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Search results for the GEO ID: GSE19299

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GSM479031

GPL1261

MC3T3 Wild type, biological rep1

Primary cultured wild-type Mus musculus osteoblast cells immortalized

tissue: osteoblast cells genotype: Wild type

Expression data from wild-type mouse osteoblast cell .

Sample_geo_accession	GSM479031
Sample_status	Public on Dec 04 2009
Sample_submission_date	Dec 03 2009
Sample_last_update_date	Dec 03 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Calvarial cell preparation and cultures. Primary osteoblasts were isolated from embryonic day 18.5 mice calvarial bone. Briefly, calvariae (topmost skull bones) were removed from mice, rinsed with PBS and digested in 0.05% Trypsin/EDTA plus 0.1% collagenase P (Boehringer Mannheim) at 37oC with shaking. Cell suspensions were collected from the digestion reaction at 10 minutes intervals, centrifuged at 1,600 K for 5 minutes, and the resulting cell pellet was resuspended in Minimum Essential Medium-alpha Medium (a-MEM) (GIBCO®/Invitrogen) supplemented with 10% fetal bovine serum (FBS, Invitrogen) and 1% penicillin-streptomycin (Sigma), and plated in 6 cm culture plates. 3T3-immortalized osteoblasts (MC3T3 cells) were obtained by culturing primary osteoblasts using the 3T3 protocol, in which 3 x 105 cells were plated in 6 cm culture plates and passaged every 3 days. The population doubling level during each passage was calculated according to the formula log (final cell number/3 x 105)/log2. MC3T3 cells were maintained in a-MEM supplemented with 10% FBS and and 1% penicillin-streptomycin.
Sample_growth_protocol_ch1	Animals. The ﬂox19-RB1 mice were obtained from the laboratory of Doug Hanahan (San Francisco, CA) and maintained in a C57BL/6 background. 2.3- and 3.6-Col1a1-Cre transgenic mice were obtained from the laboratory of Barbara Kream (Farmington, CT). The F1 RBf19/WT;Col1a1-Cre mice were self-crossed and the resulting F2 mice were used in our studies.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted and purified using the RNeasy kit (Qiagen, Valencia, CA), followed by DNase treatment.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned with AGCC Scan Control using the Affymetrix GCS3000 Scanner.
Sample_data_processing	The AGCC format .cel files were analyzed with Expression Console 1.1 using Affymetrix MAS5 algorithm with default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL1261
Sample_contact_name	Douglas,,Cress
Sample_contact_email	Douglas.cress@moffitt.org
Sample_contact_phone	8137456703
Sample_contact_laboratory	4073D
Sample_contact_department	Molecular Oncology
Sample_contact_institute	Moffitt Cancer Institute
Sample_contact_address	12902 Magnolia Drive
Sample_contact_city	Tampa
Sample_contact_state	FL
Sample_contact_zip/postal_code	33612
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479031/suppl/GSM479031.CEL.gz
Sample_series_id	GSE19299
Sample_data_row_count	45101

GSM479032

GPL1261

MC3T3 Wild type, biological rep2

Primary cultured wild-type Mus musculus osteoblast cells immortalized

tissue: osteoblast cells genotype: Wild type

Expression data from wild-type mouse osteoblast cell .

