Search results for the GEO ID: GSE16020 |
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(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM400913 | GPL570 |
|
PMN_control_1_RNeasy
|
polymorphonuclear leukocytes, control, patient 1, RNeasy RNA isolation
|
disease state: control
patient: 1
cell type: polymorphonuclear leukocytes
rna isolation method: RNeasy
|
control PMNs
|
Sample_geo_accession | GSM400913
| Sample_status | Public on Jan 01 2010
| Sample_submission_date | May 08 2009
| Sample_last_update_date | Nov 30 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of affected patients and healthy donors.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit (or with STAT60) according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 100 in at least one group. For probe sets more highly expressed in healthy control samples, the call must be present/marginal in at least 5 of 7 samples; for probe sets more highly expressed in test samples, the call must be present/marginal in at least 2 of 3 samples. At least a 1.5-fold change and a T test p-value of less than 0.05 are required.
| Sample_platform_id | GPL570
| Sample_contact_name | Addie,,Whitney
| Sample_contact_email | awhitney@niaid.nih.gov
| Sample_contact_laboratory | DeLeo
| Sample_contact_department | LHBP
| Sample_contact_institute | NIH/NIAID/RML
| Sample_contact_address | 903 S 4th St
| Sample_contact_city | Hamilton
| Sample_contact_state | MT
| Sample_contact_zip/postal_code | 59840
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400913/suppl/GSM400913.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400913/suppl/GSM400913.CHP.gz
| Sample_series_id | GSE16020
| Sample_data_row_count | 54675
| |
|
GSM400914 | GPL570 |
|
PMN_control_2_RNeasy
|
polymorphonuclear leukocytes, control, patient 2, RNeasy RNA isolation
|
disease state: control
patient: 2
cell type: polymorphonuclear leukocytes
rna isolation method: RNeasy
|
control PMNs
|
Sample_geo_accession | GSM400914
| Sample_status | Public on Jan 01 2010
| Sample_submission_date | May 08 2009
| Sample_last_update_date | Nov 30 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of affected patients and healthy donors.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit (or with STAT60) according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 100 in at least one group. For probe sets more highly expressed in healthy control samples, the call must be present/marginal in at least 5 of 7 samples; for probe sets more highly expressed in test samples, the call must be present/marginal in at least 2 of 3 samples. At least a 1.5-fold change and a T test p-value of less than 0.05 are required.
| Sample_platform_id | GPL570
| Sample_contact_name | Addie,,Whitney
| Sample_contact_email | awhitney@niaid.nih.gov
| Sample_contact_laboratory | DeLeo
| Sample_contact_department | LHBP
| Sample_contact_institute | NIH/NIAID/RML
| Sample_contact_address | 903 S 4th St
| Sample_contact_city | Hamilton
| Sample_contact_state | MT
| Sample_contact_zip/postal_code | 59840
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400914/suppl/GSM400914.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400914/suppl/GSM400914.CHP.gz
| Sample_series_id | GSE16020
| Sample_data_row_count | 54675
| |
|
GSM400915 | GPL570 |
|
PMN_control_3_RNeasy
|
polymorphonuclear leukocytes, control, patient 3, RNeasy RNA isolation
|
disease state: control
patient: 3
cell type: polymorphonuclear leukocytes
rna isolation method: RNeasy
|
control PMNs
|
Sample_geo_accession | GSM400915
| Sample_status | Public on Jan 01 2010
| Sample_submission_date | May 08 2009
| Sample_last_update_date | Nov 30 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of affected patients and healthy donors.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit (or with STAT60) according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 100 in at least one group. For probe sets more highly expressed in healthy control samples, the call must be present/marginal in at least 5 of 7 samples; for probe sets more highly expressed in test samples, the call must be present/marginal in at least 2 of 3 samples. At least a 1.5-fold change and a T test p-value of less than 0.05 are required.
