Search results for the GEO ID: GSE29628  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM734300 | GPL570 |
|
PMA-treated THP-1 cells as non-infection control
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PMA-treated THP-1 cells as non-infection control
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cell line: THP-1 cells
m. tuberculosis strain: Control
infection time: 0h
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PMA-treated THP-1 cells as non-infection control
|
| Sample_geo_accession | GSM734300
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734300/suppl/GSM734300.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734301 | GPL570 |
|
THP1-cells infected by R1.4 strains at 4h
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THP1-cells infected by R1.4 strains at 4h
|
cell line: THP-1 cells
m. tuberculosis strain: R1.4
infection time: 4h
|
THP1-cells infected by R1.4 strains at 4h
|
| Sample_geo_accession | GSM734301
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734301/suppl/GSM734301.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734302 | GPL570 |
|
THP1-cells infected by R1.4 strains at 18h
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THP1-cells infected by R1.4 strains at 18h
|
cell line: THP-1 cells
m. tuberculosis strain: R1.4
infection time: 18h
|
THP1-cells infected by R1.4 strains at 18h
|
| Sample_geo_accession | GSM734302
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734302/suppl/GSM734302.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734303 | GPL570 |
|
THP1-cells infected by R1.4 strains at 48h
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THP1-cells infected by R1.4 strains at 48h
|
cell line: THP-1 cells
m. tuberculosis strain: R1.4
infection time: 48h
|
THP1-cells infected by R1.4 strains at 48h
|
| Sample_geo_accession | GSM734303
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734303/suppl/GSM734303.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734304 | GPL570 |
|
THP1-cells infected by R17.1 strains at 4h
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THP1-cells infected by R17.1 strains at 4h
|
cell line: THP-1 cells
m. tuberculosis strain: R17.1
infection time: 4h
|
THP1-cells infected by R17.1 strains at 4h
|
| Sample_geo_accession | GSM734304
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734304/suppl/GSM734304.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734305 | GPL570 |
|
THP1-cells infected by R17.1 strains at 18h
|
THP1-cells infected by R17.1 strains at 18h
|
cell line: THP-1 cells
m. tuberculosis strain: R17.1
infection time: 18h
|
THP1-cells infected by R17.1 strains at 18h
|
| Sample_geo_accession | GSM734305
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734305/suppl/GSM734305.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734306 | GPL570 |
|
THP1-cells infected by R17.1 strains at 48h
|
THP1-cells infected by R17.1 strains at 48h
|
cell line: THP-1 cells
m. tuberculosis strain: R17.1
infection time: 48h
|
THP1-cells infected by R17.1 strains at 48h
|
| Sample_geo_accession | GSM734306
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734306/suppl/GSM734306.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734307 | GPL570 |
|
THP1-cells infected by ZA9.2 strains at 4h
|
THP1-cells infected by ZA9.2 strains at 4h
|
cell line: THP-1 cells
m. tuberculosis strain: ZA9.2
infection time: 4h
|
THP1-cells infected by ZA9.2 strains at 4h
|
| Sample_geo_accession | GSM734307
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734307/suppl/GSM734307.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734308 | GPL570 |
|
THP1-cells infected by ZA9.2 strains at 18h
|
THP1-cells infected by ZA9.2 strains at 18h
|
cell line: THP-1 cells
m. tuberculosis strain: ZA9.2
infection time: 18h
|
THP1-cells infected by ZA9.2 strains at 18h
|
| Sample_geo_accession | GSM734308
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734308/suppl/GSM734308.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734309 | GPL570 |
|
THP1-cells infected by ZA9.2 strains at 48h
|
THP1-cells infected by ZA9.2 strains at 48h
|
cell line: THP-1 cells
m. tuberculosis strain: ZA9.2
infection time: 48h
|