Sample_geo_accession	GSM479032
Sample_status	Public on Dec 04 2009
Sample_submission_date	Dec 03 2009
Sample_last_update_date	Dec 03 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Calvarial cell preparation and cultures. Primary osteoblasts were isolated from embryonic day 18.5 mice calvarial bone. Briefly, calvariae (topmost skull bones) were removed from mice, rinsed with PBS and digested in 0.05% Trypsin/EDTA plus 0.1% collagenase P (Boehringer Mannheim) at 37oC with shaking. Cell suspensions were collected from the digestion reaction at 10 minutes intervals, centrifuged at 1,600 K for 5 minutes, and the resulting cell pellet was resuspended in Minimum Essential Medium-alpha Medium (a-MEM) (GIBCO®/Invitrogen) supplemented with 10% fetal bovine serum (FBS, Invitrogen) and 1% penicillin-streptomycin (Sigma), and plated in 6 cm culture plates. 3T3-immortalized osteoblasts (MC3T3 cells) were obtained by culturing primary osteoblasts using the 3T3 protocol, in which 3 x 105 cells were plated in 6 cm culture plates and passaged every 3 days. The population doubling level during each passage was calculated according to the formula log (final cell number/3 x 105)/log2. MC3T3 cells were maintained in a-MEM supplemented with 10% FBS and and 1% penicillin-streptomycin.
Sample_growth_protocol_ch1	Animals. The ﬂox19-RB1 mice were obtained from the laboratory of Doug Hanahan (San Francisco, CA) and maintained in a C57BL/6 background. 2.3- and 3.6-Col1a1-Cre transgenic mice were obtained from the laboratory of Barbara Kream (Farmington, CT). The F1 RBf19/WT;Col1a1-Cre mice were self-crossed and the resulting F2 mice were used in our studies.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted and purified using the RNeasy kit (Qiagen, Valencia, CA), followed by DNase treatment.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned with AGCC Scan Control using the Affymetrix GCS3000 Scanner.
Sample_data_processing	The AGCC format .cel files were analyzed with Expression Console 1.1 using Affymetrix MAS5 algorithm with default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL1261
Sample_contact_name	Douglas,,Cress
Sample_contact_email	Douglas.cress@moffitt.org
Sample_contact_phone	8137456703
Sample_contact_laboratory	4073D
Sample_contact_department	Molecular Oncology
Sample_contact_institute	Moffitt Cancer Institute
Sample_contact_address	12902 Magnolia Drive
Sample_contact_city	Tampa
Sample_contact_state	FL
Sample_contact_zip/postal_code	33612
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479032/suppl/GSM479032.CEL.gz
Sample_series_id	GSE19299
Sample_data_row_count	45101

GSM479033

GPL1261

MC3T3 Wild type, biological rep3

Primary cultured wild-type Mus musculus osteoblast cells immortalized

tissue: osteoblast cells genotype: Wild type

Expression data from wild-type mouse osteoblast cell .

Sample_geo_accession	GSM479033
Sample_status	Public on Dec 04 2009
Sample_submission_date	Dec 03 2009
Sample_last_update_date	Dec 03 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Calvarial cell preparation and cultures. Primary osteoblasts were isolated from embryonic day 18.5 mice calvarial bone. Briefly, calvariae (topmost skull bones) were removed from mice, rinsed with PBS and digested in 0.05% Trypsin/EDTA plus 0.1% collagenase P (Boehringer Mannheim) at 37oC with shaking. Cell suspensions were collected from the digestion reaction at 10 minutes intervals, centrifuged at 1,600 K for 5 minutes, and the resulting cell pellet was resuspended in Minimum Essential Medium-alpha Medium (a-MEM) (GIBCO®/Invitrogen) supplemented with 10% fetal bovine serum (FBS, Invitrogen) and 1% penicillin-streptomycin (Sigma), and plated in 6 cm culture plates. 3T3-immortalized osteoblasts (MC3T3 cells) were obtained by culturing primary osteoblasts using the 3T3 protocol, in which 3 x 105 cells were plated in 6 cm culture plates and passaged every 3 days. The population doubling level during each passage was calculated according to the formula log (final cell number/3 x 105)/log2. MC3T3 cells were maintained in a-MEM supplemented with 10% FBS and and 1% penicillin-streptomycin.
Sample_growth_protocol_ch1	Animals. The ﬂox19-RB1 mice were obtained from the laboratory of Doug Hanahan (San Francisco, CA) and maintained in a C57BL/6 background. 2.3- and 3.6-Col1a1-Cre transgenic mice were obtained from the laboratory of Barbara Kream (Farmington, CT). The F1 RBf19/WT;Col1a1-Cre mice were self-crossed and the resulting F2 mice were used in our studies.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted and purified using the RNeasy kit (Qiagen, Valencia, CA), followed by DNase treatment.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned with AGCC Scan Control using the Affymetrix GCS3000 Scanner.
Sample_data_processing	The AGCC format .cel files were analyzed with Expression Console 1.1 using Affymetrix MAS5 algorithm with default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL1261
Sample_contact_name	Douglas,,Cress
Sample_contact_email	Douglas.cress@moffitt.org
Sample_contact_phone	8137456703
Sample_contact_laboratory	4073D
Sample_contact_department	Molecular Oncology
Sample_contact_institute	Moffitt Cancer Institute
Sample_contact_address	12902 Magnolia Drive
Sample_contact_city	Tampa
Sample_contact_state	FL
Sample_contact_zip/postal_code	33612
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479033/suppl/GSM479033.CEL.gz
Sample_series_id	GSE19299
Sample_data_row_count	45101

GSM479034

GPL1261

MC3T3 Rb Knockout, biological rep1

Primary cultured Rb-knockout Mus musculus osteoblast cells immortalized

tissue: osteoblast cells genotype: Rb Knockout

Expression data from mouse osteoblast cell with retinoblastoma tumor suppressor(Rb) knock-out.