| Sample_platform_id | GPL570
| Sample_contact_name | Addie,,Whitney
| Sample_contact_email | awhitney@niaid.nih.gov
| Sample_contact_laboratory | DeLeo
| Sample_contact_department | LHBP
| Sample_contact_institute | NIH/NIAID/RML
| Sample_contact_address | 903 S 4th St
| Sample_contact_city | Hamilton
| Sample_contact_state | MT
| Sample_contact_zip/postal_code | 59840
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400915/suppl/GSM400915.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400915/suppl/GSM400915.CHP.gz
| Sample_series_id | GSE16020
| Sample_data_row_count | 54675
| |
|
GSM400916 | GPL570 |
|
PMN_control_4_RNeasy
|
polymorphonuclear leukocytes, control, patient 4, RNeasy RNA isolation
|
disease state: control
patient: 4
cell type: polymorphonuclear leukocytes
rna isolation method: RNeasy
|
control PMNs
|
Sample_geo_accession | GSM400916
| Sample_status | Public on Jan 01 2010
| Sample_submission_date | May 08 2009
| Sample_last_update_date | Nov 30 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of affected patients and healthy donors.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit (or with STAT60) according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 100 in at least one group. For probe sets more highly expressed in healthy control samples, the call must be present/marginal in at least 5 of 7 samples; for probe sets more highly expressed in test samples, the call must be present/marginal in at least 2 of 3 samples. At least a 1.5-fold change and a T test p-value of less than 0.05 are required.
| Sample_platform_id | GPL570
| Sample_contact_name | Addie,,Whitney
| Sample_contact_email | awhitney@niaid.nih.gov
| Sample_contact_laboratory | DeLeo
| Sample_contact_department | LHBP
| Sample_contact_institute | NIH/NIAID/RML
| Sample_contact_address | 903 S 4th St
| Sample_contact_city | Hamilton
| Sample_contact_state | MT
| Sample_contact_zip/postal_code | 59840
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400916/suppl/GSM400916.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400916/suppl/GSM400916.CHP.gz
| Sample_series_id | GSE16020
| Sample_data_row_count | 54675
| |
|
GSM400917 | GPL570 |
|
PMN_control_5_RNeasy
|
polymorphonuclear leukocytes, control, patient 5, RNeasy RNA isolation
|
disease state: control
patient: 5
cell type: polymorphonuclear leukocytes
rna isolation method: RNeasy
|
control PMNs
|
Sample_geo_accession | GSM400917
| Sample_status | Public on Jan 01 2010
| Sample_submission_date | May 08 2009
| Sample_last_update_date | Nov 30 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of affected patients and healthy donors.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit (or with STAT60) according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 100 in at least one group. For probe sets more highly expressed in healthy control samples, the call must be present/marginal in at least 5 of 7 samples; for probe sets more highly expressed in test samples, the call must be present/marginal in at least 2 of 3 samples. At least a 1.5-fold change and a T test p-value of less than 0.05 are required.
| Sample_platform_id | GPL570
| Sample_contact_name | Addie,,Whitney
| Sample_contact_email | awhitney@niaid.nih.gov
| Sample_contact_laboratory | DeLeo
| Sample_contact_department | LHBP
| Sample_contact_institute | NIH/NIAID/RML
| Sample_contact_address | 903 S 4th St
| Sample_contact_city | Hamilton
| Sample_contact_state | MT
| Sample_contact_zip/postal_code | 59840
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400917/suppl/GSM400917.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400917/suppl/GSM400917.CHP.gz
| Sample_series_id | GSE16020
| Sample_data_row_count | 54675
| |
|
GSM400918 | GPL570 |
|
PMN_control_6_RNeasy
|
polymorphonuclear leukocytes, control, patient 6, RNeasy RNA isolation
|
disease state: control
patient: 6
cell type: polymorphonuclear leukocytes
rna isolation method: RNeasy
|
control PMNs
|
Sample_geo_accession | GSM400918
| Sample_status | Public on Jan 01 2010
| Sample_submission_date | May 08 2009
| Sample_last_update_date | Nov 30 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of affected patients and healthy donors.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit (or with STAT60) according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 100 in at least one group. For probe sets more highly expressed in healthy control samples, the call must be present/marginal in at least 5 of 7 samples; for probe sets more highly expressed in test samples, the call must be present/marginal in at least 2 of 3 samples. At least a 1.5-fold change and a T test p-value of less than 0.05 are required.
