Search results for the GEO ID: GSE6453  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM148464 | GPL339 |
|
3wkA
|
mammary gland, 3wk
|
Strain: CD1
Gender: female
Age: 3 weeks
Tissue: mammary gland
|
Recommended Affymetrix protocols were followed.
|
| Sample_geo_accession | GSM148464
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Dec 05 2006
| | Sample_last_update_date | May 01 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | The Biomedical Facility, University College Dublin
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | All animals were housed in accordance with accepted standards of humane animal care and grown to the appropriate age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Whole mammary glands (4th inguinal) were dissected and lymph nodes removed. Total RNA was extracted with TriReagent (Molecular Probes) according to the manufacturer's instructions. Total RNA was cleaned with lithium chloride by adding an equal volume of 8M LiCl pH5.2 and storing at -20degreesC for a minimum of 3 hours. After centrifugation, pellet was washed twice with cold 70% ethanol, dried and resuspended in DEPC-treated water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 micrograms RNA were used to synthesise double stranded cDNA as per Affymetrix guidelines. cDNA was cleaned with phenol chloroform. A 5 hour in vitro transcription reaction was carried out to produce biotin-labelled cRNA. Labelled cRNA was cleaned with Qiagen RNeasy columns.
| | Sample_hyb_protocol | Following fragmentation, 15 micrograms cRNA were hybridised for 16 hours at 45degreesC to GeneChip MOE430A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 2500.
| | Sample_data_processing | Data was imported into Genespring. Per chip normalisation to 50th percentile, per gene normalisation to median and data transformation to set all measurements below 0.001 to 0.001 were performed.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Finian,,Martin
| | Sample_contact_email | finian.martin@ucd.ie
| | Sample_contact_department | UCD School of Biomolecular and Biomedical Science
| | Sample_contact_institute | University College Dublin
| | Sample_contact_address | Conway Institute, Belfield
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM148nnn/GSM148464/suppl/GSM148464.CEL.gz
| | Sample_series_id | GSE6453
| | Sample_data_row_count | 22690
| | |
|
GSM148465 | GPL339 |
|
3wkB
|
mammary gland, 3wk
|
Strain: CD1
Gender: female
Age: 3 weeks
Tissue: mammary gland
|
Recommended Affymetrix protocols were followed.
|
| Sample_geo_accession | GSM148465
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Dec 05 2006
| | Sample_last_update_date | May 01 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | The Biomedical Facility, University College Dublin
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | All animals were housed in accordance with accepted standards of humane animal care and grown to the appropriate age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Whole mammary glands (4th inguinal) were dissected and lymph nodes removed. Total RNA was extracted with TriReagent (Molecular Probes) according to the manufacturer's instructions. Total RNA was cleaned with lithium chloride by adding an equal volume of 8M LiCl pH5.2 and storing at -20degreesC for a minimum of 3 hours. After centrifugation, pellet was washed twice with cold 70% ethanol, dried and resuspended in DEPC-treated water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 micrograms RNA were used to synthesise double stranded cDNA as per Affymetrix guidelines. cDNA was cleaned with phenol chloroform. A 5 hour in vitro transcription reaction was carried out to produce biotin-labelled cRNA. Labelled cRNA was cleaned with Qiagen RNeasy columns.
| | Sample_hyb_protocol | Following fragmentation, 15 micrograms cRNA were hybridised for 16 hours at 45degreesC to GeneChip MOE430A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 2500.
| | Sample_data_processing | Data was imported into Genespring. Per chip normalisation to 50th percentile, per gene normalisation to median and data transformation to set all measurements below 0.001 to 0.001 were performed.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Finian,,Martin
| | Sample_contact_email | finian.martin@ucd.ie
| | Sample_contact_department | UCD School of Biomolecular and Biomedical Science
| | Sample_contact_institute | University College Dublin
| | Sample_contact_address | Conway Institute, Belfield
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM148nnn/GSM148465/suppl/GSM148465.CEL.gz
| | Sample_series_id | GSE6453
| | Sample_data_row_count | 22690
| | |
|
GSM148466 | GPL339 |
|
3wkC
|
mammary gland, 3wk
|
Strain: CD1
Gender: female
Age: 3 weeks
Tissue: mammary gland
|
Recommended Affymetrix protocols were followed.
