Search results for the GEO ID: GSE17654  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM440761 | GPL339 |
|
Buds_WT_rep1
|
WT mammary buds
|
strain: CD-1
tissue: Embryonic mammary buds
age: E15
group: WT
|
WT murine embryonic mammary buds.
WTB1
|
| Sample_geo_accession | GSM440761
| | Sample_status | Public on Aug 15 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Aug 14 2009
| | 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 | Embryonic mammary buds and ventral skin were dissected from WT, PTHrP-/- and K14-PTHrP transgenic embryos harvested on E15. Dissections were performed on an icepack and tissue samples stored in RNA Later (Ambion, Austin, TX) at -20°C. After genotyping the embryos, like samples were pooled and RNA was isolated using the RNeasy Mini Protocol with a Qiashredder column (Qiagen, Valencia, CA). Mechanical disruption of tissue was performed with a Kontes Pellet Pestle and a cordless motor (Thermo Fisher Scientific, Waltham, MA) prior to homogenizing with the Qiashredder. MessageClean (GenHunter Corporation, Nashville, TN) was used to remove contaminating DNA. On average, 120 mammary buds were required to produce approximately 20 ug total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | Affymetrix generic hybridization.
| | Sample_scan_protocol | Arrays were scanned using the Hewlett-Packard GeneArray Scanner.
| | Sample_data_processing | Data were normalized by GC-RMA in R/Bioconductor. MAS5 presence calls were generated by the affy package in R/Bioconductor. Genes were filtered by retaining only probe sets with at least one MAS5 present call and more than 1.2 fold dynamic range across all samples. Differential expression of genes was assessed by Cyber-T. Gene lists were generated at false discovery rate (FDR) of 10% for comparisons among the ventral skin sample groups, and at FDR of 5% for all other comparisons.
| | Sample_data_processing |
| | Sample_data_processing | Lists of differentially expressed genes are linked to the Series GSE17654 record as supplementary files.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lewis,,Chodosh
| | Sample_contact_email | chodosh@mail.med.upenn.edu
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 612 BRB II/III 421 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440761/suppl/GSM440761.CEL.gz
| | Sample_series_id | GSE17654
| | Sample_data_row_count | 22690
| | |
|
GSM440762 | GPL339 |
|
Buds_WT_rep2
|
WT mammary buds
|
strain: CD-1
tissue: Embryonic mammary buds
age: E15
group: WT
|
WT murine embryonic mammary buds.
WTB2
|
| Sample_geo_accession | GSM440762
| | Sample_status | Public on Aug 15 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Aug 14 2009
| | 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 | Embryonic mammary buds and ventral skin were dissected from WT, PTHrP-/- and K14-PTHrP transgenic embryos harvested on E15. Dissections were performed on an icepack and tissue samples stored in RNA Later (Ambion, Austin, TX) at -20°C. After genotyping the embryos, like samples were pooled and RNA was isolated using the RNeasy Mini Protocol with a Qiashredder column (Qiagen, Valencia, CA). Mechanical disruption of tissue was performed with a Kontes Pellet Pestle and a cordless motor (Thermo Fisher Scientific, Waltham, MA) prior to homogenizing with the Qiashredder. MessageClean (GenHunter Corporation, Nashville, TN) was used to remove contaminating DNA. On average, 120 mammary buds were required to produce approximately 20 ug total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | Affymetrix generic hybridization.
| | Sample_scan_protocol | Arrays were scanned using the Hewlett-Packard GeneArray Scanner.
| | Sample_data_processing | Data were normalized by GC-RMA in R/Bioconductor. MAS5 presence calls were generated by the affy package in R/Bioconductor. Genes were filtered by retaining only probe sets with at least one MAS5 present call and more than 1.2 fold dynamic range across all samples. Differential expression of genes was assessed by Cyber-T. Gene lists were generated at false discovery rate (FDR) of 10% for comparisons among the ventral skin sample groups, and at FDR of 5% for all other comparisons.
| | Sample_data_processing |
| | Sample_data_processing | Lists of differentially expressed genes are linked to the Series GSE17654 record as supplementary files.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lewis,,Chodosh
| | Sample_contact_email | chodosh@mail.med.upenn.edu
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 612 BRB II/III 421 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440762/suppl/GSM440762.CEL.gz
| | Sample_series_id | GSE17654
| | Sample_data_row_count | 22690
| | |
|
GSM440763 | GPL339 |
|
Buds_WT_rep3
|
WT mammary buds
|
strain: CD-1
tissue: Embryonic mammary buds
age: E15
group: WT
|
WT murine embryonic mammary buds.
