Search results for the GEO ID: GSE12367  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM310448 | GPL1261 |
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cDeaf
|
cDeaf
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C1 clone infected with Deaf-1-expressing retrovirus.
|
Arrays were processed at the Australian Genome Research Facility (AGRF).
|
| Sample_geo_accession | GSM310448
| | Sample_status | Public on Aug 21 2008
| | Sample_submission_date | Aug 06 2008
| | Sample_last_update_date | Aug 21 2008
| | 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 harvested from two independent clones (C1 and E1) infected with either control or Deaf-1-expressing retrovirus. RNA was purified using using the QIAGEN RNeasy Kit (Qiagen, Hilden, Germany)
| | Sample_extract_protocol_ch1 | and quality assessed by spectrophotometry and gel electrophoresis before
| | Sample_extract_protocol_ch1 | hybridisation to Affymetrix slides.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT Labeling Kit
| | Sample_hyb_protocol | Affymetrix
| | Sample_scan_protocol | Affymetrix scanner 3000 7G
| | Sample_data_processing | Statistical analysis was undertaken using R (www.r-project.org) and Bioconductor
| | Sample_data_processing | (www.bioconductor.org) software. The expression values were checked for quality and consistency using statistical quality assessment and were normalized using the RMA algorithm. Control probes and a small number (147) of probe-sets showing no variability between arrays were filtered out before subsequent analysis. For the differential expression analysis, the Deaf-1 and control samples for each clone were treated as paired observations, to reflect the biological variation between clones. Statistical significance was assessed using empirical Bayes moderated paired t-tests as implemented in the limma package within the Bioconductor software.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Jane,,Visvader
| | Sample_contact_email | barker@wehi.edu.au, visvader@wehi.edu.au
| | Sample_contact_laboratory | Lindeman/Visvader Lab
| | Sample_contact_department | Victorian Breast Cancer Research Consortium
| | Sample_contact_institute | Walter and Eliza Hall Institute of Medical Research
| | Sample_contact_address | 1G Royal Pde
| | Sample_contact_city | Parkville
| | Sample_contact_state | Vic
| | Sample_contact_zip/postal_code | 3050
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310448/suppl/GSM310448.CEL.gz
| | Sample_series_id | GSE12367
| | Sample_data_row_count | 45101
| | |
|
GSM310449 | GPL1261 |
|
cPuro
|
cPuro
|
C1 clone infected with control retrovirus.
|
Arrays were processed at the Australian Genome Research Facility (AGRF).
|
| Sample_geo_accession | GSM310449
| | Sample_status | Public on Aug 21 2008
| | Sample_submission_date | Aug 06 2008
| | Sample_last_update_date | Aug 21 2008
| | 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 harvested from two independent clones (C1 and E1) infected with either control or Deaf-1-expressing retrovirus. RNA was purified using using the QIAGEN RNeasy Kit (Qiagen, Hilden, Germany)
| | Sample_extract_protocol_ch1 | and quality assessed by spectrophotometry and gel electrophoresis before
| | Sample_extract_protocol_ch1 | hybridisation to Affymetrix slides.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT Labelling Kit
| | Sample_hyb_protocol | Affymetrix
| | Sample_scan_protocol | Affymetrix scanner 3000 7G
| | Sample_data_processing | Statistical analysis was undertaken using R (www.r-project.org) and Bioconductor
| | Sample_data_processing | (www.bioconductor.org) software. The expression values were checked for quality and consistency using statistical quality assessment and were normalized using the RMA algorithm. Control probes and a small number (147) of probe-sets showing no variability between arrays were filtered out before subsequent analysis. For the differential expression analysis, the Deaf-1 and control samples for each clone were treated as paired observations, to reflect the biological variation between clones. Statistical significance was assessed using empirical Bayes moderated paired t-tests as implemented in the limma package within the Bioconductor software.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Jane,,Visvader
| | Sample_contact_email | barker@wehi.edu.au, visvader@wehi.edu.au
| | Sample_contact_laboratory | Lindeman/Visvader Lab
| | Sample_contact_department | Victorian Breast Cancer Research Consortium
| | Sample_contact_institute | Walter and Eliza Hall Institute of Medical Research
| | Sample_contact_address | 1G Royal Pde
| | Sample_contact_city | Parkville
| | Sample_contact_state | Vic
| | Sample_contact_zip/postal_code | 3050
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310449/suppl/GSM310449.CEL.gz
| | Sample_series_id | GSE12367
| | Sample_data_row_count | 45101
| | |
|
GSM310450 | GPL1261 |
|
eDeaf
|
eDeaf
|
E1 clone infected with Deaf-1-expressing retrovirus.