|
| Sample_geo_accession | GSM148466
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Dec 05 2006
| | Sample_last_update_date | May 01 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | The Biomedical Facility, University College Dublin
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | All animals were housed in accordance with accepted standards of humane animal care and grown to the appropriate age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Whole mammary glands (4th inguinal) were dissected and lymph nodes removed. Total RNA was extracted with TriReagent (Molecular Probes) according to the manufacturer's instructions. Total RNA was cleaned with lithium chloride by adding an equal volume of 8M LiCl pH5.2 and storing at -20degreesC for a minimum of 3 hours. After centrifugation, pellet was washed twice with cold 70% ethanol, dried and resuspended in DEPC-treated water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 micrograms RNA were used to synthesise double stranded cDNA as per Affymetrix guidelines. cDNA was cleaned with phenol chloroform. A 5 hour in vitro transcription reaction was carried out to produce biotin-labelled cRNA. Labelled cRNA was cleaned with Qiagen RNeasy columns.
| | Sample_hyb_protocol | Following fragmentation, 15 micrograms cRNA were hybridised for 16 hours at 45degreesC to GeneChip MOE430A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 2500.
| | Sample_data_processing | Data was imported into Genespring. Per chip normalisation to 50th percentile, per gene normalisation to median and data transformation to set all measurements below 0.001 to 0.001 were performed.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Finian,,Martin
| | Sample_contact_email | finian.martin@ucd.ie
| | Sample_contact_department | UCD School of Biomolecular and Biomedical Science
| | Sample_contact_institute | University College Dublin
| | Sample_contact_address | Conway Institute, Belfield
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM148nnn/GSM148466/suppl/GSM148466.CEL.gz
| | Sample_series_id | GSE6453
| | Sample_data_row_count | 22690
| | |
|
GSM148467 | GPL339 |
|
4wkA
|
mammary gland, 4wk
|
Strain: CD1
Gender: female
Age: 4 weeks
Tissue: mammary gland
|
Recommended Affymetrix protocols were followed.
|
| Sample_geo_accession | GSM148467
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Dec 05 2006
| | Sample_last_update_date | May 01 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | The Biomedical Facility, University College Dublin
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | All animals were housed in accordance with accepted standards of humane animal care and grown to the appropriate age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Whole mammary glands (4th inguinal) were dissected and lymph nodes removed. Total RNA was extracted with TriReagent (Molecular Probes) according to the manufacturer's instructions. Total RNA was cleaned with lithium chloride by adding an equal volume of 8M LiCl pH5.2 and storing at -20degreesC for a minimum of 3 hours. After centrifugation, pellet was washed twice with cold 70% ethanol, dried and resuspended in DEPC-treated water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 micrograms RNA were used to synthesise double stranded cDNA as per Affymetrix guidelines. cDNA was cleaned with phenol chloroform. A 5 hour in vitro transcription reaction was carried out to produce biotin-labelled cRNA. Labelled cRNA was cleaned with Qiagen RNeasy columns.
| | Sample_hyb_protocol | Following fragmentation, 15 micrograms cRNA were hybridised for 16 hours at 45degreesC to GeneChip MOE430A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 2500.
| | Sample_data_processing | Data was imported into Genespring. Per chip normalisation to 50th percentile, per gene normalisation to median and data transformation to set all measurements below 0.001 to 0.001 were performed.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Finian,,Martin
| | Sample_contact_email | finian.martin@ucd.ie
| | Sample_contact_department | UCD School of Biomolecular and Biomedical Science
| | Sample_contact_institute | University College Dublin
| | Sample_contact_address | Conway Institute, Belfield
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM148nnn/GSM148467/suppl/GSM148467.CEL.gz
| | Sample_series_id | GSE6453
| | Sample_data_row_count | 22690
| | |
|
GSM148468 | GPL339 |
|
4wkB
|
mammary gland, 4wk
|
Strain: CD1
Gender: female
Age: 4 weeks
Tissue: mammary gland
|
Recommended Affymetrix protocols were followed.
