Search results for the GEO ID: GSE42088  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1032235 | GPL570 |
|
Human Dendritic Cell uninfected 2hrs biological rep1
|
Human Dendritic Cell uninfected 2hrs
|
cell type: monocyte-derived dendritic cells
leishmania major infected: no
time point: 2 hrs
|
Gene expression data from human monocyte derived dendritic cells, uninfected
|
| Sample_geo_accession | GSM1032235
| | Sample_status | Public on Nov 08 2012
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | L. major parasites were maintained in complete M199 media (supplemented with 20% FBS). Metacyclic promastigotes were isolated using a ficol density gradient protocol and opsonized by treatment with 5% human serum for 30 min at 37°C. Metacyclic promastigotes were utilized for infection of the monocyte-derived human dendritic cells
| | Sample_growth_protocol_ch1 | Monocyte-derived human dendritic cells were maintained in RPMI-complete media (10% FBS, 2mM l-glutamine 100U/ml, 1% penicillin/streptomycin) at 37°C
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Uninfected and L. major infected samples were harvested at 2, 4, 8, or 24hrs post infection. Total RNA was extracted from each sample utilzing an RNEasy kit according to manufacturer's protocols (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to standard Affymetrix protocol from 2μg of total RNA according to manufacturer's protocols (Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Purified cRNA was fragmented in 5X fragmentation buffer (200mM Tris-Acetate, pH8.1, 500mM potassium acetate, 150mM magnesium acetate) at 94ºC for 35 min prior to cRNA chip hybridization. Gene chips were washed and stained utilizing the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | Gene chips were scanned with the Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA)
| | Sample_data_processing | The Affymetrix data files (.cel) were processed using Bioconductor software package (http://www.bioconductor.org/, Seattle, WA) [13]. Probe set signal intensities were subjected to background correction by GCRMA (Genespring GX 7.0) normalization across all 15 chips. The mean fluorescence intensity was derived from a log2 transformation of the raw data. Probe sets with “present” call in at least 7 of the 15 chips were retained, which filtered our list of 54,000 probe sets down to ~14,000. Statistical significance was determined using a one-way ANOVA and Benjamini-Yekutieli multiple correction test to control false discovery rates. A final set of 848 candidate probe set were identified as significantly expressed in at least one time point compared to non-infected samples (p<0.05).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michelle,A,Favila
| | Sample_contact_email | michellefavila@gmail.com
| | Sample_contact_laboratory | Mary Ann McDowell
| | Sample_contact_department | Biology
| | Sample_contact_institute | University of Notre Dame
| | Sample_contact_address | 210 Galvin Life Science Center
| | Sample_contact_city | Notre Dame
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46556
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1032nnn/GSM1032235/suppl/GSM1032235.CEL.gz
| | Sample_series_id | GSE42088
| | Sample_data_row_count | 54613
| | |
|
GSM1032236 | GPL570 |
|
Human Dendritic Cell uninfected 2hrs biological rep2
|
Human Dendritic Cell uninfected 2hrs
|
cell type: monocyte-derived dendritic cells
leishmania major infected: no
time point: 2 hrs
|
Gene expression data from human monocyte derived dendritic cells, uninfected
|
| Sample_geo_accession | GSM1032236
| | Sample_status | Public on Nov 08 2012
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | L. major parasites were maintained in complete M199 media (supplemented with 20% FBS). Metacyclic promastigotes were isolated using a ficol density gradient protocol and opsonized by treatment with 5% human serum for 30 min at 37°C. Metacyclic promastigotes were utilized for infection of the monocyte-derived human dendritic cells
| | Sample_growth_protocol_ch1 | Monocyte-derived human dendritic cells were maintained in RPMI-complete media (10% FBS, 2mM l-glutamine 100U/ml, 1% penicillin/streptomycin) at 37°C
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Uninfected and L. major infected samples were harvested at 2, 4, 8, or 24hrs post infection. Total RNA was extracted from each sample utilzing an RNEasy kit according to manufacturer's protocols (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to standard Affymetrix protocol from 2μg of total RNA according to manufacturer's protocols (Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Purified cRNA was fragmented in 5X fragmentation buffer (200mM Tris-Acetate, pH8.1, 500mM potassium acetate, 150mM magnesium acetate) at 94ºC for 35 min prior to cRNA chip hybridization. Gene chips were washed and stained utilizing the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | Gene chips were scanned with the Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA)
| | Sample_data_processing | The Affymetrix data files (.cel) were processed using Bioconductor software package (http://www.bioconductor.org/, Seattle, WA) [13]. Probe set signal intensities were subjected to background correction by GCRMA (Genespring GX 7.0) normalization across all 15 chips. The mean fluorescence intensity was derived from a log2 transformation of the raw data. Probe sets with “present” call in at least 7 of the 15 chips were retained, which filtered our list of 54,000 probe sets down to ~14,000. Statistical significance was determined using a one-way ANOVA and Benjamini-Yekutieli multiple correction test to control false discovery rates. A final set of 848 candidate probe set were identified as significantly expressed in at least one time point compared to non-infected samples (p<0.05).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michelle,A,Favila
| | Sample_contact_email | michellefavila@gmail.com
| | Sample_contact_laboratory | Mary Ann McDowell
