Search results for the GEO ID: GSE19314 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM479917 | GPL570 |
|
ILD Study Number 1281
|
Human peripheral blood mononuclear cells
|
age_years: 31
sex: M
ethnicity: Asian
diagnosis: Sarcoidosis
dx: sarc_high_lung_fx
array_batch: 1
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479917
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479917/suppl/GSM479917.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479918 | GPL570 |
|
ILD Study Number 1178
|
Human peripheral blood mononuclear cells
|
age_years: 42
sex: M
ethnicity: White
diagnosis: Hypersensitivity Pnemonitis
dx: hp
array_batch: 1
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479918
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479918/suppl/GSM479918.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479919 | GPL570 |
|
ILD Study Number S012
|
Human peripheral blood mononuclear cells
|
age_years: 39
sex: F
ethnicity: Latino
diagnosis: Healthy
dx: health
array_batch: 1
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479919
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479919/suppl/GSM479919.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479920 | GPL570 |
|
ILD Study Number 1245
|
Human peripheral blood mononuclear cells
|
age_years: 66
sex: F
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_low_lung_fx
array_batch: 1
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479920
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479920/suppl/GSM479920.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479921 | GPL570 |
|
ILD Study Number S014
|
Human peripheral blood mononuclear cells
|
age_years: 66
sex: F
ethnicity: Latino
diagnosis: Healthy
dx: health
array_batch: 1
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479921
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479921/suppl/GSM479921.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479922 | GPL570 |
|
ILD Study Number S020
|
Human peripheral blood mononuclear cells
|
age_years: 43
sex: F
ethnicity: White
diagnosis: Healthy
dx: health
array_batch: 1
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479922
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479922/suppl/GSM479922.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479923 | GPL570 |
|
ILD Study Number S037
|
Human peripheral blood mononuclear cells
|
age_years: 48
sex: M
ethnicity: Black
diagnosis: Healthy
dx: health
array_batch: 1
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479923
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479923/suppl/GSM479923.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479924 | GPL570 |
|
ILD Study Number 1196
|
Human peripheral blood mononuclear cells
|
age_years: 53
sex: F
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_low_lung_fx
array_batch: 1
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479924
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479924/suppl/GSM479924.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479925 | GPL570 |
|
ILD Study Number S024
|
Human peripheral blood mononuclear cells
|
age_years: 34
sex: F
ethnicity: Black
diagnosis: Healthy
dx: health
array_batch: 1
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479925
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479925/suppl/GSM479925.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479926 | GPL570 |
|
ILD Study Number 558
|
Human peripheral blood mononuclear cells
|
age_years: 63
sex: F
ethnicity: Latino
diagnosis: Sarcoidosis
dx: sarc_high_lung_fx
array_batch: 1
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479926
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479926/suppl/GSM479926.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479927 | GPL570 |
|
ILD Study Number 1237
|
Human peripheral blood mononuclear cells
|
age_years: 57
sex: F
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_low_lung_fx
array_batch: 1
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479927
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479927/suppl/GSM479927.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479928 | GPL570 |
|
ILD Study Number S027
|
Human peripheral blood mononuclear cells
|
age_years: 55
sex: F
ethnicity: White
diagnosis: Healthy
dx: health
array_batch: 1
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479928
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479928/suppl/GSM479928.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479929 | GPL570 |
|
ILD Study Number 907
|
Human peripheral blood mononuclear cells
|
age_years: 54
sex: M
ethnicity: White
diagnosis: Hypersensitivity Pnemonitis
dx: hp
array_batch: 1
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479929
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479929/suppl/GSM479929.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479930 | GPL570 |
|
ILD Study Number 1111
|
Human peripheral blood mononuclear cells
|
age_years: 66
sex: F
ethnicity: White
diagnosis: Hypersensitivity Pnemonitis
dx: hp
array_batch: 1
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479930
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479930/suppl/GSM479930.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479931 | GPL570 |
|
ILD Study Number 1299
|
Human peripheral blood mononuclear cells
|
age_years: 43
sex: M
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_low_lung_fx
array_batch: 1
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479931
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479931/suppl/GSM479931.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479932 | GPL570 |
|
ILD Study Number 1222
|
Human peripheral blood mononuclear cells
|
age_years: 46
sex: F
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_high_lung_fx
array_batch: 1
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479932
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479932/suppl/GSM479932.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479933 | GPL570 |
|
ILD Study Number 1164
|
Human peripheral blood mononuclear cells
|
age_years: 66
sex: M
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_low_lung_fx
array_batch: 1
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479933
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479933/suppl/GSM479933.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479934 | GPL570 |
|