|
| Sample_geo_accession | GSM148468
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Dec 05 2006
| | Sample_last_update_date | May 01 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | The Biomedical Facility, University College Dublin
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | All animals were housed in accordance with accepted standards of humane animal care and grown to the appropriate age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Whole mammary glands (4th inguinal) were dissected and lymph nodes removed. Total RNA was extracted with TriReagent (Molecular Probes) according to the manufacturer's instructions. Total RNA was cleaned with lithium chloride by adding an equal volume of 8M LiCl pH5.2 and storing at -20degreesC for a minimum of 3 hours. After centrifugation, pellet was washed twice with cold 70% ethanol, dried and resuspended in DEPC-treated water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 micrograms RNA were used to synthesise double stranded cDNA as per Affymetrix guidelines. cDNA was cleaned with phenol chloroform. A 5 hour in vitro transcription reaction was carried out to produce biotin-labelled cRNA. Labelled cRNA was cleaned with Qiagen RNeasy columns.
| | Sample_hyb_protocol | Following fragmentation, 15 micrograms cRNA were hybridised for 16 hours at 45degreesC to GeneChip MOE430A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 2500.
| | Sample_data_processing | Data was imported into Genespring. Per chip normalisation to 50th percentile, per gene normalisation to median and data transformation to set all measurements below 0.001 to 0.001 were performed.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Finian,,Martin
| | Sample_contact_email | finian.martin@ucd.ie
| | Sample_contact_department | UCD School of Biomolecular and Biomedical Science
| | Sample_contact_institute | University College Dublin
| | Sample_contact_address | Conway Institute, Belfield
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM148nnn/GSM148468/suppl/GSM148468.CEL.gz
| | Sample_series_id | GSE6453
| | Sample_data_row_count | 22690
| | |
|
GSM148469 | GPL339 |
|
4wkC
|
mammary gland, 4wk
|
Strain: CD1
Gender: female
Age: 4 weeks
Tissue: mammary gland
|
Recommended Affymetrix protocols were followed.
|
| Sample_geo_accession | GSM148469
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Dec 05 2006
| | Sample_last_update_date | May 01 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | The Biomedical Facility, University College Dublin
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | All animals were housed in accordance with accepted standards of humane animal care and grown to the appropriate age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Whole mammary glands (4th inguinal) were dissected and lymph nodes removed. Total RNA was extracted with TriReagent (Molecular Probes) according to the manufacturer's instructions. Total RNA was cleaned with lithium chloride by adding an equal volume of 8M LiCl pH5.2 and storing at -20degreesC for a minimum of 3 hours. After centrifugation, pellet was washed twice with cold 70% ethanol, dried and resuspended in DEPC-treated water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 micrograms RNA were used to synthesise double stranded cDNA as per Affymetrix guidelines. cDNA was cleaned with phenol chloroform. A 5 hour in vitro transcription reaction was carried out to produce biotin-labelled cRNA. Labelled cRNA was cleaned with Qiagen RNeasy columns.
| | Sample_hyb_protocol | Following fragmentation, 15 micrograms cRNA were hybridised for 16 hours at 45degreesC to GeneChip MOE430A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 2500.
| | Sample_data_processing | Data was imported into Genespring. Per chip normalisation to 50th percentile, per gene normalisation to median and data transformation to set all measurements below 0.001 to 0.001 were performed.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Finian,,Martin
| | Sample_contact_email | finian.martin@ucd.ie
| | Sample_contact_department | UCD School of Biomolecular and Biomedical Science
| | Sample_contact_institute | University College Dublin
| | Sample_contact_address | Conway Institute, Belfield
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM148nnn/GSM148469/suppl/GSM148469.CEL.gz
| | Sample_series_id | GSE6453
| | Sample_data_row_count | 22690
| | |
|
GSM148470 | GPL339 |
|
5wkA
|
mammary gland, 5wk
|
Strain: CD1
Gender: female
Age: 5 weeks
Tissue: mammary gland
|
Recommended Affymetrix protocols were followed.