| Sample_platform_id | GPL570
| Sample_contact_name | Addie,,Whitney
| Sample_contact_email | awhitney@niaid.nih.gov
| Sample_contact_laboratory | DeLeo
| Sample_contact_department | LHBP
| Sample_contact_institute | NIH/NIAID/RML
| Sample_contact_address | 903 S 4th St
| Sample_contact_city | Hamilton
| Sample_contact_state | MT
| Sample_contact_zip/postal_code | 59840
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400918/suppl/GSM400918.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400918/suppl/GSM400918.CHP.gz
| Sample_series_id | GSE16020
| Sample_data_row_count | 54675
| |
|
GSM400919 | GPL570 |
|
PMN_control_7_RNeasy
|
polymorphonuclear leukocytes, control, patient 7, RNeasy RNA isolation
|
disease state: control
patient: 7
cell type: polymorphonuclear leukocytes
rna isolation method: RNeasy
|
control PMNs
|
Sample_geo_accession | GSM400919
| Sample_status | Public on Jan 01 2010
| Sample_submission_date | May 08 2009
| Sample_last_update_date | Nov 30 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of affected patients and healthy donors.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit (or with STAT60) according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 100 in at least one group. For probe sets more highly expressed in healthy control samples, the call must be present/marginal in at least 5 of 7 samples; for probe sets more highly expressed in test samples, the call must be present/marginal in at least 2 of 3 samples. At least a 1.5-fold change and a T test p-value of less than 0.05 are required.
| Sample_platform_id | GPL570
| Sample_contact_name | Addie,,Whitney
| Sample_contact_email | awhitney@niaid.nih.gov
| Sample_contact_laboratory | DeLeo
| Sample_contact_department | LHBP
| Sample_contact_institute | NIH/NIAID/RML
| Sample_contact_address | 903 S 4th St
| Sample_contact_city | Hamilton
| Sample_contact_state | MT
| Sample_contact_zip/postal_code | 59840
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400919/suppl/GSM400919.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400919/suppl/GSM400919.CHP.gz
| Sample_series_id | GSE16020
| Sample_data_row_count | 54675
| |
|
GSM400920 | GPL570 |
|
PMN_test_1_RNeasy
|
polymorphonuclear leukocytes, test, patient 1, RNeasy RNA isolation
|
disease state: autosomal dominant monocytopenia
patient: 1
cell type: polymorphonuclear leukocytes
rna isolation method: RNeasy
|
test PMNs
|
Sample_geo_accession | GSM400920
| Sample_status | Public on Jan 01 2010
| Sample_submission_date | May 08 2009
| Sample_last_update_date | Nov 30 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of affected patients and healthy donors.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit (or with STAT60) according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 100 in at least one group. For probe sets more highly expressed in healthy control samples, the call must be present/marginal in at least 5 of 7 samples; for probe sets more highly expressed in test samples, the call must be present/marginal in at least 2 of 3 samples. At least a 1.5-fold change and a T test p-value of less than 0.05 are required.
| Sample_platform_id | GPL570
| Sample_contact_name | Addie,,Whitney
| Sample_contact_email | awhitney@niaid.nih.gov
| Sample_contact_laboratory | DeLeo
| Sample_contact_department | LHBP
| Sample_contact_institute | NIH/NIAID/RML
| Sample_contact_address | 903 S 4th St
| Sample_contact_city | Hamilton
| Sample_contact_state | MT
| Sample_contact_zip/postal_code | 59840
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400920/suppl/GSM400920.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400920/suppl/GSM400920.CHP.gz
| Sample_series_id | GSE16020
| Sample_data_row_count | 54675
| |
|
GSM400921 | GPL570 |
|
PMN_test_2_RNeasy
|
polymorphonuclear leukocytes, test, patient 2, RNeasy RNA isolation
|
disease state: autosomal dominant monocytopenia
patient: 2
cell type: polymorphonuclear leukocytes
rna isolation method: RNeasy
|
test PMNs
|
Sample_geo_accession | GSM400921
| Sample_status | Public on Jan 01 2010
| Sample_submission_date | May 08 2009
| Sample_last_update_date | Nov 30 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of affected patients and healthy donors.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit (or with STAT60) according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 100 in at least one group. For probe sets more highly expressed in healthy control samples, the call must be present/marginal in at least 5 of 7 samples; for probe sets more highly expressed in test samples, the call must be present/marginal in at least 2 of 3 samples. At least a 1.5-fold change and a T test p-value of less than 0.05 are required.
