Search results for the GEO ID: GSE28807  |
(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 |
GSM713392 | GPL570 |
|
untreated
|
primary Wilms tumor cells ws568li
|
cell type: primary Wilms tumor cells ws568li
treatment: untreated
|
Gene expression data from primary Wilms tumor cells ws568li, untreated
|
| Sample_geo_accession | GSM713392
| | Sample_status | Public on Apr 21 2012
| | Sample_submission_date | Apr 22 2011
| | Sample_last_update_date | Apr 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated with 10 µM all-trans retinoic acid for 4 days, untreated control cells received 1 µl/ml DMSO.
| | Sample_growth_protocol_ch1 | Primary Wilms tumor cells were established from fresh tumor material and maintained in Dulbecco’s Modified Eagle Medium supplemented with 10 % FCS and 1 % penicillin/streptomycin in a humidified chamber at 37C and 5 % CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with RNeasy Mini Kit (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (IVT-Express Kit, Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on a 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 GeneArray Scanner 3000
| | Sample_data_processing | The data were analyzed with Bioconductor packages (under R) and variance stabilization normalization (VSN) as normalization method
| | Sample_platform_id | GPL570
| | Sample_contact_name | Susanne,Elma,Kneitz
| | Sample_contact_email | susanne.kneitz@uni-wuerzburg.de
| | Sample_contact_phone | +49-931-31 86526
| | Sample_contact_department | Physiologigcal Chemistry
| | Sample_contact_institute | University of Wuerzburg
| | Sample_contact_address | Biozentrum, Am Hubland
| | Sample_contact_city | Wuerzburg
| | Sample_contact_zip/postal_code | 97074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM713nnn/GSM713392/suppl/GSM713392.CEL.gz
| | Sample_series_id | GSE28807
| | Sample_data_row_count | 54675
| | |
|
GSM713393 | GPL570 |
|
ATRA
|
primary Wilms tumor cells ws568li
|
cell type: primary Wilms tumor cells ws568li
treatment: ATRA
|
Gene expression from primary Wilms tumor cells ws568li, treated with ATRA
|
| Sample_geo_accession | GSM713393
| | Sample_status | Public on Apr 21 2012
| | Sample_submission_date | Apr 22 2011
| | Sample_last_update_date | Apr 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated with 10 µM all-trans retinoic acid for 4 days, untreated control cells received 1 µl/ml DMSO.
| | Sample_growth_protocol_ch1 | Primary Wilms tumor cells were established from fresh tumor material and maintained in Dulbecco’s Modified Eagle Medium supplemented with 10 % FCS and 1 % penicillin/streptomycin in a humidified chamber at 37C and 5 % CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with RNeasy Mini Kit (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (IVT-Express Kit, Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on a 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 GeneArray Scanner 3000
| | Sample_data_processing | The data were analyzed with Bioconductor packages (under R) and variance stabilization normalization (VSN) as normalization method
| | Sample_platform_id | GPL570
| | Sample_contact_name | Susanne,Elma,Kneitz
| | Sample_contact_email | susanne.kneitz@uni-wuerzburg.de
| | Sample_contact_phone | +49-931-31 86526
| | Sample_contact_department | Physiologigcal Chemistry
| | Sample_contact_institute | University of Wuerzburg
| | Sample_contact_address | Biozentrum, Am Hubland
| | Sample_contact_city | Wuerzburg
| | Sample_contact_zip/postal_code | 97074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM713nnn/GSM713393/suppl/GSM713393.CEL.gz
| | Sample_series_id | GSE28807
| | 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 |
|
|