|
| Sample_geo_accession | GSM148470
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Dec 05 2006
| | Sample_last_update_date | May 01 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | The Biomedical Facility, University College Dublin
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | All animals were housed in accordance with accepted standards of humane animal care and grown to the appropriate age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Whole mammary glands (4th inguinal) were dissected and lymph nodes removed. Total RNA was extracted with TriReagent (Molecular Probes) according to the manufacturer's instructions. Total RNA was cleaned with lithium chloride by adding an equal volume of 8M LiCl pH5.2 and storing at -20degreesC for a minimum of 3 hours. After centrifugation, pellet was washed twice with cold 70% ethanol, dried and resuspended in DEPC-treated water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 micrograms RNA were used to synthesise double stranded cDNA as per Affymetrix guidelines. cDNA was cleaned with phenol chloroform. A 5 hour in vitro transcription reaction was carried out to produce biotin-labelled cRNA. Labelled cRNA was cleaned with Qiagen RNeasy columns.
| | Sample_hyb_protocol | Following fragmentation, 15 micrograms cRNA were hybridised for 16 hours at 45degreesC to GeneChip MOE430A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 2500.
| | Sample_data_processing | Data was imported into Genespring. Per chip normalisation to 50th percentile, per gene normalisation to median and data transformation to set all measurements below 0.001 to 0.001 were performed.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Finian,,Martin
| | Sample_contact_email | finian.martin@ucd.ie
| | Sample_contact_department | UCD School of Biomolecular and Biomedical Science
| | Sample_contact_institute | University College Dublin
| | Sample_contact_address | Conway Institute, Belfield
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM148nnn/GSM148470/suppl/GSM148470.CEL.gz
| | Sample_series_id | GSE6453
| | Sample_data_row_count | 22690
| | |
|
GSM148471 | GPL339 |
|
5wkB
|
mammary gland, 5wk
|
Strain: CD1
Gender: female
Age: 5 weeks
Tissue: mammary gland
|
Recommended Affymetrix protocols were followed.
|
| Sample_geo_accession | GSM148471
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Dec 05 2006
| | Sample_last_update_date | May 01 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | The Biomedical Facility, University College Dublin
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | All animals were housed in accordance with accepted standards of humane animal care and grown to the appropriate age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Whole mammary glands (4th inguinal) were dissected and lymph nodes removed. Total RNA was extracted with TriReagent (Molecular Probes) according to the manufacturer's instructions. Total RNA was cleaned with lithium chloride by adding an equal volume of 8M LiCl pH5.2 and storing at -20degreesC for a minimum of 3 hours. After centrifugation, pellet was washed twice with cold 70% ethanol, dried and resuspended in DEPC-treated water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 micrograms RNA were used to synthesise double stranded cDNA as per Affymetrix guidelines. cDNA was cleaned with phenol chloroform. A 5 hour in vitro transcription reaction was carried out to produce biotin-labelled cRNA. Labelled cRNA was cleaned with Qiagen RNeasy columns.
| | Sample_hyb_protocol | Following fragmentation, 15 micrograms cRNA were hybridised for 16 hours at 45degreesC to GeneChip MOE430A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 2500.
| | Sample_data_processing | Data was imported into Genespring. Per chip normalisation to 50th percentile, per gene normalisation to median and data transformation to set all measurements below 0.001 to 0.001 were performed.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Finian,,Martin
| | Sample_contact_email | finian.martin@ucd.ie
| | Sample_contact_department | UCD School of Biomolecular and Biomedical Science
| | Sample_contact_institute | University College Dublin
| | Sample_contact_address | Conway Institute, Belfield
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM148nnn/GSM148471/suppl/GSM148471.CEL.gz
| | Sample_series_id | GSE6453
| | Sample_data_row_count | 22690
| | |
|
GSM148472 | GPL339 |
|
6wkA
|
mammary gland, 6wk
|
Strain: CD1
Gender: female
Age: 6 weeks
Tissue: mammary gland
|
Recommended Affymetrix protocols were followed.
