Search results for the GEO ID: GSE10738  |
(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 |
GSM257586 | GPL570 |
|
MM6 cyclin T1 knockdown Mock treated 1
|
MM6 cell line
|
Monocytic cell line.
|
All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 6486.
|
| Sample_geo_accession | GSM257586
| | Sample_status | Public on Jul 31 2008
| | Sample_submission_date | Jan 17 2008
| | Sample_last_update_date | May 16 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MM6 cells were transduced with shRNA against cyclin T1 and then mock treated.
| | Sample_growth_protocol_ch1 | MM6 cells were maintained in RPMI 1640 medium (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Hyclone), ), non-essential amino acids (Invitrogen), l-glutamine (Invitrogen), and OPI media supplement (Sigma) containing 0.15 mg of oxalacetate, 0.5 g of pyruvate and 8.2 mg of bovine insulin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using the Qiagen RNeasy kit according to the manufacturer's protocol and RNA quality was determined using an Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | See affymetrix protocol.
| | Sample_hyb_protocol | See affymetrix protocol.
| | Sample_scan_protocol | Affymetrix Gene Chip Scanner 3100.
| | Sample_data_processing | MAS5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andrew ,P.,Rice
| | Sample_contact_laboratory | Rice
| | Sample_contact_department | Molecular Virology and Microbiology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77025
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM257nnn/GSM257586/suppl/GSM257586.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM257nnn/GSM257586/suppl/GSM257586.CHP.gz
| | Sample_series_id | GSE10738
| | Sample_series_id | GSE11462
| | Sample_data_row_count | 54675
| | |
|
GSM257588 | GPL570 |
|
MM6 cyclin T1 knockdown Mock treated 2
|
MM6 cell line
|
Monocytic cell line.
|
All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 6888.
|
| Sample_geo_accession | GSM257588
| | Sample_status | Public on Jul 31 2008
| | Sample_submission_date | Jan 17 2008
| | Sample_last_update_date | May 16 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MM6 cells were transduced with shRNA against cyclin T1 and then mock treated.
| | Sample_growth_protocol_ch1 | MM6 cells were maintained in RPMI 1640 medium (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Hyclone), ), non-essential amino acids (Invitrogen), l-glutamine (Invitrogen), and OPI media supplement (Sigma) containing 0.15 mg of oxalacetate, 0.5 g of pyruvate and 8.2 mg of bovine insulin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using the Qiagen RNeasy kit according to the manufacturer's protocol and RNA quality was determined using an Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | See affymetrix protocol.
| | Sample_hyb_protocol | See affymetrix protocol.
| | Sample_scan_protocol | Affymetrix Gene Chip Scanner 3100.
| | Sample_data_processing | MAS5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andrew ,P.,Rice
| | Sample_contact_laboratory | Rice
| | Sample_contact_department | Molecular Virology and Microbiology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77025
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM257nnn/GSM257588/suppl/GSM257588.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM257nnn/GSM257588/suppl/GSM257588.CHP.gz
| | Sample_series_id | GSE10738
| | Sample_series_id | GSE11462
| | Sample_data_row_count | 54675
| | |
|
GSM257614 | GPL570 |
|
MM6 control shRNA Mock treated 1
|
MM6 cell line
|
Monocytic Cell line
|
All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 6488.
|
| Sample_geo_accession | GSM257614
| | Sample_status | Public on Jul 31 2008
| | Sample_submission_date | Jan 17 2008
| | Sample_last_update_date | May 16 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MM6 cells were transduced with a control shRNA and then mock treated.
| | Sample_growth_protocol_ch1 | MM6 cells were maintained in RPMI 1640 medium (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Hyclone), ), non-essential amino acids (Invitrogen), l-glutamine (Invitrogen), and OPI media supplement (Sigma) containing 0.15 mg of oxalacetate, 0.5 g of pyruvate and 8.2 mg of bovine insulin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using the Qiagen RNeasy kit according to the manufacturer's protocol and RNA quality was determined using an Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | See affymetrix protocol.
| | Sample_hyb_protocol | See affymetrix protocol.
| | Sample_scan_protocol | Affymetrix Gene Chip Scanner 3100.
| | Sample_data_processing | MAS5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andrew ,P.,Rice
| | Sample_contact_laboratory | Rice
| | Sample_contact_department | Molecular Virology and Microbiology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77025
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM257nnn/GSM257614/suppl/GSM257614.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM257nnn/GSM257614/suppl/GSM257614.CHP.gz
| | Sample_series_id | GSE10738
| | Sample_series_id | GSE11462
| | Sample_data_row_count | 54675
| | |
|
GSM257616 | GPL570 |
|
MM6 control shRNA Mock treated 2
|
MM6 cell line
|
Monocytic cell line
|
All the above steps after RNA extraction were done by the Microarray Core Facility at Baylor College of Medicine. This sample is numbered as 6890.
|
| Sample_geo_accession | GSM257616
| | Sample_status | Public on Jul 31 2008
| | Sample_submission_date | Jan 17 2008
| | Sample_last_update_date | May 16 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MM6 cells were transduced with a control shRNA and then mock treated.
| | Sample_growth_protocol_ch1 | MM6 cells were maintained in RPMI 1640 medium (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Hyclone), ), non-essential amino acids (Invitrogen), l-glutamine (Invitrogen), and OPI media supplement (Sigma) containing 0.15 mg of oxalacetate, 0.5 g of pyruvate and 8.2 mg of bovine insulin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using the Qiagen RNeasy kit according to the manufacturer's protocol and RNA quality was determined using an Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | See affymetrix protocol.
| | Sample_hyb_protocol | See affymetrix protocol.
| | Sample_scan_protocol | Affymetrix Gene Chip Scanner 3100.
| | Sample_data_processing | MAS5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andrew ,P.,Rice
| | Sample_contact_laboratory | Rice
| | Sample_contact_department | Molecular Virology and Microbiology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77025
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM257nnn/GSM257616/suppl/GSM257616.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM257nnn/GSM257616/suppl/GSM257616.CHP.gz
| | Sample_series_id | GSE10738
| | Sample_series_id | GSE11462
| | 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 |
|
|
