Search results for the GEO ID: GSE10595  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(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 |
GSM267077 | GPL570 |
|
HS5-rep1
|
HS5, no CD14
|
NA
|
n/a
|
| Sample_geo_accession | GSM267077
| | Sample_status | Public on Feb 22 2008
| | Sample_submission_date | Feb 21 2008
| | Sample_last_update_date | Feb 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stromal cells were cultured with and without monocytes (CD14+ cells isolated with Tuek4 Ab and IgG2a+b magnetic beads with AutoMacs).
| | Sample_growth_protocol_ch1 | All cells were cultured for 2 days in RPMI1640 medium supplemented with 10% FBS/0.4 mg/ml glutamine at 37ºC in 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with Qiagen RNeasy kits according to manufacturer's protocols.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared from 2-5 ug total RNA according to Affymetrix protocols using the SuperScriptChoice kit (Invitrogen) and the High Yield RNA transcription labeling kit (Enzo Diagnostics).
| | Sample_hyb_protocol | standard Affymetrix protocol and reagents
| | Sample_scan_protocol | standard Affymetrix protocol and instruments
| | Sample_data_processing | Affymetrix CEL files were imported into GeneSpring 7.3.1 and samples were preprocessed with GC-RMA to obtain the normalized natural hybridization values. The Per gene normalization feature of Genespring, in which each measurement is divided by the median of its measurements in all samples, was also applied.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lynn,,Graf
| | Sample_contact_email | lgraf@fhcrc.org
| | Sample_contact_phone | 206-667-4545
| | Sample_contact_fax | 206-667-5978
| | Sample_contact_laboratory | Torok-Storb
| | Sample_contact_department | Clinical Research Division
| | Sample_contact_institute | Fred Hutchinson Cancer Research Center
| | Sample_contact_address | 1100 Fairview Ave. N. D1-100
| | Sample_contact_city | Seattle
| | Sample_contact_state | WA
| | Sample_contact_zip/postal_code | 98109
| | Sample_contact_country | USA
| | Sample_contact_web_link | none
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267077/suppl/GSM267077.CEL.gz
| | Sample_series_id | GSE10595
| | Sample_data_row_count | 54675
| | |
|
GSM267078 | GPL570 |
|
HS5-rep2
|
HS5, no CD14
|
NA
|
n/a
|
| Sample_geo_accession | GSM267078
| | Sample_status | Public on Feb 22 2008
| | Sample_submission_date | Feb 21 2008
| | Sample_last_update_date | Feb 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stromal cells were cultured with and without monocytes (CD14+ cells isolated with Tuek4 Ab and IgG2a+b magnetic beads with AutoMacs).
| | Sample_growth_protocol_ch1 | All cells were cultured for 2 days in RPMI1640 medium supplemented with 10% FBS/0.4 mg/ml glutamine at 37ºC in 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with Qiagen RNeasy kits according to manufacturer's protocols.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared from 2-5 ug total RNA according to Affymetrix protocols using the SuperScriptChoice kit (Invitrogen) and the High Yield RNA transcription labeling kit (Enzo Diagnostics).
| | Sample_hyb_protocol | standard Affymetrix protocol and reagents
| | Sample_scan_protocol | standard Affymetrix protocol and instruments
| | Sample_data_processing | Affymetrix CEL files were imported into GeneSpring 7.3.1 and samples were preprocessed with GC-RMA to obtain the normalized natural hybridization values. The Per gene normalization feature of Genespring, in which each measurement is divided by the median of its measurements in all samples, was also applied.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lynn,,Graf
| | Sample_contact_email | lgraf@fhcrc.org
| | Sample_contact_phone | 206-667-4545
| | Sample_contact_fax | 206-667-5978
| | Sample_contact_laboratory | Torok-Storb
| | Sample_contact_department | Clinical Research Division
| | Sample_contact_institute | Fred Hutchinson Cancer Research Center
| | Sample_contact_address | 1100 Fairview Ave. N. D1-100
| | Sample_contact_city | Seattle
| | Sample_contact_state | WA
| | Sample_contact_zip/postal_code | 98109
| | Sample_contact_country | USA
| | Sample_contact_web_link | none
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267078/suppl/GSM267078.CEL.gz
| | Sample_series_id | GSE10595
| | Sample_data_row_count | 54675
| | |
|
GSM267079 | GPL570 |
|
HS5+MO-donor3
|
HS5, +CD14 donor 3
|
Gender: M, age: 24
|
n/a
|
| Sample_geo_accession | GSM267079
| | Sample_status | Public on Feb 22 2008
| | Sample_submission_date | Feb 21 2008
| | Sample_last_update_date | Feb 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stromal cells were cultured with and without monocytes (CD14+ cells isolated with Tuek4 Ab and IgG2a+b magnetic beads with AutoMacs).
