Result

Search results for the GEO ID: GSE24121

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM593404

GPL1261

DCs-C1

Dendritic cells

strain: C57BL/6 gender: Female tissue: Bone marrow cell type: Dendritic cells infection: control

Sample_geo_accession	GSM593404
Sample_status	Public on Oct 20 2010
Sample_submission_date	Sep 13 2010
Sample_last_update_date	Sep 16 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA extracted and purified with RNeasy mini kit (Qiagen).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotin-labeled cRNAs were generated using the GeneChip IVT Labeling Kit (in vitro transcription using T7 RNA polymerase at 37°C for 16 hours) in a thermal cycler. The biotinylated cRNA was subsequently treated with RNeasy clean-up kit (Qiagen) to remove any unincorporated biotinylated ribonucleotides from the cRNA samples and quantitated spectrophotometrically.
Sample_hyb_protocol	The fragmented target cRNA (20 ug) was mixed with 200 ul of hybridization cocktail (100 mM 2-morpholino-ethanesulfonic acid (MES), 1 M NaCl, 20 mM ethylenediaminetetraacetic acid, 0.01% Tween 20, 0.1 mg/ml herring sperm DNA, 500 g/ml acetylated bovine serum albumin) and hybridized to the Affymetrix chip at 45C for 16 h in a rotisserie oven at 60 rpm. Following hybridization, the target cRNA was removed; the arrays washed in 6X SSPE at 25C and then with 100 mM MES, 0.1 M NaCl, and 0.01% Tween 20 at 50C. The arrays were then be stained with streptavidin IgG (3 ug/ml), followed by a a second staining with streptavidin phycoerthrin and then rinsed in 100 mM MES, 0.1 M NaCl and 0.01% Tween 20 at 50C.
Sample_scan_protocol	The arrays were scanned by using Gene Array scanner (Affymetrix, Santa Clara, Calif, USA).
Sample_data_processing	Data was normalized using CEL files followed by RMA normalization, median polishing and the raw data filtered. The normalized array intensities were employed to compare expression intensities between samples.
Sample_data_processing	Changes in gene expression were detected using Affymetrix software (Microarray Suite v5.0 and Data Mining Tool v2.0). Only significantly changed probe sets (P < 0.05) were be considered. Up regulated and down regulated genes were clustered depending upon their functions using NetAffyx Gene Ontology Mining Tool software. Data was also be analyzed using the GeneSpring Suite 7 software package.
Sample_platform_id	GPL1261
Sample_contact_name	Hanping,,Feng
Sample_contact_email	hanping.feng@tufts.edu
Sample_contact_institute	Tufts University
Sample_contact_address	200 Westboro Rd.
Sample_contact_city	North Grafton
Sample_contact_zip/postal_code	01536
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM593nnn/GSM593404/suppl/GSM593404.CEL.gz
Sample_series_id	GSE24121
Sample_data_row_count	45101

GSM593405

GPL1261

DCs-C2

Dendritic cells

strain: C57BL/6 gender: Female tissue: Bone marrow cell type: Dendritic cells infection: control