WTB3
|
| Sample_geo_accession | GSM440763
| | Sample_status | Public on Aug 15 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Aug 14 2009
| | 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 | Embryonic mammary buds and ventral skin were dissected from WT, PTHrP-/- and K14-PTHrP transgenic embryos harvested on E15. Dissections were performed on an icepack and tissue samples stored in RNA Later (Ambion, Austin, TX) at -20°C. After genotyping the embryos, like samples were pooled and RNA was isolated using the RNeasy Mini Protocol with a Qiashredder column (Qiagen, Valencia, CA). Mechanical disruption of tissue was performed with a Kontes Pellet Pestle and a cordless motor (Thermo Fisher Scientific, Waltham, MA) prior to homogenizing with the Qiashredder. MessageClean (GenHunter Corporation, Nashville, TN) was used to remove contaminating DNA. On average, 120 mammary buds were required to produce approximately 20 ug total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | Affymetrix generic hybridization.
| | Sample_scan_protocol | Arrays were scanned using the Hewlett-Packard GeneArray Scanner.
| | Sample_data_processing | Data were normalized by GC-RMA in R/Bioconductor. MAS5 presence calls were generated by the affy package in R/Bioconductor. Genes were filtered by retaining only probe sets with at least one MAS5 present call and more than 1.2 fold dynamic range across all samples. Differential expression of genes was assessed by Cyber-T. Gene lists were generated at false discovery rate (FDR) of 10% for comparisons among the ventral skin sample groups, and at FDR of 5% for all other comparisons.
| | Sample_data_processing |
| | Sample_data_processing | Lists of differentially expressed genes are linked to the Series GSE17654 record as supplementary files.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lewis,,Chodosh
| | Sample_contact_email | chodosh@mail.med.upenn.edu
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 612 BRB II/III 421 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440763/suppl/GSM440763.CEL.gz
| | Sample_series_id | GSE17654
| | Sample_data_row_count | 22690
| | |
|
GSM440764 | GPL339 |
|
Buds_PTHrP-KO_rep1
|
PTHrP-/- mammary buds
|
strain: CD-1
tissue: Embryonic mammary buds
age: E15
group: PTHrP-/-
|
PTHrP-/- murine embryonic mammary buds.
KOB1
|
| Sample_geo_accession | GSM440764
| | Sample_status | Public on Aug 15 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Aug 14 2009
| | 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 | Embryonic mammary buds and ventral skin were dissected from WT, PTHrP-/- and K14-PTHrP transgenic embryos harvested on E15. Dissections were performed on an icepack and tissue samples stored in RNA Later (Ambion, Austin, TX) at -20°C. After genotyping the embryos, like samples were pooled and RNA was isolated using the RNeasy Mini Protocol with a Qiashredder column (Qiagen, Valencia, CA). Mechanical disruption of tissue was performed with a Kontes Pellet Pestle and a cordless motor (Thermo Fisher Scientific, Waltham, MA) prior to homogenizing with the Qiashredder. MessageClean (GenHunter Corporation, Nashville, TN) was used to remove contaminating DNA. On average, 120 mammary buds were required to produce approximately 20 ug total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | Affymetrix generic hybridization.
| | Sample_scan_protocol | Arrays were scanned using the Hewlett-Packard GeneArray Scanner.
| | Sample_data_processing | Data were normalized by GC-RMA in R/Bioconductor. MAS5 presence calls were generated by the affy package in R/Bioconductor. Genes were filtered by retaining only probe sets with at least one MAS5 present call and more than 1.2 fold dynamic range across all samples. Differential expression of genes was assessed by Cyber-T. Gene lists were generated at false discovery rate (FDR) of 10% for comparisons among the ventral skin sample groups, and at FDR of 5% for all other comparisons.
