Search results for the GEO ID: GSE31166  |
(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 |
GSM772504 | GPL1261 |
|
CTL, biological replicate 1
|
inducible ES stable cell line grown in medium containing Tetracycline
|
cell line: mouse Embryonic Stem (ES) cells
|
Gene expression data from mouse inducible ES stable control clone
Raw data file: CTL 1.CEL
|
| Sample_geo_accession | GSM772504
| | Sample_status | Public on Dec 13 2012
| | Sample_submission_date | Aug 03 2011
| | Sample_last_update_date | Dec 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | The growth of each inducible clone was performed in medium deprived of Tetracycline for 48 hours, while the control clones were grown in medium containing Tetracycline and the total RNA was extracted
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNAs from either undifferentiated ES cells were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Biotinylated cRNAs were generated using the GeneChip IVT labelling kit (Affymetrix). 20µg of Biotinylated cRNA was fragmented and 10µg hybridised to the Affymetrix GeneChip Mouse Genome 430_2 array for 16hrs at 45°C using an Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’ standard protocols.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000 .
| | Sample_data_processing | The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Rossella,,De Cegli
| | Sample_contact_email | decegli@tigem.it
| | Sample_contact_institute | Tigem
| | Sample_contact_address | via Castellino
| | Sample_contact_city | Naples
| | Sample_contact_zip/postal_code | 80131
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM772nnn/GSM772504/suppl/GSM772504.CEL.gz
| | Sample_series_id | GSE31166
| | Sample_series_id | GSE31701
| | Sample_data_row_count | 45101
| | |
|
GSM772505 | GPL1261 |
|
CTL, biological replicate 2
|
inducible ES stable cell line grown in medium containing Tetracycline
|
cell line: mouse Embryonic Stem (ES) cells
|
Gene expression data from mouse inducible ES stable control clone
Raw data file: CTL 2.CEL
|
| Sample_geo_accession | GSM772505
| | Sample_status | Public on Dec 13 2012
| | Sample_submission_date | Aug 03 2011
| | Sample_last_update_date | Dec 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | The growth of each inducible clone was performed in medium deprived of Tetracycline for 48 hours, while the control clones were grown in medium containing Tetracycline and the total RNA was extracted
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNAs from either undifferentiated ES cells were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Biotinylated cRNAs were generated using the GeneChip IVT labelling kit (Affymetrix). 20µg of Biotinylated cRNA was fragmented and 10µg hybridised to the Affymetrix GeneChip Mouse Genome 430_2 array for 16hrs at 45°C using an Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’ standard protocols.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000 .
| | Sample_data_processing | The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Rossella,,De Cegli
| | Sample_contact_email | decegli@tigem.it
| | Sample_contact_institute | Tigem
| | Sample_contact_address | via Castellino
| | Sample_contact_city | Naples
| | Sample_contact_zip/postal_code | 80131
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM772nnn/GSM772505/suppl/GSM772505.CEL.gz
| | Sample_series_id | GSE31166
| | Sample_series_id | GSE31701
| | Sample_data_row_count | 45101
| | |
|
GSM772506 | GPL1261 |
|
CTL, biological replicate 3
|
inducible ES stable cell line grown in medium containing Tetracycline
|
cell line: mouse Embryonic Stem (ES) cells
|
Gene expression data from mouse inducible ES stable control clone
Raw data file: CTL 3.CEL
|
| Sample_geo_accession | GSM772506
| | Sample_status | Public on Dec 13 2012
| | Sample_submission_date | Aug 03 2011
| | Sample_last_update_date | Dec 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | The growth of each inducible clone was performed in medium deprived of Tetracycline for 48 hours, while the control clones were grown in medium containing Tetracycline and the total RNA was extracted
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNAs from either undifferentiated ES cells were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Biotinylated cRNAs were generated using the GeneChip IVT labelling kit (Affymetrix). 20µg of Biotinylated cRNA was fragmented and 10µg hybridised to the Affymetrix GeneChip Mouse Genome 430_2 array for 16hrs at 45°C using an Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’ standard protocols.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000 .