Sample_geo_accession	GSM593405
Sample_status	Public on Oct 20 2010
Sample_submission_date	Sep 13 2010
Sample_last_update_date	Sep 16 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA extracted and purified with RNeasy mini kit (Qiagen).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotin-labeled cRNAs were generated using the GeneChip IVT Labeling Kit (in vitro transcription using T7 RNA polymerase at 37°C for 16 hours) in a thermal cycler. The biotinylated cRNA was subsequently treated with RNeasy clean-up kit (Qiagen) to remove any unincorporated biotinylated ribonucleotides from the cRNA samples and quantitated spectrophotometrically.
Sample_hyb_protocol	The fragmented target cRNA (20 ug) was mixed with 200 ul of hybridization cocktail (100 mM 2-morpholino-ethanesulfonic acid (MES), 1 M NaCl, 20 mM ethylenediaminetetraacetic acid, 0.01% Tween 20, 0.1 mg/ml herring sperm DNA, 500 g/ml acetylated bovine serum albumin) and hybridized to the Affymetrix chip at 45C for 16 h in a rotisserie oven at 60 rpm. Following hybridization, the target cRNA was removed; the arrays washed in 6X SSPE at 25C and then with 100 mM MES, 0.1 M NaCl, and 0.01% Tween 20 at 50C. The arrays were then be stained with streptavidin IgG (3 ug/ml), followed by a a second staining with streptavidin phycoerthrin and then rinsed in 100 mM MES, 0.1 M NaCl and 0.01% Tween 20 at 50C.
Sample_scan_protocol	The arrays were scanned by using Gene Array scanner (Affymetrix, Santa Clara, Calif, USA).
Sample_data_processing	Data was normalized using CEL files followed by RMA normalization, median polishing and the raw data filtered. The normalized array intensities were employed to compare expression intensities between samples.
Sample_data_processing	Changes in gene expression were detected using Affymetrix software (Microarray Suite v5.0 and Data Mining Tool v2.0). Only significantly changed probe sets (P < 0.05) were be considered. Up regulated and down regulated genes were clustered depending upon their functions using NetAffyx Gene Ontology Mining Tool software. Data was also be analyzed using the GeneSpring Suite 7 software package.
Sample_platform_id	GPL1261
Sample_contact_name	Hanping,,Feng
Sample_contact_email	hanping.feng@tufts.edu
Sample_contact_institute	Tufts University
Sample_contact_address	200 Westboro Rd.
Sample_contact_city	North Grafton
Sample_contact_zip/postal_code	01536
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM593nnn/GSM593405/suppl/GSM593405.CEL.gz
Sample_series_id	GSE24121
Sample_data_row_count	45101

GSM593406

GPL1261

DCs-C3

Dendritic cells

strain: C57BL/6 gender: Female tissue: Bone marrow cell type: Dendritic cells infection: control

Sample_geo_accession	GSM593406
Sample_status	Public on Oct 20 2010
Sample_submission_date	Sep 13 2010
Sample_last_update_date	Sep 16 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA extracted and purified with RNeasy mini kit (Qiagen).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotin-labeled cRNAs were generated using the GeneChip IVT Labeling Kit (in vitro transcription using T7 RNA polymerase at 37°C for 16 hours) in a thermal cycler. The biotinylated cRNA was subsequently treated with RNeasy clean-up kit (Qiagen) to remove any unincorporated biotinylated ribonucleotides from the cRNA samples and quantitated spectrophotometrically.
Sample_hyb_protocol	The fragmented target cRNA (20 ug) was mixed with 200 ul of hybridization cocktail (100 mM 2-morpholino-ethanesulfonic acid (MES), 1 M NaCl, 20 mM ethylenediaminetetraacetic acid, 0.01% Tween 20, 0.1 mg/ml herring sperm DNA, 500 g/ml acetylated bovine serum albumin) and hybridized to the Affymetrix chip at 45C for 16 h in a rotisserie oven at 60 rpm. Following hybridization, the target cRNA was removed; the arrays washed in 6X SSPE at 25C and then with 100 mM MES, 0.1 M NaCl, and 0.01% Tween 20 at 50C. The arrays were then be stained with streptavidin IgG (3 ug/ml), followed by a a second staining with streptavidin phycoerthrin and then rinsed in 100 mM MES, 0.1 M NaCl and 0.01% Tween 20 at 50C.
Sample_scan_protocol	The arrays were scanned by using Gene Array scanner (Affymetrix, Santa Clara, Calif, USA).
Sample_data_processing	Data was normalized using CEL files followed by RMA normalization, median polishing and the raw data filtered. The normalized array intensities were employed to compare expression intensities between samples.
Sample_data_processing	Changes in gene expression were detected using Affymetrix software (Microarray Suite v5.0 and Data Mining Tool v2.0). Only significantly changed probe sets (P < 0.05) were be considered. Up regulated and down regulated genes were clustered depending upon their functions using NetAffyx Gene Ontology Mining Tool software. Data was also be analyzed using the GeneSpring Suite 7 software package.
Sample_platform_id	GPL1261
Sample_contact_name	Hanping,,Feng
Sample_contact_email	hanping.feng@tufts.edu
Sample_contact_institute	Tufts University
Sample_contact_address	200 Westboro Rd.
Sample_contact_city	North Grafton
Sample_contact_zip/postal_code	01536
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM593nnn/GSM593406/suppl/GSM593406.CEL.gz
Sample_series_id	GSE24121
Sample_data_row_count	45101

