Search results for the GEO ID: GSE44825 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1092119 | GPL1261 |
|
lung_not_treated_rep1
|
Lung from Infected mice not treated
|
strain: Balb/c
gender: female
tissue: lung
initial age (infection day): eight weeks old
infection (microorganism): 1.0 x 10e5 colony-forming units of Mycobacterium tuberculosis H37Rv
infection (route): intra-tracheal
final age at death: approximately 18 weeks old
death day: ten days after the end of therapy
|
Gene expression data from lung of mice infected with M. tuberculosis and not treated
|
Sample_geo_accession | GSM1092119
| Sample_status | Public on Apr 08 2013
| Sample_submission_date | Mar 04 2013
| Sample_last_update_date | Apr 08 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 100 ng total RNA (Affymetrix User Manual GeneChip 3’ IVT Express Kit).
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Array for 16 hr at 45°C and 60 rpm in GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| Sample_data_processing = Gene expression levels were normalized using the GC-RMA algorithm and flags were computed using MAS5. Quality assessment of the chips has been performed with affyQCReport R package. The “P50” probe list has been used for comparison according to flagged (A= absent; P | present) measurement in the chips. The “P50” list has been created filtering probes flagged as “Present” for at least two of the three chips of each group.
| Sample_platform_id | GPL1261
| Sample_contact_name | Rodrigo,Ferracine,Rodrigues
| Sample_contact_email | ferracine.rodrigues@gmail.com
| Sample_contact_institute | University of Sao Paulo
| Sample_contact_address | Avenida bandeirantes 3900
| Sample_contact_city | Ribeirao Preto
| Sample_contact_zip/postal_code | 14049-900
| Sample_contact_country | Brazil
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1092nnn/GSM1092119/suppl/GSM1092119_A_17.CEL.gz
| Sample_series_id | GSE44825
| Sample_data_row_count | 45101
| |
|
GSM1092120 | GPL1261 |
|
lung_not_treated_rep2
|
Lung from Infected mice not treated
|
strain: Balb/c
gender: female
tissue: lung
initial age (infection day): eight weeks old
infection (microorganism): 1.0 x 10e5 colony-forming units of Mycobacterium tuberculosis H37Rv
infection (route): intra-tracheal
final age at death: approximately 18 weeks old
death day: ten days after the end of therapy
|
Gene expression data from lung of mice infected with M. tuberculosis and not treated
|
Sample_geo_accession | GSM1092120
| Sample_status | Public on Apr 08 2013
| Sample_submission_date | Mar 04 2013
| Sample_last_update_date | Apr 08 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 100 ng total RNA (Affymetrix User Manual GeneChip 3’ IVT Express Kit).
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Array for 16 hr at 45°C and 60 rpm in GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| Sample_data_processing = Gene expression levels were normalized using the GC-RMA algorithm and flags were computed using MAS5. Quality assessment of the chips has been performed with affyQCReport R package. The “P50” probe list has been used for comparison according to flagged (A= absent; P | present) measurement in the chips. The “P50” list has been created filtering probes flagged as “Present” for at least two of the three chips of each group.
| Sample_platform_id | GPL1261
| Sample_contact_name | Rodrigo,Ferracine,Rodrigues
| Sample_contact_email | ferracine.rodrigues@gmail.com
| Sample_contact_institute | University of Sao Paulo
| Sample_contact_address | Avenida bandeirantes 3900
| Sample_contact_city | Ribeirao Preto
| Sample_contact_zip/postal_code | 14049-900
| Sample_contact_country | Brazil
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1092nnn/GSM1092120/suppl/GSM1092120_A_18.CEL.gz
| Sample_series_id | GSE44825
| Sample_data_row_count | 45101
| |
|
GSM1092121 | GPL1261 |
|
lung_not_treated_rep3
|
Lung from Infected mice not treated
|
strain: Balb/c
gender: female
tissue: lung
initial age (infection day): eight weeks old
infection (microorganism): 1.0 x 10e5 colony-forming units of Mycobacterium tuberculosis H37Rv
infection (route): intra-tracheal
final age at death: approximately 18 weeks old
death day: ten days after the end of therapy
|
Gene expression data from lung of mice infected with M. tuberculosis and not treated
|
Sample_geo_accession | GSM1092121
| Sample_status | Public on Apr 08 2013
| Sample_submission_date | Mar 04 2013
| Sample_last_update_date | Apr 08 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 100 ng total RNA (Affymetrix User Manual GeneChip 3’ IVT Express Kit).