| | Sample_data_processing |
| | Sample_data_processing | Lists of differentially expressed genes are linked to the Series GSE17654 record as supplementary files.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lewis,,Chodosh
| | Sample_contact_email | chodosh@mail.med.upenn.edu
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 612 BRB II/III 421 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440764/suppl/GSM440764.CEL.gz
| | Sample_series_id | GSE17654
| | Sample_data_row_count | 22690
| | |
|
GSM440765 | GPL339 |
|
Buds_PTHrP-KO_rep2
|
PTHrP-/- mammary buds
|
strain: CD-1
tissue: Embryonic mammary buds
age: E15
group: PTHrP-/-
|
PTHrP-/- murine embryonic mammary buds.
KOB2
|
| Sample_geo_accession | GSM440765
| | Sample_status | Public on Aug 15 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Aug 14 2009
| | 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 | Embryonic mammary buds and ventral skin were dissected from WT, PTHrP-/- and K14-PTHrP transgenic embryos harvested on E15. Dissections were performed on an icepack and tissue samples stored in RNA Later (Ambion, Austin, TX) at -20°C. After genotyping the embryos, like samples were pooled and RNA was isolated using the RNeasy Mini Protocol with a Qiashredder column (Qiagen, Valencia, CA). Mechanical disruption of tissue was performed with a Kontes Pellet Pestle and a cordless motor (Thermo Fisher Scientific, Waltham, MA) prior to homogenizing with the Qiashredder. MessageClean (GenHunter Corporation, Nashville, TN) was used to remove contaminating DNA. On average, 120 mammary buds were required to produce approximately 20 ug total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | Affymetrix generic hybridization.
| | Sample_scan_protocol | Arrays were scanned using the Hewlett-Packard GeneArray Scanner.
| | Sample_data_processing | Data were normalized by GC-RMA in R/Bioconductor. MAS5 presence calls were generated by the affy package in R/Bioconductor. Genes were filtered by retaining only probe sets with at least one MAS5 present call and more than 1.2 fold dynamic range across all samples. Differential expression of genes was assessed by Cyber-T. Gene lists were generated at false discovery rate (FDR) of 10% for comparisons among the ventral skin sample groups, and at FDR of 5% for all other comparisons.
| | Sample_data_processing |
| | Sample_data_processing | Lists of differentially expressed genes are linked to the Series GSE17654 record as supplementary files.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lewis,,Chodosh
| | Sample_contact_email | chodosh@mail.med.upenn.edu
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 612 BRB II/III 421 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440765/suppl/GSM440765.CEL.gz
| | Sample_series_id | GSE17654
| | Sample_data_row_count | 22690
| | |
|
GSM440766 | GPL339 |
|
Buds_PTHrP-KO_rep3
|
PTHrP-/- mammary buds
|
strain: CD-1
tissue: Embryonic mammary buds
age: E15
group: PTHrP-/-
|
PTHrP-/- murine embryonic mammary buds.
KOB3
|
| Sample_geo_accession | GSM440766
| | Sample_status | Public on Aug 15 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Aug 14 2009
| | 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 | Embryonic mammary buds and ventral skin were dissected from WT, PTHrP-/- and K14-PTHrP transgenic embryos harvested on E15. Dissections were performed on an icepack and tissue samples stored in RNA Later (Ambion, Austin, TX) at -20°C. After genotyping the embryos, like samples were pooled and RNA was isolated using the RNeasy Mini Protocol with a Qiashredder column (Qiagen, Valencia, CA). Mechanical disruption of tissue was performed with a Kontes Pellet Pestle and a cordless motor (Thermo Fisher Scientific, Waltham, MA) prior to homogenizing with the Qiashredder. MessageClean (GenHunter Corporation, Nashville, TN) was used to remove contaminating DNA. On average, 120 mammary buds were required to produce approximately 20 ug total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | Affymetrix generic hybridization.
| | Sample_scan_protocol | Arrays were scanned using the Hewlett-Packard GeneArray Scanner.