GSM593672

GPL1261

DCs-EC1

Dendritic cells treated with E. cuniculi

strain: C57BL/6 gender: Female tissue: Bone marrow cell type: Dendritic cells infection: E. cuniculi

Sample_geo_accession	GSM593672
Sample_status	Public on Oct 20 2010
Sample_submission_date	Sep 14 2010
Sample_last_update_date	Sep 16 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA extracted and purified with RNeasy mini kit (Qiagen).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotin-labeled cRNAs were generated using the GeneChip IVT Labeling Kit (in vitro transcription using T7 RNA polymerase at 37°C for 16 hours) in a thermal cycler. The biotinylated cRNA was subsequently treated with RNeasy clean-up kit (Qiagen) to remove any unincorporated biotinylated ribonucleotides from the cRNA samples and quantitated spectrophotometrically
Sample_hyb_protocol	The fragmented target cRNA (20 ug) was mixed with 200 ul of hybridization cocktail (100 mM 2-morpholino-ethanesulfonic acid (MES), 1 M NaCl, 20 mM ethylenediaminetetraacetic acid, 0.01% Tween 20, 0.1 mg/ml herring sperm DNA, 500 g/ml acetylated bovine serum albumin) and hybridized to the Affymetrix chip at 45°C for 16 h in a rotisserie oven at 60 rpm. Following hybridization, the target cRNA was removed; the arrays washed in 6X SSPE at 25°C and then with 100 mM MES, 0.1 M NaCl, and 0.01% Tween 20 at 50C. The arrays were then be stained with streptavidin IgG (3 ug/ml), followed by a a second staining with streptavidin phycoerthrin and then rinsed in 100 mM MES, 0.1 M NaCl and 0.01% Tween 20 at 50°C.
Sample_scan_protocol	The arrays were scanned by using Gene Array scanner (Affymetrix, Santa Clara, Calif, USA).
Sample_data_processing	Data was normalized using CEL files followed by RMA normalization, median polishing and the raw data filtered. The normalized array intensities were employed to compare expression intensities between samples.
Sample_data_processing	Changes in gene expression were detected using Affymetrix software (Microarray Suite v5.0 and Data Mining Tool v2.0). Only significantly changed probe sets (P < 0.05) were be considered. Up regulated and down regulated genes were clustered depending upon their functions using NetAffyx Gene Ontology Mining Tool software. Data was also be analyzed using the GeneSpring Suite 7 software package.
Sample_platform_id	GPL1261
Sample_contact_name	Hanping,,Feng
Sample_contact_email	hanping.feng@tufts.edu
Sample_contact_institute	Tufts University
Sample_contact_address	200 Westboro Rd.
Sample_contact_city	North Grafton
Sample_contact_zip/postal_code	01536
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM593nnn/GSM593672/suppl/GSM593672.CEL.gz
Sample_series_id	GSE24121
Sample_data_row_count	45101

GSM593673

GPL1261

DCs-EC2

Dendritic cells treated with E. cuniculi

strain: C57BL/6 gender: Female tissue: Bone marrow cell type: Dendritic cells infection: E. cuniculi

