Search results for the GEO ID: GSE42637  |
(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 |
GSM1047005 | GPL570 |
|
A1_scrb
|
BL2
|
cell line: BL2
transfection: scrb siRNA
batch: 1
|
Gene expression data.
|
| Sample_geo_accession | GSM1047005
| | Sample_status | Public on Jun 01 2013
| | Sample_submission_date | Nov 29 2012
| | Sample_last_update_date | Jun 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | electroporation of BL2 cells
| | Sample_growth_protocol_ch1 | complete RPMI
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047005/suppl/GSM1047005_A330b_A1.CEL.gz
| | Sample_series_id | GSE42637
| | Sample_data_row_count | 54675
| | |
|
GSM1047006 | GPL570 |
|
A2_LEF1
|
BL2
|
cell line: BL2
transfection: LEF siRNA
batch: 1
|
Gene expression data.
|
| Sample_geo_accession | GSM1047006
| | Sample_status | Public on Jun 01 2013
| | Sample_submission_date | Nov 29 2012
| | Sample_last_update_date | Jun 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | electroporation of BL2 cells
| | Sample_growth_protocol_ch1 | complete RPMI
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047006/suppl/GSM1047006_A330b_A2.CEL.gz
| | Sample_series_id | GSE42637
| | Sample_data_row_count | 54675
| | |
|
GSM1047007 | GPL570 |
|
A3_scrb
|
BL2
|
cell line: BL2
transfection: scrb siRNA
batch: 2
|
Gene expression data.
|
| Sample_geo_accession | GSM1047007
| | Sample_status | Public on Jun 01 2013
| | Sample_submission_date | Nov 29 2012
| | Sample_last_update_date | Jun 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | electroporation of BL2 cells
| | Sample_growth_protocol_ch1 | complete RPMI
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047007/suppl/GSM1047007_A330b_A3.CEL.gz
| | Sample_series_id | GSE42637
| | Sample_data_row_count | 54675
| | |
|
GSM1047008 | GPL570 |
|
A4_LEF1
|
BL2
|
cell line: BL2
transfection: LEF siRNA
batch: 2
|
Gene expression data.
|
| Sample_geo_accession | GSM1047008
| | Sample_status | Public on Jun 01 2013
| | Sample_submission_date | Nov 29 2012
| | Sample_last_update_date | Jun 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | electroporation of BL2 cells
| | Sample_growth_protocol_ch1 | complete RPMI
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047008/suppl/GSM1047008_A330b_A4.CEL.gz
| | Sample_series_id | GSE42637
| | Sample_data_row_count | 54675
| | |
|
GSM1047009 | GPL570 |
|
A5_scrb
|
BL2
|
cell line: BL2
transfection: scrb siRNA
batch: 3
|
Gene expression data.
|
| Sample_geo_accession | GSM1047009
| | Sample_status | Public on Jun 01 2013
| | Sample_submission_date | Nov 29 2012
| | Sample_last_update_date | Jun 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | electroporation of BL2 cells
| | Sample_growth_protocol_ch1 | complete RPMI
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047009/suppl/GSM1047009_A330c_A5.CEL.gz
| | Sample_series_id | GSE42637
| | Sample_data_row_count | 54675
| | |
|
GSM1047010 | GPL570 |
|
A6_LEF1
|
BL2
|
cell line: BL2
transfection: LEF siRNA
batch: 3
|
Gene expression data.
|
| Sample_geo_accession | GSM1047010
| | Sample_status | Public on Jun 01 2013
| | Sample_submission_date | Nov 29 2012
| | Sample_last_update_date | Jun 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | electroporation of BL2 cells
| | Sample_growth_protocol_ch1 | complete RPMI
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047010/suppl/GSM1047010_A330c_A6.CEL.gz
| | Sample_series_id | GSE42637
| | 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 |
|
|