| | Sample_data_processing | Data were normalized by GC-RMA in R/Bioconductor. MAS5 presence calls were generated by the affy package in R/Bioconductor. Genes were filtered by retaining only probe sets with at least one MAS5 present call and more than 1.2 fold dynamic range across all samples. Differential expression of genes was assessed by Cyber-T. Gene lists were generated at false discovery rate (FDR) of 10% for comparisons among the ventral skin sample groups, and at FDR of 5% for all other comparisons.
| | Sample_data_processing |
| | Sample_data_processing | Lists of differentially expressed genes are linked to the Series GSE17654 record as supplementary files.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lewis,,Chodosh
| | Sample_contact_email | chodosh@mail.med.upenn.edu
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 612 BRB II/III 421 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440766/suppl/GSM440766.CEL.gz
| | Sample_series_id | GSE17654
| | Sample_data_row_count | 22690
| | |
|
GSM440767 | GPL339 |
|
VentralSkin_WT_rep1
|
WT ventral skin
|
strain: CD-1
tissue: Embryonic ventral skin
age: E15
group: WT
|
WT murine embryonic ventral skin.
WTS1
|
| Sample_geo_accession | GSM440767
| | Sample_status | Public on Aug 15 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Aug 14 2009
| | 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 | Embryonic mammary buds and ventral skin were dissected from WT, PTHrP-/- and K14-PTHrP transgenic embryos harvested on E15. Dissections were performed on an icepack and tissue samples stored in RNA Later (Ambion, Austin, TX) at -20°C. After genotyping the embryos, like samples were pooled and RNA was isolated using the RNeasy Mini Protocol with a Qiashredder column (Qiagen, Valencia, CA). Mechanical disruption of tissue was performed with a Kontes Pellet Pestle and a cordless motor (Thermo Fisher Scientific, Waltham, MA) prior to homogenizing with the Qiashredder. MessageClean (GenHunter Corporation, Nashville, TN) was used to remove contaminating DNA. On average, 120 mammary buds were required to produce approximately 20 ug total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | Affymetrix generic hybridization.
| | Sample_scan_protocol | Arrays were scanned using the Hewlett-Packard GeneArray Scanner.
| | Sample_data_processing | Data were normalized by GC-RMA in R/Bioconductor. MAS5 presence calls were generated by the affy package in R/Bioconductor. Genes were filtered by retaining only probe sets with at least one MAS5 present call and more than 1.2 fold dynamic range across all samples. Differential expression of genes was assessed by Cyber-T. Gene lists were generated at false discovery rate (FDR) of 10% for comparisons among the ventral skin sample groups, and at FDR of 5% for all other comparisons.
| | Sample_data_processing |
| | Sample_data_processing | Lists of differentially expressed genes are linked to the Series GSE17654 record as supplementary files.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lewis,,Chodosh
| | Sample_contact_email | chodosh@mail.med.upenn.edu
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 612 BRB II/III 421 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440767/suppl/GSM440767.CEL.gz
| | Sample_series_id | GSE17654
| | Sample_data_row_count | 22690
| | |
|
GSM440768 | GPL339 |
|
VentralSkin_WT_rep2
|
WT ventral skin
|
strain: CD-1
tissue: Embryonic ventral skin
age: E15
group: WT
|
WT murine embryonic ventral skin.
WTS2
|
| Sample_geo_accession | GSM440768
| | Sample_status | Public on Aug 15 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Aug 14 2009
| | 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 | Embryonic mammary buds and ventral skin were dissected from WT, PTHrP-/- and K14-PTHrP transgenic embryos harvested on E15. Dissections were performed on an icepack and tissue samples stored in RNA Later (Ambion, Austin, TX) at -20°C. After genotyping the embryos, like samples were pooled and RNA was isolated using the RNeasy Mini Protocol with a Qiashredder column (Qiagen, Valencia, CA). Mechanical disruption of tissue was performed with a Kontes Pellet Pestle and a cordless motor (Thermo Fisher Scientific, Waltham, MA) prior to homogenizing with the Qiashredder. MessageClean (GenHunter Corporation, Nashville, TN) was used to remove contaminating DNA. On average, 120 mammary buds were required to produce approximately 20 ug total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | Affymetrix generic hybridization.
