Search results for the GEO ID: GSE49680  |
(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 |
GSM1204822 | GPL339 |
|
LM8 hPHD4 clone
|
LM8 osteosarcoma cells
|
treatment: stable transfected clone
cell line: LM8
|
|
| Sample_geo_accession | GSM1204822
| | Sample_status | Public on Aug 09 2013
| | Sample_submission_date | Aug 08 2013
| | Sample_last_update_date | Aug 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | and selected in medium supplemented with 0,5 mg/ml G418. Cells transfected with empty pcDNA3.1 vector served as control for all experiments.
| | Sample_growth_protocol_ch1 | LM8 osteosarcoma cells were transfected eith a full length hPHD4 cDNA clone in a pcDNA3.1 vector using transfection reagent (Lipofectamine TM 200; Invitrogen, Carlsbad),
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolatedfrom cell pellets using the Rneasy Mini Kit (Quiagen, Hilden, Germany) according to the manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylatetd targets were prepared according to the Affymetrix Eukaryotic Hybridization protocol (Affymetrix, Santa Clara, CA, http:\\www.affymetrix.com) from 5 µg total RNA.
| | Sample_hyb_protocol | The fragmented cRNA was hybridized to the GeneChip array MOE430A over night at 45°C under rotation (60 rpm).
| | Sample_scan_protocol | The arrays were washed, stained and scanned ba standard Affymetrix protocols using the Affymetrix GeneChip Fluidic station 400 and the Agilent GeneArray scanner 2500 (Agilent, Technologies, Palo Alto, CA, USA
| | Sample_data_processing | Images were quantified with MAS 5.0 software and GeneSpring software 9.0, using MAS5 normalisation and no baseline transformation.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Georg,,Breier
| | Sample_contact_email | georg.breier@uniklinikum-dresden.de
| | Sample_contact_phone | ++493514585278
| | Sample_contact_department | Institut für Pathologie
| | Sample_contact_institute | TU Dresden
| | Sample_contact_address | Fetscherstr.74
| | Sample_contact_city | Dresden
| | Sample_contact_zip/postal_code | 01307
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1204nnn/GSM1204822/suppl/GSM1204822_LM8_hPHD4.CEL.gz
| | Sample_series_id | GSE49680
| | Sample_data_row_count | 22690
| | |
|
GSM1204823 | GPL339 |
|
LM8 control clone
|
LM8 osteosarcoma cells
|
treatment: control clone transfected with empty vector
cell line: LM8
|
|
| Sample_geo_accession | GSM1204823
| | Sample_status | Public on Aug 09 2013
| | Sample_submission_date | Aug 08 2013
| | Sample_last_update_date | Aug 09 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | and selected in medium supplemented with 0,5 mg/ml G418. Cells transfected with empty pcDNA3.1 vector served as control for all experiments.
| | Sample_growth_protocol_ch1 | LM8 osteosarcoma cells were transfected eith a full length hPHD4 cDNA clone in a pcDNA3.1 vector using transfection reagent (Lipofectamine TM 200; Invitrogen, Carlsbad),
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolatedfrom cell pellets using the Rneasy Mini Kit (Quiagen, Hilden, Germany) according to the manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylatetd targets were prepared according to the Affymetrix Eukaryotic Hybridization protocol (Affymetrix, Santa Clara, CA, http:\\www.affymetrix.com) from 5 µg total RNA.
| | Sample_hyb_protocol | The fragmented cRNA was hybridized to the GeneChip array MOE430A over night at 45°C under rotation (60 rpm).
| | Sample_scan_protocol | The arrays were washed, stained and scanned ba standard Affymetrix protocols using the Affymetrix GeneChip Fluidic station 400 and the Agilent GeneArray scanner 2500 (Agilent, Technologies, Palo Alto, CA, USA
| | Sample_data_processing | Images were quantified with MAS 5.0 software and GeneSpring software 9.0, using MAS5 normalisation and no baseline transformation.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Georg,,Breier
| | Sample_contact_email | georg.breier@uniklinikum-dresden.de
| | Sample_contact_phone | ++493514585278
| | Sample_contact_department | Institut für Pathologie
| | Sample_contact_institute | TU Dresden
| | Sample_contact_address | Fetscherstr.74
| | Sample_contact_city | Dresden
| | Sample_contact_zip/postal_code | 01307
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1204nnn/GSM1204823/suppl/GSM1204823_LM8_control.CEL.gz
| | Sample_series_id | GSE49680
| | Sample_data_row_count | 22690
| | |
|
| |
| |
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 |
|
|