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Array for 16 hr at 45°C and 60 rpm in GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| Sample_data_processing = Gene expression levels were normalized using the GC-RMA algorithm and flags were computed using MAS5. Quality assessment of the chips has been performed with affyQCReport R package. The “P50” probe list has been used for comparison according to flagged (A= absent; P | present) measurement in the chips. The “P50” list has been created filtering probes flagged as “Present” for at least two of the three chips of each group.
| Sample_platform_id | GPL1261
| Sample_contact_name | Rodrigo,Ferracine,Rodrigues
| Sample_contact_email | ferracine.rodrigues@gmail.com
| Sample_contact_institute | University of Sao Paulo
| Sample_contact_address | Avenida bandeirantes 3900
| Sample_contact_city | Ribeirao Preto
| Sample_contact_zip/postal_code | 14049-900
| Sample_contact_country | Brazil
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1092nnn/GSM1092121/suppl/GSM1092121_A_21.CEL.gz
| Sample_series_id | GSE44825
| Sample_data_row_count | 45101
| |
|
GSM1092122 | GPL1261 |
|
lung_immunotherapy_rep1
|
Lung from Infected mice that received DNAhsp65 immunotherapy
|
strain: Balb/c
gender: female
tissue: lung
initial age (infection day): eight weeks old
infection (microorganism): 1.0 x 10e5 colony-forming units of Mycobacterium tuberculosis H37Rv
infection (route): intra-tracheal
final age at death: approximately 18 weeks old
death day: ten days after the end of therapy
|
Gene expression data from lung of mice infected with M. tuberculosis and treated with DNAhsp65 immunotherapy
|
Sample_geo_accession | GSM1092122
| Sample_status | Public on Apr 08 2013
| Sample_submission_date | Mar 04 2013
| Sample_last_update_date | Apr 08 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 100 ng total RNA (Affymetrix User Manual GeneChip 3’ IVT Express Kit).
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Array for 16 hr at 45°C and 60 rpm in GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| Sample_data_processing = Gene expression levels were normalized using the GC-RMA algorithm and flags were computed using MAS5. Quality assessment of the chips has been performed with affyQCReport R package. The “P50” probe list has been used for comparison according to flagged (A= absent; P | present) measurement in the chips. The “P50” list has been created filtering probes flagged as “Present” for at least two of the three chips of each group.
| Sample_platform_id | GPL1261
| Sample_contact_name | Rodrigo,Ferracine,Rodrigues
| Sample_contact_email | ferracine.rodrigues@gmail.com
| Sample_contact_institute | University of Sao Paulo
| Sample_contact_address | Avenida bandeirantes 3900
| Sample_contact_city | Ribeirao Preto
| Sample_contact_zip/postal_code | 14049-900
| Sample_contact_country | Brazil
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1092nnn/GSM1092122/suppl/GSM1092122_B_24.CEL.gz
| Sample_series_id | GSE44825
| Sample_data_row_count | 45101
| |
|
GSM1092123 | GPL1261 |
|
lung_immunotherapy_rep2
|
Lung from Infected mice that received DNAhsp65 immunotherapy
|
strain: Balb/c
gender: female
tissue: lung
initial age (infection day): eight weeks old
infection (microorganism): 1.0 x 10e5 colony-forming units of Mycobacterium tuberculosis H37Rv
infection (route): intra-tracheal
final age at death: approximately 18 weeks old
death day: ten days after the end of therapy
|
Gene expression data from lung of mice infected with M. tuberculosis and treated with DNAhsp65 immunotherapy
|
Sample_geo_accession | GSM1092123
| Sample_status | Public on Apr 08 2013
| Sample_submission_date | Mar 04 2013
| Sample_last_update_date | Apr 08 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 100 ng total RNA (Affymetrix User Manual GeneChip 3’ IVT Express Kit).
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Array for 16 hr at 45°C and 60 rpm in GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| Sample_data_processing = Gene expression levels were normalized using the GC-RMA algorithm and flags were computed using MAS5. Quality assessment of the chips has been performed with affyQCReport R package. The “P50” probe list has been used for comparison according to flagged (A= absent; P | present) measurement in the chips. The “P50” list has been created filtering probes flagged as “Present” for at least two of the three chips of each group.