Sample_geo_accession	GSM593673
Sample_status	Public on Oct 20 2010
Sample_submission_date	Sep 14 2010
Sample_last_update_date	Sep 16 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA extracted and purified with RNeasy mini kit (Qiagen).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotin-labeled cRNAs were generated using the GeneChip IVT Labeling Kit (in vitro transcription using T7 RNA polymerase at 37°C for 16 hours) in a thermal cycler. The biotinylated cRNA was subsequently treated with RNeasy clean-up kit (Qiagen) to remove any unincorporated biotinylated ribonucleotides from the cRNA samples and quantitated spectrophotometrically
Sample_hyb_protocol	The fragmented target cRNA (20 ug) was mixed with 200 ul of hybridization cocktail (100 mM 2-morpholino-ethanesulfonic acid (MES), 1 M NaCl, 20 mM ethylenediaminetetraacetic acid, 0.01% Tween 20, 0.1 mg/ml herring sperm DNA, 500 g/ml acetylated bovine serum albumin) and hybridized to the Affymetrix chip at 45°C for 16 h in a rotisserie oven at 60 rpm. Following hybridization, the target cRNA was removed; the arrays washed in 6X SSPE at 25°C and then with 100 mM MES, 0.1 M NaCl, and 0.01% Tween 20 at 50C. The arrays were then be stained with streptavidin IgG (3 ug/ml), followed by a a second staining with streptavidin phycoerthrin and then rinsed in 100 mM MES, 0.1 M NaCl and 0.01% Tween 20 at 50°C.
Sample_scan_protocol	The arrays were scanned by using Gene Array scanner (Affymetrix, Santa Clara, Calif, USA).
Sample_data_processing	Data was normalized using CEL files followed by RMA normalization, median polishing and the raw data filtered. The normalized array intensities were employed to compare expression intensities between samples.
Sample_data_processing	Changes in gene expression were detected using Affymetrix software (Microarray Suite v5.0 and Data Mining Tool v2.0). Only significantly changed probe sets (P < 0.05) were be considered. Up regulated and down regulated genes were clustered depending upon their functions using NetAffyx Gene Ontology Mining Tool software. Data was also be analyzed using the GeneSpring Suite 7 software package.
Sample_platform_id	GPL1261
Sample_contact_name	Hanping,,Feng
Sample_contact_email	hanping.feng@tufts.edu
Sample_contact_institute	Tufts University
Sample_contact_address	200 Westboro Rd.
Sample_contact_city	North Grafton
Sample_contact_zip/postal_code	01536
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM593nnn/GSM593673/suppl/GSM593673.CEL.gz
Sample_series_id	GSE24121
Sample_data_row_count	45101

GSM593674

GPL1261

DCs-EC3

Dendritic cells treated with E. cuniculi

strain: C57BL/6 gender: Female tissue: Bone marrow cell type: Dendritic cells infection: E. cuniculi

Sample_geo_accession	GSM593674
Sample_status	Public on Oct 20 2010
Sample_submission_date	Sep 14 2010
Sample_last_update_date	Sep 16 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA extracted and purified with RNeasy mini kit (Qiagen).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotin-labeled cRNAs were generated using the GeneChip IVT Labeling Kit (in vitro transcription using T7 RNA polymerase at 37°C for 16 hours) in a thermal cycler. The biotinylated cRNA was subsequently treated with RNeasy clean-up kit (Qiagen) to remove any unincorporated biotinylated ribonucleotides from the cRNA samples and quantitated spectrophotometrically
Sample_hyb_protocol	The fragmented target cRNA (20 ug) was mixed with 200 ul of hybridization cocktail (100 mM 2-morpholino-ethanesulfonic acid (MES), 1 M NaCl, 20 mM ethylenediaminetetraacetic acid, 0.01% Tween 20, 0.1 mg/ml herring sperm DNA, 500 g/ml acetylated bovine serum albumin) and hybridized to the Affymetrix chip at 45°C for 16 h in a rotisserie oven at 60 rpm. Following hybridization, the target cRNA was removed; the arrays washed in 6X SSPE at 25°C and then with 100 mM MES, 0.1 M NaCl, and 0.01% Tween 20 at 50C. The arrays were then be stained with streptavidin IgG (3 ug/ml), followed by a a second staining with streptavidin phycoerthrin and then rinsed in 100 mM MES, 0.1 M NaCl and 0.01% Tween 20 at 50°C.
Sample_scan_protocol	The arrays were scanned by using Gene Array scanner (Affymetrix, Santa Clara, Calif, USA).
Sample_data_processing	Data was normalized using CEL files followed by RMA normalization, median polishing and the raw data filtered. The normalized array intensities were employed to compare expression intensities between samples.
Sample_data_processing	Changes in gene expression were detected using Affymetrix software (Microarray Suite v5.0 and Data Mining Tool v2.0). Only significantly changed probe sets (P < 0.05) were be considered. Up regulated and down regulated genes were clustered depending upon their functions using NetAffyx Gene Ontology Mining Tool software. Data was also be analyzed using the GeneSpring Suite 7 software package.
Sample_platform_id	GPL1261
Sample_contact_name	Hanping,,Feng
Sample_contact_email	hanping.feng@tufts.edu
Sample_contact_institute	Tufts University
Sample_contact_address	200 Westboro Rd.
Sample_contact_city	North Grafton
Sample_contact_zip/postal_code	01536
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM593nnn/GSM593674/suppl/GSM593674.CEL.gz
Sample_series_id	GSE24121
Sample_data_row_count	45101

