Search results for the GEO ID: GSE18598 |
(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 |
GSM462488 | GPL1261 |
|
L1-GL3-2
|
differentiating 3T3-L1 cells with control siRNA
|
cell type: differentiating 3T3-L1 adipocytes
|
3T3-L1, control siRNA
|
Sample_geo_accession | GSM462488
| Sample_status | Public on Apr 05 2012
| Sample_submission_date | Oct 16 2009
| Sample_last_update_date | Apr 05 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Cells were washed twice with PBS, and were collected in cell lysis buffer RLT (RNeasy Mini Kit) and homogenized.
| Sample_growth_protocol_ch1 | Cells were grown in DMEM containing 25mM glucose and 10% FBS. For adipogenic induction, insulin, dexamethaone and 3- isobutyl-1-methylxanthine were added.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Mini Kit according to manufacturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3'IVT Express Kit User Manual, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GCS3000.
| Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| Sample_platform_id | GPL1261
| Sample_contact_name | Mitsuyoshi,,Nakao
| Sample_contact_email | mnakao@gpo.kumamoto-u.ac.jp
| Sample_contact_institute | Kumamoto University
| Sample_contact_address | 2-2-1 Honjo
| Sample_contact_city | Kumamoto
| Sample_contact_zip/postal_code | 860-0811
| Sample_contact_country | Japan
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM462nnn/GSM462488/suppl/GSM462488_L2-GL3.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM462nnn/GSM462488/suppl/GSM462488_L2-GL3.mas5.CHP.gz
| Sample_series_id | GSE18598
| Sample_series_id | GSE18600
| Sample_data_row_count | 45101
| |
|
GSM462489 | GPL1261 |
|
L1-AOF2
|
differentiating 3T3-L1 cells with aof2-specific siRNA
|
cell type: differentiating 3T3-L1 adipocytes
|
3T3-L1, aof2 siRNA
|
Sample_geo_accession | GSM462489
| Sample_status | Public on Apr 05 2012
| Sample_submission_date | Oct 16 2009
| Sample_last_update_date | Apr 05 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Cells were washed twice with PBS, and were collected in cell lysis buffer RLT (RNeasy Mini Kit) and homogenized.
| Sample_growth_protocol_ch1 | Cells were grown in DMEM containing 25mM glucose and 10% FBS. For adipogenic induction, insulin, dexamethaone and 3- isobutyl-1-methylxanthine were added.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Mini Kit according to manufacturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3'IVT Express Kit User Manual, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GCS3000.
| Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| Sample_platform_id | GPL1261
| Sample_contact_name | Mitsuyoshi,,Nakao
| Sample_contact_email | mnakao@gpo.kumamoto-u.ac.jp
| Sample_contact_institute | Kumamoto University
| Sample_contact_address | 2-2-1 Honjo
| Sample_contact_city | Kumamoto
| Sample_contact_zip/postal_code | 860-0811
| Sample_contact_country | Japan
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM462nnn/GSM462489/suppl/GSM462489_L2-AOF2.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM462nnn/GSM462489/suppl/GSM462489_L2-AOF2.mas5.CHP.gz
| Sample_series_id | GSE18598
| Sample_series_id | GSE18600
| Sample_data_row_count | 45101
| |
|
GSM462490 | GPL1261 |
|
L1-RFK
|
differentiating 3T3-L1 cells with rfk-specific siRNA
|
cell type: differentiating 3T3-L1 adipocytes
|
3T3-L1, rfk siRNA
|
Sample_geo_accession | GSM462490
| Sample_status | Public on Apr 05 2012
| Sample_submission_date | Oct 16 2009
| Sample_last_update_date | Apr 05 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Cells were washed twice with PBS, and were collected in cell lysis buffer RLT (RNeasy Mini Kit) and homogenized.
| Sample_growth_protocol_ch1 | Cells were grown in DMEM containing 25mM glucose and 10% FBS. For adipogenic induction, insulin, dexamethaone and 3- isobutyl-1-methylxanthine were added.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Mini Kit according to manufacturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3'IVT Express Kit User Manual, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GCS3000.
| Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| Sample_platform_id | GPL1261
| Sample_contact_name | Mitsuyoshi,,Nakao
| Sample_contact_email | mnakao@gpo.kumamoto-u.ac.jp
| Sample_contact_institute | Kumamoto University
| Sample_contact_address | 2-2-1 Honjo
| Sample_contact_city | Kumamoto
| Sample_contact_zip/postal_code | 860-0811
| Sample_contact_country | Japan
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM462nnn/GSM462490/suppl/GSM462490_L2-RFK.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM462nnn/GSM462490/suppl/GSM462490_L2-RFK.mas5.CHP.gz
| Sample_series_id | GSE18598
| Sample_series_id | GSE18600
| Sample_data_row_count | 45101
| |
|
GSM462491 | GPL1261 |
|
L1-TC
|
differentiating 3T3-L1 cells treated with tranylcypromine
|
cell type: differentiating 3T3-L1 adipocytes
|
3T3-L1, TC-treated
|
Sample_geo_accession | GSM462491
| Sample_status | Public on Apr 05 2012
| Sample_submission_date | Oct 16 2009
| Sample_last_update_date | Apr 05 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Cells were washed twice with PBS, and were collected in cell lysis buffer RLT (RNeasy Mini Kit) and homogenized.
| Sample_growth_protocol_ch1 | Cells were grown in DMEM containing 25mM glucose and 10% FBS. For adipogenic induction, insulin, dexamethaone and 3- isobutyl-1-methylxanthine were added.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Mini Kit according to manufacturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3'IVT Express Kit User Manual, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GCS3000.
| Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| Sample_platform_id | GPL1261
| Sample_contact_name | Mitsuyoshi,,Nakao
| Sample_contact_email | mnakao@gpo.kumamoto-u.ac.jp
| Sample_contact_institute | Kumamoto University
| Sample_contact_address | 2-2-1 Honjo
| Sample_contact_city | Kumamoto
| Sample_contact_zip/postal_code | 860-0811
| Sample_contact_country | Japan
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM462nnn/GSM462491/suppl/GSM462491_L2-TC.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM462nnn/GSM462491/suppl/GSM462491_L2-TC.mas5.CHP.gz
| Sample_series_id | GSE18598
| Sample_series_id | GSE18600
| 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: |
|
|
|
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 |
|
|