| Sample_platform_id | GPL570
| Sample_contact_name | Addie,,Whitney
| Sample_contact_email | awhitney@niaid.nih.gov
| Sample_contact_laboratory | DeLeo
| Sample_contact_department | LHBP
| Sample_contact_institute | NIH/NIAID/RML
| Sample_contact_address | 903 S 4th St
| Sample_contact_city | Hamilton
| Sample_contact_state | MT
| Sample_contact_zip/postal_code | 59840
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400921/suppl/GSM400921.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400921/suppl/GSM400921.CHP.gz
| Sample_series_id | GSE16020
| Sample_data_row_count | 54675
| |
|
GSM400922 | GPL570 |
|
PMN_test_3_RNeasy
|
polymorphonuclear leukocytes, test, patient 3, RNeasy RNA isolation
|
disease state: autosomal dominant monocytopenia
patient: 3
cell type: polymorphonuclear leukocytes
rna isolation method: RNeasy
|
test PMNs
|
Sample_geo_accession | GSM400922
| Sample_status | Public on Jan 01 2010
| Sample_submission_date | May 08 2009
| Sample_last_update_date | Nov 30 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of affected patients and healthy donors.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit (or with STAT60) according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 100 in at least one group. For probe sets more highly expressed in healthy control samples, the call must be present/marginal in at least 5 of 7 samples; for probe sets more highly expressed in test samples, the call must be present/marginal in at least 2 of 3 samples. At least a 1.5-fold change and a T test p-value of less than 0.05 are required.
| Sample_platform_id | GPL570
| Sample_contact_name | Addie,,Whitney
| Sample_contact_email | awhitney@niaid.nih.gov
| Sample_contact_laboratory | DeLeo
| Sample_contact_department | LHBP
| Sample_contact_institute | NIH/NIAID/RML
| Sample_contact_address | 903 S 4th St
| Sample_contact_city | Hamilton
| Sample_contact_state | MT
| Sample_contact_zip/postal_code | 59840
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400922/suppl/GSM400922.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400922/suppl/GSM400922.CHP.gz
| Sample_series_id | GSE16020
| Sample_data_row_count | 54675
| |
|
GSM400923 | GPL570 |
|
PMN_control_1_STAT60
|
polymorphonuclear leukocytes, control, patient 1, STAT60 RNA isolation
|
disease state: control
patient: 1
cell type: polymorphonuclear leukocytes
rna isolation method: STAT60
|
control PMNs
|
Sample_geo_accession | GSM400923
| Sample_status | Public on Jan 01 2010
| Sample_submission_date | May 08 2009
| Sample_last_update_date | Nov 30 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of affected patients and healthy donors.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit (or with STAT60) according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 100 in at least one group.
| Sample_platform_id | GPL570
| Sample_contact_name | Addie,,Whitney
| Sample_contact_email | awhitney@niaid.nih.gov
| Sample_contact_laboratory | DeLeo
| Sample_contact_department | LHBP
| Sample_contact_institute | NIH/NIAID/RML
| Sample_contact_address | 903 S 4th St
| Sample_contact_city | Hamilton
| Sample_contact_state | MT
| Sample_contact_zip/postal_code | 59840
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400923/suppl/GSM400923.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400923/suppl/GSM400923.CHP.gz
| Sample_series_id | GSE16020
| Sample_data_row_count | 54675
| |
|
GSM400924 | GPL570 |
|
PMN_control_2_STAT60
|
polymorphonuclear leukocytes, control, patient 2, STAT60 RNA isolation
|
disease state: control
patient: 2
cell type: polymorphonuclear leukocytes
rna isolation method: STAT60
|
control PMNs
|
Sample_geo_accession | GSM400924
| Sample_status | Public on Jan 01 2010
| Sample_submission_date | May 08 2009
| Sample_last_update_date | Nov 30 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of affected patients and healthy donors.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit (or with STAT60) according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 100 in at least one group.
| Sample_platform_id | GPL570
| Sample_contact_name | Addie,,Whitney
| Sample_contact_email | awhitney@niaid.nih.gov
| Sample_contact_laboratory | DeLeo
| Sample_contact_department | LHBP
| Sample_contact_institute | NIH/NIAID/RML
| Sample_contact_address | 903 S 4th St
| Sample_contact_city | Hamilton
| Sample_contact_state | MT
| Sample_contact_zip/postal_code | 59840
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400924/suppl/GSM400924.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400924/suppl/GSM400924.CHP.gz
| Sample_series_id | GSE16020
| Sample_data_row_count | 54675
| |
|
GSM400925 | GPL570 |
|
PMN_control_3_STAT60
|
polymorphonuclear leukocytes, control, patient 3, STAT60 RNA isolation
|
disease state: control
patient: 3
cell type: polymorphonuclear leukocytes
rna isolation method: STAT60
|
control PMNs
|
Sample_geo_accession | GSM400925
| Sample_status | Public on Jan 01 2010
| Sample_submission_date | May 08 2009
| Sample_last_update_date | Nov 30 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of affected patients and healthy donors.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit (or with STAT60) according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 100 in at least one group.