| Sample_platform_id | GPL1261
| Sample_contact_name | Rodrigo,Ferracine,Rodrigues
| Sample_contact_email | ferracine.rodrigues@gmail.com
| Sample_contact_institute | University of Sao Paulo
| Sample_contact_address | Avenida bandeirantes 3900
| Sample_contact_city | Ribeirao Preto
| Sample_contact_zip/postal_code | 14049-900
| Sample_contact_country | Brazil
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1092nnn/GSM1092123/suppl/GSM1092123_B_25.CEL.gz
| Sample_series_id | GSE44825
| Sample_data_row_count | 45101
| |
|
GSM1092124 | GPL1261 |
|
lung_immunotherapy_rep3
|
Lung from Infected mice that received DNAhsp65 immunotherapy
|
strain: Balb/c
gender: female
tissue: lung
initial age (infection day): eight weeks old
infection (microorganism): 1.0 x 10e5 colony-forming units of Mycobacterium tuberculosis H37Rv
infection (route): intra-tracheal
final age at death: approximately 18 weeks old
death day: ten days after the end of therapy
|
Gene expression data from lung of mice infected with M. tuberculosis and treated with DNAhsp65 immunotherapy
|
Sample_geo_accession | GSM1092124
| Sample_status | Public on Apr 08 2013
| Sample_submission_date | Mar 04 2013
| Sample_last_update_date | Apr 08 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 100 ng total RNA (Affymetrix User Manual GeneChip 3’ IVT Express Kit).
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Array for 16 hr at 45°C and 60 rpm in GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| Sample_data_processing = Gene expression levels were normalized using the GC-RMA algorithm and flags were computed using MAS5. Quality assessment of the chips has been performed with affyQCReport R package. The “P50” probe list has been used for comparison according to flagged (A= absent; P | present) measurement in the chips. The “P50” list has been created filtering probes flagged as “Present” for at least two of the three chips of each group.
| Sample_platform_id | GPL1261
| Sample_contact_name | Rodrigo,Ferracine,Rodrigues
| Sample_contact_email | ferracine.rodrigues@gmail.com
| Sample_contact_institute | University of Sao Paulo
| Sample_contact_address | Avenida bandeirantes 3900
| Sample_contact_city | Ribeirao Preto
| Sample_contact_zip/postal_code | 14049-900
| Sample_contact_country | Brazil
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1092nnn/GSM1092124/suppl/GSM1092124_B_28.CEL.gz
| Sample_series_id | GSE44825
| Sample_data_row_count | 45101
| |
|
GSM1092125 | GPL1261 |
|
lung_chemotherapy_rep1
|
Lung from Infected mice that received isoniazid and rifampicin chemotherapy
|
strain: Balb/c
gender: female
tissue: lung
initial age (infection day): eight weeks old
infection (microorganism): 1.0 x 10e5 colony-forming units of Mycobacterium tuberculosis H37Rv
infection (route): intra-tracheal
final age at death: approximately 18 weeks old
death day: ten days after the end of therapy
|
Gene expression data from lung of mice infected with M. tuberculosis and treated with isoniazid and rifampicin drugs
|
Sample_geo_accession | GSM1092125
| Sample_status | Public on Apr 08 2013
| Sample_submission_date | Mar 04 2013
| Sample_last_update_date | Apr 08 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 100 ng total RNA (Affymetrix User Manual GeneChip 3’ IVT Express Kit).
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Array for 16 hr at 45°C and 60 rpm in GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| Sample_data_processing = Gene expression levels were normalized using the GC-RMA algorithm and flags were computed using MAS5. Quality assessment of the chips has been performed with affyQCReport R package. The “P50” probe list has been used for comparison according to flagged (A= absent; P | present) measurement in the chips. The “P50” list has been created filtering probes flagged as “Present” for at least two of the three chips of each group.
| Sample_platform_id | GPL1261
| Sample_contact_name | Rodrigo,Ferracine,Rodrigues
| Sample_contact_email | ferracine.rodrigues@gmail.com
| Sample_contact_institute | University of Sao Paulo
| Sample_contact_address | Avenida bandeirantes 3900
| Sample_contact_city | Ribeirao Preto
| Sample_contact_zip/postal_code | 14049-900
| Sample_contact_country | Brazil
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1092nnn/GSM1092125/suppl/GSM1092125_C_29.CEL.gz
| Sample_series_id | GSE44825
| Sample_data_row_count | 45101
| |
|
GSM1092126 | GPL1261 |
|
lung_chemotherapy_rep2
|
Lung from Infected mice that received isoniazid and rifampicin chemotherapy
|
strain: Balb/c
gender: female
tissue: lung
initial age (infection day): eight weeks old
infection (microorganism): 1.0 x 10e5 colony-forming units of Mycobacterium tuberculosis H37Rv
infection (route): intra-tracheal
final age at death: approximately 18 weeks old
death day: ten days after the end of therapy
|
Gene expression data from lung of mice infected with M. tuberculosis and treated with isoniazid and rifampicin drugs
|
Sample_geo_accession | GSM1092126
| Sample_status | Public on Apr 08 2013
| Sample_submission_date | Mar 04 2013
| Sample_last_update_date | Apr 08 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 100 ng total RNA (Affymetrix User Manual GeneChip 3’ IVT Express Kit).