| | Sample_contact_department | Biology
| | Sample_contact_institute | University of Notre Dame
| | Sample_contact_address | 210 Galvin Life Science Center
| | Sample_contact_city | Notre Dame
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46556
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1032nnn/GSM1032236/suppl/GSM1032236.CEL.gz
| | Sample_series_id | GSE42088
| | Sample_data_row_count | 54613
| | |
|
GSM1032237 | GPL570 |
|
Human Dendritic Cell uninfected 2hrs biological rep3
|
Human Dendritic Cell uninfected 2hrs
|
cell type: monocyte-derived dendritic cells
leishmania major infected: no
time point: 2 hrs
|
Gene expression data from human monocyte derived dendritic cells, uninfected
|
| Sample_geo_accession | GSM1032237
| | Sample_status | Public on Nov 08 2012
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | L. major parasites were maintained in complete M199 media (supplemented with 20% FBS). Metacyclic promastigotes were isolated using a ficol density gradient protocol and opsonized by treatment with 5% human serum for 30 min at 37°C. Metacyclic promastigotes were utilized for infection of the monocyte-derived human dendritic cells
| | Sample_growth_protocol_ch1 | Monocyte-derived human dendritic cells were maintained in RPMI-complete media (10% FBS, 2mM l-glutamine 100U/ml, 1% penicillin/streptomycin) at 37°C
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Uninfected and L. major infected samples were harvested at 2, 4, 8, or 24hrs post infection. Total RNA was extracted from each sample utilzing an RNEasy kit according to manufacturer's protocols (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to standard Affymetrix protocol from 2μg of total RNA according to manufacturer's protocols (Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Purified cRNA was fragmented in 5X fragmentation buffer (200mM Tris-Acetate, pH8.1, 500mM potassium acetate, 150mM magnesium acetate) at 94ºC for 35 min prior to cRNA chip hybridization. Gene chips were washed and stained utilizing the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | Gene chips were scanned with the Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA)
| | Sample_data_processing | The Affymetrix data files (.cel) were processed using Bioconductor software package (http://www.bioconductor.org/, Seattle, WA) [13]. Probe set signal intensities were subjected to background correction by GCRMA (Genespring GX 7.0) normalization across all 15 chips. The mean fluorescence intensity was derived from a log2 transformation of the raw data. Probe sets with “present” call in at least 7 of the 15 chips were retained, which filtered our list of 54,000 probe sets down to ~14,000. Statistical significance was determined using a one-way ANOVA and Benjamini-Yekutieli multiple correction test to control false discovery rates. A final set of 848 candidate probe set were identified as significantly expressed in at least one time point compared to non-infected samples (p<0.05).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michelle,A,Favila
| | Sample_contact_email | michellefavila@gmail.com
| | Sample_contact_laboratory | Mary Ann McDowell
| | Sample_contact_department | Biology
| | Sample_contact_institute | University of Notre Dame
| | Sample_contact_address | 210 Galvin Life Science Center
| | Sample_contact_city | Notre Dame
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46556
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1032nnn/GSM1032237/suppl/GSM1032237.CEL.gz
| | Sample_series_id | GSE42088
| | Sample_data_row_count | 54613
| | |
|
GSM1032238 | GPL570 |
|
Human Dendritic Cell L. major 2hrs biological rep1
|
Human Dendritic Cell L. major 2hrs
|
cell type: monocyte-derived dendritic cells
leishmania major infected: yes
time point: 2 hrs
|
Gene expression data from human monocyte derived dendritic cells, L. major infected, 2hrs
|
| Sample_geo_accession | GSM1032238
| | Sample_status | Public on Nov 08 2012
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | L. major parasites were maintained in complete M199 media (supplemented with 20% FBS). Metacyclic promastigotes were isolated using a ficol density gradient protocol and opsonized by treatment with 5% human serum for 30 min at 37°C. Metacyclic promastigotes were utilized for infection of the monocyte-derived human dendritic cells
| | Sample_growth_protocol_ch1 | Monocyte-derived human dendritic cells were maintained in RPMI-complete media (10% FBS, 2mM l-glutamine 100U/ml, 1% penicillin/streptomycin) at 37°C
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Uninfected and L. major infected samples were harvested at 2, 4, 8, or 24hrs post infection. Total RNA was extracted from each sample utilzing an RNEasy kit according to manufacturer's protocols (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to standard Affymetrix protocol from 2μg of total RNA according to manufacturer's protocols (Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Purified cRNA was fragmented in 5X fragmentation buffer (200mM Tris-Acetate, pH8.1, 500mM potassium acetate, 150mM magnesium acetate) at 94ºC for 35 min prior to cRNA chip hybridization. Gene chips were washed and stained utilizing the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | Gene chips were scanned with the Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA)
| | Sample_data_processing | The Affymetrix data files (.cel) were processed using Bioconductor software package (http://www.bioconductor.org/, Seattle, WA) [13]. Probe set signal intensities were subjected to background correction by GCRMA (Genespring GX 7.0) normalization across all 15 chips. The mean fluorescence intensity was derived from a log2 transformation of the raw data. Probe sets with “present” call in at least 7 of the 15 chips were retained, which filtered our list of 54,000 probe sets down to ~14,000. Statistical significance was determined using a one-way ANOVA and Benjamini-Yekutieli multiple correction test to control false discovery rates. A final set of 848 candidate probe set were identified as significantly expressed in at least one time point compared to non-infected samples (p<0.05).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michelle,A,Favila
