Search results for the GEO ID: GSE9296  |
(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 |
GSM236935 | GPL339 |
|
CD45+/Sca1+_BM_rep1
|
CD45+/Sca1+ cells isolated from the bone marrow
|
Strain: C57BL/6, Age: 6-8 weeks old, Tissue: bone marrow
|
Synthesis of biotinylated cRNA targets, arrays hybridization (Mouse430A GeneChip, Affymetrix, Santa Clara,CA), staining and scanning were performed using Affymetrix standard protocols starting from 1μg of total RNA.
|
| Sample_geo_accession | GSM236935
| | Sample_status | Public on Apr 06 2010
| | Sample_submission_date | Oct 11 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | One-cycle target labeling assays were performed, using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 1 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (20 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | The fragmented cRNA was then hybridized to an identical lot of Affymetrix Mouse430A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | Scaling to TGT value=250. The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM236nnn/GSM236935/suppl/GSM236935.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM236nnn/GSM236935/suppl/GSM236935.CHP.gz
| | Sample_series_id | GSE9296
| | Sample_data_row_count | 22690
| | |
|
GSM236936 | GPL339 |
|
CD45+/Sca1+_BM_rep2
|
CD45+/Sca1+ cells isolated from the bone marrow
|
Strain: C57BL/6, Age: 6-8 weeks old, Tissue: bone marrow
|
Synthesis of biotinylated cRNA targets, arrays hybridization (Mouse430A GeneChip, Affymetrix, Santa Clara,CA), staining and scanning were performed using Affymetrix standard protocols starting from 1μg of total RNA.
|
| Sample_geo_accession | GSM236936
| | Sample_status | Public on Apr 06 2010
| | Sample_submission_date | Oct 11 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | One-cycle target labeling assays were performed, using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 1 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (20 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | The fragmented cRNA was then hybridized to an identical lot of Affymetrix Mouse430A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | Scaling to TGT value=250. The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM236nnn/GSM236936/suppl/GSM236936.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM236nnn/GSM236936/suppl/GSM236936.CHP.gz
| | Sample_series_id | GSE9296
| | Sample_data_row_count | 22690
| | |
|
GSM236937 | GPL339 |
|
CD45+/Sca1+_Muscle_rep1
|
CD45+/Sca1+ cells isolated from the muscle
|
Strain: C57BL/6, Age: 6-8 weeks old, Tissue: muscle
|
Synthesis of biotinylated cRNA targets, arrays hybridization (Mouse430A GeneChip, Affymetrix, Santa Clara,CA), staining and scanning were performed using Affymetrix standard protocols starting from 1μg of total RNA.
|
| Sample_geo_accession | GSM236937
| | Sample_status | Public on Apr 06 2010
| | Sample_submission_date | Oct 11 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | One-cycle target labeling assays were performed, using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 1 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (20 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | The fragmented cRNA was then hybridized to an identical lot of Affymetrix Mouse430A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | Scaling to TGT value=250. The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM236nnn/GSM236937/suppl/GSM236937.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM236nnn/GSM236937/suppl/GSM236937.CHP.gz
| | Sample_series_id | GSE9296
| | Sample_data_row_count | 22690
| | |
|
GSM236938 | GPL339 |
|
CD45+/Sca1+_Muscle_rep2
|
CD45+/Sca1+ cells isolated from the muscle
|
Strain: C57BL/6, Age: 6-8 weeks old, Tissue: muscle
|
Synthesis of biotinylated cRNA targets, arrays hybridization (Mouse430A GeneChip, Affymetrix, Santa Clara,CA), staining and scanning were performed using Affymetrix standard protocols starting from 1μg of total RNA.
|
| Sample_geo_accession | GSM236938
| | Sample_status | Public on Apr 06 2010
| | Sample_submission_date | Oct 11 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | One-cycle target labeling assays were performed, using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 1 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (20 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | The fragmented cRNA was then hybridized to an identical lot of Affymetrix Mouse430A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | Scaling to TGT value=250. The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM236nnn/GSM236938/suppl/GSM236938.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM236nnn/GSM236938/suppl/GSM236938.CHP.gz
| | Sample_series_id | GSE9296
| | Sample_data_row_count | 22690
| | |
|
GSM236939 | GPL339 |
|
CD45+/Sca1+_Muscle_+Ctx/BMT_rep1
|
CD45+/Sca1+ cells isolated from the muscle
|
strain: C57BL/6, Age: 6-8 weeks old, Tissue: muscle
|
Synthesis of biotinylated cRNA targets, arrays hybridization (Mouse430A GeneChip, Affymetrix, Santa Clara,CA), staining and scanning were performed using Affymetrix standard protocols starting from 1μg of total RNA.
