Search results for the GEO ID: GSE37917  |
(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 |
GSM688705 | GPL1261 |
|
Max-null ES Dox untreated ver2
|
Max-null ES Dox untreated
|
gender: male
strain: 129SV
tissue: ES cells
|
Reference sample for Max-null ES cells Dox-treated for 6 and 8 days
|
| Sample_geo_accession | GSM688705
| | Sample_status | Public on Jul 20 2011
| | Sample_submission_date | Mar 10 2011
| | Sample_last_update_date | Jul 20 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Dox-untread or -treated Max-null ESCs cultured under conventional ES culture condition with LIF and serum or 2i/Nam condition. Nanog-rescued Max-null ESCs and wild-type ESCs were cultured under conventional and 2i/Nam conditions, respectively.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNAs were prepared by using TRIzol reagent from invitrogen (15596-026).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol. (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Labelled samples were hybridized to the microarrays according to the manufacturer’s protocol with Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneArray Scanner 3000. Scanning was preformed as described elsewhere. (Irizarry et al, Nucleic Acids Res 31, e15, 2003)
| | Sample_data_processing | The data was background-subtracted and normalized with the robust multi-array analysis (RMA; Irizarry et al. Nucleic Acids Res 31(4): e15, 2003) via R/Bioconductor 2.7 affy package using default analysis settings.
| | Sample_data_processing | Matrix values are logarithmic (log2) of expression measure from CEL files.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Akihiko,,Okuda
| | Sample_contact_email | akiokuda@saitama-med.a.jp
| | Sample_contact_phone | 81-42-984-4787
| | Sample_contact_fax | 81-42-984-4763
| | Sample_contact_laboratory | Division of Developmental Biology
| | Sample_contact_department | Research Center for Genomic Medicine
| | Sample_contact_institute | Saitama Medical University
| | Sample_contact_address | 1397-1 Yamane
| | Sample_contact_city | Hidaka
| | Sample_contact_state | Saitama
| | Sample_contact_zip/postal_code | 3501241
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.saitama-med.ac.jp/genome
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM688nnn/GSM688705/suppl/GSM688705.CEL.gz
| | Sample_series_id | GSE27881
| | Sample_series_id | GSE37917
| | Sample_data_row_count | 45101
| | |
|
GSM688706 | GPL1261 |
|
Max-null ES Dox-treated (6 day)
|
Max-null ES Dox treated for 6 days
|
gender: male
strain: 129SV
tissue: ES cells
|
|
| Sample_geo_accession | GSM688706
| | Sample_status | Public on Jul 20 2011
| | Sample_submission_date | Mar 10 2011
| | Sample_last_update_date | Jul 20 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Dox-untread or -treated Max-null ESCs cultured under conventional ES culture condition with LIF and serum or 2i/Nam condition. Nanog-rescued Max-null ESCs and wild-type ESCs were cultured under conventional and 2i/Nam conditions, respectively.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNAs were prepared by using TRIzol reagent from invitrogen (15596-026).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol. (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Labelled samples were hybridized to the microarrays according to the manufacturer’s protocol with Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneArray Scanner 3000. Scanning was preformed as described elsewhere. (Irizarry et al, Nucleic Acids Res 31, e15, 2003)
| | Sample_data_processing | The data was background-subtracted and normalized with the robust multi-array analysis (RMA; Irizarry et al. Nucleic Acids Res 31(4): e15, 2003) via R/Bioconductor 2.7 affy package using default analysis settings.
| | Sample_data_processing | Matrix values are logarithmic (log2) of expression measure from CEL files.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Akihiko,,Okuda
| | Sample_contact_email | akiokuda@saitama-med.a.jp
| | Sample_contact_phone | 81-42-984-4787
| | Sample_contact_fax | 81-42-984-4763
| | Sample_contact_laboratory | Division of Developmental Biology
| | Sample_contact_department | Research Center for Genomic Medicine
| | Sample_contact_institute | Saitama Medical University
| | Sample_contact_address | 1397-1 Yamane
| | Sample_contact_city | Hidaka
| | Sample_contact_state | Saitama
| | Sample_contact_zip/postal_code | 3501241
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.saitama-med.ac.jp/genome
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM688nnn/GSM688706/suppl/GSM688706.CEL.gz
| | Sample_series_id | GSE27881
| | Sample_series_id | GSE37917
| | Sample_data_row_count | 45101
| | |
|
GSM929906 | GPL1261 |
|
Max-null ES cells (Nam+)(Dox-)
|
Max-expressing ES cells with Nam
|
gender: male
strain: 129sv
cell type: embryonic stem (ES) cells
treatment: nicotinamide (Nam)
max expression: yes
|
Gene expression data of Nam-treated, Dox-untreated Max-null ES cells.