| | Sample_contact_email | michellefavila@gmail.com
| | Sample_contact_laboratory | Mary Ann McDowell
| | Sample_contact_department | Biology
| | Sample_contact_institute | University of Notre Dame
| | Sample_contact_address | 210 Galvin Life Science Center
| | Sample_contact_city | Notre Dame
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46556
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1032nnn/GSM1032238/suppl/GSM1032238.CEL.gz
| | Sample_series_id | GSE42088
| | Sample_data_row_count | 54613
| | |
|
GSM1032239 | GPL570 |
|
Human Dendritic Cell L. major 2hrs biological rep2
|
Human Dendritic Cell L. major 2hrs
|
cell type: monocyte-derived dendritic cells
leishmania major infected: yes
time point: 2 hrs
|
Gene expression data from human monocyte derived dendritic cells, L. major infected, 2hrs
|
| Sample_geo_accession | GSM1032239
| | Sample_status | Public on Nov 08 2012
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | L. major parasites were maintained in complete M199 media (supplemented with 20% FBS). Metacyclic promastigotes were isolated using a ficol density gradient protocol and opsonized by treatment with 5% human serum for 30 min at 37°C. Metacyclic promastigotes were utilized for infection of the monocyte-derived human dendritic cells
| | Sample_growth_protocol_ch1 | Monocyte-derived human dendritic cells were maintained in RPMI-complete media (10% FBS, 2mM l-glutamine 100U/ml, 1% penicillin/streptomycin) at 37°C
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Uninfected and L. major infected samples were harvested at 2, 4, 8, or 24hrs post infection. Total RNA was extracted from each sample utilzing an RNEasy kit according to manufacturer's protocols (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to standard Affymetrix protocol from 2μg of total RNA according to manufacturer's protocols (Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Purified cRNA was fragmented in 5X fragmentation buffer (200mM Tris-Acetate, pH8.1, 500mM potassium acetate, 150mM magnesium acetate) at 94ºC for 35 min prior to cRNA chip hybridization. Gene chips were washed and stained utilizing the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | Gene chips were scanned with the Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA)
| | Sample_data_processing | The Affymetrix data files (.cel) were processed using Bioconductor software package (http://www.bioconductor.org/, Seattle, WA) [13]. Probe set signal intensities were subjected to background correction by GCRMA (Genespring GX 7.0) normalization across all 15 chips. The mean fluorescence intensity was derived from a log2 transformation of the raw data. Probe sets with “present” call in at least 7 of the 15 chips were retained, which filtered our list of 54,000 probe sets down to ~14,000. Statistical significance was determined using a one-way ANOVA and Benjamini-Yekutieli multiple correction test to control false discovery rates. A final set of 848 candidate probe set were identified as significantly expressed in at least one time point compared to non-infected samples (p<0.05).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michelle,A,Favila
| | Sample_contact_email | michellefavila@gmail.com
| | Sample_contact_laboratory | Mary Ann McDowell
| | Sample_contact_department | Biology
| | Sample_contact_institute | University of Notre Dame
| | Sample_contact_address | 210 Galvin Life Science Center
| | Sample_contact_city | Notre Dame
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46556
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1032nnn/GSM1032239/suppl/GSM1032239.CEL.gz
| | Sample_series_id | GSE42088
| | Sample_data_row_count | 54613
| | |
|
GSM1032240 | GPL570 |
|
Human Dendritic Cell L. major 2hrs biological rep3
|
Human Dendritic Cell L. major 2hrs
|
cell type: monocyte-derived dendritic cells
leishmania major infected: yes
time point: 2 hrs
|
Gene expression data from human monocyte derived dendritic cells, L. major infected, 2hrs
|
| Sample_geo_accession | GSM1032240
| | Sample_status | Public on Nov 08 2012
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | L. major parasites were maintained in complete M199 media (supplemented with 20% FBS). Metacyclic promastigotes were isolated using a ficol density gradient protocol and opsonized by treatment with 5% human serum for 30 min at 37°C. Metacyclic promastigotes were utilized for infection of the monocyte-derived human dendritic cells
| | Sample_growth_protocol_ch1 | Monocyte-derived human dendritic cells were maintained in RPMI-complete media (10% FBS, 2mM l-glutamine 100U/ml, 1% penicillin/streptomycin) at 37°C
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Uninfected and L. major infected samples were harvested at 2, 4, 8, or 24hrs post infection. Total RNA was extracted from each sample utilzing an RNEasy kit according to manufacturer's protocols (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to standard Affymetrix protocol from 2μg of total RNA according to manufacturer's protocols (Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Purified cRNA was fragmented in 5X fragmentation buffer (200mM Tris-Acetate, pH8.1, 500mM potassium acetate, 150mM magnesium acetate) at 94ºC for 35 min prior to cRNA chip hybridization. Gene chips were washed and stained utilizing the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | Gene chips were scanned with the Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA)
