vs_N'Dama179_T._congolense_infected_21_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama179, 21dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama179) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 21 days post-infection


title: PBMC_Common_ref_vs_N'Dama179_T._congolense_infected_25_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama179, 25dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama179) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 25 days post-infection


title: PBMC_Common_ref_vs_N'Dama178_T._congolense_infected_25_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama178, 25dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama178) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 25 days post-infection


title: PBMC_Common_ref_vs_N'Dama178_pre-T._congolense_infection

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama178, pre-infection

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama178) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected prior to infection


title: PBMC_Common_ref_vs_N'Dama178_T._congolense_infected_14_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama178, 14dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama178) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 14 days post-infection


title: PBMC_Common_ref_vs_N'Dama176_pre-T._congolense_infection

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama176, pre-infection

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama176) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected prior to infection


title: PBMC_Common_ref_vs_N'Dama178_T._congolense_infected_21_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama178, 21dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama178) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 21 days post-infection


title: PBMC_Common_ref_vs_N'Dama176_T._congolense_infected_34_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama176, 34dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama176) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 34 days post-infection


title: PBMC_Common_ref_vs_N'Dama179_T._congolense_infected_34_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama179, 34dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama179) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 34 days post-infection


title: PBMC_Common_ref_vs_N'Dama175_T._congolense_infected_25_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama175, 25dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama175) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 25 days post-infection


title: PBMC_Common_ref_vs_N'Dama175_pre-T._congolense_infection

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama175, pre-infection

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama175) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected prior to infection


title: PBMC_Common_ref_vs_N'Dama176_T._congolense_infected_29_dpi

description: No additional information.

source_name: African Bos taurus and Bos indicus pooled PBMC from a Trypanosoma congolense infection time course.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama176, 29dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama176) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 29 days post-infection


title: PBMC_Common_ref_vs_N'Dama175_T._congolense_infected_29_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama175, 29dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama175) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 29 days post-infection


title: PBMC_Common_ref_vs_N'Dama175_T._congolense_infected_14_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama175, 14dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama175) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 14 days post-infection


title: PBMC_Common_ref_vs_N'Dama176_T._congolense_infected_14_dpi

description: No additional information.

value: Pooled peripheral blood mononuclear cells from eight Boran (B. indicus, trypanosusceptible) and eight N’Dama (B. taurus, trypanotolerant) female cattle aged between 19-28 months, raised together at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The cattle were each experimentally infected with the T. congolense clone IL1180, which was delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected before infection and at 14, 21, 25, 29 and 34 days post infection.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama176, 14dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama176) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 14 days post-infection


title: PBMC_Common_ref_vs_N'Dama175_T._congolense_infected_21_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama175, 21dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama175) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 21 days post-infection


title: PBMC_Common_ref_vs_N'Dama172_pre-T._congolense_infection

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama172, pre-infection

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama172) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected prior to infection


title: PBMC_Common_ref_vs_N'Dama176_T._congolense_infected_21_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama176, 21dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama176) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 21 days post-infection


title: PBMC_Common_ref_vs_N'Dama175_T._congolense_infected_34_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama175, 34dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama175) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 34 days post-infection


title: PBMC_Common_ref_vs_N'Dama172_T._congolense_infected_25_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama172, 25dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama172) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 25 days post-infection


title: PBMC_Common_ref_vs_N'Dama172_T._congolense_infected_29_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama172, 29dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama172) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 29 days post-infection


title: PBMC_Common_ref_vs_N'Dama172_T._congolense_infected_21_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama172, 21dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama172) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 21 days post-infection


title: PBMC_Common_ref_vs_N'Dama172_T._congolense_infected_14_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama172, 14dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama172) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 14 days post-infection


title: PBMC_Common_ref_vs_N'Dama172_T._congolense_infected_34_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama172, 34dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama172) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 34 days post-infection


title: PBMC_Common_ref_vs_Boran99_T._congolense_infected_34_dpi

description: No additional information.

organism: Bos indicus

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran99, 34dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran99) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 34 days post-infection


title: PBMC_Common_ref_vs_Boran98_T._congolense_infected_25_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran98, 25dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran98) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 25 days post-infection


title: PBMC_Common_ref_vs_N'Dama189_T._congolense_infected_29_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama189, 29dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama189) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 29 days post-infection


title: PBMC_Common_ref_vs_Boran98_T._congolense_infected_21_dpi

description: No additional information.

source_name: African Bos taurus and Bos indicus pooled PBMC from a Trypanosoma congolense infection time course.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran98, 21dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran98) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 21 days post-infection


title: PBMC_Common_ref_vs_Boran98_T._congolense_infected_29_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran98, 29dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran98) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 29 days post-infection


title: PBMC_Common_ref_vs_Boran98_T._congolense_infected_34_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran98, 34dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran98) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 34 days post-infection


title: Patient F CMV 48h

city: Nantes

first: Franck

last: Halary

address: 30, bd Jean Monnet

department: ITERT - CHU Hotel Dieu

country: France

institute: INSERM UMR643

hyb_protocol: The Whole Human genome (4x44K) Oligo Microarray were hybridized according to the instructions of Agilent protocol (One color-Agilent Microarray 5,5-February 2007) for 17 h at 65 °C . Stabilization and drying solution was used to protect against Ozone.

