Result

Search results for the GEO ID: GSE20050

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM501249

GPL1352

Caseum 1

Caseous human pulmonary TB granuloma

tissue: caseous granuloma

Gene expression data from caseous human pulmonary TB granuloma

Sample_geo_accession	GSM501249
Sample_status	Public on Jun 02 2010
Sample_submission_date	Jan 26 2010
Sample_last_update_date	Jun 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Cryosections were made from human lung tissues. After fixation in graded alcohol containing 0.5% sodium azide, caseous granuloma or normal lung parenchyma was dissected out by using laser capture microdissection. The dissected materials were stored at -80°C until further processing.
Sample_growth_protocol_ch1	Human pulmonary TB tissues and normal lung tissues were excised from TB patients who underwent surgery.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA were isolated using PicoPure RNA Isolation Kit (Molecular devices), and sufficient quantities of messenger RNA were produced by two-rounds of linear amplification using RiboAmp HS Amplification Kit (Molecular Devices).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated aRNA were generated by using BioArray High Yield RNA Transcript Lableing Kit (Enzo Life Sciences).
Sample_hyb_protocol	Fifteen microgram of fragmented aRNA were hybridized onto GeneChip Human X3P array (Affymetrix) for 16 hours at 45°C. Genechips were washed and stained in Affymetrix Fluidics Station FS450.
Sample_scan_protocol	Genechips were scanned using Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	The data for caseous granulomas only were analyzed using R and Bioconductor, and the raw PM probes only were subjected to background correction using MAS5 method, log-transformed and median-centered. And informative PM probes from each probe set were selected as having the highest mean across all arrays. The data for caseous granulomas and normal lung parenchyma were analyzed using GeneSpring GX 10.0.2 program. MAS5 method was used to summarize raw CEL files, the normalization was done by scaling to median of all samples and the baseline was transformed to the median of all samples.
Sample_platform_id	GPL1352
Sample_contact_name	Mi-Jeong,,Kim
Sample_contact_email	mk376@cornell.edu
Sample_contact_phone	6072534060
Sample_contact_fax	6072399124
Sample_contact_department	Microbiology and Immunology
Sample_contact_institute	Cornell University
Sample_contact_address	C5 104 VMC Cornell University
Sample_contact_city	Ithaca
Sample_contact_state	NY
Sample_contact_zip/postal_code	14853
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM501nnn/GSM501249/suppl/GSM501249.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM501nnn/GSM501249/suppl/GSM501249.CHP.gz
Sample_series_id	GSE20050
Sample_data_row_count	61359

GSM501250

GPL1352

Caseum 2-A

Caseous human pulmonary TB granuloma

tissue: caseous granuloma

Gene expression data from caseous human pulmonary TB granuloma

Sample_geo_accession	GSM501250
Sample_status	Public on Jun 02 2010
Sample_submission_date	Jan 26 2010
Sample_last_update_date	Jun 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Cryosections were made from human lung tissues. After fixation in graded alcohol containing 0.5% sodium azide, caseous granuloma or normal lung parenchyma was dissected out by using laser capture microdissection. The dissected materials were stored at -80°C until further processing.
Sample_growth_protocol_ch1	Human pulmonary TB tissues and normal lung tissues were excised from TB patients who underwent surgery.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA were isolated using PicoPure RNA Isolation Kit (Molecular devices), and sufficient quantities of messenger RNA were produced by two-rounds of linear amplification using RiboAmp HS Amplification Kit (Molecular Devices).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated aRNA were generated by using BioArray High Yield RNA Transcript Lableing Kit (Enzo Life Sciences).
Sample_hyb_protocol	Fifteen microgram of fragmented aRNA were hybridized onto GeneChip Human X3P array (Affymetrix) for 16 hours at 45°C. Genechips were washed and stained in Affymetrix Fluidics Station FS450.
Sample_scan_protocol	Genechips were scanned using Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	The data for caseous granulomas only were analyzed using R and Bioconductor, and the raw PM probes only were subjected to background correction using MAS5 method, log-transformed and median-centered. And informative PM probes from each probe set were selected as having the highest mean across all arrays. The data for caseous granulomas and normal lung parenchyma were analyzed using GeneSpring GX 10.0.2 program. MAS5 method was used to summarize raw CEL files, the normalization was done by scaling to median of all samples and the baseline was transformed to the median of all samples.
Sample_platform_id	GPL1352
Sample_contact_name	Mi-Jeong,,Kim
Sample_contact_email	mk376@cornell.edu
Sample_contact_phone	6072534060
Sample_contact_fax	6072399124
Sample_contact_department	Microbiology and Immunology
Sample_contact_institute	Cornell University
Sample_contact_address	C5 104 VMC Cornell University
Sample_contact_city	Ithaca
Sample_contact_state	NY
Sample_contact_zip/postal_code	14853
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM501nnn/GSM501250/suppl/GSM501250.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM501nnn/GSM501250/suppl/GSM501250.CHP.gz
Sample_series_id	GSE20050
Sample_data_row_count	61359