ILD Study Number 1236
|
Human peripheral blood mononuclear cells
|
age_years: 31
sex: F
ethnicity: Black
diagnosis: Sarcoidosis
dx: sarc_low_lung_fx
array_batch: 1
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479934
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479934/suppl/GSM479934.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479935 | GPL570 |
|
ILD Study Number 1226
|
Human peripheral blood mononuclear cells
|
age_years: 37
sex: F
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_high_lung_fx
array_batch: 1
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479935
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479935/suppl/GSM479935.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479936 | GPL570 |
|
ILD Study Number S011
|
Human peripheral blood mononuclear cells
|
age_years: 61
sex: F
ethnicity: White
diagnosis: Healthy
dx: health
array_batch: 1
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479936
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479936/suppl/GSM479936.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479937 | GPL570 |
|
ILD Study Number S036
|
Human peripheral blood mononuclear cells
|
age_years: 56
sex: F
ethnicity: White
diagnosis: Healthy
dx: health
array_batch: 1
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479937
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479937/suppl/GSM479937.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479938 | GPL570 |
|
ILD Study Number 1090
|
Human peripheral blood mononuclear cells
|
age_years: 50
sex: F
ethnicity: White
diagnosis: Hypersensitivity Pnemonitis
dx: hp
array_batch: 1
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479938
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479938/suppl/GSM479938.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479939 | GPL570 |
|
ILD Study Number S031
|
Human peripheral blood mononuclear cells
|
age_years: 45
sex: M
ethnicity: White
diagnosis: Healthy
dx: health
array_batch: 1
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479939
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479939/suppl/GSM479939.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479940 | GPL570 |
|
ILD Study Number S030
|
Human peripheral blood mononuclear cells
|
age_years: 59
sex: M
ethnicity: White
diagnosis: Healthy
dx: health
array_batch: 1
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479940
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479940/suppl/GSM479940.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479941 | GPL570 |
|
ILD Study Number S038
|
Human peripheral blood mononuclear cells
|
age_years: 34
sex: F
ethnicity: White
diagnosis: Healthy
dx: health
array_batch: 2
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479941
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479941/suppl/GSM479941.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479942 | GPL570 |
|
ILD Study Number 998
|
Human peripheral blood mononuclear cells
|
age_years: 60
sex: M
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_low_lung_fx
array_batch: 2
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479942
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479942/suppl/GSM479942.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479943 | GPL570 |
|
ILD Study Number 1113
|
Human peripheral blood mononuclear cells
|
age_years: 47
sex: F
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_high_lung_fx
array_batch: 2
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479943
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479943/suppl/GSM479943.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479944 | GPL570 |
|
ILD Study Number 901
|
Human peripheral blood mononuclear cells
|
age_years: 32
sex: M
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_low_lung_fx
array_batch: 2
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479944
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479944/suppl/GSM479944.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479945 | GPL570 |
|
ILD Study Number 1235
|
Human peripheral blood mononuclear cells
|
age_years: 73
sex: F
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_high_lung_fx
array_batch: 2
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479945
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479945/suppl/GSM479945.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479946 | GPL570 |
|
ILD Study Number 1074
|
Human peripheral blood mononuclear cells
|
age_years: 63
sex: M
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_low_lung_fx
array_batch: 2
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479946
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479946/suppl/GSM479946.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479947 | GPL570 |
|
ILD Study Number S032
|
Human peripheral blood mononuclear cells
|
age_years: 53
sex: F
ethnicity: White
diagnosis: Healthy
dx: health
array_batch: 2
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479947
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479947/suppl/GSM479947.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479948 | GPL570 |
|
ILD Study Number S033
|
Human peripheral blood mononuclear cells
|
age_years: 55
sex: M
ethnicity: White
diagnosis: Healthy
dx: health
array_batch: 2
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479948
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479948/suppl/GSM479948.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479949 | GPL570 |
|
ILD Study Number 1243
|
Human peripheral blood mononuclear cells
|
age_years: 37
sex: F
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_low_lung_fx
array_batch: 2
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479949
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479949/suppl/GSM479949.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479950 | GPL570 |
|
ILD Study Number 1064
|
Human peripheral blood mononuclear cells
|
age_years: 63
sex: M
ethnicity: White
diagnosis: Hypersensitivity Pnemonitis
dx: hp
array_batch: 2
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479950
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479950/suppl/GSM479950.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479951 | GPL570 |
|
ILD Study Number 1319
|
Human peripheral blood mononuclear cells
|
age_years: 35
sex: M
ethnicity: Black
diagnosis: Sarcoidosis
dx: sarc_low_lung_fx