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Array for 16 hr at 45°C and 60 rpm in GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| Sample_data_processing = Gene expression levels were normalized using the GC-RMA algorithm and flags were computed using MAS5. Quality assessment of the chips has been performed with affyQCReport R package. The “P50” probe list has been used for comparison according to flagged (A= absent; P | present) measurement in the chips. The “P50” list has been created filtering probes flagged as “Present” for at least two of the three chips of each group.
| Sample_platform_id | GPL1261
| Sample_contact_name | Rodrigo,Ferracine,Rodrigues
| Sample_contact_email | ferracine.rodrigues@gmail.com
| Sample_contact_institute | University of Sao Paulo
| Sample_contact_address | Avenida bandeirantes 3900
| Sample_contact_city | Ribeirao Preto
| Sample_contact_zip/postal_code | 14049-900
| Sample_contact_country | Brazil
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1092nnn/GSM1092126/suppl/GSM1092126_C_31.CEL.gz
| Sample_series_id | GSE44825
| Sample_data_row_count | 45101
| |
|
GSM1092127 | GPL1261 |
|
lung_chemotherapy_rep3
|
Lung from Infected mice that received isoniazid and rifampicin chemotherapy
|
strain: Balb/c
gender: female
tissue: lung
initial age (infection day): eight weeks old
infection (microorganism): 1.0 x 10e5 colony-forming units of Mycobacterium tuberculosis H37Rv
infection (route): intra-tracheal
final age at death: approximately 18 weeks old
death day: ten days after the end of therapy
|
Gene expression data from lung of mice infected with M. tuberculosis and treated with isoniazid and rifampicin drugs
|
Sample_geo_accession | GSM1092127
| Sample_status | Public on Apr 08 2013
| Sample_submission_date | Mar 04 2013
| Sample_last_update_date | Apr 08 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 100 ng total RNA (Affymetrix User Manual GeneChip 3’ IVT Express Kit).
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Array for 16 hr at 45°C and 60 rpm in GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| Sample_data_processing = Gene expression levels were normalized using the GC-RMA algorithm and flags were computed using MAS5. Quality assessment of the chips has been performed with affyQCReport R package. The “P50” probe list has been used for comparison according to flagged (A= absent; P | present) measurement in the chips. The “P50” list has been created filtering probes flagged as “Present” for at least two of the three chips of each group.
| Sample_platform_id | GPL1261
| Sample_contact_name | Rodrigo,Ferracine,Rodrigues
| Sample_contact_email | ferracine.rodrigues@gmail.com
| Sample_contact_institute | University of Sao Paulo
| Sample_contact_address | Avenida bandeirantes 3900
| Sample_contact_city | Ribeirao Preto
| Sample_contact_zip/postal_code | 14049-900
| Sample_contact_country | Brazil
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1092nnn/GSM1092127/suppl/GSM1092127_C_34.CEL.gz
| Sample_series_id | GSE44825
| Sample_data_row_count | 45101
| |
|
GSM1092128 | GPL1261 |
|
lung_immunotherapy_and_chemotherapy_rep1
|
Lung from Infected mice that received DNAhsp65 immunotherapy and isoniazid and rifampicin chemotherapy
|
strain: Balb/c
gender: female
tissue: lung
initial age (infection day): eight weeks old
infection (microorganism): 1.0 x 10e5 colony-forming units of Mycobacterium tuberculosis H37Rv
infection (route): intra-tracheal
final age at death: approximately 18 weeks old
death day: ten days after the end of therapy
|
Gene expression data from lung of mice infected with M. tuberculosis and treated with DNAhsp65 immunotherapy and isoniazid and rifampicin drugs
|
Sample_geo_accession | GSM1092128
| Sample_status | Public on Apr 08 2013
| Sample_submission_date | Mar 04 2013
| Sample_last_update_date | Apr 08 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 100 ng total RNA (Affymetrix User Manual GeneChip 3’ IVT Express Kit).