GSM501251

GPL1352

Caseum 2-B

Caseous human pulmonary TB granuloma

tissue: caseous granuloma

Gene expression data from caseous human pulmonary TB granuloma

Sample_geo_accession	GSM501251
Sample_status	Public on Jun 02 2010
Sample_submission_date	Jan 26 2010
Sample_last_update_date	Jun 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Cryosections were made from human lung tissues. After fixation in graded alcohol containing 0.5% sodium azide, caseous granuloma or normal lung parenchyma was dissected out by using laser capture microdissection. The dissected materials were stored at -80°C until further processing.
Sample_growth_protocol_ch1	Human pulmonary TB tissues and normal lung tissues were excised from TB patients who underwent surgery.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA were isolated using PicoPure RNA Isolation Kit (Molecular devices), and sufficient quantities of messenger RNA were produced by two-rounds of linear amplification using RiboAmp HS Amplification Kit (Molecular Devices).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated aRNA were generated by using BioArray High Yield RNA Transcript Lableing Kit (Enzo Life Sciences).
Sample_hyb_protocol	Fifteen microgram of fragmented aRNA were hybridized onto GeneChip Human X3P array (Affymetrix) for 16 hours at 45°C. Genechips were washed and stained in Affymetrix Fluidics Station FS450.
Sample_scan_protocol	Genechips were scanned using Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	The data for caseous granulomas only were analyzed using R and Bioconductor, and the raw PM probes only were subjected to background correction using MAS5 method, log-transformed and median-centered. And informative PM probes from each probe set were selected as having the highest mean across all arrays. The data for caseous granulomas and normal lung parenchyma were analyzed using GeneSpring GX 10.0.2 program. MAS5 method was used to summarize raw CEL files, the normalization was done by scaling to median of all samples and the baseline was transformed to the median of all samples.
Sample_platform_id	GPL1352
Sample_contact_name	Mi-Jeong,,Kim
Sample_contact_email	mk376@cornell.edu
Sample_contact_phone	6072534060
Sample_contact_fax	6072399124
Sample_contact_department	Microbiology and Immunology
Sample_contact_institute	Cornell University
Sample_contact_address	C5 104 VMC Cornell University
Sample_contact_city	Ithaca
Sample_contact_state	NY
Sample_contact_zip/postal_code	14853
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM501nnn/GSM501251/suppl/GSM501251.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM501nnn/GSM501251/suppl/GSM501251.CHP.gz
Sample_series_id	GSE20050
Sample_data_row_count	61359

GSM501253

GPL1352

Caseum 3

Caseous human pulmonary TB granuloma

tissue: caseous granuloma

Gene expression data from caseous human pulmonary TB granuloma

Sample_geo_accession	GSM501253
Sample_status	Public on Jun 02 2010
Sample_submission_date	Jan 26 2010
Sample_last_update_date	Jun 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Cryosections were made from human lung tissues. After fixation in graded alcohol containing 0.5% sodium azide, caseous granuloma or normal lung parenchyma was dissected out by using laser capture microdissection. The dissected materials were stored at -80°C until further processing.
Sample_growth_protocol_ch1	Human pulmonary TB tissues and normal lung tissues were excised from TB patients who underwent surgery.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA were isolated using PicoPure RNA Isolation Kit (Molecular devices), and sufficient quantities of messenger RNA were produced by two-rounds of linear amplification using RiboAmp HS Amplification Kit (Molecular Devices).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated aRNA were generated by using BioArray High Yield RNA Transcript Lableing Kit (Enzo Life Sciences).
Sample_hyb_protocol	Fifteen microgram of fragmented aRNA were hybridized onto GeneChip Human X3P array (Affymetrix) for 16 hours at 45°C. Genechips were washed and stained in Affymetrix Fluidics Station FS450.
Sample_scan_protocol	Genechips were scanned using Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	The data for caseous granulomas only were analyzed using R and Bioconductor, and the raw PM probes only were subjected to background correction using MAS5 method, log-transformed and median-centered. And informative PM probes from each probe set were selected as having the highest mean across all arrays. The data for caseous granulomas and normal lung parenchyma were analyzed using GeneSpring GX 10.0.2 program. MAS5 method was used to summarize raw CEL files, the normalization was done by scaling to median of all samples and the baseline was transformed to the median of all samples.
Sample_platform_id	GPL1352
Sample_contact_name	Mi-Jeong,,Kim
Sample_contact_email	mk376@cornell.edu
Sample_contact_phone	6072534060
Sample_contact_fax	6072399124
Sample_contact_department	Microbiology and Immunology
Sample_contact_institute	Cornell University
Sample_contact_address	C5 104 VMC Cornell University
Sample_contact_city	Ithaca
Sample_contact_state	NY
Sample_contact_zip/postal_code	14853
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM501nnn/GSM501253/suppl/GSM501253.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM501nnn/GSM501253/suppl/GSM501253.CHP.gz
Sample_series_id	GSE20050
Sample_data_row_count	61359