| | Sample_growth_protocol_ch1 | All cells were cultured for 2 days in RPMI1640 medium supplemented with 10% FBS/0.4 mg/ml glutamine at 37ºC in 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with Qiagen RNeasy kits according to manufacturer's protocols.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared from 2-5 ug total RNA according to Affymetrix protocols using the SuperScriptChoice kit (Invitrogen) and the High Yield RNA transcription labeling kit (Enzo Diagnostics).
| | Sample_hyb_protocol | standard Affymetrix protocol and reagents
| | Sample_scan_protocol | standard Affymetrix protocol and instruments
| | Sample_data_processing | Affymetrix CEL files were imported into GeneSpring 7.3.1 and samples were preprocessed with GC-RMA to obtain the normalized natural hybridization values. The Per gene normalization feature of Genespring, in which each measurement is divided by the median of its measurements in all samples, was also applied.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lynn,,Graf
| | Sample_contact_email | lgraf@fhcrc.org
| | Sample_contact_phone | 206-667-4545
| | Sample_contact_fax | 206-667-5978
| | Sample_contact_laboratory | Torok-Storb
| | Sample_contact_department | Clinical Research Division
| | Sample_contact_institute | Fred Hutchinson Cancer Research Center
| | Sample_contact_address | 1100 Fairview Ave. N. D1-100
| | Sample_contact_city | Seattle
| | Sample_contact_state | WA
| | Sample_contact_zip/postal_code | 98109
| | Sample_contact_country | USA
| | Sample_contact_web_link | none
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267079/suppl/GSM267079.CEL.gz
| | Sample_series_id | GSE10595
| | Sample_data_row_count | 54675
| | |
|
GSM267080 | GPL570 |
|
HS5+MO-donor4
|
HS5, +CD14 donor 4
|
Gender: M, age: 31
|
n/a
|
| Sample_geo_accession | GSM267080
| | Sample_status | Public on Feb 22 2008
| | Sample_submission_date | Feb 21 2008
| | Sample_last_update_date | Feb 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stromal cells were cultured with and without monocytes (CD14+ cells isolated with Tuek4 Ab and IgG2a+b magnetic beads with AutoMacs).
| | Sample_growth_protocol_ch1 | All cells were cultured for 2 days in RPMI1640 medium supplemented with 10% FBS/0.4 mg/ml glutamine at 37ºC in 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with Qiagen RNeasy kits according to manufacturer's protocols.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared from 2-5 ug total RNA according to Affymetrix protocols using the SuperScriptChoice kit (Invitrogen) and the High Yield RNA transcription labeling kit (Enzo Diagnostics).
| | Sample_hyb_protocol | standard Affymetrix protocol and reagents
| | Sample_scan_protocol | standard Affymetrix protocol and instruments
| | Sample_data_processing | Affymetrix CEL files were imported into GeneSpring 7.3.1 and samples were preprocessed with GC-RMA to obtain the normalized natural hybridization values. The Per gene normalization feature of Genespring, in which each measurement is divided by the median of its measurements in all samples, was also applied.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lynn,,Graf
| | Sample_contact_email | lgraf@fhcrc.org
| | Sample_contact_phone | 206-667-4545
| | Sample_contact_fax | 206-667-5978
| | Sample_contact_laboratory | Torok-Storb
| | Sample_contact_department | Clinical Research Division
| | Sample_contact_institute | Fred Hutchinson Cancer Research Center
| | Sample_contact_address | 1100 Fairview Ave. N. D1-100
| | Sample_contact_city | Seattle
| | Sample_contact_state | WA
| | Sample_contact_zip/postal_code | 98109
| | Sample_contact_country | USA
| | Sample_contact_web_link | none
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267080/suppl/GSM267080.CEL.gz
| | Sample_series_id | GSE10595
| | Sample_data_row_count | 54675
| | |
|
GSM267081 | GPL570 |
|
HS27a-rep1
|
HS27a, no CD14
|
NA
|
n/a
|
| Sample_geo_accession | GSM267081
| | Sample_status | Public on Feb 22 2008
| | Sample_submission_date | Feb 21 2008
| | Sample_last_update_date | Feb 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stromal cells were cultured with and without monocytes (CD14+ cells isolated with Tuek4 Ab and IgG2a+b magnetic beads with AutoMacs).
