Result

Search results for the GEO ID: GSE20070

(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

GSM501704

GPL570

negative control siRNA

Seg-1 cells

cell type: lung adenocarcinoma cell line cell line: Seg-1 sirna: negative control

Seg-1 cells transfected with negative control siRNA for 72hrs

Sample_geo_accession	GSM501704
Sample_status	Public on Jan 28 2010
Sample_submission_date	Jan 27 2010
Sample_last_update_date	Jan 27 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Seg-1 cells were reverse transfected with pre-designed siRNA from Ambion according to Invitrogen’s Lipofectamine™ RNAiMAX Reverse Transfection protocol. Briefly, transfection complexes were formed in 6-well culture plates in OPTI-1 MEM culture media to give final siRNA concentrations of 25-200 nM. A control siRNA, with no homology to any known gene sequence, was included as a negative control. Cell suspensions were added to formed complexes to give a seeding density of 1.0x105 cells per well and incubated at 37°C with 5% C02 for 72 hours. Cells were then harvested for RNA.
Sample_growth_protocol_ch1	Adherent human Seg-1 cells (generously provided by David Beer, Ph.D., University of Michigan, Ann Arbor, MI) were cultured in DMEM supplemented with 8% fetal bovine serum at 37°C with 5% CO2. Although originally believed to be an esophageal adenocarcinoma cell line, Seg-1 has recently been confirmed to be the human lung adenocarcinoma cell line H460 (Dr. David Beer, personal communication).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted with the Qiagen Rneasy mini RNA extraction kit.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Total RNA (5 μg) was used for 1st- and 2nd -strand cDNA synthesis with oligo-dT containing T7 promoter from the One-Cycle Target Labeling and Control Reagents kit (Affymetrix Cat. No. 900493). Synthesized double stranded cDNA was used as template to generate Biotin-labeled cRNA which was then fragmented to 35-200 bases in size using fragmentation buffer (Affymetrix Cat. No. 900493).
Sample_hyb_protocol	15 μg of Biotin-labeled cRNA in 250 μl hybridization cocktail was injected into each array and hybridized at 45oC for 16 hours with rotation of 60 rpm in an Affymetrix GeneChip Hybridization Oven 640. After hybridization, the staining and washing of each array was performed on Affymetrix GeneChip Fluidics Station 450 using Streptavidin Phycoerythrin, goat IgG, and Biotinylated anti-streptavidin antibody.
Sample_scan_protocol	Each array was scanned with an Affymetrix GeneChip 7G 2 Plus Scanner.
Sample_data_processing	Expression values were processed using GeneChip Operating Software (GCOS) v 1.4, MAS5, Baseline level: 100 fluorescence unit.
Sample_platform_id	GPL570
Sample_contact_name	Paul ,R,Murphy
Sample_contact_email	prmurphy@dal.ca
Sample_contact_phone	902-494-1579
Sample_contact_department	Physiology and Biophysics
Sample_contact_institute	Dalhousie University
Sample_contact_address	5850 College Street
Sample_contact_city	Halifax
Sample_contact_state	Nova Scotia
Sample_contact_zip/postal_code	B3H 1X5
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM501nnn/GSM501704/suppl/GSM501704.CEL.gz
Sample_series_id	GSE20070
Sample_data_row_count	54675

GSM501705

GPL570

FGF-AS siRNA

Seg-1 cells

cell type: lung adenocarcinoma cell line cell line: Seg-1 sirna: FGF-AS

Seg-1 cells transfected with FGF-AS siRNA for 72hrs

Sample_geo_accession	GSM501705
Sample_status	Public on Jan 28 2010
Sample_submission_date	Jan 27 2010
Sample_last_update_date	Jan 27 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Seg-1 cells were reverse transfected with pre-designed siRNA from Ambion according to Invitrogen’s Lipofectamine™ RNAiMAX Reverse Transfection protocol. Briefly, transfection complexes were formed in 6-well culture plates in OPTI-1 MEM culture media to give final siRNA concentrations of 25-200 nM. A control siRNA, with no homology to any known gene sequence, was included as a negative control. Cell suspensions were added to formed complexes to give a seeding density of 1.0x105 cells per well and incubated at 37°C with 5% C02 for 72 hours. Cells were then harvested for RNA.
Sample_growth_protocol_ch1	Adherent human Seg-1 cells (generously provided by David Beer, Ph.D., University of Michigan, Ann Arbor, MI) were cultured in DMEM supplemented with 8% fetal bovine serum at 37°C with 5% CO2. Although originally believed to be an esophageal adenocarcinoma cell line, Seg-1 has recently been confirmed to be the human lung adenocarcinoma cell line H460 (Dr. David Beer, personal communication).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted with the Qiagen Rneasy mini RNA extraction kit.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Total RNA (5 μg) was used for 1st- and 2nd -strand cDNA synthesis with oligo-dT containing T7 promoter from the One-Cycle Target Labeling and Control Reagents kit (Affymetrix Cat. No. 900493). Synthesized double stranded cDNA was used as template to generate Biotin-labeled cRNA which was then fragmented to 35-200 bases in size using fragmentation buffer (Affymetrix Cat. No. 900493).
Sample_hyb_protocol	15 μg of Biotin-labeled cRNA in 250 μl hybridization cocktail was injected into each array and hybridized at 45oC for 16 hours with rotation of 60 rpm in an Affymetrix GeneChip Hybridization Oven 640. After hybridization, the staining and washing of each array was performed on Affymetrix GeneChip Fluidics Station 450 using Streptavidin Phycoerythrin, goat IgG, and Biotinylated anti-streptavidin antibody.
Sample_scan_protocol	Each array was scanned with an Affymetrix GeneChip 7G 2 Plus Scanner.
Sample_data_processing	Expression values were processed using GeneChip Operating Software (GCOS) v 1.4, MAS5, Baseline level: 100 fluorescence unit.
Sample_platform_id	GPL570
Sample_contact_name	Paul ,R,Murphy
Sample_contact_email	prmurphy@dal.ca
Sample_contact_phone	902-494-1579
Sample_contact_department	Physiology and Biophysics
Sample_contact_institute	Dalhousie University
Sample_contact_address	5850 College Street
Sample_contact_city	Halifax
Sample_contact_state	Nova Scotia
Sample_contact_zip/postal_code	B3H 1X5
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM501nnn/GSM501705/suppl/GSM501705.CEL.gz
Sample_series_id	GSE20070
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)

B. Absolute calls (Transcribed/Not-detected)

Filter results by number of probes