| | Sample_scan_protocol | Arrays were scanned using the Hewlett-Packard GeneArray Scanner.
| | Sample_data_processing | Data were normalized by GC-RMA in R/Bioconductor. MAS5 presence calls were generated by the affy package in R/Bioconductor. Genes were filtered by retaining only probe sets with at least one MAS5 present call and more than 1.2 fold dynamic range across all samples. Differential expression of genes was assessed by Cyber-T. Gene lists were generated at false discovery rate (FDR) of 10% for comparisons among the ventral skin sample groups, and at FDR of 5% for all other comparisons.
| | Sample_data_processing |
| | Sample_data_processing | Lists of differentially expressed genes are linked to the Series GSE17654 record as supplementary files.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lewis,,Chodosh
| | Sample_contact_email | chodosh@mail.med.upenn.edu
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 612 BRB II/III 421 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440768/suppl/GSM440768.CEL.gz
| | Sample_series_id | GSE17654
| | Sample_data_row_count | 22690
| | |
|
GSM440769 | GPL339 |
|
VentralSkin_WT_rep3
|
WT ventral skin
|
strain: CD-1
tissue: Embryonic ventral skin
age: E15
group: WT
|
WT murine embryonic ventral skin.
WTS3
|
| Sample_geo_accession | GSM440769
| | Sample_status | Public on Aug 15 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Aug 14 2009
| | 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 | Embryonic mammary buds and ventral skin were dissected from WT, PTHrP-/- and K14-PTHrP transgenic embryos harvested on E15. Dissections were performed on an icepack and tissue samples stored in RNA Later (Ambion, Austin, TX) at -20°C. After genotyping the embryos, like samples were pooled and RNA was isolated using the RNeasy Mini Protocol with a Qiashredder column (Qiagen, Valencia, CA). Mechanical disruption of tissue was performed with a Kontes Pellet Pestle and a cordless motor (Thermo Fisher Scientific, Waltham, MA) prior to homogenizing with the Qiashredder. MessageClean (GenHunter Corporation, Nashville, TN) was used to remove contaminating DNA. On average, 120 mammary buds were required to produce approximately 20 ug total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | Affymetrix generic hybridization.
| | Sample_scan_protocol | Arrays were scanned using the Hewlett-Packard GeneArray Scanner.
| | Sample_data_processing | Data were normalized by GC-RMA in R/Bioconductor. MAS5 presence calls were generated by the affy package in R/Bioconductor. Genes were filtered by retaining only probe sets with at least one MAS5 present call and more than 1.2 fold dynamic range across all samples. Differential expression of genes was assessed by Cyber-T. Gene lists were generated at false discovery rate (FDR) of 10% for comparisons among the ventral skin sample groups, and at FDR of 5% for all other comparisons.
| | Sample_data_processing |
| | Sample_data_processing | Lists of differentially expressed genes are linked to the Series GSE17654 record as supplementary files.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lewis,,Chodosh
| | Sample_contact_email | chodosh@mail.med.upenn.edu
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 612 BRB II/III 421 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440769/suppl/GSM440769.CEL.gz
| | Sample_series_id | GSE17654
| | Sample_data_row_count | 22690
| | |
|
GSM440770 | GPL339 |
|
VentralSkin_K14WT_rep1
|
WT ventral skin
|
strain: CD-1
tissue: Embryonic ventral skin
age: E15
group: K14WT
|
WT murine embryonic ventral skin. Used in comparison with K14-PTHrP murine embryonic ventral skin.
K14WTS1
|
| Sample_geo_accession | GSM440770
| | Sample_status | Public on Aug 15 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Aug 14 2009
| | 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 | Embryonic mammary buds and ventral skin were dissected from WT, PTHrP-/- and K14-PTHrP transgenic embryos harvested on E15. Dissections were performed on an icepack and tissue samples stored in RNA Later (Ambion, Austin, TX) at -20°C. After genotyping the embryos, like samples were pooled and RNA was isolated using the RNeasy Mini Protocol with a Qiashredder column (Qiagen, Valencia, CA). Mechanical disruption of tissue was performed with a Kontes Pellet Pestle and a cordless motor (Thermo Fisher Scientific, Waltham, MA) prior to homogenizing with the Qiashredder. MessageClean (GenHunter Corporation, Nashville, TN) was used to remove contaminating DNA. On average, 120 mammary buds were required to produce approximately 20 ug total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | Affymetrix generic hybridization.
