Search results for the GEO ID: GSE45210  |
(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 |
GSM1099153 | GPL570 |
|
Against CDK8 and CDK19 rep1
|
Against CDK8 and CDK19 double transfected cell
|
cell line: HeLa s3
|
|
| Sample_geo_accession | GSM1099153
| | Sample_status | Public on Mar 16 2013
| | Sample_submission_date | Mar 15 2013
| | Sample_last_update_date | Mar 16 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | We transfect two siRNA against CDK8 and CDK19 at a same time using Lipofectamine 2000 (invitrogen) according to its manual and siRNA final concentration in the medium was 10nM each. After culturing for 48hr, transfection medium was changed to fresh antibiotic containing medium. Then the cells were incubated for additional 12hr
| | Sample_growth_protocol_ch1 | HeLa S3 cells were seeded on 6-well plate at 4 x 104 cells per well in 2ml antibiotic free DMEM medium before 24hr transfection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using RNeazy column (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with RMA using GeneSpring software. Base line was created as median of all sample.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Taiki,,Tsutsui
| | Sample_contact_email | ttsutsui@ucsd.edu
| | Sample_contact_phone | 858-534-4926
| | Sample_contact_department | CMM
| | Sample_contact_institute | UCSD
| | Sample_contact_address | 9500 Gilman Dr
| | Sample_contact_city | San Diego
| | Sample_contact_state | California
| | Sample_contact_zip/postal_code | 92093
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1099nnn/GSM1099153/suppl/GSM1099153_CDK8+19_W_knockdown-1.CEL.gz
| | Sample_series_id | GSE45210
| | Sample_data_row_count | 54675
| | |
|
GSM1099154 | GPL570 |
|
Against CDK8 and CDK19 rep2
|
Against CDK8 and CDK19 double transfected cell
|
cell line: HeLa s3
|
|
| Sample_geo_accession | GSM1099154
| | Sample_status | Public on Mar 16 2013
| | Sample_submission_date | Mar 15 2013
| | Sample_last_update_date | Mar 16 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | We transfect two siRNA against CDK8 and CDK19 at a same time using Lipofectamine 2000 (invitrogen) according to its manual and siRNA final concentration in the medium was 10nM each. After culturing for 48hr, transfection medium was changed to fresh antibiotic containing medium. Then the cells were incubated for additional 12hr
| | Sample_growth_protocol_ch1 | HeLa S3 cells were seeded on 6-well plate at 4 x 104 cells per well in 2ml antibiotic free DMEM medium before 24hr transfection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using RNeazy column (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with RMA using GeneSpring software. Base line was created as median of all sample.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Taiki,,Tsutsui
| | Sample_contact_email | ttsutsui@ucsd.edu
| | Sample_contact_phone | 858-534-4926
| | Sample_contact_department | CMM
| | Sample_contact_institute | UCSD
| | Sample_contact_address | 9500 Gilman Dr
| | Sample_contact_city | San Diego
| | Sample_contact_state | California
| | Sample_contact_zip/postal_code | 92093
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1099nnn/GSM1099154/suppl/GSM1099154_CDK8+19_W_knockdown-2.CEL.gz
| | Sample_series_id | GSE45210
| | Sample_data_row_count | 54675
| | |
|
GSM1099155 | GPL570 |
|
Against CDK8 and CDK19 rep3
|
Against CDK8 and CDK19 double transfected cell
|
cell line: HeLa s3
|
|
| Sample_geo_accession | GSM1099155
| | Sample_status | Public on Mar 16 2013
| | Sample_submission_date | Mar 15 2013
| | Sample_last_update_date | Mar 16 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | We transfect two siRNA against CDK8 and CDK19 at a same time using Lipofectamine 2000 (invitrogen) according to its manual and siRNA final concentration in the medium was 10nM each. After culturing for 48hr, transfection medium was changed to fresh antibiotic containing medium. Then the cells were incubated for additional 12hr
| | Sample_growth_protocol_ch1 | HeLa S3 cells were seeded on 6-well plate at 4 x 104 cells per well in 2ml antibiotic free DMEM medium before 24hr transfection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using RNeazy column (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with RMA using GeneSpring software. Base line was created as median of all sample.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Taiki,,Tsutsui
| | Sample_contact_email | ttsutsui@ucsd.edu
| | Sample_contact_phone | 858-534-4926
| | Sample_contact_department | CMM
| | Sample_contact_institute | UCSD
| | Sample_contact_address | 9500 Gilman Dr
| | Sample_contact_city | San Diego
| | Sample_contact_state | California
| | Sample_contact_zip/postal_code | 92093
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1099nnn/GSM1099155/suppl/GSM1099155_CDK8+19_W_knockdown-3.CEL.gz
| | Sample_series_id | GSE45210
| | 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 |
|
|