THP1-cells infected by ZA9.2 strains at 48h
|
| Sample_geo_accession | GSM734309
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734309/suppl/GSM734309.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734310 | GPL570 |
|
THP1-cells infected by ZA9.4 strains at 4h
|
THP1-cells infected by ZA9.4 strains at 4h
|
cell line: THP-1 cells
m. tuberculosis strain: ZA9.4
infection time: 4h
|
THP1-cells infected by ZA9.4 strains at 4h
|
| Sample_geo_accession | GSM734310
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734310/suppl/GSM734310.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734311 | GPL570 |
|
THP1-cells infected by ZA9.4 strains at 18h
|
THP1-cells infected by ZA9.4 strains at 18h
|
cell line: THP-1 cells
m. tuberculosis strain: ZA9.4
infection time: 18h
|
THP1-cells infected by ZA9.4 strains at 18h
|
| Sample_geo_accession | GSM734311
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734311/suppl/GSM734311.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734312 | GPL570 |
|
THP1-cells infected by ZA9.4 strains at 48h
|
THP1-cells infected by ZA9.4 strains at 48h
|
cell line: THP-1 cells
m. tuberculosis strain: ZA9.4
infection time: 48h
|
THP1-cells infected by ZA9.4 strains at 48h
|
| Sample_geo_accession | GSM734312
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734312/suppl/GSM734312.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734313 | GPL570 |
|
THP1-cells infected by R19.4 strains at 4h
|
THP1-cells infected by R19.4 strains at 4h
|
cell line: THP-1 cells
m. tuberculosis strain: R19.4
infection time: 4h
|
THP1-cells infected by R19.4 strains at 4h
|
| Sample_geo_accession | GSM734313
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734313/suppl/GSM734313.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734314 | GPL570 |
|
THP1-cells infected by R19.4 strains at 18h
|
THP1-cells infected by R19.4 strains at 18h
|
cell line: THP-1 cells
m. tuberculosis strain: R19.4
infection time: 18h
|
THP1-cells infected by R19.4 strains at 18h
|
| Sample_geo_accession | GSM734314
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734314/suppl/GSM734314.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734315 | GPL570 |
|
THP1-cells infected by R19.4 strains at 48h
|
THP1-cells infected by R19.4 strains at 48h
|
cell line: THP-1 cells
m. tuberculosis strain: R19.4
infection time: 48h
|
THP1-cells infected by R19.4 strains at 48h
|
| Sample_geo_accession | GSM734315
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734315/suppl/GSM734315.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734316 | GPL570 |
|
THP1-cells infected by CHN50.1 strains at 4h
|
THP1-cells infected by CHN50.1 strains at 4h
|
cell line: THP-1 cells
m. tuberculosis strain: CHN50.1
infection time: 4h
|
THP1-cells infected by CHN50.1 strains at 4h
|
| Sample_geo_accession | GSM734316
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734316/suppl/GSM734316.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734317 | GPL570 |
|
THP1-cells infected by CHN50.1 strains at 18h
|
THP1-cells infected by CHN50.1 strains at 18h
|
cell line: THP-1 cells
m. tuberculosis strain: CHN50.1
infection time: 18h
|
THP1-cells infected by CHN50.1 strains at 18h
|
| Sample_geo_accession | GSM734317
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734317/suppl/GSM734317.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734318 | GPL570 |
|
THP1-cells infected by CHN50.1 strains at 48h
|
THP1-cells infected by CHN50.1 strains at 48h
|
cell line: THP-1 cells
m. tuberculosis strain: CHN50.1
infection time: 48h
|
THP1-cells infected by CHN50.1 strains at 48h
|
| Sample_geo_accession | GSM734318
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734318/suppl/GSM734318.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734319 | GPL570 |
|
THP1-cells infected by MAD2.1 strains at 4h
|
THP1-cells infected by MAD2.1 strains at 4h
|
cell line: THP-1 cells
m. tuberculosis strain: MAD2.1
infection time: 4h
|
THP1-cells infected by MAD2.1 strains at 4h
|
| Sample_geo_accession | GSM734319
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734319/suppl/GSM734319.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734320 | GPL570 |
|
THP1-cells infected by MAD2.1 strains at 18h