|
| Sample_geo_accession | GSM929906
| | Sample_status | Public on Aug 28 2012
| | Sample_submission_date | May 10 2012
| | Sample_last_update_date | Aug 28 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Nam (4mM) was added, but doxycycline was not added.
| | Sample_growth_protocol_ch1 | ES cells were cultured under conventional ES culture conditions with LIF and serum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNAs were prepared using TRIzol reagent from Invitrogen (15596-026).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual 2001, Affymetrix).
| | Sample_hyb_protocol | Labeled samples were hybridized to the microarrays according to the manufacturer's protocol with Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneArray Scanner 3000. Scanning was performed as described elsewhere (Irizarry et al. Nucleic Acids Res. e15, 2003).
| | Sample_data_processing | The intensity data was background-subtracted and normalized with the robust multi-array analysis (RMA; Irizarry et al. Nucleic Acids Res. e15, 2003) via the R/Bioconductor affy 2.13.1 package using default analysis settings.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Akihiko,,Okuda
| | Sample_contact_email | akiokuda@saitama-med.a.jp
| | Sample_contact_phone | 81-42-984-4787
| | Sample_contact_fax | 81-42-984-4763
| | Sample_contact_laboratory | Division of Developmental Biology
| | Sample_contact_department | Research Center for Genomic Medicine
| | Sample_contact_institute | Saitama Medical University
| | Sample_contact_address | 1397-1 Yamane
| | Sample_contact_city | Hidaka
| | Sample_contact_state | Saitama
| | Sample_contact_zip/postal_code | 3501241
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.saitama-med.ac.jp/genome
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM929nnn/GSM929906/suppl/GSM929906_Okuda_Max_null_Nam_plus_Dox_minus.CEL.gz
| | Sample_series_id | GSE37917
| | Sample_data_row_count | 45101
| | |
|
GSM929907 | GPL1261 |
|
Max-null ES cells (Nam+)(Dox+)
|
Max-non-expressing ES cells with Nam
|
gender: male
strain: 129sv
cell type: embryonic stem (ES) cells
treatment: nicotinamide (Nam)
max expression: no
|
Gene expression data of Nam- and Dox-treated Max-null ES cells.
|
| Sample_geo_accession | GSM929907
| | Sample_status | Public on Aug 28 2012
| | Sample_submission_date | May 10 2012
| | Sample_last_update_date | Aug 28 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Nam (4mM) and doxycycline were added.
| | Sample_growth_protocol_ch1 | ES cells were cultured under conventional ES culture conditions with LIF and serum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNAs were prepared using TRIzol reagent from Invitrogen (15596-026).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual 2001, Affymetrix).
| | Sample_hyb_protocol | Labeled samples were hybridized to the microarrays according to the manufacturer's protocol with Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneArray Scanner 3000. Scanning was performed as described elsewhere (Irizarry et al. Nucleic Acids Res. e15, 2003).
| | Sample_data_processing | The intensity data was background-subtracted and normalized with the robust multi-array analysis (RMA; Irizarry et al. Nucleic Acids Res. e15, 2003) via the R/Bioconductor affy 2.13.1 package using default analysis settings.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Akihiko,,Okuda
| | Sample_contact_email | akiokuda@saitama-med.a.jp
| | Sample_contact_phone | 81-42-984-4787
| | Sample_contact_fax | 81-42-984-4763
| | Sample_contact_laboratory | Division of Developmental Biology
| | Sample_contact_department | Research Center for Genomic Medicine
| | Sample_contact_institute | Saitama Medical University
| | Sample_contact_address | 1397-1 Yamane
| | Sample_contact_city | Hidaka
| | Sample_contact_state | Saitama
| | Sample_contact_zip/postal_code | 3501241
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.saitama-med.ac.jp/genome
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM929nnn/GSM929907/suppl/GSM929907_Okuda_Max_null_Nam_plus_Dox_plus.CEL.gz
| | Sample_series_id | GSE37917
| | 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: |
|
|
|
