Search results for the GEO ID: GSE17563  |
(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 |
GSM437715 | GPL339 |
|
Mouses bone marrow treated with hRANKL 0 hr
|
bone marrow cells
|
development stage: Precursor
strain: C57/BL6
time: 0 hr
|
Osteoclastogenesis
|
| Sample_geo_accession | GSM437715
| | Sample_status | Public on Aug 08 2009
| | Sample_submission_date | Aug 07 2009
| | Sample_last_update_date | Aug 07 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Macrophages were treated with hRANKL (150 ng/ml) for 0, 24, and 72 h.
| | Sample_growth_protocol_ch1 | Mouse (C57/BL6) bone marrow cells were harvested and cultured in the presence of hM-CSF (50 ng/ml) for 3 days to induce macrophages.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy mini kit (Quiagen) 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 5 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 Mouse 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 | GPL339
| | Sample_contact_name | Masamichi,,Takami
| | Sample_contact_laboratory | Biochemistry
| | Sample_contact_department | School of Dentistry
| | Sample_contact_institute | Showa University
| | Sample_contact_address | 1-5-8, Hatanodai, Shinagawa
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 142-8555
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437715/suppl/GSM437715.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437715/suppl/GSM437715.CHP.gz
| | Sample_series_id | GSE17563
| | Sample_data_row_count | 22690
| | |
|
GSM437716 | GPL339 |
|
Mouses bone marrow treated with hRANKL 24 h
|
bone marrow cells
|
development stage: Differentiating precursor
strain: C57/BL6
time: 24 hr
|
Osteoclastogenesis
|
| Sample_geo_accession | GSM437716
| | Sample_status | Public on Aug 08 2009
| | Sample_submission_date | Aug 07 2009
| | Sample_last_update_date | Aug 07 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Macrophages were treated with hRANKL (150 ng/ml) for 0, 24, and 72 h.
| | Sample_growth_protocol_ch1 | Mouse (C57/BL6) bone marrow cells were harvested and cultured in the presence of hM-CSF (50 ng/ml) for 3 days to induce macrophages.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy mini kit (Quiagen) 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 5 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 Mouse 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 | GPL339
| | Sample_contact_name | Masamichi,,Takami
| | Sample_contact_laboratory | Biochemistry
| | Sample_contact_department | School of Dentistry
| | Sample_contact_institute | Showa University
| | Sample_contact_address | 1-5-8, Hatanodai, Shinagawa
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 142-8555
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437716/suppl/GSM437716.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437716/suppl/GSM437716.CHP.gz
| | Sample_series_id | GSE17563
| | Sample_data_row_count | 22690
| | |
|
GSM437717 | GPL339 |
|
Mouses bone marrow treated with hRANKL 72h
|
bone marrow cells
|
development stage: Osteoclast
strain: C57/BL6
time: 72 hr
|
Osteoclastogenesis
|
| Sample_geo_accession | GSM437717
| | Sample_status | Public on Aug 08 2009
| | Sample_submission_date | Aug 07 2009
| | Sample_last_update_date | Aug 07 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Macrophages were treated with hRANKL (150 ng/ml) for 0, 24, and 72 h.
| | Sample_growth_protocol_ch1 | Mouse (C57/BL6) bone marrow cells were harvested and cultured in the presence of hM-CSF (50 ng/ml) for 3 days to induce macrophages.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy mini kit (Quiagen) 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 5 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 Mouse 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 | GPL339
| | Sample_contact_name | Masamichi,,Takami
| | Sample_contact_laboratory | Biochemistry
| | Sample_contact_department | School of Dentistry
| | Sample_contact_institute | Showa University
| | Sample_contact_address | 1-5-8, Hatanodai, Shinagawa
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 142-8555
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437717/suppl/GSM437717.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437717/suppl/GSM437717.CHP.gz
| | Sample_series_id | GSE17563
| | Sample_data_row_count | 22690
| | |
|
| |
| |
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 |
|
|