| | Sample_scan_protocol | Arrays were scanned using the Hewlett-Packard GeneArray Scanner.
| | Sample_data_processing | Data were normalized by GC-RMA in R/Bioconductor. MAS5 presence calls were generated by the affy package in R/Bioconductor. Genes were filtered by retaining only probe sets with at least one MAS5 present call and more than 1.2 fold dynamic range across all samples. Differential expression of genes was assessed by Cyber-T. Gene lists were generated at false discovery rate (FDR) of 10% for comparisons among the ventral skin sample groups, and at FDR of 5% for all other comparisons.
| | Sample_data_processing |
| | Sample_data_processing | Lists of differentially expressed genes are linked to the Series GSE17654 record as supplementary files.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lewis,,Chodosh
| | Sample_contact_email | chodosh@mail.med.upenn.edu
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 612 BRB II/III 421 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440770/suppl/GSM440770.CEL.gz
| | Sample_series_id | GSE17654
| | Sample_data_row_count | 22690
| | |
|
GSM440771 | GPL339 |
|
VentralSkin_K14WT_rep2
|
WT ventral skin
|
strain: CD-1
tissue: Embryonic ventral skin
age: E15
group: K14WT
|
WT murine embryonic ventral skin. Used in comparison with K14-PTHrP murine embryonic ventral skin.
K14WTS2
|
| Sample_geo_accession | GSM440771
| | Sample_status | Public on Aug 15 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Aug 14 2009
| | 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 | Embryonic mammary buds and ventral skin were dissected from WT, PTHrP-/- and K14-PTHrP transgenic embryos harvested on E15. Dissections were performed on an icepack and tissue samples stored in RNA Later (Ambion, Austin, TX) at -20°C. After genotyping the embryos, like samples were pooled and RNA was isolated using the RNeasy Mini Protocol with a Qiashredder column (Qiagen, Valencia, CA). Mechanical disruption of tissue was performed with a Kontes Pellet Pestle and a cordless motor (Thermo Fisher Scientific, Waltham, MA) prior to homogenizing with the Qiashredder. MessageClean (GenHunter Corporation, Nashville, TN) was used to remove contaminating DNA. On average, 120 mammary buds were required to produce approximately 20 ug total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | Affymetrix generic hybridization.
| | Sample_scan_protocol | Arrays were scanned using the Hewlett-Packard GeneArray Scanner.
| | Sample_data_processing | Data were normalized by GC-RMA in R/Bioconductor. MAS5 presence calls were generated by the affy package in R/Bioconductor. Genes were filtered by retaining only probe sets with at least one MAS5 present call and more than 1.2 fold dynamic range across all samples. Differential expression of genes was assessed by Cyber-T. Gene lists were generated at false discovery rate (FDR) of 10% for comparisons among the ventral skin sample groups, and at FDR of 5% for all other comparisons.
| | Sample_data_processing |
| | Sample_data_processing | Lists of differentially expressed genes are linked to the Series GSE17654 record as supplementary files.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lewis,,Chodosh
| | Sample_contact_email | chodosh@mail.med.upenn.edu
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 612 BRB II/III 421 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440771/suppl/GSM440771.CEL.gz
| | Sample_series_id | GSE17654
| | Sample_data_row_count | 22690
| | |
|
GSM440772 | GPL339 |
|
VentralSkin_K14WT_rep3
|
WT ventral skin
|
strain: CD-1
tissue: Embryonic ventral skin
age: E15
group: K14WT
|
WT murine embryonic ventral skin. Used in comparison with K14-PTHrP murine embryonic ventral skin.