Sample_geo_accession	GSM479034
Sample_status	Public on Dec 04 2009
Sample_submission_date	Dec 03 2009
Sample_last_update_date	Dec 03 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Calvarial cell preparation and cultures. Primary osteoblasts were isolated from embryonic day 18.5 mice calvarial bone. Briefly, calvariae (topmost skull bones) were removed from mice, rinsed with PBS and digested in 0.05% Trypsin/EDTA plus 0.1% collagenase P (Boehringer Mannheim) at 37oC with shaking. Cell suspensions were collected from the digestion reaction at 10 minutes intervals, centrifuged at 1,600 K for 5 minutes, and the resulting cell pellet was resuspended in Minimum Essential Medium-alpha Medium (a-MEM) (GIBCO®/Invitrogen) supplemented with 10% fetal bovine serum (FBS, Invitrogen) and 1% penicillin-streptomycin (Sigma), and plated in 6 cm culture plates. 3T3-immortalized osteoblasts (MC3T3 cells) were obtained by culturing primary osteoblasts using the 3T3 protocol, in which 3 x 105 cells were plated in 6 cm culture plates and passaged every 3 days. The population doubling level during each passage was calculated according to the formula log (final cell number/3 x 105)/log2. MC3T3 cells were maintained in a-MEM supplemented with 10% FBS and and 1% penicillin-streptomycin.
Sample_growth_protocol_ch1	Animals. The ﬂox19-RB1 mice were obtained from the laboratory of Doug Hanahan (San Francisco, CA) and maintained in a C57BL/6 background. 2.3- and 3.6-Col1a1-Cre transgenic mice were obtained from the laboratory of Barbara Kream (Farmington, CT). The F1 RBf19/WT;Col1a1-Cre mice were self-crossed and the resulting F2 mice were used in our studies.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted and purified using the RNeasy kit (Qiagen, Valencia, CA), followed by DNase treatment.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned with AGCC Scan Control using the Affymetrix GCS3000 Scanner.
Sample_data_processing	The AGCC format .cel files were analyzed with Expression Console 1.1 using Affymetrix MAS5 algorithm with default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL1261
Sample_contact_name	Douglas,,Cress
Sample_contact_email	Douglas.cress@moffitt.org
Sample_contact_phone	8137456703
Sample_contact_laboratory	4073D
Sample_contact_department	Molecular Oncology
Sample_contact_institute	Moffitt Cancer Institute
Sample_contact_address	12902 Magnolia Drive
Sample_contact_city	Tampa
Sample_contact_state	FL
Sample_contact_zip/postal_code	33612
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479034/suppl/GSM479034.CEL.gz
Sample_series_id	GSE19299
Sample_data_row_count	45101

GSM479035

GPL1261

MC3T3 Rb Knockout, biological rep2

Primary cultured Rb-knockout Mus musculus osteoblast cells immortalized

tissue: osteoblast cells genotype: Rb Knockout

Expression data from mouse osteoblast cell with retinoblastoma tumor suppressor(Rb) knock-out.