| | Sample_growth_protocol_ch1 | All cells were cultured for 2 days in RPMI1640 medium supplemented with 10% FBS/0.4 mg/ml glutamine at 37ºC in 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with Qiagen RNeasy kits according to manufacturer's protocols.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared from 2-5 ug total RNA according to Affymetrix protocols using the SuperScriptChoice kit (Invitrogen) and the High Yield RNA transcription labeling kit (Enzo Diagnostics).
| | Sample_hyb_protocol | standard Affymetrix protocol and reagents
| | Sample_scan_protocol | standard Affymetrix protocol and instruments
| | Sample_data_processing | Affymetrix CEL files were imported into GeneSpring 7.3.1 and samples were preprocessed with GC-RMA to obtain the normalized natural hybridization values. The Per gene normalization feature of Genespring, in which each measurement is divided by the median of its measurements in all samples, was also applied.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lynn,,Graf
| | Sample_contact_email | lgraf@fhcrc.org
| | Sample_contact_phone | 206-667-4545
| | Sample_contact_fax | 206-667-5978
| | Sample_contact_laboratory | Torok-Storb
| | Sample_contact_department | Clinical Research Division
| | Sample_contact_institute | Fred Hutchinson Cancer Research Center
| | Sample_contact_address | 1100 Fairview Ave. N. D1-100
| | Sample_contact_city | Seattle
| | Sample_contact_state | WA
| | Sample_contact_zip/postal_code | 98109
| | Sample_contact_country | USA
| | Sample_contact_web_link | none
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267081/suppl/GSM267081.CEL.gz
| | Sample_series_id | GSE10595
| | Sample_data_row_count | 54675
| | |
|
GSM267082 | GPL570 |
|
HS27a-rep2
|
HS27a, no CD14
|
NA
|
n/a
|
| Sample_geo_accession | GSM267082
| | Sample_status | Public on Feb 22 2008
| | Sample_submission_date | Feb 21 2008
| | Sample_last_update_date | Feb 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stromal cells were cultured with and without monocytes (CD14+ cells isolated with Tuek4 Ab and IgG2a+b magnetic beads with AutoMacs).
| | Sample_growth_protocol_ch1 | All cells were cultured for 2 days in RPMI1640 medium supplemented with 10% FBS/0.4 mg/ml glutamine at 37ºC in 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with Qiagen RNeasy kits according to manufacturer's protocols.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared from 2-5 ug total RNA according to Affymetrix protocols using the SuperScriptChoice kit (Invitrogen) and the High Yield RNA transcription labeling kit (Enzo Diagnostics).
| | Sample_hyb_protocol | standard Affymetrix protocol and reagents
| | Sample_scan_protocol | standard Affymetrix protocol and instruments
| | Sample_data_processing | Affymetrix CEL files were imported into GeneSpring 7.3.1 and samples were preprocessed with GC-RMA to obtain the normalized natural hybridization values. The Per gene normalization feature of Genespring, in which each measurement is divided by the median of its measurements in all samples, was also applied.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lynn,,Graf
| | Sample_contact_email | lgraf@fhcrc.org
| | Sample_contact_phone | 206-667-4545
| | Sample_contact_fax | 206-667-5978
| | Sample_contact_laboratory | Torok-Storb
| | Sample_contact_department | Clinical Research Division
| | Sample_contact_institute | Fred Hutchinson Cancer Research Center
| | Sample_contact_address | 1100 Fairview Ave. N. D1-100
| | Sample_contact_city | Seattle
| | Sample_contact_state | WA
| | Sample_contact_zip/postal_code | 98109
| | Sample_contact_country | USA
| | Sample_contact_web_link | none
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267082/suppl/GSM267082.CEL.gz
| | Sample_series_id | GSE10595
| | Sample_data_row_count | 54675
| | |
|
GSM267083 | GPL570 |
|
HS27a+MO-donor3
|
HS27a, +CD14 donor 3
|
Gender: M, age: 24
|
n/a
|
| Sample_geo_accession | GSM267083
| | Sample_status | Public on Feb 22 2008
| | Sample_submission_date | Feb 21 2008
| | Sample_last_update_date | Feb 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stromal cells were cultured with and without monocytes (CD14+ cells isolated with Tuek4 Ab and IgG2a+b magnetic beads with AutoMacs).
