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Sample GSM1575435 Query DataSets for GSM1575435
Status Public on Jan 02, 2015
Title MDDC_Leishmania-major-strain-FV1-infected_4HR-post-infection_donor-706
Sample type RNA
 
Source name human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-infected_4HR-post-infection
Organism Homo sapiens
Characteristics host cell type: Monocyte derived dendritic cell
donor id number: 706
infecting parasite species: Leishmania major
parasite strain: FV1
time post-infection: 4 hours
Treatment protocol After 4, 8, or 24 hours post-infection, MDDCs were harvested washing in medium and application of 0.5 mM EDTA (Gibco) in 1X PBS (Cellgro). Cell harvests were spun down, washed, and pellets resuspended in RNAlater RNA Stabilization Solution (Applied Biosystems).
Growth protocol CD14+ monocytes of four anonymous healthy adult female human donors (Central Indiana Regional Blood Center, Indianapolis, IN) were isolated from peripheral blood mononuclear cells by positive selection using an AutoMACS separator (Miltenyi Biotec) after isolation using lymphocyte separating media (Cellgro) following manufacturer protocols. The purity of separated monocytes was determined by flow cytometry analysis on a MCL500 flow cytometer (Beckman Coulter) using fluorescent antibody staining for CD14, CD19, CD45, and CD3 (Biolegend). Enriched monocytes were differentiated into dendritic cells (MDDC) by treatment with granulocyte-macrophage colony-stimulating factor (GM-CSF; 2,000 U/mL) and interleukin-4 (IL-4; 800 U/mL) recombinant cytokines (Peprotech) on days 0, 3, and 6 after plating in six-well plates at 2.5 × 10^6 cells/mL in complete RPMI medium (10% fetal bovine serum, 100 U/mL penicillin, 100 μg/mL streptomycin, 2 mM L-glutamine). Immature MDDC were harvested on day 7 and plated in 6-well plates at 2 × 10^6 cells in 2 mL complete RPMI medium per well in the absence of exogenous cytokine. The phenotype puritiess of DCs was determined by flow cytometry analysis of CD1a, CD14, HLA-DR, CD40, CD80, and CD86 expression. All infections were performed with Leishmania major Friedlin V1 strain (NIH) and Leishmania donovani 1S strain (ATCC #30142) parasites. All parasites were cultured at 26°C without CO2 in complete medium 199 (20% heat-inactivated fetal bovine serum, 100 U/mL penicillin, 100 μg/mL streptomycin, 2 mM L-glutamine, 40 mM HEPES, 0.1 mM adenine in 50 mM HEPES, 5 mg/mL hemin in 50% triethanolamine, and 1 mg/mL biotin). Parasites tested negative for mycoplasma using a Mycoplasma PCR detection set (Takara) and tested below the detection limits for endotoxin using a Limulus Amoebocyte Lysate kit (Charles River Laboratories). Infective-stage metacyclic promastigotes were isolated by use of a Ficoll gradient as previously described (PMID: 11748963) and opsonized with 5% normal human serum prior to infection at a concentration of ten parasites to one host cell. Infection rates were determined at the end of each experiment by DiffQuick staining of cytospin whole cell preparations and visualization by light microscopy.
Extracted molecule total RNA
Extraction protocol Total RNA from uninfected or Leishmania-infected human MDDCs was isolated using an RNEasy kit (Qiagen). Bioanalyzer 2100 (Agilent Technologies) and RNA 6000 Nano kits (Agilent Technologies) were used to determine total RNA integrity.
Label Cy3
Label protocol 25ng of high quality RNA was converted to double stranded cDNA using Sigma TransPlex Complete Whole Transcriptome Amplification Kit (Sigma). RNA degradation, double stranded cDNA purification, and cDNA precipitation was conducted following NimbleGen Gene Expression Array user’s guide protocols (Roche NimbleGen). A Nanodrop ND-2000 (ThermoScientific) was used to determine total RNA and double stranded cDNA concentrations. Sample cDNAs were Cy3-labeled using NimbleGen Single Color Labeling Kit (Roche NimbleGen) per manufacturer's recommendations.
 
Hybridization protocol Labeled cDNAs were hybridized to 12-plex NimbleGen Homo sapiens Expression Arrays (platform accession number GPL16025), featuring 45,033 probes representing 23,752 gene transcripts, using Hybridization Kit, LS (Roche NimbleGen) and Wash Buffer Kit (Roche NimbleGen) per manufacturer's recommendations.
Scan protocol Image acquisition of arrays was performed using a NimbleGen MS 200 Microarray Scanner, at a 2 micron resolution.
Description 706-FV1-04h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-infected_4HR-post-infection_donor-706
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania major (FV1 strain) parasites for 4 hours and is the first of five biological replicates
Data processing NimbleGen array image data were processed using NimbleScan (version 2.5) to extract intensity values for each gene. NimbleScan software automates the pre-processing of NimbleGen microarray image data, including identifying the location of each probe, extraction of intensity data from the image, background correction, and obtaining expression summary values for each gene using a probe-level summarization method RMA (Robust Multi-Array Average).
Averages of RMA normalized gene probeset (consisting of three probes per gene) with intensity values two times greater than that of each array background values were retained for downstream analysis. Any values that did not pass this filter are listed as NULL.
 
Submission date Dec 31, 2014
Last update date Jan 02, 2015
Contact name Mary Ann McDowell
E-mail(s) mcdowell.11@nd.edu
Organization name University of Notre Dame
Department Biological Sciences
Street address 210 Galvin Life Science Center
City Notre Dame
State/province Indiana
ZIP/Postal code 46556
Country USA
 
Platform ID GPL16025
Series (1)
GSE64610 Differential gene transcript expression profiles among human monocyte-derived dendritic cells infected with Leishmania major Friedlin V1 strain and Leishmania donovani 1S strain parasites at early infection time points

Data table header descriptions
ID_REF
VALUE RMA signal

Data table
ID_REF VALUE
AB000409 9850.810
AB000463 2546.889
AB000781 NULL
AB001328 NULL
AB002294 2098.852
AB002308 7891.765
AB002311 5026.248
AB002313 11463.994
AB002360 NULL
AB002377 2224.638
AB002381 1650.710
AB002382 2419.603
AB002384 NULL
AB003177 1961.518
AB003333 14650.736
AB006589 NULL
AB006590 NULL
AB006621 NULL
AB006625 NULL
AB007457 5621.015

Total number of rows: 45033

Table truncated, full table size 731 Kbytes.




Supplementary file Size Download File type/resource
GSM1575435_563417_2013-10-04_Cycle11_532_706-FV1-04h.pair.gz 2.9 Mb (ftp)(http) PAIR
Processed data included within Sample table

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