Sample_geo_accession	GSM479035
Sample_status	Public on Dec 04 2009
Sample_submission_date	Dec 03 2009
Sample_last_update_date	Dec 03 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Calvarial cell preparation and cultures. Primary osteoblasts were isolated from embryonic day 18.5 mice calvarial bone. Briefly, calvariae (topmost skull bones) were removed from mice, rinsed with PBS and digested in 0.05% Trypsin/EDTA plus 0.1% collagenase P (Boehringer Mannheim) at 37oC with shaking. Cell suspensions were collected from the digestion reaction at 10 minutes intervals, centrifuged at 1,600 K for 5 minutes, and the resulting cell pellet was resuspended in Minimum Essential Medium-alpha Medium (a-MEM) (GIBCO®/Invitrogen) supplemented with 10% fetal bovine serum (FBS, Invitrogen) and 1% penicillin-streptomycin (Sigma), and plated in 6 cm culture plates. 3T3-immortalized osteoblasts (MC3T3 cells) were obtained by culturing primary osteoblasts using the 3T3 protocol, in which 3 x 105 cells were plated in 6 cm culture plates and passaged every 3 days. The population doubling level during each passage was calculated according to the formula log (final cell number/3 x 105)/log2. MC3T3 cells were maintained in a-MEM supplemented with 10% FBS and and 1% penicillin-streptomycin.
Sample_growth_protocol_ch1	Animals. The ﬂox19-RB1 mice were obtained from the laboratory of Doug Hanahan (San Francisco, CA) and maintained in a C57BL/6 background. 2.3- and 3.6-Col1a1-Cre transgenic mice were obtained from the laboratory of Barbara Kream (Farmington, CT). The F1 RBf19/WT;Col1a1-Cre mice were self-crossed and the resulting F2 mice were used in our studies.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted and purified using the RNeasy kit (Qiagen, Valencia, CA), followed by DNase treatment.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned with AGCC Scan Control using the Affymetrix GCS3000 Scanner.
Sample_data_processing	The AGCC format .cel files were analyzed with Expression Console 1.1 using Affymetrix MAS5 algorithm with default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL1261
Sample_contact_name	Douglas,,Cress
Sample_contact_email	Douglas.cress@moffitt.org
Sample_contact_phone	8137456703
Sample_contact_laboratory	4073D
Sample_contact_department	Molecular Oncology
Sample_contact_institute	Moffitt Cancer Institute
Sample_contact_address	12902 Magnolia Drive
Sample_contact_city	Tampa
Sample_contact_state	FL
Sample_contact_zip/postal_code	33612
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479035/suppl/GSM479035.CEL.gz
Sample_series_id	GSE19299
Sample_data_row_count	45101

GSM479036

GPL1261

MC3T3 Rb Knockout, biological rep3

Primary cultured Rb-knockout Mus musculus osteoblast cells immortalized

tissue: osteoblast cells genotype: Rb Knockout

Expression data from mouse osteoblast cell with retinoblastoma tumor suppressor(Rb) knock-out.

Sample_geo_accession	GSM479036
Sample_status	Public on Dec 04 2009
Sample_submission_date	Dec 03 2009
Sample_last_update_date	Dec 03 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Calvarial cell preparation and cultures. Primary osteoblasts were isolated from embryonic day 18.5 mice calvarial bone. Briefly, calvariae (topmost skull bones) were removed from mice, rinsed with PBS and digested in 0.05% Trypsin/EDTA plus 0.1% collagenase P (Boehringer Mannheim) at 37oC with shaking. Cell suspensions were collected from the digestion reaction at 10 minutes intervals, centrifuged at 1,600 K for 5 minutes, and the resulting cell pellet was resuspended in Minimum Essential Medium-alpha Medium (a-MEM) (GIBCO®/Invitrogen) supplemented with 10% fetal bovine serum (FBS, Invitrogen) and 1% penicillin-streptomycin (Sigma), and plated in 6 cm culture plates. 3T3-immortalized osteoblasts (MC3T3 cells) were obtained by culturing primary osteoblasts using the 3T3 protocol, in which 3 x 105 cells were plated in 6 cm culture plates and passaged every 3 days. The population doubling level during each passage was calculated according to the formula log (final cell number/3 x 105)/log2. MC3T3 cells were maintained in a-MEM supplemented with 10% FBS and and 1% penicillin-streptomycin.
Sample_growth_protocol_ch1	Animals. The ﬂox19-RB1 mice were obtained from the laboratory of Doug Hanahan (San Francisco, CA) and maintained in a C57BL/6 background. 2.3- and 3.6-Col1a1-Cre transgenic mice were obtained from the laboratory of Barbara Kream (Farmington, CT). The F1 RBf19/WT;Col1a1-Cre mice were self-crossed and the resulting F2 mice were used in our studies.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted and purified using the RNeasy kit (Qiagen, Valencia, CA), followed by DNase treatment.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned with AGCC Scan Control using the Affymetrix GCS3000 Scanner.
Sample_data_processing	The AGCC format .cel files were analyzed with Expression Console 1.1 using Affymetrix MAS5 algorithm with default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL1261
Sample_contact_name	Douglas,,Cress
Sample_contact_email	Douglas.cress@moffitt.org
Sample_contact_phone	8137456703
Sample_contact_laboratory	4073D
Sample_contact_department	Molecular Oncology
Sample_contact_institute	Moffitt Cancer Institute
Sample_contact_address	12902 Magnolia Drive
Sample_contact_city	Tampa
Sample_contact_state	FL
Sample_contact_zip/postal_code	33612
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479036/suppl/GSM479036.CEL.gz
Sample_series_id	GSE19299
Sample_data_row_count	45101

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