| | Sample_growth_protocol_ch1 | All cells were cultured for 2 days in RPMI1640 medium supplemented with 10% FBS/0.4 mg/ml glutamine at 37ºC in 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with Qiagen RNeasy kits according to manufacturer's protocols.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared from 2-5 ug total RNA according to Affymetrix protocols using the SuperScriptChoice kit (Invitrogen) and the High Yield RNA transcription labeling kit (Enzo Diagnostics).
| | Sample_hyb_protocol | standard Affymetrix protocol and reagents
| | Sample_scan_protocol | standard Affymetrix protocol and instruments
| | Sample_data_processing | Affymetrix CEL files were imported into GeneSpring 7.3.1 and samples were preprocessed with GC-RMA to obtain the normalized natural hybridization values. The Per gene normalization feature of Genespring, in which each measurement is divided by the median of its measurements in all samples, was also applied.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lynn,,Graf
| | Sample_contact_email | lgraf@fhcrc.org
| | Sample_contact_phone | 206-667-4545
| | Sample_contact_fax | 206-667-5978
| | Sample_contact_laboratory | Torok-Storb
| | Sample_contact_department | Clinical Research Division
| | Sample_contact_institute | Fred Hutchinson Cancer Research Center
| | Sample_contact_address | 1100 Fairview Ave. N. D1-100
| | Sample_contact_city | Seattle
| | Sample_contact_state | WA
| | Sample_contact_zip/postal_code | 98109
| | Sample_contact_country | USA
| | Sample_contact_web_link | none
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267083/suppl/GSM267083.CEL.gz
| | Sample_series_id | GSE10595
| | Sample_data_row_count | 54675
| | |
|
GSM267084 | GPL570 |
|
HS27a+MO-donor4
|
HS27a, +CD14 donor 4
|
Gender: M, age: 31
|
n/a
|
| Sample_geo_accession | GSM267084
| | Sample_status | Public on Feb 22 2008
| | Sample_submission_date | Feb 21 2008
| | Sample_last_update_date | Feb 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stromal cells were cultured with and without monocytes (CD14+ cells isolated with Tuek4 Ab and IgG2a+b magnetic beads with AutoMacs).
| | Sample_growth_protocol_ch1 | All cells were cultured for 2 days in RPMI1640 medium supplemented with 10% FBS/0.4 mg/ml glutamine at 37ºC in 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with Qiagen RNeasy kits according to manufacturer's protocols.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared from 2-5 ug total RNA according to Affymetrix protocols using the SuperScriptChoice kit (Invitrogen) and the High Yield RNA transcription labeling kit (Enzo Diagnostics).
| | Sample_hyb_protocol | standard Affymetrix protocol and reagents
| | Sample_scan_protocol | standard Affymetrix protocol and instruments
| | Sample_data_processing | Affymetrix CEL files were imported into GeneSpring 7.3.1 and samples were preprocessed with GC-RMA to obtain the normalized natural hybridization values. The Per gene normalization feature of Genespring, in which each measurement is divided by the median of its measurements in all samples, was also applied.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lynn,,Graf
| | Sample_contact_email | lgraf@fhcrc.org
| | Sample_contact_phone | 206-667-4545
| | Sample_contact_fax | 206-667-5978
| | Sample_contact_laboratory | Torok-Storb
| | Sample_contact_department | Clinical Research Division
| | Sample_contact_institute | Fred Hutchinson Cancer Research Center
| | Sample_contact_address | 1100 Fairview Ave. N. D1-100
| | Sample_contact_city | Seattle
| | Sample_contact_state | WA
| | Sample_contact_zip/postal_code | 98109
| | Sample_contact_country | USA
| | Sample_contact_web_link | none
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267084/suppl/GSM267084.CEL.gz
| | Sample_series_id | GSE10595
| | Sample_data_row_count | 54675
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
Select expression type |
| Transcripts profile based on; |
A. Differential status (Up/Down regulation) |
|
|
Regulation type |
|
Fold change |
|
p-value |
|
|
|
B. Absolute calls (Transcribed/Not-detected) |
|
|
| Derive calls within/across groups |
Within groups |
|
|
Detection status |
|
Percentage detection |
|
|
Across groups |
|
|
Detection status |
First group: |
- |
Second group:
|
Percentage detection |
First group: |
- |
Second group:
|
|
|
| |
Filter results by number of probes |
|
|