| | Sample_data_processing | The Affymetrix data files (.cel) were processed using Bioconductor software package (http://www.bioconductor.org/, Seattle, WA) [13]. Probe set signal intensities were subjected to background correction by GCRMA (Genespring GX 7.0) normalization across all 15 chips. The mean fluorescence intensity was derived from a log2 transformation of the raw data. Probe sets with “present” call in at least 7 of the 15 chips were retained, which filtered our list of 54,000 probe sets down to ~14,000. Statistical significance was determined using a one-way ANOVA and Benjamini-Yekutieli multiple correction test to control false discovery rates. A final set of 848 candidate probe set were identified as significantly expressed in at least one time point compared to non-infected samples (p<0.05).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michelle,A,Favila
| | Sample_contact_email | michellefavila@gmail.com
| | Sample_contact_laboratory | Mary Ann McDowell
| | Sample_contact_department | Biology
| | Sample_contact_institute | University of Notre Dame
| | Sample_contact_address | 210 Galvin Life Science Center
| | Sample_contact_city | Notre Dame
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46556
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1032nnn/GSM1032240/suppl/GSM1032240.CEL.gz
| | Sample_series_id | GSE42088
| | Sample_data_row_count | 54613
| | |
|
GSM1032241 | GPL570 |
|
Human Dendritic Cell L. major 4hrs biological rep1
|
Human Dendritic Cell L. major 4hrs
|
cell type: monocyte-derived dendritic cells
leishmania major infected: yes
time point: 4 hrs
|
Gene expression data from human monocyte derived dendritic cells, L. major infected, 4hrs
|
| Sample_geo_accession | GSM1032241
| | Sample_status | Public on Nov 08 2012
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | L. major parasites were maintained in complete M199 media (supplemented with 20% FBS). Metacyclic promastigotes were isolated using a ficol density gradient protocol and opsonized by treatment with 5% human serum for 30 min at 37°C. Metacyclic promastigotes were utilized for infection of the monocyte-derived human dendritic cells
| | Sample_growth_protocol_ch1 | Monocyte-derived human dendritic cells were maintained in RPMI-complete media (10% FBS, 2mM l-glutamine 100U/ml, 1% penicillin/streptomycin) at 37°C
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Uninfected and L. major infected samples were harvested at 2, 4, 8, or 24hrs post infection. Total RNA was extracted from each sample utilzing an RNEasy kit according to manufacturer's protocols (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to standard Affymetrix protocol from 2μg of total RNA according to manufacturer's protocols (Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Purified cRNA was fragmented in 5X fragmentation buffer (200mM Tris-Acetate, pH8.1, 500mM potassium acetate, 150mM magnesium acetate) at 94ºC for 35 min prior to cRNA chip hybridization. Gene chips were washed and stained utilizing the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | Gene chips were scanned with the Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA)
| | Sample_data_processing | The Affymetrix data files (.cel) were processed using Bioconductor software package (http://www.bioconductor.org/, Seattle, WA) [13]. Probe set signal intensities were subjected to background correction by GCRMA (Genespring GX 7.0) normalization across all 15 chips. The mean fluorescence intensity was derived from a log2 transformation of the raw data. Probe sets with “present” call in at least 7 of the 15 chips were retained, which filtered our list of 54,000 probe sets down to ~14,000. Statistical significance was determined using a one-way ANOVA and Benjamini-Yekutieli multiple correction test to control false discovery rates. A final set of 848 candidate probe set were identified as significantly expressed in at least one time point compared to non-infected samples (p<0.05).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michelle,A,Favila
| | Sample_contact_email | michellefavila@gmail.com
| | Sample_contact_laboratory | Mary Ann McDowell
| | Sample_contact_department | Biology
| | Sample_contact_institute | University of Notre Dame
| | Sample_contact_address | 210 Galvin Life Science Center
| | Sample_contact_city | Notre Dame
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46556
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1032nnn/GSM1032241/suppl/GSM1032241.CEL.gz
| | Sample_series_id | GSE42088
| | Sample_data_row_count | 54613
| | |
|
GSM1032242 | GPL570 |
|
Human Dendritic Cell L. major 4hrs biological rep2
|
Human Dendritic Cell L. major 4hrs
|
cell type: monocyte-derived dendritic cells
leishmania major infected: yes
time point: 4 hrs
|
Gene expression data from human monocyte derived dendritic cells, L. major infected, 4hrs
|
| Sample_geo_accession | GSM1032242
| | Sample_status | Public on Nov 08 2012
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | L. major parasites were maintained in complete M199 media (supplemented with 20% FBS). Metacyclic promastigotes were isolated using a ficol density gradient protocol and opsonized by treatment with 5% human serum for 30 min at 37°C. Metacyclic promastigotes were utilized for infection of the monocyte-derived human dendritic cells
| | Sample_growth_protocol_ch1 | Monocyte-derived human dendritic cells were maintained in RPMI-complete media (10% FBS, 2mM l-glutamine 100U/ml, 1% penicillin/streptomycin) at 37°C
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Uninfected and L. major infected samples were harvested at 2, 4, 8, or 24hrs post infection. Total RNA was extracted from each sample utilzing an RNEasy kit according to manufacturer's protocols (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to standard Affymetrix protocol from 2μg of total RNA according to manufacturer's protocols (Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Purified cRNA was fragmented in 5X fragmentation buffer (200mM Tris-Acetate, pH8.1, 500mM potassium acetate, 150mM magnesium acetate) at 94ºC for 35 min prior to cRNA chip hybridization. Gene chips were washed and stained utilizing the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | Gene chips were scanned with the Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA)