|
THP1-cells infected by MAD2.1 strains at 18h
|
cell line: THP-1 cells
m. tuberculosis strain: MAD2.1
infection time: 18h
|
THP1-cells infected by MAD2.1 strains at 18h
|
| Sample_geo_accession | GSM734320
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734320/suppl/GSM734320.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734321 | GPL570 |
|
THP1-cells infected by MAD2.1 strains at 48h
|
THP1-cells infected by MAD2.1 strains at 48h
|
cell line: THP-1 cells
m. tuberculosis strain: MAD2.1
infection time: 48h
|
THP1-cells infected by MAD2.1 strains at 48h
|
| Sample_geo_accession | GSM734321
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734321/suppl/GSM734321.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734322 | GPL570 |
|
THP1-cells infected by CHN50.2 strains at 4h
|
THP1-cells infected by CHN50.2 strains at 4h
|
cell line: THP-1 cells
m. tuberculosis strain: CHN50.2
infection time: 4h
|
THP1-cells infected by CHN50.2 strains at 4h
|
| Sample_geo_accession | GSM734322
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734322/suppl/GSM734322.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734323 | GPL570 |
|
THP1-cells infected by CHN50.2 strains at 18h
|
THP1-cells infected by CHN50.2 strains at 18h
|
cell line: THP-1 cells
m. tuberculosis strain: CHN50.2
infection time: 18h
|
THP1-cells infected by CHN50.2 strains at 18h
|
| Sample_geo_accession | GSM734323
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734323/suppl/GSM734323.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734324 | GPL570 |
|
THP1-cells infected by CHN50.2 strains at 48h
|
THP1-cells infected by CHN50.2 strains at 48h
|
cell line: THP-1 cells
m. tuberculosis strain: CHN50.2
infection time: 48h
|
THP1-cells infected by CHN50.2 strains at 48h
|
| Sample_geo_accession | GSM734324
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734324/suppl/GSM734324.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734325 | GPL570 |
|
THP1-cells infected by R17.3 strains at 4h
|
THP1-cells infected by R17.3 strains at 4h
|
cell line: THP-1 cells
m. tuberculosis strain: R17.3
infection time: 4h
|
THP1-cells infected by R17.3 strains at 4h
|
| Sample_geo_accession | GSM734325
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734325/suppl/GSM734325.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734326 | GPL570 |
|
THP1-cells infected by R17.3 strains at 18h
|
THP1-cells infected by R17.3 strains at 18h
|
cell line: THP-1 cells
m. tuberculosis strain: R17.3
infection time: 18h
|
THP1-cells infected by R17.3 strains at 18h
|
| Sample_geo_accession | GSM734326
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734326/suppl/GSM734326.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734327 | GPL570 |
|
THP1-cells infected by R17.3 strains at 48h
|
THP1-cells infected by R17.3 strains at 48h
|
cell line: THP-1 cells
m. tuberculosis strain: R17.3
infection time: 48h
|
THP1-cells infected by R17.3 strains at 48h
|
| Sample_geo_accession | GSM734327
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734327/suppl/GSM734327.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734328 | GPL570 |
|
THP1-cells infected by 19.5 strains at 4h
|
THP1-cells infected by 19.5 strains at 4h
|
cell line: THP-1 cells
m. tuberculosis strain: R19.5
infection time: 4h
|
THP1-cells infected by 19.5 strains at 4h
|
| Sample_geo_accession | GSM734328
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734328/suppl/GSM734328.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734329 | GPL570 |
|
THP1-cells infected by 19.5 strains at 18h
|
THP1-cells infected by 19.5 strains at 18h
|
cell line: THP-1 cells
m. tuberculosis strain: R19.5
infection time: 18h
|
THP1-cells infected by 19.5 strains at 18h
|
| Sample_geo_accession | GSM734329
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734329/suppl/GSM734329.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734330 | GPL570 |
|
THP1-cells infected by 19.5 strains at 48h
|
THP1-cells infected by 19.5 strains at 48h
|
cell line: THP-1 cells
m. tuberculosis strain: R19.5
infection time: 48h
|
THP1-cells infected by 19.5 strains at 48h
|
| Sample_geo_accession | GSM734330