| | Sample_data_processing | The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Rossella,,De Cegli
| | Sample_contact_email | decegli@tigem.it
| | Sample_contact_institute | Tigem
| | Sample_contact_address | via Castellino
| | Sample_contact_city | Naples
| | Sample_contact_zip/postal_code | 80131
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM772nnn/GSM772506/suppl/GSM772506.CEL.gz
| | Sample_series_id | GSE31166
| | Sample_series_id | GSE31701
| | Sample_data_row_count | 45101
| | |
|
GSM772507 | GPL1261 |
|
inducible clone, biological replicate1
|
inducible ES stable cell line grown in medium deprived of Tetracycline
|
cell line: mouse Embryonic Stem (ES) cells
|
Gene expression data from mouse inducible ES stable clone
Raw data file: induction 1.CEL
|
| Sample_geo_accession | GSM772507
| | Sample_status | Public on Dec 13 2012
| | Sample_submission_date | Aug 03 2011
| | Sample_last_update_date | Dec 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | The growth of each inducible clone was performed in medium deprived of Tetracycline for 48 hours, while the control clones were grown in medium containing Tetracycline and the total RNA was extracted
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNAs from either undifferentiated ES cells were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Biotinylated cRNAs were generated using the GeneChip IVT labelling kit (Affymetrix). 20µg of Biotinylated cRNA was fragmented and 10µg hybridised to the Affymetrix GeneChip Mouse Genome 430_2 array for 16hrs at 45°C using an Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’ standard protocols.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000 .
| | Sample_data_processing | The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Rossella,,De Cegli
| | Sample_contact_email | decegli@tigem.it
| | Sample_contact_institute | Tigem
| | Sample_contact_address | via Castellino
| | Sample_contact_city | Naples
| | Sample_contact_zip/postal_code | 80131
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM772nnn/GSM772507/suppl/GSM772507.CEL.gz
| | Sample_series_id | GSE31166
| | Sample_series_id | GSE31701
| | Sample_data_row_count | 45101
| | |
|
GSM772508 | GPL1261 |
|
inducible clone, biological replicate2
|
inducible ES stable cell line grown in medium deprived of Tetracycline
|
cell line: mouse Embryonic Stem (ES) cells
|
Gene expression data from mouse inducible ES stable clone
Raw data file: induction 2.CEL
|
| Sample_geo_accession | GSM772508
| | Sample_status | Public on Dec 13 2012
| | Sample_submission_date | Aug 03 2011
| | Sample_last_update_date | Dec 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | The growth of each inducible clone was performed in medium deprived of Tetracycline for 48 hours, while the control clones were grown in medium containing Tetracycline and the total RNA was extracted
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNAs from either undifferentiated ES cells were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Biotinylated cRNAs were generated using the GeneChip IVT labelling kit (Affymetrix). 20µg of Biotinylated cRNA was fragmented and 10µg hybridised to the Affymetrix GeneChip Mouse Genome 430_2 array for 16hrs at 45°C using an Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’ standard protocols.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000 .
| | Sample_data_processing | The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Rossella,,De Cegli
| | Sample_contact_email | decegli@tigem.it
| | Sample_contact_institute | Tigem
| | Sample_contact_address | via Castellino
| | Sample_contact_city | Naples
| | Sample_contact_zip/postal_code | 80131
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM772nnn/GSM772508/suppl/GSM772508.CEL.gz
| | Sample_series_id | GSE31166
| | Sample_series_id | GSE31701
| | Sample_data_row_count | 45101
| | |
|
GSM772509 | GPL1261 |
|
inducible clone, biological replicate3
|
inducible ES stable cell line grown in medium deprived of Tetracycline
|
cell line: mouse Embryonic Stem (ES) cells
|
Gene expression data from mouse inducible ES stable clone
Raw data file: induction 3.CEL
|
| Sample_geo_accession | GSM772509
| | Sample_status | Public on Dec 13 2012
| | Sample_submission_date | Aug 03 2011
| | Sample_last_update_date | Dec 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | The growth of each inducible clone was performed in medium deprived of Tetracycline for 48 hours, while the control clones were grown in medium containing Tetracycline and the total RNA was extracted
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNAs from either undifferentiated ES cells were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Biotinylated cRNAs were generated using the GeneChip IVT labelling kit (Affymetrix). 20µg of Biotinylated cRNA was fragmented and 10µg hybridised to the Affymetrix GeneChip Mouse Genome 430_2 array for 16hrs at 45°C using an Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’ standard protocols.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000 .
| | Sample_data_processing | The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Rossella,,De Cegli
| | Sample_contact_email | decegli@tigem.it
| | Sample_contact_institute | Tigem
| | Sample_contact_address | via Castellino
| | Sample_contact_city | Naples
| | Sample_contact_zip/postal_code | 80131
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM772nnn/GSM772509/suppl/GSM772509.CEL.gz
| | Sample_series_id | GSE31166
| | Sample_series_id | GSE31701
| | Sample_data_row_count | 45101
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
