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Search results for the GEO ID: GSE23496

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GSM575568

GPL1261

osteocytes_virgin_rep1

purifed tibiae osteocytes from virgin by enzyme digestions

tissue: tibiae bone genotype: CD1 wild type age: 16-18week

Sample_geo_accession	GSM575568
Sample_status	Public on Dec 31 2011
Sample_submission_date	Aug 06 2010
Sample_last_update_date	Dec 31 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Twelve-week-old, CD1 mice purchased from Charles River Laboratories Wilmington, MA were allowed to become pregnant, deliver and lactate. Litter size was adjusted to 8–13 pups to equalize suckling intensity between dams. Pups were removed on the 12th day of lactation to induce the weaning response. Age-matched, virgin CD1 mice were used as controls. Mice were sacrificed on the 12th day of lactation or the 7th day after forced weaning. Age-matched, virgin CD1 mice were used as controls.
Sample_growth_protocol_ch1	All mice were housed in standard conditions of temperature 23 ± 2°C and light-controlled environment 12-h light/12-h dark cycle, and had free access to water and pelleted food UAR rodent diet No.R03-25; UAR, Epinay/Orge. All animal experiments were approved by the University of Missouri at Kansas City IACUC committee in accordance with regulations and guidelines.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Tibiae from CD1 mice in Virgin, Lactation and Post lactation groups were processed immediately after sacrifice. Osteocyte RNA was extracted from tibia diaphyses with all surface cells such as osteoclasts and osteoblasts removed by sequential digestion. The digestion procedure generally followed the published procedure. Namely, soft tissue and periosteum were removed from the femurs. Epiphyses were cut off and bone marrows were removed by centrifuging. Diaphyses were incubated at 37°C with 0.2% type 1 collagenase Sigma/ 0.05% trypsin Sigma for 30 minutes for 3 times, and then washed with PBS. Remaining diaphyses were digested in 0.53 mM EDTA/ 0.05 % trypsin Cellgro, Mediatech,Inc, Manassas, VA at 37°C for 30 min, and then were rinsed with PBS and digested with 0.2 % collagenase/ 0.05% trypsin solution at 37°C for 30 min. Finally the remaining diaphyses are rinsed with PBS and pulverized in liquid nitrogen, and bone powder was added to Trizol reagent Invitrogen, Carlsbad, CA. Total RNA was isolated as per the Trizol manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA reversely transcribed to cDNA, subjected to T7 mediated invitro-transcription amplification and labeling
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were 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 using the GeneChip® Scanner 3000 7G with autoloader.
Sample_data_processing	The data were analyzed with Genepattern using RMA analysis with quantile normalization and background correct. After preprocess, the data were statistical analyzed with bioconductor software package using ANOVA analysis.
Sample_platform_id	GPL1261
Sample_contact_name	Lynda,F,Bonewald
Sample_contact_email	bonewaldl@umkc.edu
Sample_contact_department	Department of Oral Biology
Sample_contact_institute	School of dentistry University of Missouri-Kansas City
Sample_contact_address	650 E 25th Street
Sample_contact_city	KANSAS CITY
Sample_contact_state	MO
Sample_contact_zip/postal_code	64108
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM575nnn/GSM575568/suppl/GSM575568.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM575nnn/GSM575568/suppl/GSM575568.CHP.gz
Sample_series_id	GSE23496
Sample_data_row_count	45101