GSM501254

GPL1352

Normal-A

Normal lung parenchyma

tissue: normal lung parenchyma

Gene expression data from human normal lung parenchyma

Sample_geo_accession	GSM501254
Sample_status	Public on Jun 02 2010
Sample_submission_date	Jan 26 2010
Sample_last_update_date	Jun 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Cryosections were made from human lung tissues. After fixation in graded alcohol containing 0.5% sodium azide, caseous granuloma or normal lung parenchyma was dissected out by using laser capture microdissection. The dissected materials were stored at -80°C until further processing.
Sample_growth_protocol_ch1	Human pulmonary TB tissues and normal lung tissues were excised from TB patients who underwent surgery.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA were isolated using PicoPure RNA Isolation Kit (Molecular devices), and sufficient quantities of messenger RNA were produced by two-rounds of linear amplification using RiboAmp HS Amplification Kit (Molecular Devices).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated aRNA were generated by using BioArray High Yield RNA Transcript Lableing Kit (Enzo Life Sciences).
Sample_hyb_protocol	Fifteen microgram of fragmented aRNA were hybridized onto GeneChip Human X3P array (Affymetrix) for 16 hours at 45°C. Genechips were washed and stained in Affymetrix Fluidics Station FS450.
Sample_scan_protocol	Genechips were scanned using Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	The data for caseous granulomas only were analyzed using R and Bioconductor, and the raw PM probes only were subjected to background correction using MAS5 method, log-transformed and median-centered. And informative PM probes from each probe set were selected as having the highest mean across all arrays. The data for caseous granulomas and normal lung parenchyma were analyzed using GeneSpring GX 10.0.2 program. MAS5 method was used to summarize raw CEL files, the normalization was done by scaling to median of all samples and the baseline was transformed to the median of all samples.
Sample_platform_id	GPL1352
Sample_contact_name	Mi-Jeong,,Kim
Sample_contact_email	mk376@cornell.edu
Sample_contact_phone	6072534060
Sample_contact_fax	6072399124
Sample_contact_department	Microbiology and Immunology
Sample_contact_institute	Cornell University
Sample_contact_address	C5 104 VMC Cornell University
Sample_contact_city	Ithaca
Sample_contact_state	NY
Sample_contact_zip/postal_code	14853
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM501nnn/GSM501254/suppl/GSM501254.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM501nnn/GSM501254/suppl/GSM501254.CHP.gz
Sample_series_id	GSE20050
Sample_data_row_count	61359

GSM501255

GPL1352

Normal-B

Normal lung parenchyma

tissue: normal lung parenchyma

Gene expression data from human normal lung parenchyma

Sample_geo_accession	GSM501255
Sample_status	Public on Jun 02 2010
Sample_submission_date	Jan 26 2010
Sample_last_update_date	Jun 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Cryosections were made from human lung tissues. After fixation in graded alcohol containing 0.5% sodium azide, caseous granuloma or normal lung parenchyma was dissected out by using laser capture microdissection. The dissected materials were stored at -80°C until further processing.
Sample_growth_protocol_ch1	Human pulmonary TB tissues and normal lung tissues were excised from TB patients who underwent surgery.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA were isolated using PicoPure RNA Isolation Kit (Molecular devices), and sufficient quantities of messenger RNA were produced by two-rounds of linear amplification using RiboAmp HS Amplification Kit (Molecular Devices).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated aRNA were generated by using BioArray High Yield RNA Transcript Lableing Kit (Enzo Life Sciences).
Sample_hyb_protocol	Fifteen microgram of fragmented aRNA were hybridized onto GeneChip Human X3P array (Affymetrix) for 16 hours at 45°C. Genechips were washed and stained in Affymetrix Fluidics Station FS450.
Sample_scan_protocol	Genechips were scanned using Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	The data for caseous granulomas only were analyzed using R and Bioconductor, and the raw PM probes only were subjected to background correction using MAS5 method, log-transformed and median-centered. And informative PM probes from each probe set were selected as having the highest mean across all arrays. The data for caseous granulomas and normal lung parenchyma were analyzed using GeneSpring GX 10.0.2 program. MAS5 method was used to summarize raw CEL files, the normalization was done by scaling to median of all samples and the baseline was transformed to the median of all samples.
Sample_platform_id	GPL1352
Sample_contact_name	Mi-Jeong,,Kim
Sample_contact_email	mk376@cornell.edu
Sample_contact_phone	6072534060
Sample_contact_fax	6072399124
Sample_contact_department	Microbiology and Immunology
Sample_contact_institute	Cornell University
Sample_contact_address	C5 104 VMC Cornell University
Sample_contact_city	Ithaca
Sample_contact_state	NY
Sample_contact_zip/postal_code	14853
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM501nnn/GSM501255/suppl/GSM501255.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM501nnn/GSM501255/suppl/GSM501255.CHP.gz
Sample_series_id	GSE20050
Sample_data_row_count	61359

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