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Array for 16 hr at 45°C and 60 rpm in GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| Sample_data_processing = Gene expression levels were normalized using the GC-RMA algorithm and flags were computed using MAS5. Quality assessment of the chips has been performed with affyQCReport R package. The “P50” probe list has been used for comparison according to flagged (A= absent; P | present) measurement in the chips. The “P50” list has been created filtering probes flagged as “Present” for at least two of the three chips of each group.
| Sample_platform_id | GPL1261
| Sample_contact_name | Rodrigo,Ferracine,Rodrigues
| Sample_contact_email | ferracine.rodrigues@gmail.com
| Sample_contact_institute | University of Sao Paulo
| Sample_contact_address | Avenida bandeirantes 3900
| Sample_contact_city | Ribeirao Preto
| Sample_contact_zip/postal_code | 14049-900
| Sample_contact_country | Brazil
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1092nnn/GSM1092128/suppl/GSM1092128_D_37.CEL.gz
| Sample_series_id | GSE44825
| Sample_data_row_count | 45101
| |
|
GSM1092129 | GPL1261 |
|
lung_immunotherapy_and_chemotherapy_rep2
|
Lung from Infected mice that received DNAhsp65 immunotherapy and isoniazid and rifampicin chemotherapy
|
strain: Balb/c
gender: female
tissue: lung
initial age (infection day): eight weeks old
infection (microorganism): 1.0 x 10e5 colony-forming units of Mycobacterium tuberculosis H37Rv
infection (route): intra-tracheal
final age at death: approximately 18 weeks old
death day: ten days after the end of therapy
|
Gene expression data from lung of mice infected with M. tuberculosis and treated with DNAhsp65 immunotherapy and isoniazid and rifampicin drugs
|
Sample_geo_accession | GSM1092129
| Sample_status | Public on Apr 08 2013
| Sample_submission_date | Mar 04 2013
| Sample_last_update_date | Apr 08 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 100 ng total RNA (Affymetrix User Manual GeneChip 3’ IVT Express Kit).
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Array for 16 hr at 45°C and 60 rpm in GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| Sample_data_processing = Gene expression levels were normalized using the GC-RMA algorithm and flags were computed using MAS5. Quality assessment of the chips has been performed with affyQCReport R package. The “P50” probe list has been used for comparison according to flagged (A= absent; P | present) measurement in the chips. The “P50” list has been created filtering probes flagged as “Present” for at least two of the three chips of each group.
| Sample_platform_id | GPL1261
| Sample_contact_name | Rodrigo,Ferracine,Rodrigues
| Sample_contact_email | ferracine.rodrigues@gmail.com
| Sample_contact_institute | University of Sao Paulo
| Sample_contact_address | Avenida bandeirantes 3900
| Sample_contact_city | Ribeirao Preto
| Sample_contact_zip/postal_code | 14049-900
| Sample_contact_country | Brazil
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1092nnn/GSM1092129/suppl/GSM1092129_D_38.CEL.gz
| Sample_series_id | GSE44825
| Sample_data_row_count | 45101
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GSM1092130 | GPL1261 |
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lung_immunotherapy_and_chemotherapy_rep3
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Lung from Infected mice that received DNAhsp65 immunotherapy and isoniazid and rifampicin chemotherapy
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strain: Balb/c
gender: female
tissue: lung
initial age (infection day): eight weeks old
infection (microorganism): 1.0 x 10e5 colony-forming units of Mycobacterium tuberculosis H37Rv
infection (route): intra-tracheal
final age at death: approximately 18 weeks old
death day: ten days after the end of therapy
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Gene expression data from lung of mice infected with M. tuberculosis and treated with DNAhsp65 immunotherapy and isoniazid and rifampicin drugs
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Sample_geo_accession | GSM1092130
| Sample_status | Public on Apr 08 2013
| Sample_submission_date | Mar 04 2013
| Sample_last_update_date | Apr 08 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 100 ng total RNA (Affymetrix User Manual GeneChip 3’ IVT Express Kit).
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Array for 16 hr at 45°C and 60 rpm in GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| Sample_data_processing = Gene expression levels were normalized using the GC-RMA algorithm and flags were computed using MAS5. Quality assessment of the chips has been performed with affyQCReport R package. The “P50” probe list has been used for comparison according to flagged (A= absent; P | present) measurement in the chips. The “P50” list has been created filtering probes flagged as “Present” for at least two of the three chips of each group.
| Sample_platform_id | GPL1261
| Sample_contact_name | Rodrigo,Ferracine,Rodrigues
| Sample_contact_email | ferracine.rodrigues@gmail.com
| Sample_contact_institute | University of Sao Paulo
| Sample_contact_address | Avenida bandeirantes 3900
| Sample_contact_city | Ribeirao Preto
| Sample_contact_zip/postal_code | 14049-900
| Sample_contact_country | Brazil
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1092nnn/GSM1092130/suppl/GSM1092130_D_39.CEL.gz
| Sample_series_id | GSE44825
| Sample_data_row_count | 45101
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