GSM575569

GPL1261

osteocytes_virgin_rep2

purifed tibiae osteocytes from virgin by enzyme digestions

tissue: tibiae bone genotype: CD1 wild type age: 16-18week

Sample_geo_accession	GSM575569
Sample_status	Public on Dec 31 2011
Sample_submission_date	Aug 06 2010
Sample_last_update_date	Dec 31 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Twelve-week-old, CD1 mice purchased from Charles River Laboratories Wilmington, MA were allowed to become pregnant, deliver and lactate. Litter size was adjusted to 8–13 pups to equalize suckling intensity between dams. Pups were removed on the 12th day of lactation to induce the weaning response. Age-matched, virgin CD1 mice were used as controls. Mice were sacrificed on the 12th day of lactation or the 7th day after forced weaning. Age-matched, virgin CD1 mice were used as controls.
Sample_growth_protocol_ch1	All mice were housed in standard conditions of temperature 23 ± 2°C and light-controlled environment 12-h light/12-h dark cycle, and had free access to water and pelleted food UAR rodent diet No.R03-25; UAR, Epinay/Orge. All animal experiments were approved by the University of Missouri at Kansas City IACUC committee in accordance with regulations and guidelines.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Tibiae from CD1 mice in Virgin, Lactation and Post lactation groups were processed immediately after sacrifice. Osteocyte RNA was extracted from tibia diaphyses with all surface cells such as osteoclasts and osteoblasts removed by sequential digestion. The digestion procedure generally followed the published procedure. Namely, soft tissue and periosteum were removed from the femurs. Epiphyses were cut off and bone marrows were removed by centrifuging. Diaphyses were incubated at 37°C with 0.2% type 1 collagenase Sigma/ 0.05% trypsin Sigma for 30 minutes for 3 times, and then washed with PBS. Remaining diaphyses were digested in 0.53 mM EDTA/ 0.05 % trypsin Cellgro, Mediatech,Inc, Manassas, VA at 37°C for 30 min, and then were rinsed with PBS and digested with 0.2 % collagenase/ 0.05% trypsin solution at 37°C for 30 min. Finally the remaining diaphyses are rinsed with PBS and pulverized in liquid nitrogen, and bone powder was added to Trizol reagent Invitrogen, Carlsbad, CA. Total RNA was isolated as per the Trizol manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA reversely transcribed to cDNA, subjected to T7 mediated invitro-transcription amplification and labeling
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were 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 using the GeneChip® Scanner 3000 7G with autoloader.
Sample_data_processing	The data were analyzed with Genepattern using RMA analysis with quantile normalization and background correct. After preprocess, the data were statistical analyzed with bioconductor software package using ANOVA analysis.
Sample_platform_id	GPL1261
Sample_contact_name	Lynda,F,Bonewald
Sample_contact_email	bonewaldl@umkc.edu
Sample_contact_department	Department of Oral Biology
Sample_contact_institute	School of dentistry University of Missouri-Kansas City
Sample_contact_address	650 E 25th Street
Sample_contact_city	KANSAS CITY
Sample_contact_state	MO
Sample_contact_zip/postal_code	64108
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM575nnn/GSM575569/suppl/GSM575569.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM575nnn/GSM575569/suppl/GSM575569.CHP.gz
Sample_series_id	GSE23496
Sample_data_row_count	45101