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734330/suppl/GSM734330.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734331 | GPL570 |
|
THP1-cells infected by H37Rv strains at 4h, Replication 1
|
THP1-cells infected by H37Rv strains at 4h, Replication 1
|
cell line: THP-1 cells
m. tuberculosis strain: H37Rv
infection time: 4h
|
THP1-cells infected by H37Rv strains at 4h, Replication 1
|
| Sample_geo_accession | GSM734331
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734331/suppl/GSM734331.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734332 | GPL570 |
|
THP1-cells infected by H37Rv strains at 18h, Replication 1
|
THP1-cells infected by H37Rv strains at 18h, Replication 1
|
cell line: THP-1 cells
m. tuberculosis strain: H37Rv
infection time: 18h
|
THP1-cells infected by H37Rv strains at 18h, Replication 1
|
| Sample_geo_accession | GSM734332
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734332/suppl/GSM734332.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734333 | GPL570 |
|
THP1-cells infected by H37Rv strains at 48h, Replication 1
|
THP1-cells infected by H37Rv strains at 48h, Replication 1
|
cell line: THP-1 cells
m. tuberculosis strain: H37Rv
infection time: 48h
|
THP1-cells infected by H37Rv strains at 48h, Replication 1
|
| Sample_geo_accession | GSM734333
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734333/suppl/GSM734333.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734334 | GPL570 |
|
THP1-cells infected by H37Rv strains at 4h, Replication 2
|
THP1-cells infected by H37Rv strains at 4h, Replication 2
|
cell line: THP-1 cells
m. tuberculosis strain: H37Rv
infection time: 4h
|
THP1-cells infected by H37Rv strains at 4h, Replication 2
|
| Sample_geo_accession | GSM734334
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734334/suppl/GSM734334.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734335 | GPL570 |
|
THP1-cells infected by H37Rv strains at 18h, Replication 2
|
THP1-cells infected by H37Rv strains at 18h, Replication 2
|
cell line: THP-1 cells
m. tuberculosis strain: H37Rv
infection time: 18h
|
THP1-cells infected by H37Rv strains at 18h, Replication 2
|
| Sample_geo_accession | GSM734335
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734335/suppl/GSM734335.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734336 | GPL570 |
|
THP1-cells infected by H37Rv strains at 48h, Replication 2
|
THP1-cells infected by H37Rv strains at 48h, Replication 2
|
cell line: THP-1 cells
m. tuberculosis strain: H37Rv
infection time: 48h
|
THP1-cells infected by H37Rv strains at 48h, Replication 2
|
| Sample_geo_accession | GSM734336
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734336/suppl/GSM734336.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734337 | GPL570 |
|
THP1-cells infected by MAD2.2 strains at 4h
|
THP1-cells infected by MAD2.2 strains at 4h
|
cell line: THP-1 cells
m. tuberculosis strain: MAD2.2
infection time: 4h
|
THP1-cells infected by MAD2.2 strains at 4h
|
| Sample_geo_accession | GSM734337
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734337/suppl/GSM734337.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734338 | GPL570 |
|
THP1-cells infected by MAD2.2 strains at 18h
|
THP1-cells infected by MAD2.2 strains at 18h
|
cell line: THP-1 cells
m. tuberculosis strain: MAD2.2
infection time: 18h
|
THP1-cells infected by MAD2.2 strains at 18h
|
| Sample_geo_accession | GSM734338
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734338/suppl/GSM734338.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
|
GSM734339 | GPL570 |
|
THP1-cells infected by MAD2.2 strains at 48h
|
THP1-cells infected by MAD2.2 strains at 48h
|
cell line: THP-1 cells
m. tuberculosis strain: MAD2.2
infection time: 48h
|
THP1-cells infected by MAD2.2 strains at 48h
|
| Sample_geo_accession | GSM734339
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | May 31 2011
| | Sample_last_update_date | Dec 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
| | Sample_data_processing | These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734339/suppl/GSM734339.CEL.gz
| | Sample_series_id | GSE29628
| | Sample_data_row_count | 54675
| | |
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