array_batch: 2
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479951
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479951/suppl/GSM479951.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479952 | GPL570 |
|
ILD Study Number 1039
|
Human peripheral blood mononuclear cells
|
age_years: 62
sex: F
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_high_lung_fx
array_batch: 2
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479952
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479952/suppl/GSM479952.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479953 | GPL570 |
|
ILD Study Number 1274
|
Human peripheral blood mononuclear cells
|
age_years: 53
sex: F
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_high_lung_fx
array_batch: 2
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479953
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479953/suppl/GSM479953.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479954 | GPL570 |
|
ILD Study Number S034
|
Human peripheral blood mononuclear cells
|
age_years: 70
sex: F
ethnicity: White
diagnosis: Healthy
dx: health
array_batch: 2
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479954
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479954/suppl/GSM479954.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479955 | GPL570 |
|
ILD Study Number 945
|
Human peripheral blood mononuclear cells
|
age_years: 49
sex: F
ethnicity: Latino
diagnosis: Hypersensitivity Pnemonitis
dx: hp
array_batch: 2
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479955
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479955/suppl/GSM479955.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479956 | GPL570 |
|
ILD Study Number 1040
|
Human peripheral blood mononuclear cells
|
age_years: 40
sex: M
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_low_lung_fx
array_batch: 2
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479956
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479956/suppl/GSM479956.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479957 | GPL570 |
|
ILD Study Number 1107
|
Human peripheral blood mononuclear cells
|
age_years: 41
sex: F
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_low_lung_fx
array_batch: 2
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479957
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479957/suppl/GSM479957.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479958 | GPL570 |
|
ILD Study Number S001
|
Human peripheral blood mononuclear cells
|
age_years: 42
sex: M
ethnicity: White
diagnosis: Healthy
dx: health
array_batch: 2
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479958
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479958/suppl/GSM479958.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479959 | GPL570 |
|
ILD Study Number 942
|
Human peripheral blood mononuclear cells
|
age_years: 44
sex: M
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_high_lung_fx
array_batch: 2
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479959
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479959/suppl/GSM479959.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479960 | GPL570 |
|
ILD Study Number 917
|
Human peripheral blood mononuclear cells
|
age_years: 56
sex: M
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_low_lung_fx
array_batch: 2
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479960
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479960/suppl/GSM479960.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479961 | GPL570 |
|
ILD Study Number 1239
|
Human peripheral blood mononuclear cells
|
age_years: 40
sex: M
ethnicity: Asian
diagnosis: Sarcoidosis
dx: sarc_low_lung_fx
array_batch: 2
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479961
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479961/suppl/GSM479961.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479962 | GPL570 |
|
ILD Study Number 1000
|
Human peripheral blood mononuclear cells
|
age_years: 56
sex: F
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_high_lung_fx
array_batch: 2
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479962
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479962/suppl/GSM479962.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479963 | GPL570 |
|
ILD Study Number 1021
|
Human peripheral blood mononuclear cells
|
age_years: 57
sex: F
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_high_lung_fx
array_batch: 3
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479963
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479963/suppl/GSM479963.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479964 | GPL570 |
|
ILD Study Number 1259
|
Human peripheral blood mononuclear cells
|
age_years: 53
sex: F
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_high_lung_fx
array_batch: 3
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479964
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479964/suppl/GSM479964.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479965 | GPL570 |
|
ILD Study Number 1035
|
Human peripheral blood mononuclear cells
|
age_years: 60
sex: F
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_high_lung_fx
array_batch: 3
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479965
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479965/suppl/GSM479965.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479966 | GPL570 |
|
ILD Study Number S019
|
Human peripheral blood mononuclear cells
|
age_years: 55
sex: F
ethnicity: White
diagnosis: Healthy
dx: health
array_batch: 3
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479966
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479966/suppl/GSM479966.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479967 | GPL570 |
|
ILD Study Number S017
|
Human peripheral blood mononuclear cells
|
age_years: 43
sex: F
ethnicity: White
diagnosis: Healthy
dx: health
array_batch: 3
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479967
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479967/suppl/GSM479967.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479968 | GPL570 |
|
ILD Study Number 660
|
Human peripheral blood mononuclear cells
|
age_years: 47
sex: F
ethnicity: Black
diagnosis: Sarcoidosis
dx: sarc_high_lung_fx
array_batch: 3
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479968