GSM575570

GPL1261

osteocytes_virgin_rep3

purifed tibiae osteocytes from virgin by enzyme digestions

tissue: tibiae bone genotype: CD1 wild type age: 16-18week

Sample_geo_accession	GSM575570
Sample_status	Public on Dec 31 2011
Sample_submission_date	Aug 06 2010
Sample_last_update_date	Dec 31 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Twelve-week-old, CD1 mice purchased from Charles River Laboratories Wilmington, MA were allowed to become pregnant, deliver and lactate. Litter size was adjusted to 8–13 pups to equalize suckling intensity between dams. Pups were removed on the 12th day of lactation to induce the weaning response. Age-matched, virgin CD1 mice were used as controls. Mice were sacrificed on the 12th day of lactation or the 7th day after forced weaning. Age-matched, virgin CD1 mice were used as controls.
Sample_growth_protocol_ch1	All mice were housed in standard conditions of temperature 23 ± 2°C and light-controlled environment 12-h light/12-h dark cycle, and had free access to water and pelleted food UAR rodent diet No.R03-25; UAR, Epinay/Orge. All animal experiments were approved by the University of Missouri at Kansas City IACUC committee in accordance with regulations and guidelines.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Tibiae from CD1 mice in Virgin, Lactation and Post lactation groups were processed immediately after sacrifice. Osteocyte RNA was extracted from tibia diaphyses with all surface cells such as osteoclasts and osteoblasts removed by sequential digestion. The digestion procedure generally followed the published procedure. Namely, soft tissue and periosteum were removed from the femurs. Epiphyses were cut off and bone marrows were removed by centrifuging. Diaphyses were incubated at 37°C with 0.2% type 1 collagenase Sigma/ 0.05% trypsin Sigma for 30 minutes for 3 times, and then washed with PBS. Remaining diaphyses were digested in 0.53 mM EDTA/ 0.05 % trypsin Cellgro, Mediatech,Inc, Manassas, VA at 37°C for 30 min, and then were rinsed with PBS and digested with 0.2 % collagenase/ 0.05% trypsin solution at 37°C for 30 min. Finally the remaining diaphyses are rinsed with PBS and pulverized in liquid nitrogen, and bone powder was added to Trizol reagent Invitrogen, Carlsbad, CA. Total RNA was isolated as per the Trizol manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA reversely transcribed to cDNA, subjected to T7 mediated invitro-transcription amplification and labeling
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were 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 using the GeneChip® Scanner 3000 7G with autoloader.
Sample_data_processing	The data were analyzed with Genepattern using RMA analysis with quantile normalization and background correct. After preprocess, the data were statistical analyzed with bioconductor software package using ANOVA analysis.
Sample_platform_id	GPL1261
Sample_contact_name	Lynda,F,Bonewald
Sample_contact_email	bonewaldl@umkc.edu
Sample_contact_department	Department of Oral Biology
Sample_contact_institute	School of dentistry University of Missouri-Kansas City
Sample_contact_address	650 E 25th Street
Sample_contact_city	KANSAS CITY
Sample_contact_state	MO
Sample_contact_zip/postal_code	64108
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM575nnn/GSM575570/suppl/GSM575570.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM575nnn/GSM575570/suppl/GSM575570.CHP.gz
Sample_series_id	GSE23496
Sample_data_row_count	45101

GSM575571

GPL1261

osteocytes_lactation_rep1

purifed tibiae osteocytes from lactation mice by enzyme digestions

tissue: tibiae bone genotype: CD1 wild type age: 16-18week

Sample_geo_accession	GSM575571
Sample_status	Public on Dec 31 2011
Sample_submission_date	Aug 06 2010
Sample_last_update_date	Dec 31 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Twelve-week-old, CD1 mice purchased from Charles River Laboratories Wilmington, MA were allowed to become pregnant, deliver and lactate. Litter size was adjusted to 8–13 pups to equalize suckling intensity between dams. Pups were removed on the 12th day of lactation to induce the weaning response. Age-matched, virgin CD1 mice were used as controls. Mice were sacrificed on the 12th day of lactation or the 7th day after forced weaning. Age-matched, virgin CD1 mice were used as controls.
Sample_growth_protocol_ch1	All mice were housed in standard conditions of temperature 23 ± 2°C and light-controlled environment 12-h light/12-h dark cycle, and had free access to water and pelleted food UAR rodent diet No.R03-25; UAR, Epinay/Orge. All animal experiments were approved by the University of Missouri at Kansas City IACUC committee in accordance with regulations and guidelines.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Tibiae from CD1 mice in Virgin, Lactation and Post lactation groups were processed immediately after sacrifice. Osteocyte RNA was extracted from tibia diaphyses with all surface cells such as osteoclasts and osteoblasts removed by sequential digestion. The digestion procedure generally followed the published procedure. Namely, soft tissue and periosteum were removed from the femurs. Epiphyses were cut off and bone marrows were removed by centrifuging. Diaphyses were incubated at 37°C with 0.2% type 1 collagenase Sigma/ 0.05% trypsin Sigma for 30 minutes for 3 times, and then washed with PBS. Remaining diaphyses were digested in 0.53 mM EDTA/ 0.05 % trypsin Cellgro, Mediatech,Inc, Manassas, VA at 37°C for 30 min, and then were rinsed with PBS and digested with 0.2 % collagenase/ 0.05% trypsin solution at 37°C for 30 min. Finally the remaining diaphyses are rinsed with PBS and pulverized in liquid nitrogen, and bone powder was added to Trizol reagent Invitrogen, Carlsbad, CA. Total RNA was isolated as per the Trizol manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA reversely transcribed to cDNA, subjected to T7 mediated invitro-transcription amplification and labeling
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were 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 using the GeneChip® Scanner 3000 7G with autoloader.
Sample_data_processing	The data were analyzed with Genepattern using RMA analysis with quantile normalization and background correct. After preprocess, the data were statistical analyzed with bioconductor software package using ANOVA analysis.
Sample_platform_id	GPL1261
Sample_contact_name	Lynda,F,Bonewald
Sample_contact_email	bonewaldl@umkc.edu
Sample_contact_department	Department of Oral Biology
Sample_contact_institute	School of dentistry University of Missouri-Kansas City
Sample_contact_address	650 E 25th Street
Sample_contact_city	KANSAS CITY
Sample_contact_state	MO
Sample_contact_zip/postal_code	64108
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM575nnn/GSM575571/suppl/GSM575571.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM575nnn/GSM575571/suppl/GSM575571.CHP.gz
Sample_series_id	GSE23496
Sample_data_row_count	45101

