Search results for the GEO ID: GSE37982  |
(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 |
GSM931295 | GPL570 |
|
CML-iPS1
|
human iPS cells
|
cell type: iPS cells
disease status: CML
|
Gene expression data from iPS cells
|
| Sample_geo_accession | GSM931295
| | Sample_status | Public on May 16 2012
| | Sample_submission_date | May 15 2012
| | Sample_last_update_date | May 16 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DNA was removed by RNAse-freeDNAse treatment using standard procedure.
| | Sample_growth_protocol_ch1 | iPS cells were maintained on MEF.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with RNAeasy reagents (QIAGEN, Hilden, Germany) according to the manufacture's instructions. The integrity of RNA was checked by Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system. Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system. Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system. Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system. Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system. Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system.
| | Sample_hyb_protocol | Following amplification, 5 ug of cRNA were hybridized to HG-U133 Plus 2.0 GeneChip arrays (Affymetrix).
| | Sample_scan_protocol | Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G. Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G. Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G. Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G. Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G.
| | 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_data_processing | Expression data were extracted from image files produced on Affymetrix® GeneChip Operating Software 1.0® (GCOS®).Background subtraction, normalization and expression values of our data were calculated using the rma algorithm, available as a part of the Affymetrix package of the Bioconductor open-source software library for the statistical language R (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Keiki,,Kumano
| | Sample_contact_email | kumano-tky@umin.ac.jp
| | Sample_contact_phone | +81-3-3815-5411
| | Sample_contact_fax | +81-3-5804-6261
| | Sample_contact_institute | University of Tokyo
| | Sample_contact_address | 7-3-1, Hongo, Bunkyo-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 1138655
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM931nnn/GSM931295/suppl/GSM931295_14U0010354-H01_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE37982
| | Sample_data_row_count | 54675
| | |
|
GSM931296 | GPL570 |
|
CML-iPS 2
|
human iPS cells
|
cell type: iPS cells
disease status: CML
|
Gene expression data from iPS cells
|
| Sample_geo_accession | GSM931296
| | Sample_status | Public on May 16 2012
| | Sample_submission_date | May 15 2012
| | Sample_last_update_date | May 16 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DNA was removed by RNAse-freeDNAse treatment using standard procedure.
| | Sample_growth_protocol_ch1 | iPS cells were maintained on MEF.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with RNAeasy reagents (QIAGEN, Hilden, Germany) according to the manufacture's instructions. The integrity of RNA was checked by Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system. Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system. Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system. Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system. Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system. Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system.
| | Sample_hyb_protocol | Following amplification, 5 ug of cRNA were hybridized to HG-U133 Plus 2.0 GeneChip arrays (Affymetrix).
| | Sample_scan_protocol | Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G. Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G. Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G. Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G. Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G.
| | 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_data_processing | Expression data were extracted from image files produced on Affymetrix® GeneChip Operating Software 1.0® (GCOS®).Background subtraction, normalization and expression values of our data were calculated using the rma algorithm, available as a part of the Affymetrix package of the Bioconductor open-source software library for the statistical language R (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Keiki,,Kumano
| | Sample_contact_email | kumano-tky@umin.ac.jp
| | Sample_contact_phone | +81-3-3815-5411
| | Sample_contact_fax | +81-3-5804-6261
| | Sample_contact_institute | University of Tokyo
| | Sample_contact_address | 7-3-1, Hongo, Bunkyo-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 1138655
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM931nnn/GSM931296/suppl/GSM931296_14U0010354-H02_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE37982
| | Sample_data_row_count | 54675
| | |
|
GSM931297 | GPL570 |
|
normal iPS
|
human iPS cells
|
cell type: iPS cells
disease status: normal cord blood
|
Gene expression data from iPS cells
|
| Sample_geo_accession | GSM931297
| | Sample_status | Public on May 16 2012
| | Sample_submission_date | May 15 2012
| | Sample_last_update_date | May 16 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DNA was removed by RNAse-freeDNAse treatment using standard procedure.
| | Sample_growth_protocol_ch1 | iPS cells were maintained on MEF.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with RNAeasy reagents (QIAGEN, Hilden, Germany) according to the manufacture's instructions. The integrity of RNA was checked by Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system. Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system. Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system. Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system. Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system. Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system.
| | Sample_hyb_protocol | Following amplification, 5 ug of cRNA were hybridized to HG-U133 Plus 2.0 GeneChip arrays (Affymetrix).
| | Sample_scan_protocol | Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G. Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G. Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G. Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G. Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G.
| | 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_data_processing | Expression data were extracted from image files produced on Affymetrix® GeneChip Operating Software 1.0® (GCOS®).Background subtraction, normalization and expression values of our data were calculated using the rma algorithm, available as a part of the Affymetrix package of the Bioconductor open-source software library for the statistical language R (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Keiki,,Kumano
| | Sample_contact_email | kumano-tky@umin.ac.jp
| | Sample_contact_phone | +81-3-3815-5411
| | Sample_contact_fax | +81-3-5804-6261
| | Sample_contact_institute | University of Tokyo
| | Sample_contact_address | 7-3-1, Hongo, Bunkyo-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 1138655
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM931nnn/GSM931297/suppl/GSM931297_14U0010354-H03_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE37982
| | 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 |
|
|