scan_protocol: Agilent Technologies Scanner G2505B US22502687-GE1-v5_95_Feb07 + Feature Extraction 9.5

data_processing: The raw data were normalized and scaled with lowess algorithm.

source_name: immature monocyte-derived dendritic cells

label_protocol: 500 ng of total RNA was reverse-transcribed according to the instructions of Agilent protocol (One color-Agilent Microarray 5,5-February 2007). Agilent's Low RNA Input Linear Amplification Kit PLUS generates fluorescent cRNA (complimentary RNA) and  uses T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3-labeled CTP.

growth_protocol: human blood monocytes were isolated by elutriation from CMV, HBV, HCV and HIV seronegative healthy individuals. DC differentiation was allowed by culturing monocytes for 6 days in a IL-4/GM-CSF supplemented medium (see Sallusto et al, J Exp Med, 1994).

extract_protocol: Total RNA were extracted from each sample on Nucleospin II column according to the manufacturer's instructions (Macherey-Nagel, France).

treatment_protocol: At day 6, cells were harvested and either infected at a moi of 10 with an endotheliotropic CMV strain for additional 6 or 48 hours or subcultured in mediul alone for 48 hours. The percentage of infected cells was evaluated for each sample by immunocytochemistry. The infectious percentages ranged from 75 to 98% (median=87%).

tag: Age

tag: Sex

value: F

tag: CMV seronegative donor

tag: HIV neg

tag: HBs 28

tag: HCV neg


title: PBMC_Common_ref_vs_Boran99_pre-T._congolense_infection

description: No additional information.

value: Pooled peripheral blood mononuclear cells from eight Boran (B. indicus, trypanosusceptible) and eight N’Dama (B. taurus, trypanotolerant) female cattle aged between 19-28 months, raised together at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The cattle were each experimentally infected with the T. congolense clone IL1180, which was delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected before infection and at 14, 21, 25, 29 and 34 days post infection.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran99, pre-infection

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran99) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected prior to infection


title: PBMC_Common_ref_vs_Boran99_T._congolense_infected_29_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran99, 29dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran99) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 29 days post-infection


title: CTB-5

city: Vienna

first: Martin

last: Bilban

country: Austria

institute: Medical University of Vienna

description: Affymetrix

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: Affymetrix MAS5.0

source_name: First trimester cytotrophoblast cells grown in culture for 24 hours

label_protocol: Affymetrix

extract_protocol: trizol and RNeasy Mini kit

tag: First trimester placental villous material was digested with a 0.125% (v/v) trypsin solution (GIBCO, Life Technologies, Paisley, UK). The released cells were loaded on top of a Percoll (Pharmacia, Uppsala, Sweden) gradient ranging from 70 to 10% (v/v). After centrifugation, the band containing the trophoblasts was collected and sequentially purified using immunomagnetic beads (Dynabeads M-450, Dynal) conjugated to CD45 RB leukocyte common antigen (Dako, CA) and to fibroblast specific antibody A 502 (Dianova, Hamburg).

tag: Trophoblasts were cultured for 24 h in DMEM (GIBCO)

tag: with 10% FCS, 100 mg/ml streptomycin and 100 IU/ml penicillin

tag: (GIBCO).


title: Patient A CMV 48h (replicate)

tag: HBV neg


title: PBMC_Common_ref_vs_Boran98_pre-T._congolense_infection

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran98, pre-infection

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran98) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected prior to infection


title: PBMC_Common_ref_vs_Boran99_T._congolense_infected_21_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran99, 21dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran99) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 21 days post-infection


title: PBMC_Common_ref_vs_Boran99_T._congolense_infected_25_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran99, 25dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran99) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 25 days post-infection


title: PBMC_Common_ref_vs_Boran99_T._congolense_infected_14_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran99, 14dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran99) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 14 days post-infection


title: CTB-4

description: Affymetrix


title: PBMC_Common_ref_vs_N'Dama176_T._congolense_infected_25_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama176, 25dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama176) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 25 days post-infection


title: EVT-5

description: Affymetrix

source_name: First trimester placental organ explants grown on matrigel

tag: Dissected mesenchymal villous tissue of early pregnancy was arranged radially on 80 μl drops of growth-factor-reduced Matrigel™ (BD, Bedford, MA) in 24 well plates (SFM; DMEM:Ham's F12 (Gibco) 1:1, supplemented with 100 µg/ml streptomycin/penicillin (Gibco) and incubated for 4 hours at 37°C, 5% CO2 to allow attachment. Wells were then carefully flooded with 500 µl SFM, incubated at 37°C, 5% CO2 and subsequent growth characteristics were monitored by light microscopy. Total RNA or tissue sections were prepared after 72 hours of incubation.