| Sample_platform_id | GPL570
| Sample_contact_name | Addie,,Whitney
| Sample_contact_email | awhitney@niaid.nih.gov
| Sample_contact_laboratory | DeLeo
| Sample_contact_department | LHBP
| Sample_contact_institute | NIH/NIAID/RML
| Sample_contact_address | 903 S 4th St
| Sample_contact_city | Hamilton
| Sample_contact_state | MT
| Sample_contact_zip/postal_code | 59840
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400925/suppl/GSM400925.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400925/suppl/GSM400925.CHP.gz
| Sample_series_id | GSE16020
| Sample_data_row_count | 54675
| |
|
GSM400926 | GPL570 |
|
PMN_control_4_STAT60
|
polymorphonuclear leukocytes, control, patient 4, STAT60 RNA isolation
|
disease state: control
patient: 4
cell type: polymorphonuclear leukocytes
rna isolation method: STAT60
|
control PMNs
|
Sample_geo_accession | GSM400926
| Sample_status | Public on Jan 01 2010
| Sample_submission_date | May 08 2009
| Sample_last_update_date | Nov 30 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of affected patients and healthy donors.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit (or with STAT60) according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 100 in at least one group.
| Sample_platform_id | GPL570
| Sample_contact_name | Addie,,Whitney
| Sample_contact_email | awhitney@niaid.nih.gov
| Sample_contact_laboratory | DeLeo
| Sample_contact_department | LHBP
| Sample_contact_institute | NIH/NIAID/RML
| Sample_contact_address | 903 S 4th St
| Sample_contact_city | Hamilton
| Sample_contact_state | MT
| Sample_contact_zip/postal_code | 59840
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400926/suppl/GSM400926.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400926/suppl/GSM400926.CHP.gz
| Sample_series_id | GSE16020
| Sample_data_row_count | 54675
| |
|
GSM400927 | GPL570 |
|
PMN_control_5_STAT60
|
polymorphonuclear leukocytes, control, patient 5, STAT60 RNA isolation
|
disease state: control
patient: 5
cell type: polymorphonuclear leukocytes
rna isolation method: STAT60
|
control PMNs
|
Sample_geo_accession | GSM400927
| Sample_status | Public on Jan 01 2010
| Sample_submission_date | May 08 2009
| Sample_last_update_date | Nov 30 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of affected patients and healthy donors.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit (or with STAT60) according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 100 in at least one group.
| Sample_platform_id | GPL570
| Sample_contact_name | Addie,,Whitney
| Sample_contact_email | awhitney@niaid.nih.gov
| Sample_contact_laboratory | DeLeo
| Sample_contact_department | LHBP
| Sample_contact_institute | NIH/NIAID/RML
| Sample_contact_address | 903 S 4th St
| Sample_contact_city | Hamilton
| Sample_contact_state | MT
| Sample_contact_zip/postal_code | 59840
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400927/suppl/GSM400927.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400927/suppl/GSM400927.CHP.gz
| Sample_series_id | GSE16020
| Sample_data_row_count | 54675
| |
|
GSM400928 | GPL570 |
|
PMN_test_1_STAT60
|
polymorphonuclear leukocytes, test, patient 1, STAT60 RNA isolation
|
disease state: autosomal dominant monocytopenia
patient: 1
cell type: polymorphonuclear leukocytes
rna isolation method: STAT60
|
test PMNs
|
Sample_geo_accession | GSM400928
| Sample_status | Public on Jan 01 2010
| Sample_submission_date | May 08 2009
| Sample_last_update_date | Nov 30 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of affected patients and healthy donors.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit (or with STAT60) according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 100 in at least one group.
| Sample_platform_id | GPL570
| Sample_contact_name | Addie,,Whitney
| Sample_contact_email | awhitney@niaid.nih.gov
| Sample_contact_laboratory | DeLeo
| Sample_contact_department | LHBP
| Sample_contact_institute | NIH/NIAID/RML
| Sample_contact_address | 903 S 4th St
| Sample_contact_city | Hamilton
| Sample_contact_state | MT
| Sample_contact_zip/postal_code | 59840
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400928/suppl/GSM400928.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400928/suppl/GSM400928.CHP.gz
| Sample_series_id | GSE16020
| Sample_data_row_count | 54675
| |
|
GSM400929 | GPL570 |
|
PMN_test_2_STAT60
|
polymorphonuclear leukocytes, test, patient 2, STAT60 RNA isolation
|
disease state: autosomal dominant monocytopenia
patient: 2
cell type: polymorphonuclear leukocytes
rna isolation method: STAT60
|
test PMNs
|
Sample_geo_accession | GSM400929
| Sample_status | Public on Jan 01 2010
| Sample_submission_date | May 08 2009
| Sample_last_update_date | Nov 30 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of affected patients and healthy donors.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit (or with STAT60) according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 100 in at least one group.