GSM593675

GPL1261

DCs-CP1 IOWA

Dendritic cells treated with C. parvum

strain: C57BL/6 gender: Female tissue: Bone marrow cell type: Dendritic cells infection: C. parvum (strain Iowa)

Sample_geo_accession	GSM593675
Sample_status	Public on Oct 20 2010
Sample_submission_date	Sep 14 2010
Sample_last_update_date	Sep 16 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA extracted and purified with RNeasy mini kit (Qiagen).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotin-labeled cRNAs were generated using the GeneChip IVT Labeling Kit (in vitro transcription using T7 RNA polymerase at 37°C for 16 hours) in a thermal cycler. The biotinylated cRNA was subsequently treated with RNeasy clean-up kit (Qiagen) to remove any unincorporated biotinylated ribonucleotides from the cRNA samples and quantitated spectrophotometrically
Sample_hyb_protocol	The fragmented target cRNA (20 ug) was mixed with 200 ul of hybridization cocktail (100 mM 2-morpholino-ethanesulfonic acid (MES), 1 M NaCl, 20 mM ethylenediaminetetraacetic acid, 0.01% Tween 20, 0.1 mg/ml herring sperm DNA, 500 g/ml acetylated bovine serum albumin) and hybridized to the Affymetrix chip at 45°C for 16 h in a rotisserie oven at 60 rpm. Following hybridization, the target cRNA was removed; the arrays washed in 6X SSPE at 25°C and then with 100 mM MES, 0.1 M NaCl, and 0.01% Tween 20 at 50C. The arrays were then be stained with streptavidin IgG (3 ug/ml), followed by a a second staining with streptavidin phycoerthrin and then rinsed in 100 mM MES, 0.1 M NaCl and 0.01% Tween 20 at 50°C.
Sample_scan_protocol	The arrays were scanned by using Gene Array scanner (Affymetrix, Santa Clara, Calif, USA).
Sample_data_processing	Data was normalized using CEL files followed by RMA normalization, median polishing and the raw data filtered. The normalized array intensities were employed to compare expression intensities between samples.
Sample_data_processing	Changes in gene expression were detected using Affymetrix software (Microarray Suite v5.0 and Data Mining Tool v2.0). Only significantly changed probe sets (P < 0.05) were be considered. Up regulated and down regulated genes were clustered depending upon their functions using NetAffyx Gene Ontology Mining Tool software. Data was also be analyzed using the GeneSpring Suite 7 software package.
Sample_platform_id	GPL1261
Sample_contact_name	Hanping,,Feng
Sample_contact_email	hanping.feng@tufts.edu
Sample_contact_institute	Tufts University
Sample_contact_address	200 Westboro Rd.
Sample_contact_city	North Grafton
Sample_contact_zip/postal_code	01536
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM593nnn/GSM593675/suppl/GSM593675.CEL.gz
Sample_series_id	GSE24121
Sample_data_row_count	45101

GSM593676

GPL1261

DCs-CP2 IOWA

Dendritic cells treated with C. parvum

strain: C57BL/6 gender: Female tissue: Bone marrow cell type: Dendritic cells infection: C. parvum (strain Iowa)