| | Sample_data_processing | The Affymetrix data files (.cel) were processed using Bioconductor software package (http://www.bioconductor.org/, Seattle, WA) [13]. Probe set signal intensities were subjected to background correction by GCRMA (Genespring GX 7.0) normalization across all 15 chips. The mean fluorescence intensity was derived from a log2 transformation of the raw data. Probe sets with “present” call in at least 7 of the 15 chips were retained, which filtered our list of 54,000 probe sets down to ~14,000. Statistical significance was determined using a one-way ANOVA and Benjamini-Yekutieli multiple correction test to control false discovery rates. A final set of 848 candidate probe set were identified as significantly expressed in at least one time point compared to non-infected samples (p<0.05).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michelle,A,Favila
| | Sample_contact_email | michellefavila@gmail.com
| | Sample_contact_laboratory | Mary Ann McDowell
| | Sample_contact_department | Biology
| | Sample_contact_institute | University of Notre Dame
| | Sample_contact_address | 210 Galvin Life Science Center
| | Sample_contact_city | Notre Dame
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46556
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1032nnn/GSM1032242/suppl/GSM1032242.CEL.gz
| | Sample_series_id | GSE42088
| | Sample_data_row_count | 54613
| | |
|
GSM1032243 | GPL570 |
|
Human Dendritic Cell L. major 4hrs biological rep3
|
Human Dendritic Cell L. major 4hrs
|
cell type: monocyte-derived dendritic cells
leishmania major infected: yes
time point: 4 hrs
|
Gene expression data from human monocyte derived dendritic cells, L. major infected, 4hrs
|
| Sample_geo_accession | GSM1032243
| | Sample_status | Public on Nov 08 2012
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | L. major parasites were maintained in complete M199 media (supplemented with 20% FBS). Metacyclic promastigotes were isolated using a ficol density gradient protocol and opsonized by treatment with 5% human serum for 30 min at 37°C. Metacyclic promastigotes were utilized for infection of the monocyte-derived human dendritic cells
| | Sample_growth_protocol_ch1 | Monocyte-derived human dendritic cells were maintained in RPMI-complete media (10% FBS, 2mM l-glutamine 100U/ml, 1% penicillin/streptomycin) at 37°C
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Uninfected and L. major infected samples were harvested at 2, 4, 8, or 24hrs post infection. Total RNA was extracted from each sample utilzing an RNEasy kit according to manufacturer's protocols (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to standard Affymetrix protocol from 2μg of total RNA according to manufacturer's protocols (Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Purified cRNA was fragmented in 5X fragmentation buffer (200mM Tris-Acetate, pH8.1, 500mM potassium acetate, 150mM magnesium acetate) at 94ºC for 35 min prior to cRNA chip hybridization. Gene chips were washed and stained utilizing the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | Gene chips were scanned with the Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA)
| | Sample_data_processing | The Affymetrix data files (.cel) were processed using Bioconductor software package (http://www.bioconductor.org/, Seattle, WA) [13]. Probe set signal intensities were subjected to background correction by GCRMA (Genespring GX 7.0) normalization across all 15 chips. The mean fluorescence intensity was derived from a log2 transformation of the raw data. Probe sets with “present” call in at least 7 of the 15 chips were retained, which filtered our list of 54,000 probe sets down to ~14,000. Statistical significance was determined using a one-way ANOVA and Benjamini-Yekutieli multiple correction test to control false discovery rates. A final set of 848 candidate probe set were identified as significantly expressed in at least one time point compared to non-infected samples (p<0.05).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michelle,A,Favila
| | Sample_contact_email | michellefavila@gmail.com
| | Sample_contact_laboratory | Mary Ann McDowell
| | Sample_contact_department | Biology
| | Sample_contact_institute | University of Notre Dame
| | Sample_contact_address | 210 Galvin Life Science Center
| | Sample_contact_city | Notre Dame
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46556
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1032nnn/GSM1032243/suppl/GSM1032243.CEL.gz
| | Sample_series_id | GSE42088
| | Sample_data_row_count | 54613
| | |
|
GSM1032244 | GPL570 |
|
Human Dendritic Cell L. major 8hrs biological rep1
|
Human Dendritic Cell L. major 8hrs
|
cell type: monocyte-derived dendritic cells
leishmania major infected: yes
time point: 8 hrs
|
Gene expression data from human monocyte derived dendritic cells, L. major infected, 8hrs
|
| Sample_geo_accession | GSM1032244
| | Sample_status | Public on Nov 08 2012
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | L. major parasites were maintained in complete M199 media (supplemented with 20% FBS). Metacyclic promastigotes were isolated using a ficol density gradient protocol and opsonized by treatment with 5% human serum for 30 min at 37°C. Metacyclic promastigotes were utilized for infection of the monocyte-derived human dendritic cells
| | Sample_growth_protocol_ch1 | Monocyte-derived human dendritic cells were maintained in RPMI-complete media (10% FBS, 2mM l-glutamine 100U/ml, 1% penicillin/streptomycin) at 37°C