title: Patient E CMV 48h

value: M


title: PBMC_Common_ref_vs_Boran98_T._congolense_infected_14_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran98, 14dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran98) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 14 days post-infection


title: Patient C CMV 6h (replicate)


title: EVT-4

description: Affymetrix


title: Patient B CMV 48h


title: Patient D CMV 48h

tag: HBs 88


title: EVT-6

description: Affymetrix

tag: Dissected mesenchymal villous tissue of early pregnancy was arranged radially on 80 μl drops of growth-factor-reduced Matrigel™ (BD, Bedford, MA) in 24 well plates (SFM; DMEM:Ham's F12 (Gibco) 1:1, supplemented with 100 µg/ml streptomycin/penicillin (Gibco) and incubated for 4 hours at 37°C, 5% CO2 to allow attachment. Wells were then carefully flooded with 500 µl SFM, incubated at 37°C, 5% CO2 and subsequent growth characteristics were monitored by light microscopy. Total RNA or tissue sections were prepared after 72 hours of incubation


title: PBMC_Common_ref_vs_Boran90_T._congolense_infected_34_dpi

description: No additional information.

tag: Source

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran90, 34dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran90) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 34 days post-infection


title: Patient E CMV 6h


title: PBMC_Common_ref_vs_Boran90_T._congolense_infected_14_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran90, 14dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran90) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 14 days post-infection


title: Patient D CMV 6h


title: PBMC_Common_ref_vs_Boran90_T._congolense_infected_21_dpi

description: No additional information.

source_name: African Bos taurus and Bos indicus pooled PBMC from a Trypanosoma congolense infection time course.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran90, 21dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran90) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 21 days post-infection


title: PBMC_Common_ref_vs_Boran89_pre-T._congolense_infection

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran89, pre-infection

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran89) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected prior to infection


title: PBMC_Common_ref_vs_Boran90_T._congolense_infected_29_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran90, 29dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran90) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 29 days post-infection


title: PBMC_Common_ref_vs_Boran90_T._congolense_infected_25_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran90, 25dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran90) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 25 days post-infection


title: Patient F CMV 6h

source_name: immature monocyte-derived dendritic cells

value: F


title: Patient A CMV 48h


title: PBMC_Common_ref_vs_N'Dama179_pre-T._congolense_infection

description: No additional information.

value: Pooled peripheral blood mononuclear cells from eight Boran (B. indicus, trypanosusceptible) and eight N’Dama (B. taurus, trypanotolerant) female cattle aged between 19-28 months, raised together at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The cattle were each experimentally infected with the T. congolense clone IL1180, which was delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected before infection and at 14, 21, 25, 29 and 34 days post infection.

source_name: PBMC from Trypanosoma congolense infection time course : African bos taurus animal N'Dama179, pre-infection

value: Peripheral blood mononuclear cells (PBMC) from a female trypanotolerant African Bos taurus N’Dama  cow (individual ID N'Dama179) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected prior to infection


title: Patient B CMV 6h


title: Patient C CMV 6h


title: Patient F non infected


title: PBMC_Common_ref_vs_Boran88_T._congolense_infected_34_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran88, 34dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran88) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 34 days post-infection


title: PBMC_Common_ref_vs_Boran89_T._congolense_infected_34_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran89, 34dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran89) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 34 days post-infection


title: PBMC_Common_ref_vs_Boran89_T._congolense_infected_14_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran89, 14dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran89) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 14 days post-infection


title: Patient B non infected


title: Patient E non infected


title: Patient E CMV 6h (replicate)


title: Patient C non infected


title: Patient D non infected


title: Patient A CMV 6h


title: PBMC_Common_ref_vs_Boran88_T._congolense_infected_29_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran88, 29dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran88) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 29 days post-infection


title: PBMC_Common_ref_vs_Boran89_T._congolense_infected_29_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran89, 29dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran89) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 29 days post-infection


title: PBMC_Common_ref_vs_Boran89_T._congolense_infected_21_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran89, 21dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran89) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 21 days post-infection


title: PBMC_Common_ref_vs_Boran89_T._congolense_infected_25_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran89, 25dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran89) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 25 days post-infection


title: PBMC_Common_ref_vs_Boran88_T._congolense_infected_25_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran88, 25dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran88) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 25 days post-infection


title: Patient A non infected


title: PBMC_Common_ref_vs_Boran88_T._congolense_infected_21_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran88, 21dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran88) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 21 days post-infection


title: PBMC_Common_ref_vs_Boran86_T._congolense_infected_29_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran86, 29dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran86) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 29 days post-infection


title: PBMC_Common_ref_vs_Boran88_T._congolense_infected_14_dpi

description: No additional information.

source_name: African Bos taurus and Bos indicus pooled PBMC from a Trypanosoma congolense infection time course.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran88, 14dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran88) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 14 days post-infection


title: PBMC_Common_ref_vs_Boran86_T._congolense_infected_34_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran86, 34dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran86) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 34 days post-infection


title: PBMC_Common_ref_vs_Boran86_T._congolense_infected_21_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran86, 21dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran86) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 21 days post-infection


title: PBMC_Common_ref_vs_Boran86_T._congolense_infected_25_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran86, 25dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran86) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 25 days post-infection