Sample_geo_accession	GSM593676
Sample_status	Public on Oct 20 2010
Sample_submission_date	Sep 14 2010
Sample_last_update_date	Sep 16 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA extracted and purified with RNeasy mini kit (Qiagen).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotin-labeled cRNAs were generated using the GeneChip IVT Labeling Kit (in vitro transcription using T7 RNA polymerase at 37°C for 16 hours) in a thermal cycler. The biotinylated cRNA was subsequently treated with RNeasy clean-up kit (Qiagen) to remove any unincorporated biotinylated ribonucleotides from the cRNA samples and quantitated spectrophotometrically
Sample_hyb_protocol	The fragmented target cRNA (20 ug) was mixed with 200 ul of hybridization cocktail (100 mM 2-morpholino-ethanesulfonic acid (MES), 1 M NaCl, 20 mM ethylenediaminetetraacetic acid, 0.01% Tween 20, 0.1 mg/ml herring sperm DNA, 500 g/ml acetylated bovine serum albumin) and hybridized to the Affymetrix chip at 45°C for 16 h in a rotisserie oven at 60 rpm. Following hybridization, the target cRNA was removed; the arrays washed in 6X SSPE at 25°C and then with 100 mM MES, 0.1 M NaCl, and 0.01% Tween 20 at 50C. The arrays were then be stained with streptavidin IgG (3 ug/ml), followed by a a second staining with streptavidin phycoerthrin and then rinsed in 100 mM MES, 0.1 M NaCl and 0.01% Tween 20 at 50°C.
Sample_scan_protocol	The arrays were scanned by using Gene Array scanner (Affymetrix, Santa Clara, Calif, USA).
Sample_data_processing	Data was normalized using CEL files followed by RMA normalization, median polishing and the raw data filtered. The normalized array intensities were employed to compare expression intensities between samples.
Sample_data_processing	Changes in gene expression were detected using Affymetrix software (Microarray Suite v5.0 and Data Mining Tool v2.0). Only significantly changed probe sets (P < 0.05) were be considered. Up regulated and down regulated genes were clustered depending upon their functions using NetAffyx Gene Ontology Mining Tool software. Data was also be analyzed using the GeneSpring Suite 7 software package.
Sample_platform_id	GPL1261
Sample_contact_name	Hanping,,Feng
Sample_contact_email	hanping.feng@tufts.edu
Sample_contact_institute	Tufts University
Sample_contact_address	200 Westboro Rd.
Sample_contact_city	North Grafton
Sample_contact_zip/postal_code	01536
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM593nnn/GSM593676/suppl/GSM593676.CEL.gz
Sample_series_id	GSE24121
Sample_data_row_count	45101

GSM593677

GPL1261

DCs-CP3 IOWA

Dendritic cells treated with C. parvum

strain: C57BL/6 gender: Female tissue: Bone marrow cell type: Dendritic cells infection: C. parvum (strain Iowa)

Sample_geo_accession	GSM593677
Sample_status	Public on Oct 20 2010
Sample_submission_date	Sep 14 2010
Sample_last_update_date	Sep 16 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA extracted and purified with RNeasy mini kit (Qiagen).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotin-labeled cRNAs were generated using the GeneChip IVT Labeling Kit (in vitro transcription using T7 RNA polymerase at 37°C for 16 hours) in a thermal cycler. The biotinylated cRNA was subsequently treated with RNeasy clean-up kit (Qiagen) to remove any unincorporated biotinylated ribonucleotides from the cRNA samples and quantitated spectrophotometrically
Sample_hyb_protocol	The fragmented target cRNA (20 ug) was mixed with 200 ul of hybridization cocktail (100 mM 2-morpholino-ethanesulfonic acid (MES), 1 M NaCl, 20 mM ethylenediaminetetraacetic acid, 0.01% Tween 20, 0.1 mg/ml herring sperm DNA, 500 g/ml acetylated bovine serum albumin) and hybridized to the Affymetrix chip at 45°C for 16 h in a rotisserie oven at 60 rpm. Following hybridization, the target cRNA was removed; the arrays washed in 6X SSPE at 25°C and then with 100 mM MES, 0.1 M NaCl, and 0.01% Tween 20 at 50C. The arrays were then be stained with streptavidin IgG (3 ug/ml), followed by a a second staining with streptavidin phycoerthrin and then rinsed in 100 mM MES, 0.1 M NaCl and 0.01% Tween 20 at 50°C.
Sample_scan_protocol	The arrays were scanned by using Gene Array scanner (Affymetrix, Santa Clara, Calif, USA).
Sample_data_processing	Data was normalized using CEL files followed by RMA normalization, median polishing and the raw data filtered. The normalized array intensities were employed to compare expression intensities between samples.
Sample_data_processing	Changes in gene expression were detected using Affymetrix software (Microarray Suite v5.0 and Data Mining Tool v2.0). Only significantly changed probe sets (P < 0.05) were be considered. Up regulated and down regulated genes were clustered depending upon their functions using NetAffyx Gene Ontology Mining Tool software. Data was also be analyzed using the GeneSpring Suite 7 software package.
Sample_platform_id	GPL1261
Sample_contact_name	Hanping,,Feng
Sample_contact_email	hanping.feng@tufts.edu
Sample_contact_institute	Tufts University
Sample_contact_address	200 Westboro Rd.
Sample_contact_city	North Grafton
Sample_contact_zip/postal_code	01536
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM593nnn/GSM593677/suppl/GSM593677.CEL.gz
Sample_series_id	GSE24121
Sample_data_row_count	45101

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