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479968/suppl/GSM479968.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479969 | GPL570 |
|
ILD Study Number 545
|
Human peripheral blood mononuclear cells
|
age_years: 53
sex: F
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_low_lung_fx
array_batch: 3
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479969
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479969/suppl/GSM479969.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479970 | GPL570 |
|
ILD Study Number S035
|
Human peripheral blood mononuclear cells
|
age_years: 60
sex: F
ethnicity: White
diagnosis: Healthy
dx: health
array_batch: 3
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479970
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479970/suppl/GSM479970.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479971 | GPL570 |
|
ILD Study Number 890
|
Human peripheral blood mononuclear cells
|
age_years: 51
sex: M
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_high_lung_fx
array_batch: 3
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479971
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479971/suppl/GSM479971.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479972 | GPL570 |
|
ILD Study Number 93
|
Human peripheral blood mononuclear cells
|
age_years: 54
sex: M
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_low_lung_fx
array_batch: 3
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479972
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479972/suppl/GSM479972.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479973 | GPL570 |
|
ILD Study Number 1078
|
Human peripheral blood mononuclear cells
|
age_years: 35
sex: F
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_high_lung_fx
array_batch: 3
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479973
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479973/suppl/GSM479973.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479974 | GPL570 |
|
ILD Study Number 1098
|
Human peripheral blood mononuclear cells
|
age_years: 67
sex: M
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_low_lung_fx
array_batch: 3
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479974
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479974/suppl/GSM479974.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479975 | GPL570 |
|
ILD Study Number S013
|
Human peripheral blood mononuclear cells
|
age_years: 57
sex: F
ethnicity: White
diagnosis: Healthy
dx: health
array_batch: 3
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479975
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479975/suppl/GSM479975.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479976 | GPL570 |
|
ILD Study Number S010
|
Human peripheral blood mononuclear cells
|
age_years: 62
sex: F
ethnicity: White
diagnosis: Healthy
dx: health
array_batch: 3
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479976
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479976/suppl/GSM479976.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479977 | GPL570 |
|
ILD Study Number 897
|
Human peripheral blood mononuclear cells
|
age_years: 58
sex: F
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_low_lung_fx
array_batch: 3
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479977
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479977/suppl/GSM479977.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479978 | GPL570 |
|
ILD Study Number 1136
|
Human peripheral blood mononuclear cells
|
age_years: 40
sex: F
ethnicity: Latino
diagnosis: sarcoid vs. BO
dx: sarc-vs-bo
array_batch: 3
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479978
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479978/suppl/GSM479978.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479979 | GPL570 |
|
ILD Study Number 908
|
Human peripheral blood mononuclear cells
|
age_years: 63
sex: M
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_high_lung_fx
array_batch: 3
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479979
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479979/suppl/GSM479979.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479980 | GPL570 |
|
ILD Study Number 774
|
Human peripheral blood mononuclear cells
|
age_years: 51
sex: M
ethnicity: White
diagnosis: Sarcoidosis
dx: sarc_low_lung_fx
array_batch: 3
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479980
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479980/suppl/GSM479980.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479981 | GPL570 |
|
ILD Study Number 1115
|
Human peripheral blood mononuclear cells
|
age_years: 50
sex: M
ethnicity: Black
diagnosis: Sarcoidosis
dx: sarc_high_lung_fx
array_batch: 3
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479981
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479981/suppl/GSM479981.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
GSM479982 | GPL570 |
|
ILD Study Number 425
|
Human peripheral blood mononuclear cells
|
age_years: 44
sex: F
ethnicity: Black
diagnosis: HCV/sarcoid
dx: sarc-hcv
array_batch: 3
|
Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients
|
Sample_geo_accession | GSM479982
| Sample_status | Public on Aug 11 2011
| Sample_submission_date | Dec 03 2009
| Sample_last_update_date | Aug 11 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix Model 3000 scanner.
| Sample_data_processing | The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037
| Sample_platform_id | GPL570
| Sample_contact_name | Prescott,Gurney,Woodruff
| Sample_contact_email | prescott.woodruff@ucsf.edu
| Sample_contact_phone | 4155142061
| Sample_contact_fax | 4154765712
| Sample_contact_laboratory | Woodruff Lab
| Sample_contact_department | Medicine
| Sample_contact_institute | UCSF
| Sample_contact_address | 505 Parnassus Ave
| Sample_contact_city | San Francisco
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 94143
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479982/suppl/GSM479982.CEL.gz
| Sample_series_id | GSE19314
| Sample_data_row_count | 54675
| |
|
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Make groups for comparisons |
(2 groups will be compared at a time) |
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Select GSMs and click on "Add groups" |
Enter the group name here: |
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