|
| Sample_geo_accession | GSM148472
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Dec 05 2006
| | Sample_last_update_date | May 01 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | The Biomedical Facility, University College Dublin
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | All animals were housed in accordance with accepted standards of humane animal care and grown to the appropriate age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Whole mammary glands (4th inguinal) were dissected and lymph nodes removed. Total RNA was extracted with TriReagent (Molecular Probes) according to the manufacturer's instructions. Total RNA was cleaned with lithium chloride by adding an equal volume of 8M LiCl pH5.2 and storing at -20degreesC for a minimum of 3 hours. After centrifugation, pellet was washed twice with cold 70% ethanol, dried and resuspended in DEPC-treated water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 micrograms RNA were used to synthesise double stranded cDNA as per Affymetrix guidelines. cDNA was cleaned with phenol chloroform. A 5 hour in vitro transcription reaction was carried out to produce biotin-labelled cRNA. Labelled cRNA was cleaned with Qiagen RNeasy columns.
| | Sample_hyb_protocol | Following fragmentation, 15 micrograms cRNA were hybridised for 16 hours at 45degreesC to GeneChip MOE430A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 2500.
| | Sample_data_processing | Data was imported into Genespring. Per chip normalisation to 50th percentile, per gene normalisation to median and data transformation to set all measurements below 0.001 to 0.001 were performed.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Finian,,Martin
| | Sample_contact_email | finian.martin@ucd.ie
| | Sample_contact_department | UCD School of Biomolecular and Biomedical Science
| | Sample_contact_institute | University College Dublin
| | Sample_contact_address | Conway Institute, Belfield
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM148nnn/GSM148472/suppl/GSM148472.CEL.gz
| | Sample_series_id | GSE6453
| | Sample_data_row_count | 22690
| | |
|
GSM148473 | GPL339 |
|
6wkB
|
mammary gland, 6wk
|
Strain: CD1
Gender: female
Age: 6 weeks
Tissue: mammary gland
|
Recommended Affymetrix protocols were followed.
|
| Sample_geo_accession | GSM148473
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Dec 05 2006
| | Sample_last_update_date | May 01 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | The Biomedical Facility, University College Dublin
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | All animals were housed in accordance with accepted standards of humane animal care and grown to the appropriate age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Whole mammary glands (4th inguinal) were dissected and lymph nodes removed. Total RNA was extracted with TriReagent (Molecular Probes) according to the manufacturer's instructions. Total RNA was cleaned with lithium chloride by adding an equal volume of 8M LiCl pH5.2 and storing at -20degreesC for a minimum of 3 hours. After centrifugation, pellet was washed twice with cold 70% ethanol, dried and resuspended in DEPC-treated water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 micrograms RNA were used to synthesise double stranded cDNA as per Affymetrix guidelines. cDNA was cleaned with phenol chloroform. A 5 hour in vitro transcription reaction was carried out to produce biotin-labelled cRNA. Labelled cRNA was cleaned with Qiagen RNeasy columns.
| | Sample_hyb_protocol | Following fragmentation, 15 micrograms cRNA were hybridised for 16 hours at 45degreesC to GeneChip MOE430A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 2500.
| | Sample_data_processing | Data was imported into Genespring. Per chip normalisation to 50th percentile, per gene normalisation to median and data transformation to set all measurements below 0.001 to 0.001 were performed.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Finian,,Martin
| | Sample_contact_email | finian.martin@ucd.ie
| | Sample_contact_department | UCD School of Biomolecular and Biomedical Science
| | Sample_contact_institute | University College Dublin
| | Sample_contact_address | Conway Institute, Belfield
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM148nnn/GSM148473/suppl/GSM148473.CEL.gz
| | Sample_series_id | GSE6453
| | Sample_data_row_count | 22690
| | |
|
GSM148474 | GPL339 |
|
6wkC
|
mammary gland, 6wk
|
Strain: CD1
Gender: female
Age: 6 weeks
Tissue: mammary gland
|
Recommended Affymetrix protocols were followed.