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Uninfected and L. major infected samples were harvested at 2, 4, 8, or 24hrs post infection. Total RNA was extracted from each sample utilzing an RNEasy kit according to manufacturer's protocols (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to standard Affymetrix protocol from 2μg of total RNA according to manufacturer's protocols (Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Purified cRNA was fragmented in 5X fragmentation buffer (200mM Tris-Acetate, pH8.1, 500mM potassium acetate, 150mM magnesium acetate) at 94ºC for 35 min prior to cRNA chip hybridization. Gene chips were washed and stained utilizing the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | Gene chips were scanned with the Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA)
| | Sample_data_processing | The Affymetrix data files (.cel) were processed using Bioconductor software package (http://www.bioconductor.org/, Seattle, WA) [13]. Probe set signal intensities were subjected to background correction by GCRMA (Genespring GX 7.0) normalization across all 15 chips. The mean fluorescence intensity was derived from a log2 transformation of the raw data. Probe sets with “present” call in at least 7 of the 15 chips were retained, which filtered our list of 54,000 probe sets down to ~14,000. Statistical significance was determined using a one-way ANOVA and Benjamini-Yekutieli multiple correction test to control false discovery rates. A final set of 848 candidate probe set were identified as significantly expressed in at least one time point compared to non-infected samples (p<0.05).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michelle,A,Favila
| | Sample_contact_email | michellefavila@gmail.com
| | Sample_contact_laboratory | Mary Ann McDowell
| | Sample_contact_department | Biology
| | Sample_contact_institute | University of Notre Dame
| | Sample_contact_address | 210 Galvin Life Science Center
| | Sample_contact_city | Notre Dame
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46556
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1032nnn/GSM1032244/suppl/GSM1032244.CEL.gz
| | Sample_series_id | GSE42088
| | Sample_data_row_count | 54613
| | |
|
GSM1032245 | GPL570 |
|
Human Dendritic Cell L. major 8hrs biological rep2
|
Human Dendritic Cell L. major 8hrs
|
cell type: monocyte-derived dendritic cells
leishmania major infected: yes
time point: 8 hrs
|
Gene expression data from human monocyte derived dendritic cells, L. major infected, 8hrs
|
| Sample_geo_accession | GSM1032245
| | Sample_status | Public on Nov 08 2012
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | L. major parasites were maintained in complete M199 media (supplemented with 20% FBS). Metacyclic promastigotes were isolated using a ficol density gradient protocol and opsonized by treatment with 5% human serum for 30 min at 37°C. Metacyclic promastigotes were utilized for infection of the monocyte-derived human dendritic cells
| | Sample_growth_protocol_ch1 | Monocyte-derived human dendritic cells were maintained in RPMI-complete media (10% FBS, 2mM l-glutamine 100U/ml, 1% penicillin/streptomycin) at 37°C
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Uninfected and L. major infected samples were harvested at 2, 4, 8, or 24hrs post infection. Total RNA was extracted from each sample utilzing an RNEasy kit according to manufacturer's protocols (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to standard Affymetrix protocol from 2μg of total RNA according to manufacturer's protocols (Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Purified cRNA was fragmented in 5X fragmentation buffer (200mM Tris-Acetate, pH8.1, 500mM potassium acetate, 150mM magnesium acetate) at 94ºC for 35 min prior to cRNA chip hybridization. Gene chips were washed and stained utilizing the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | Gene chips were scanned with the Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA)
| | Sample_data_processing | The Affymetrix data files (.cel) were processed using Bioconductor software package (http://www.bioconductor.org/, Seattle, WA) [13]. Probe set signal intensities were subjected to background correction by GCRMA (Genespring GX 7.0) normalization across all 15 chips. The mean fluorescence intensity was derived from a log2 transformation of the raw data. Probe sets with “present” call in at least 7 of the 15 chips were retained, which filtered our list of 54,000 probe sets down to ~14,000. Statistical significance was determined using a one-way ANOVA and Benjamini-Yekutieli multiple correction test to control false discovery rates. A final set of 848 candidate probe set were identified as significantly expressed in at least one time point compared to non-infected samples (p<0.05).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michelle,A,Favila
| | Sample_contact_email | michellefavila@gmail.com
| | Sample_contact_laboratory | Mary Ann McDowell
| | Sample_contact_department | Biology
| | Sample_contact_institute | University of Notre Dame
| | Sample_contact_address | 210 Galvin Life Science Center
| | Sample_contact_city | Notre Dame
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46556
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1032nnn/GSM1032245/suppl/GSM1032245.CEL.gz
| | Sample_series_id | GSE42088
| | Sample_data_row_count | 54613
| | |
|
GSM1032246 | GPL570 |
|
Human Dendritic Cell L. major 8hrs biological rep3
|
Human Dendritic Cell L. major 8hrs
|
cell type: monocyte-derived dendritic cells
leishmania major infected: yes
time point: 8 hrs
|
Gene expression data from human monocyte derived dendritic cells, L. major infected, 8hrs
|
| Sample_geo_accession | GSM1032246
| | Sample_status | Public on Nov 08 2012
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | L. major parasites were maintained in complete M199 media (supplemented with 20% FBS). Metacyclic promastigotes were isolated using a ficol density gradient protocol and opsonized by treatment with 5% human serum for 30 min at 37°C. Metacyclic promastigotes were utilized for infection of the monocyte-derived human dendritic cells
| | Sample_growth_protocol_ch1 | Monocyte-derived human dendritic cells were maintained in RPMI-complete media (10% FBS, 2mM l-glutamine 100U/ml, 1% penicillin/streptomycin) at 37°C