K14WTS3
|
| Sample_geo_accession | GSM440772
| | Sample_status | Public on Aug 15 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Aug 14 2009
| | 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 | Embryonic mammary buds and ventral skin were dissected from WT, PTHrP-/- and K14-PTHrP transgenic embryos harvested on E15. Dissections were performed on an icepack and tissue samples stored in RNA Later (Ambion, Austin, TX) at -20°C. After genotyping the embryos, like samples were pooled and RNA was isolated using the RNeasy Mini Protocol with a Qiashredder column (Qiagen, Valencia, CA). Mechanical disruption of tissue was performed with a Kontes Pellet Pestle and a cordless motor (Thermo Fisher Scientific, Waltham, MA) prior to homogenizing with the Qiashredder. MessageClean (GenHunter Corporation, Nashville, TN) was used to remove contaminating DNA. On average, 120 mammary buds were required to produce approximately 20 ug total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | Affymetrix generic hybridization.
| | Sample_scan_protocol | Arrays were scanned using the Hewlett-Packard GeneArray Scanner.
| | Sample_data_processing | Data were normalized by GC-RMA in R/Bioconductor. MAS5 presence calls were generated by the affy package in R/Bioconductor. Genes were filtered by retaining only probe sets with at least one MAS5 present call and more than 1.2 fold dynamic range across all samples. Differential expression of genes was assessed by Cyber-T. Gene lists were generated at false discovery rate (FDR) of 10% for comparisons among the ventral skin sample groups, and at FDR of 5% for all other comparisons.
| | Sample_data_processing |
| | Sample_data_processing | Lists of differentially expressed genes are linked to the Series GSE17654 record as supplementary files.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lewis,,Chodosh
| | Sample_contact_email | chodosh@mail.med.upenn.edu
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 612 BRB II/III 421 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440772/suppl/GSM440772.CEL.gz
| | Sample_series_id | GSE17654
| | Sample_data_row_count | 22690
| | |
|
GSM440773 | GPL339 |
|
VentralSkin_K14-PTHrP_rep1
|
K14-PTHrP ventral skin
|
strain: CD-1
tissue: Embryonic ventral skin
age: E15
group: K14-PTHrP
|
K14-PTHrP murine embryonic ventral skin.
K14S1
|
| Sample_geo_accession | GSM440773
| | Sample_status | Public on Aug 15 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Aug 14 2009
| | 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 | Embryonic mammary buds and ventral skin were dissected from WT, PTHrP-/- and K14-PTHrP transgenic embryos harvested on E15. Dissections were performed on an icepack and tissue samples stored in RNA Later (Ambion, Austin, TX) at -20°C. After genotyping the embryos, like samples were pooled and RNA was isolated using the RNeasy Mini Protocol with a Qiashredder column (Qiagen, Valencia, CA). Mechanical disruption of tissue was performed with a Kontes Pellet Pestle and a cordless motor (Thermo Fisher Scientific, Waltham, MA) prior to homogenizing with the Qiashredder. MessageClean (GenHunter Corporation, Nashville, TN) was used to remove contaminating DNA. On average, 120 mammary buds were required to produce approximately 20 ug total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | Affymetrix generic hybridization.
| | Sample_scan_protocol | Arrays were scanned using the Hewlett-Packard GeneArray Scanner.
| | Sample_data_processing | Data were normalized by GC-RMA in R/Bioconductor. MAS5 presence calls were generated by the affy package in R/Bioconductor. Genes were filtered by retaining only probe sets with at least one MAS5 present call and more than 1.2 fold dynamic range across all samples. Differential expression of genes was assessed by Cyber-T. Gene lists were generated at false discovery rate (FDR) of 10% for comparisons among the ventral skin sample groups, and at FDR of 5% for all other comparisons.
| | Sample_data_processing |
| | Sample_data_processing | Lists of differentially expressed genes are linked to the Series GSE17654 record as supplementary files.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lewis,,Chodosh
| | Sample_contact_email | chodosh@mail.med.upenn.edu
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 612 BRB II/III 421 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440773/suppl/GSM440773.CEL.gz
| | Sample_series_id | GSE17654
| | Sample_data_row_count | 22690
| | |
|
GSM440774 | GPL339 |
|
VentralSkin_K14-PTHrP_rep2
|
K14-PTHrP ventral skin
|
strain: CD-1
tissue: Embryonic ventral skin
age: E15
group: K14-PTHrP
|
K14-PTHrP murine embryonic ventral skin.