|
| Sample_geo_accession | GSM236939
| | Sample_status | Public on Apr 06 2010
| | Sample_submission_date | Oct 11 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Injury with Cardiotoxin (Ctx) and BM transplantation (BMT)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | One-cycle target labeling assays were performed, using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 1 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (20 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | The fragmented cRNA was then hybridized to an identical lot of Affymetrix Mouse430A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | Scaling to TGT value=250. The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM236nnn/GSM236939/suppl/GSM236939.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM236nnn/GSM236939/suppl/GSM236939.CHP.gz
| | Sample_series_id | GSE9296
| | Sample_data_row_count | 22690
| | |
|
GSM236962 | GPL339 |
|
CD45+/Sca1+_Muscle_+Ctx/BMT_rep2
|
CD45+/Sca1+ cells isolated from the muscle
|
strain: C57BL/6, Age: 6-8 weeks old, Tissue: muscle
|
Synthesis of biotinylated cRNA targets, arrays hybridization (Mouse430A GeneChip, Affymetrix, Santa Clara,CA), staining and scanning were performed using Affymetrix standard protocols starting from 1μg of total RNA.
|
| Sample_geo_accession | GSM236962
| | Sample_status | Public on Apr 06 2010
| | Sample_submission_date | Oct 11 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Injury with Cardiotoxin (Ctx) and BM transplantation (BMT)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | One-cycle target labeling assays were performed, using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 1 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (20 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | The fragmented cRNA was then hybridized to an identical lot of Affymetrix Mouse430A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | Scaling to TGT value=250. The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM236nnn/GSM236962/suppl/GSM236962.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM236nnn/GSM236962/suppl/GSM236962.CHP.gz
| | Sample_series_id | GSE9296
| | Sample_data_row_count | 22690
| | |
|
GSM236964 | GPL339 |
|
CD45+/Sca1+_Muscle_+Ctx_rep1
|
CD45+/Sca1+ cells isolated from the muscle
|
Strain: C57BL/6, Age: 6-8 weeks old, Tissue: muscle
|
Synthesis of biotinylated cRNA targets, arrays hybridization (Mouse430A GeneChip, Affymetrix, Santa Clara,CA), staining and scanning were performed using Affymetrix standard protocols starting from 1μg of total RNA.
|
| Sample_geo_accession | GSM236964
| | Sample_status | Public on Apr 06 2010
| | Sample_submission_date | Oct 11 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Injury with Cardiotoxin (Ctx)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | One-cycle target labeling assays were performed, using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 1 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (20 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | The fragmented cRNA was then hybridized to an identical lot of Affymetrix Mouse430A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | Scaling to TGT value=250. The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM236nnn/GSM236964/suppl/GSM236964.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM236nnn/GSM236964/suppl/GSM236964.CHP.gz
| | Sample_series_id | GSE9296
| | Sample_data_row_count | 22690
| | |
|
GSM236966 | GPL339 |
|
CD45+/Sca1+_Muscle_+Ctx_rep2
|
CD45+/Sca1+ cells isolated from the muscle
|
Strain: C57BL/6, Age: 6-8 weeks old, Tissue: muscle
|
Synthesis of biotinylated cRNA targets, arrays hybridization (Mouse430A GeneChip, Affymetrix, Santa Clara,CA), staining and scanning were performed using Affymetrix standard protocols starting from 1μg of total RNA.
|
| Sample_geo_accession | GSM236966
| | Sample_status | Public on Apr 06 2010
| | Sample_submission_date | Oct 11 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Injury with Cardiotoxin (Ctx)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | One-cycle target labeling assays were performed, using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 1 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (20 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | The fragmented cRNA was then hybridized to an identical lot of Affymetrix Mouse430A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | Scaling to TGT value=250. The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM236nnn/GSM236966/suppl/GSM236966.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM236nnn/GSM236966/suppl/GSM236966.CHP.gz
| | Sample_series_id | GSE9296
| | Sample_data_row_count | 22690
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