| Sample_platform_id | GPL570
| Sample_contact_name | Addie,,Whitney
| Sample_contact_email | awhitney@niaid.nih.gov
| Sample_contact_laboratory | DeLeo
| Sample_contact_department | LHBP
| Sample_contact_institute | NIH/NIAID/RML
| Sample_contact_address | 903 S 4th St
| Sample_contact_city | Hamilton
| Sample_contact_state | MT
| Sample_contact_zip/postal_code | 59840
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400929/suppl/GSM400929.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400929/suppl/GSM400929.CHP.gz
| Sample_series_id | GSE16020
| Sample_data_row_count | 54675
| |
|
GSM400930 | GPL570 |
|
PMN_test_3_STAT60
|
polymorphonuclear leukocytes, test, patient 3, STAT60 RNA isolation
|
disease state: autosomal dominant monocytopenia
patient: 3
cell type: polymorphonuclear leukocytes
rna isolation method: STAT60
|
test PMNs
|
Sample_geo_accession | GSM400930
| Sample_status | Public on Jan 01 2010
| Sample_submission_date | May 08 2009
| Sample_last_update_date | Nov 30 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of affected patients and healthy donors.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit (or with STAT60) according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 100 in at least one group.
| Sample_platform_id | GPL570
| Sample_contact_name | Addie,,Whitney
| Sample_contact_email | awhitney@niaid.nih.gov
| Sample_contact_laboratory | DeLeo
| Sample_contact_department | LHBP
| Sample_contact_institute | NIH/NIAID/RML
| Sample_contact_address | 903 S 4th St
| Sample_contact_city | Hamilton
| Sample_contact_state | MT
| Sample_contact_zip/postal_code | 59840
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400930/suppl/GSM400930.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400930/suppl/GSM400930.CHP.gz
| Sample_series_id | GSE16020
| Sample_data_row_count | 54675
| |
|
GSM400931 | GPL570 |
|
PMN_test_4_STAT60
|
polymorphonuclear leukocytes, test, patient 4, STAT60 RNA isolation
|
disease state: autosomal dominant monocytopenia
patient: 4
cell type: polymorphonuclear leukocytes
rna isolation method: STAT60
|
test PMNs
|
Sample_geo_accession | GSM400931
| Sample_status | Public on Jan 01 2010
| Sample_submission_date | May 08 2009
| Sample_last_update_date | Nov 30 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of affected patients and healthy donors.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit (or with STAT60) according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 100 in at least one group.
| Sample_platform_id | GPL570
| Sample_contact_name | Addie,,Whitney
| Sample_contact_email | awhitney@niaid.nih.gov
| Sample_contact_laboratory | DeLeo
| Sample_contact_department | LHBP
| Sample_contact_institute | NIH/NIAID/RML
| Sample_contact_address | 903 S 4th St
| Sample_contact_city | Hamilton
| Sample_contact_state | MT
| Sample_contact_zip/postal_code | 59840
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400931/suppl/GSM400931.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400931/suppl/GSM400931.CHP.gz
| Sample_series_id | GSE16020
| Sample_data_row_count | 54675
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GSM400932 | GPL570 |
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PMN_test_5_STAT60
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polymorphonuclear leukocytes, test, patient 5, STAT60 RNA isolation
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disease state: autosomal dominant monocytopenia
patient: 5
cell type: polymorphonuclear leukocytes
rna isolation method: STAT60
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test PMNs
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Sample_geo_accession | GSM400932
| Sample_status | Public on Jan 01 2010
| Sample_submission_date | May 08 2009
| Sample_last_update_date | Nov 30 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of affected patients and healthy donors.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit (or with STAT60) according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 100 in at least one group.
| Sample_platform_id | GPL570
| Sample_contact_name | Addie,,Whitney
| Sample_contact_email | awhitney@niaid.nih.gov
| Sample_contact_laboratory | DeLeo
| Sample_contact_department | LHBP
| Sample_contact_institute | NIH/NIAID/RML
| Sample_contact_address | 903 S 4th St
| Sample_contact_city | Hamilton
| Sample_contact_state | MT
| Sample_contact_zip/postal_code | 59840
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400932/suppl/GSM400932.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400932/suppl/GSM400932.CHP.gz
| Sample_series_id | GSE16020
| 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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