|
| Sample_geo_accession | GSM148474
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Dec 05 2006
| | Sample_last_update_date | May 01 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | The Biomedical Facility, University College Dublin
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | All animals were housed in accordance with accepted standards of humane animal care and grown to the appropriate age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Whole mammary glands (4th inguinal) were dissected and lymph nodes removed. Total RNA was extracted with TriReagent (Molecular Probes) according to the manufacturer's instructions. Total RNA was cleaned with lithium chloride by adding an equal volume of 8M LiCl pH5.2 and storing at -20degreesC for a minimum of 3 hours. After centrifugation, pellet was washed twice with cold 70% ethanol, dried and resuspended in DEPC-treated water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 micrograms RNA were used to synthesise double stranded cDNA as per Affymetrix guidelines. cDNA was cleaned with phenol chloroform. A 5 hour in vitro transcription reaction was carried out to produce biotin-labelled cRNA. Labelled cRNA was cleaned with Qiagen RNeasy columns.
| | Sample_hyb_protocol | Following fragmentation, 15 micrograms cRNA were hybridised for 16 hours at 45degreesC to GeneChip MOE430A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 2500.
| | Sample_data_processing | Data was imported into Genespring. Per chip normalisation to 50th percentile, per gene normalisation to median and data transformation to set all measurements below 0.001 to 0.001 were performed.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Finian,,Martin
| | Sample_contact_email | finian.martin@ucd.ie
| | Sample_contact_department | UCD School of Biomolecular and Biomedical Science
| | Sample_contact_institute | University College Dublin
| | Sample_contact_address | Conway Institute, Belfield
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM148nnn/GSM148474/suppl/GSM148474.CEL.gz
| | Sample_series_id | GSE6453
| | Sample_data_row_count | 22690
| | |
|
GSM148475 | GPL339 |
|
7wkA
|
mammary gland, 7wk
|
Strain: CD1
Gender: female
Age: 7 weeks
Tissue: mammary gland
|
Recommended Affymetrix protocols were followed.
|
| Sample_geo_accession | GSM148475
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Dec 05 2006
| | Sample_last_update_date | May 01 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | The Biomedical Facility, University College Dublin
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | All animals were housed in accordance with accepted standards of humane animal care and grown to the appropriate age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Whole mammary glands (4th inguinal) were dissected and lymph nodes removed. Total RNA was extracted with TriReagent (Molecular Probes) according to the manufacturer's instructions. Total RNA was cleaned with lithium chloride by adding an equal volume of 8M LiCl pH5.2 and storing at -20degreesC for a minimum of 3 hours. After centrifugation, pellet was washed twice with cold 70% ethanol, dried and resuspended in DEPC-treated water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 micrograms RNA were used to synthesise double stranded cDNA as per Affymetrix guidelines. cDNA was cleaned with phenol chloroform. A 5 hour in vitro transcription reaction was carried out to produce biotin-labelled cRNA. Labelled cRNA was cleaned with Qiagen RNeasy columns.
| | Sample_hyb_protocol | Following fragmentation, 15 micrograms cRNA were hybridised for 16 hours at 45degreesC to GeneChip MOE430A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 2500.
| | Sample_data_processing | Data was imported into Genespring. Per chip normalisation to 50th percentile, per gene normalisation to median and data transformation to set all measurements below 0.001 to 0.001 were performed.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Finian,,Martin
| | Sample_contact_email | finian.martin@ucd.ie
| | Sample_contact_department | UCD School of Biomolecular and Biomedical Science
| | Sample_contact_institute | University College Dublin
| | Sample_contact_address | Conway Institute, Belfield
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM148nnn/GSM148475/suppl/GSM148475.CEL.gz
| | Sample_series_id | GSE6453
| | Sample_data_row_count | 22690
| | |
|
GSM148476 | GPL339 |
|
7wkB
|
mammary gland, 7wk
|
Strain: CD1
Gender: female
Age: 7 weeks
Tissue: mammary gland
|
Recommended Affymetrix protocols were followed.