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Uninfected and L. major infected samples were harvested at 2, 4, 8, or 24hrs post infection. Total RNA was extracted from each sample utilzing an RNEasy kit according to manufacturer's protocols (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to standard Affymetrix protocol from 2μg of total RNA according to manufacturer's protocols (Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Purified cRNA was fragmented in 5X fragmentation buffer (200mM Tris-Acetate, pH8.1, 500mM potassium acetate, 150mM magnesium acetate) at 94ºC for 35 min prior to cRNA chip hybridization. Gene chips were washed and stained utilizing the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | Gene chips were scanned with the Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA)
| | Sample_data_processing | The Affymetrix data files (.cel) were processed using Bioconductor software package (http://www.bioconductor.org/, Seattle, WA) [13]. Probe set signal intensities were subjected to background correction by GCRMA (Genespring GX 7.0) normalization across all 15 chips. The mean fluorescence intensity was derived from a log2 transformation of the raw data. Probe sets with “present” call in at least 7 of the 15 chips were retained, which filtered our list of 54,000 probe sets down to ~14,000. Statistical significance was determined using a one-way ANOVA and Benjamini-Yekutieli multiple correction test to control false discovery rates. A final set of 848 candidate probe set were identified as significantly expressed in at least one time point compared to non-infected samples (p<0.05).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michelle,A,Favila
| | Sample_contact_email | michellefavila@gmail.com
| | Sample_contact_laboratory | Mary Ann McDowell
| | Sample_contact_department | Biology
| | Sample_contact_institute | University of Notre Dame
| | Sample_contact_address | 210 Galvin Life Science Center
| | Sample_contact_city | Notre Dame
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46556
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1032nnn/GSM1032246/suppl/GSM1032246.CEL.gz
| | Sample_series_id | GSE42088
| | Sample_data_row_count | 54613
| | |
|
GSM1032247 | GPL570 |
|
Human Dendritic Cell L. major 24hrs biological rep1
|
Human Dendritic Cell L. major 24hrs
|
cell type: monocyte-derived dendritic cells
leishmania major infected: yes
time point: 24 hrs
|
Gene expression data from human monocyte derived dendritic cells, L. major infected, 24hrs
|
| Sample_geo_accession | GSM1032247
| | Sample_status | Public on Nov 08 2012
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | L. major parasites were maintained in complete M199 media (supplemented with 20% FBS). Metacyclic promastigotes were isolated using a ficol density gradient protocol and opsonized by treatment with 5% human serum for 30 min at 37°C. Metacyclic promastigotes were utilized for infection of the monocyte-derived human dendritic cells
| | Sample_growth_protocol_ch1 | Monocyte-derived human dendritic cells were maintained in RPMI-complete media (10% FBS, 2mM l-glutamine 100U/ml, 1% penicillin/streptomycin) at 37°C
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Uninfected and L. major infected samples were harvested at 2, 4, 8, or 24hrs post infection. Total RNA was extracted from each sample utilzing an RNEasy kit according to manufacturer's protocols (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to standard Affymetrix protocol from 2μg of total RNA according to manufacturer's protocols (Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Purified cRNA was fragmented in 5X fragmentation buffer (200mM Tris-Acetate, pH8.1, 500mM potassium acetate, 150mM magnesium acetate) at 94ºC for 35 min prior to cRNA chip hybridization. Gene chips were washed and stained utilizing the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | Gene chips were scanned with the Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA)
| | Sample_data_processing | The Affymetrix data files (.cel) were processed using Bioconductor software package (http://www.bioconductor.org/, Seattle, WA) [13]. Probe set signal intensities were subjected to background correction by GCRMA (Genespring GX 7.0) normalization across all 15 chips. The mean fluorescence intensity was derived from a log2 transformation of the raw data. Probe sets with “present” call in at least 7 of the 15 chips were retained, which filtered our list of 54,000 probe sets down to ~14,000. Statistical significance was determined using a one-way ANOVA and Benjamini-Yekutieli multiple correction test to control false discovery rates. A final set of 848 candidate probe set were identified as significantly expressed in at least one time point compared to non-infected samples (p<0.05).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michelle,A,Favila
| | Sample_contact_email | michellefavila@gmail.com
| | Sample_contact_laboratory | Mary Ann McDowell
| | Sample_contact_department | Biology
| | Sample_contact_institute | University of Notre Dame
| | Sample_contact_address | 210 Galvin Life Science Center
| | Sample_contact_city | Notre Dame
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46556
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1032nnn/GSM1032247/suppl/GSM1032247.CEL.gz
| | Sample_series_id | GSE42088
| | Sample_data_row_count | 54613
| | |
|
GSM1032248 | GPL570 |
|
Human Dendritic Cell L. major 24hrs biological rep2
|
Human Dendritic Cell L. major 24hrs
|
cell type: monocyte-derived dendritic cells
leishmania major infected: yes
time point: 24 hrs
|
Gene expression data from human monocyte derived dendritic cells, L. major infected, 24hrs
|
| Sample_geo_accession | GSM1032248
| | Sample_status | Public on Nov 08 2012
