Search results for the GEO ID: GSE27820  |
(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 |
GSM686898 | GPL570 |
|
inactive HUMSC
|
human umbilical cord
|
tissue: umbilical cord
cell type: mesenchymal stem cell (HUMSC)
tumor suppression: low
|
Gene expression data from inactive HUMSC
HST
|
| Sample_geo_accession | GSM686898
| | Sample_status | Public on Dec 31 2012
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Dec 31 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | UCHY was UC cells but cultured in 2% O2 incubator at 37℃ for 3 days
| | Sample_growth_protocol_ch1 | HST and UC were cultured in 5% CO2 incubator at 37℃.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.
| | 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 | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | 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 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kuo-Ching,,Chao
| | Sample_contact_email | kuoching.chao@gmail.com
| | Sample_contact_department | Department of Internal Medicine
| | Sample_contact_institute | Taipei Medical University Hospital
| | Sample_contact_address | 252, Wu Hsing Street
| | Sample_contact_city | Taipei
| | Sample_contact_zip/postal_code | 110
| | Sample_contact_country | Taiwan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM686nnn/GSM686898/suppl/GSM686898.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM686nnn/GSM686898/suppl/GSM686898.CHP.gz
| | Sample_series_id | GSE27820
| | Sample_data_row_count | 54675
| | |
|
GSM686899 | GPL570 |
|
active HUMSC
|
human umbilical cord
|
tissue: umbilical cord
cell type: mesenchymal stem cell (HUMSC)
tumor suppression: high
|
Gene expression data from active HUMSC
UC
|
| Sample_geo_accession | GSM686899
| | Sample_status | Public on Dec 31 2012
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Dec 31 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | UCHY was UC cells but cultured in 2% O2 incubator at 37℃ for 3 days
| | Sample_growth_protocol_ch1 | HST and UC were cultured in 5% CO2 incubator at 37℃.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.
| | 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 | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | 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 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kuo-Ching,,Chao
| | Sample_contact_email | kuoching.chao@gmail.com
| | Sample_contact_department | Department of Internal Medicine
| | Sample_contact_institute | Taipei Medical University Hospital
| | Sample_contact_address | 252, Wu Hsing Street
| | Sample_contact_city | Taipei
| | Sample_contact_zip/postal_code | 110
| | Sample_contact_country | Taiwan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM686nnn/GSM686899/suppl/GSM686899.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM686nnn/GSM686899/suppl/GSM686899.CHP.gz
| | Sample_series_id | GSE27820
| | Sample_data_row_count | 54675
| | |
|
GSM686900 | GPL570 |
|
active HUMSC culture in hypoxia condition
|
human umbilical cord
|
tissue: umbilical cord
cell type: mesenchymal stem cell (HUMSC)
tumor suppression: high
growth condition: hypoxia
|
Gene expression data from active HUMSC
UCHY
|
| Sample_geo_accession | GSM686900
| | Sample_status | Public on Dec 31 2012
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Dec 31 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | UCHY was UC cells but cultured in 2% O2 incubator at 37℃ for 3 days
| | Sample_growth_protocol_ch1 | HST and UC were cultured in 5% CO2 incubator at 37℃.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.
| | 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 | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | 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 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kuo-Ching,,Chao
| | Sample_contact_email | kuoching.chao@gmail.com
| | Sample_contact_department | Department of Internal Medicine
| | Sample_contact_institute | Taipei Medical University Hospital
| | Sample_contact_address | 252, Wu Hsing Street
| | Sample_contact_city | Taipei
| | Sample_contact_zip/postal_code | 110
| | Sample_contact_country | Taiwan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM686nnn/GSM686900/suppl/GSM686900.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM686nnn/GSM686900/suppl/GSM686900.CHP.gz
| | Sample_series_id | GSE27820
| | 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 |
|
|