|
| Sample_geo_accession | GSM148476
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Dec 05 2006
| | Sample_last_update_date | May 01 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | The Biomedical Facility, University College Dublin
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | All animals were housed in accordance with accepted standards of humane animal care and grown to the appropriate age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Whole mammary glands (4th inguinal) were dissected and lymph nodes removed. Total RNA was extracted with TriReagent (Molecular Probes) according to the manufacturer's instructions. Total RNA was cleaned with lithium chloride by adding an equal volume of 8M LiCl pH5.2 and storing at -20degreesC for a minimum of 3 hours. After centrifugation, pellet was washed twice with cold 70% ethanol, dried and resuspended in DEPC-treated water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 micrograms RNA were used to synthesise double stranded cDNA as per Affymetrix guidelines. cDNA was cleaned with phenol chloroform. A 5 hour in vitro transcription reaction was carried out to produce biotin-labelled cRNA. Labelled cRNA was cleaned with Qiagen RNeasy columns.
| | Sample_hyb_protocol | Following fragmentation, 15 micrograms cRNA were hybridised for 16 hours at 45degreesC to GeneChip MOE430A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 2500.
| | Sample_data_processing | Data was imported into Genespring. Per chip normalisation to 50th percentile, per gene normalisation to median and data transformation to set all measurements below 0.001 to 0.001 were performed.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Finian,,Martin
| | Sample_contact_email | finian.martin@ucd.ie
| | Sample_contact_department | UCD School of Biomolecular and Biomedical Science
| | Sample_contact_institute | University College Dublin
| | Sample_contact_address | Conway Institute, Belfield
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM148nnn/GSM148476/suppl/GSM148476.CEL.gz
| | Sample_series_id | GSE6453
| | Sample_data_row_count | 22690
| | |
|
GSM148477 | GPL339 |
|
7wkC
|
mammary gland, 7wk
|
Strain: CD1
Gender: female
Age: 7 weeks
Tissue: mammary gland
|
Recommended Affymetrix protocols were followed.
|
| Sample_geo_accession | GSM148477
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Dec 05 2006
| | Sample_last_update_date | May 01 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | The Biomedical Facility, University College Dublin
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | All animals were housed in accordance with accepted standards of humane animal care and grown to the appropriate age.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Whole mammary glands (4th inguinal) were dissected and lymph nodes removed. Total RNA was extracted with TriReagent (Molecular Probes) according to the manufacturer's instructions. Total RNA was cleaned with lithium chloride by adding an equal volume of 8M LiCl pH5.2 and storing at -20degreesC for a minimum of 3 hours. After centrifugation, pellet was washed twice with cold 70% ethanol, dried and resuspended in DEPC-treated water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 micrograms RNA were used to synthesise double stranded cDNA as per Affymetrix guidelines. cDNA was cleaned with phenol chloroform. A 5 hour in vitro transcription reaction was carried out to produce biotin-labelled cRNA. Labelled cRNA was cleaned with Qiagen RNeasy columns.
| | Sample_hyb_protocol | Following fragmentation, 15 micrograms cRNA were hybridised for 16 hours at 45degreesC to GeneChip MOE430A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 2500.
| | Sample_data_processing | Data was imported into Genespring. Per chip normalisation to 50th percentile, per gene normalisation to median and data transformation to set all measurements below 0.001 to 0.001 were performed.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Finian,,Martin
| | Sample_contact_email | finian.martin@ucd.ie
| | Sample_contact_department | UCD School of Biomolecular and Biomedical Science
| | Sample_contact_institute | University College Dublin
| | Sample_contact_address | Conway Institute, Belfield
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM148nnn/GSM148477/suppl/GSM148477.CEL.gz
| | Sample_series_id | GSE6453
| | Sample_data_row_count | 22690
| | |
|
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