|
Arrays were processed at the Australian Genome Research Facility (AGRF).
|
| Sample_geo_accession | GSM310450
| | Sample_status | Public on Aug 21 2008
| | Sample_submission_date | Aug 07 2008
| | Sample_last_update_date | Aug 21 2008
| | 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 harvested from two independent clones (C1 and E1) infected with either control or Deaf-1-expressing retrovirus. RNA was purified using using the QIAGEN RNeasy Kit (Qiagen, Hilden, Germany)
| | Sample_extract_protocol_ch1 | and quality assessed by spectrophotometry and gel electrophoresis before
| | Sample_extract_protocol_ch1 | hybridisation to Affymetrix slides.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT Labelling Kit
| | Sample_hyb_protocol | Affymetrix
| | Sample_scan_protocol | Affymetrix scanner 3000 7G
| | Sample_data_processing | Statistical analysis was undertaken using R (www.r-project.org) and Bioconductor
| | Sample_data_processing | (www.bioconductor.org) software. The expression values were checked for quality and consistency using statistical quality assessment and were normalized using the RMA algorithm. Control probes and a small number (147) of probe-sets showing no variability between arrays were filtered out before subsequent analysis. For the differential expression analysis, the Deaf-1 and control samples for each clone were treated as paired observations, to reflect the biological variation between clones. Statistical significance was assessed using empirical Bayes moderated paired t-tests as implemented in the limma package within the Bioconductor software.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Jane,,Visvader
| | Sample_contact_email | barker@wehi.edu.au, visvader@wehi.edu.au
| | Sample_contact_laboratory | Lindeman/Visvader Lab
| | Sample_contact_department | Victorian Breast Cancer Research Consortium
| | Sample_contact_institute | Walter and Eliza Hall Institute of Medical Research
| | Sample_contact_address | 1G Royal Pde
| | Sample_contact_city | Parkville
| | Sample_contact_state | Vic
| | Sample_contact_zip/postal_code | 3050
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310450/suppl/GSM310450.CEL.gz
| | Sample_series_id | GSE12367
| | Sample_data_row_count | 45101
| | |
|
GSM310452 | GPL1261 |
|
ePuro
|
ePuro
|
E1 clone infected with control retrovirus.
|
Arrays were processed at the Australian Genome Research Facility (AGRF).
|
| Sample_geo_accession | GSM310452
| | Sample_status | Public on Aug 21 2008
| | Sample_submission_date | Aug 07 2008
| | Sample_last_update_date | Aug 21 2008
| | 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 harvested from two independent clones (C1 and E1) infected with either control or Deaf-1-expressing retrovirus. RNA was purified using using the QIAGEN RNeasy Kit (Qiagen, Hilden, Germany)
| | Sample_extract_protocol_ch1 | and quality assessed by spectrophotometry and gel electrophoresis before
| | Sample_extract_protocol_ch1 | hybridisation to Affymetrix slides.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix IVT Labelling Kit
| | Sample_hyb_protocol | Affymetrix
| | Sample_scan_protocol | Affymetrix scanner 3000 7G
| | Sample_data_processing | Statistical analysis was undertaken using R (www.r-project.org) and Bioconductor
| | Sample_data_processing | (www.bioconductor.org) software. The expression values were checked for quality and consistency using statistical quality assessment and were normalized using the RMA algorithm. Control probes and a small number (147) of probe-sets showing no variability between arrays were filtered out before subsequent analysis. For the differential expression analysis, the Deaf-1 and control samples for each clone were treated as paired observations, to reflect the biological variation between clones. Statistical significance was assessed using empirical Bayes moderated paired t-tests as implemented in the limma package within the Bioconductor software.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Jane,,Visvader
| | Sample_contact_email | barker@wehi.edu.au, visvader@wehi.edu.au
| | Sample_contact_laboratory | Lindeman/Visvader Lab
| | Sample_contact_department | Victorian Breast Cancer Research Consortium
| | Sample_contact_institute | Walter and Eliza Hall Institute of Medical Research
| | Sample_contact_address | 1G Royal Pde
| | Sample_contact_city | Parkville
| | Sample_contact_state | Vic
| | Sample_contact_zip/postal_code | 3050
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310452/suppl/GSM310452.CEL.gz
| | Sample_series_id | GSE12367
| | Sample_data_row_count | 45101
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