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | L. major parasites were maintained in complete M199 media (supplemented with 20% FBS). Metacyclic promastigotes were isolated using a ficol density gradient protocol and opsonized by treatment with 5% human serum for 30 min at 37°C. Metacyclic promastigotes were utilized for infection of the monocyte-derived human dendritic cells
| | Sample_growth_protocol_ch1 | Monocyte-derived human dendritic cells were maintained in RPMI-complete media (10% FBS, 2mM l-glutamine 100U/ml, 1% penicillin/streptomycin) at 37°C
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Uninfected and L. major infected samples were harvested at 2, 4, 8, or 24hrs post infection. Total RNA was extracted from each sample utilzing an RNEasy kit according to manufacturer's protocols (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to standard Affymetrix protocol from 2μg of total RNA according to manufacturer's protocols (Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Purified cRNA was fragmented in 5X fragmentation buffer (200mM Tris-Acetate, pH8.1, 500mM potassium acetate, 150mM magnesium acetate) at 94ºC for 35 min prior to cRNA chip hybridization. Gene chips were washed and stained utilizing the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | Gene chips were scanned with the Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA)
| | Sample_data_processing | The Affymetrix data files (.cel) were processed using Bioconductor software package (http://www.bioconductor.org/, Seattle, WA) [13]. Probe set signal intensities were subjected to background correction by GCRMA (Genespring GX 7.0) normalization across all 15 chips. The mean fluorescence intensity was derived from a log2 transformation of the raw data. Probe sets with “present” call in at least 7 of the 15 chips were retained, which filtered our list of 54,000 probe sets down to ~14,000. Statistical significance was determined using a one-way ANOVA and Benjamini-Yekutieli multiple correction test to control false discovery rates. A final set of 848 candidate probe set were identified as significantly expressed in at least one time point compared to non-infected samples (p<0.05).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michelle,A,Favila
| | Sample_contact_email | michellefavila@gmail.com
| | Sample_contact_laboratory | Mary Ann McDowell
| | Sample_contact_department | Biology
| | Sample_contact_institute | University of Notre Dame
| | Sample_contact_address | 210 Galvin Life Science Center
| | Sample_contact_city | Notre Dame
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46556
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1032nnn/GSM1032248/suppl/GSM1032248.CEL.gz
| | Sample_series_id | GSE42088
| | Sample_data_row_count | 54613
| | |
|
GSM1032249 | GPL570 |
|
Human Dendritic Cell L. major 24hrs biological rep3
|
Human Dendritic Cell L. major 24hrs
|
cell type: monocyte-derived dendritic cells
leishmania major infected: yes
time point: 24 hrs
|
Gene expression data from human monocyte derived dendritic cells, L. major infected, 24hrs
|
| Sample_geo_accession | GSM1032249
| | Sample_status | Public on Nov 08 2012
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Nov 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | L. major parasites were maintained in complete M199 media (supplemented with 20% FBS). Metacyclic promastigotes were isolated using a ficol density gradient protocol and opsonized by treatment with 5% human serum for 30 min at 37°C. Metacyclic promastigotes were utilized for infection of the monocyte-derived human dendritic cells
| | Sample_growth_protocol_ch1 | Monocyte-derived human dendritic cells were maintained in RPMI-complete media (10% FBS, 2mM l-glutamine 100U/ml, 1% penicillin/streptomycin) at 37°C
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Uninfected and L. major infected samples were harvested at 2, 4, 8, or 24hrs post infection. Total RNA was extracted from each sample utilzing an RNEasy kit according to manufacturer's protocols (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to standard Affymetrix protocol from 2μg of total RNA according to manufacturer's protocols (Affymetrix, Santa Clara, CA)
| | Sample_hyb_protocol | Purified cRNA was fragmented in 5X fragmentation buffer (200mM Tris-Acetate, pH8.1, 500mM potassium acetate, 150mM magnesium acetate) at 94ºC for 35 min prior to cRNA chip hybridization. Gene chips were washed and stained utilizing the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | Gene chips were scanned with the Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA)
| | Sample_data_processing | The Affymetrix data files (.cel) were processed using Bioconductor software package (http://www.bioconductor.org/, Seattle, WA) [13]. Probe set signal intensities were subjected to background correction by GCRMA (Genespring GX 7.0) normalization across all 15 chips. The mean fluorescence intensity was derived from a log2 transformation of the raw data. Probe sets with “present” call in at least 7 of the 15 chips were retained, which filtered our list of 54,000 probe sets down to ~14,000. Statistical significance was determined using a one-way ANOVA and Benjamini-Yekutieli multiple correction test to control false discovery rates. A final set of 848 candidate probe set were identified as significantly expressed in at least one time point compared to non-infected samples (p<0.05).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michelle,A,Favila
| | Sample_contact_email | michellefavila@gmail.com
| | Sample_contact_laboratory | Mary Ann McDowell
| | Sample_contact_department | Biology
| | Sample_contact_institute | University of Notre Dame
| | Sample_contact_address | 210 Galvin Life Science Center
| | Sample_contact_city | Notre Dame
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46556
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1032nnn/GSM1032249/suppl/GSM1032249.CEL.gz
| | Sample_series_id | GSE42088
| | Sample_data_row_count | 54613
| | |
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