K14S2
|
| Sample_geo_accession | GSM440774
| | Sample_status | Public on Aug 15 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Aug 14 2009
| | 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 | Embryonic mammary buds and ventral skin were dissected from WT, PTHrP-/- and K14-PTHrP transgenic embryos harvested on E15. Dissections were performed on an icepack and tissue samples stored in RNA Later (Ambion, Austin, TX) at -20°C. After genotyping the embryos, like samples were pooled and RNA was isolated using the RNeasy Mini Protocol with a Qiashredder column (Qiagen, Valencia, CA). Mechanical disruption of tissue was performed with a Kontes Pellet Pestle and a cordless motor (Thermo Fisher Scientific, Waltham, MA) prior to homogenizing with the Qiashredder. MessageClean (GenHunter Corporation, Nashville, TN) was used to remove contaminating DNA. On average, 120 mammary buds were required to produce approximately 20 ug total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | Affymetrix generic hybridization.
| | Sample_scan_protocol | Arrays were scanned using the Hewlett-Packard GeneArray Scanner.
| | Sample_data_processing | Data were normalized by GC-RMA in R/Bioconductor. MAS5 presence calls were generated by the affy package in R/Bioconductor. Genes were filtered by retaining only probe sets with at least one MAS5 present call and more than 1.2 fold dynamic range across all samples. Differential expression of genes was assessed by Cyber-T. Gene lists were generated at false discovery rate (FDR) of 10% for comparisons among the ventral skin sample groups, and at FDR of 5% for all other comparisons.
| | Sample_data_processing |
| | Sample_data_processing | Lists of differentially expressed genes are linked to the Series GSE17654 record as supplementary files.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lewis,,Chodosh
| | Sample_contact_email | chodosh@mail.med.upenn.edu
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 612 BRB II/III 421 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440774/suppl/GSM440774.CEL.gz
| | Sample_series_id | GSE17654
| | Sample_data_row_count | 22690
| | |
|
GSM440775 | GPL339 |
|
VentralSkin_K14-PTHrP_rep3
|
K14-PTHrP ventral skin
|
strain: CD-1
tissue: Embryonic ventral skin
age: E15
group: K14-PTHrP
|
K14-PTHrP murine embryonic ventral skin.
K14S3
|
| Sample_geo_accession | GSM440775
| | Sample_status | Public on Aug 15 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Aug 14 2009
| | 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 | Embryonic mammary buds and ventral skin were dissected from WT, PTHrP-/- and K14-PTHrP transgenic embryos harvested on E15. Dissections were performed on an icepack and tissue samples stored in RNA Later (Ambion, Austin, TX) at -20°C. After genotyping the embryos, like samples were pooled and RNA was isolated using the RNeasy Mini Protocol with a Qiashredder column (Qiagen, Valencia, CA). Mechanical disruption of tissue was performed with a Kontes Pellet Pestle and a cordless motor (Thermo Fisher Scientific, Waltham, MA) prior to homogenizing with the Qiashredder. MessageClean (GenHunter Corporation, Nashville, TN) was used to remove contaminating DNA. On average, 120 mammary buds were required to produce approximately 20 ug total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | Affymetrix generic hybridization.
| | Sample_scan_protocol | Arrays were scanned using the Hewlett-Packard GeneArray Scanner.
| | Sample_data_processing | Data were normalized by GC-RMA in R/Bioconductor. MAS5 presence calls were generated by the affy package in R/Bioconductor. Genes were filtered by retaining only probe sets with at least one MAS5 present call and more than 1.2 fold dynamic range across all samples. Differential expression of genes was assessed by Cyber-T. Gene lists were generated at false discovery rate (FDR) of 10% for comparisons among the ventral skin sample groups, and at FDR of 5% for all other comparisons.
| | Sample_data_processing |
| | Sample_data_processing | Lists of differentially expressed genes are linked to the Series GSE17654 record as supplementary files.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lewis,,Chodosh
| | Sample_contact_email | chodosh@mail.med.upenn.edu
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 612 BRB II/III 421 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440775/suppl/GSM440775.CEL.gz
| | Sample_series_id | GSE17654
| | Sample_data_row_count | 22690
| | |
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