GSM575572

GPL1261

osteocytes_lactation_rep2

purifed tibiae osteocytes from lactation mice by enzyme digestions

tissue: tibiae bone genotype: CD1 wild type age: 16-18week

Sample_geo_accession	GSM575572
Sample_status	Public on Dec 31 2011
Sample_submission_date	Aug 06 2010
Sample_last_update_date	Dec 31 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Twelve-week-old, CD1 mice purchased from Charles River Laboratories Wilmington, MA were allowed to become pregnant, deliver and lactate. Litter size was adjusted to 8–13 pups to equalize suckling intensity between dams. Pups were removed on the 12th day of lactation to induce the weaning response. Age-matched, virgin CD1 mice were used as controls. Mice were sacrificed on the 12th day of lactation or the 7th day after forced weaning. Age-matched, virgin CD1 mice were used as controls.
Sample_growth_protocol_ch1	All mice were housed in standard conditions of temperature 23 ± 2°C and light-controlled environment 12-h light/12-h dark cycle, and had free access to water and pelleted food UAR rodent diet No.R03-25; UAR, Epinay/Orge. All animal experiments were approved by the University of Missouri at Kansas City IACUC committee in accordance with regulations and guidelines.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Tibiae from CD1 mice in Virgin, Lactation and Post lactation groups were processed immediately after sacrifice. Osteocyte RNA was extracted from tibia diaphyses with all surface cells such as osteoclasts and osteoblasts removed by sequential digestion. The digestion procedure generally followed the published procedure. Namely, soft tissue and periosteum were removed from the femurs. Epiphyses were cut off and bone marrows were removed by centrifuging. Diaphyses were incubated at 37°C with 0.2% type 1 collagenase Sigma/ 0.05% trypsin Sigma for 30 minutes for 3 times, and then washed with PBS. Remaining diaphyses were digested in 0.53 mM EDTA/ 0.05 % trypsin Cellgro, Mediatech,Inc, Manassas, VA at 37°C for 30 min, and then were rinsed with PBS and digested with 0.2 % collagenase/ 0.05% trypsin solution at 37°C for 30 min. Finally the remaining diaphyses are rinsed with PBS and pulverized in liquid nitrogen, and bone powder was added to Trizol reagent Invitrogen, Carlsbad, CA. Total RNA was isolated as per the Trizol manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA reversely transcribed to cDNA, subjected to T7 mediated invitro-transcription amplification and labeling
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were 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 using the GeneChip® Scanner 3000 7G with autoloader.
Sample_data_processing	The data were analyzed with Genepattern using RMA analysis with quantile normalization and background correct. After preprocess, the data were statistical analyzed with bioconductor software package using ANOVA analysis.
Sample_platform_id	GPL1261
Sample_contact_name	Lynda,F,Bonewald
Sample_contact_email	bonewaldl@umkc.edu
Sample_contact_department	Department of Oral Biology
Sample_contact_institute	School of dentistry University of Missouri-Kansas City
Sample_contact_address	650 E 25th Street
Sample_contact_city	KANSAS CITY
Sample_contact_state	MO
Sample_contact_zip/postal_code	64108
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM575nnn/GSM575572/suppl/GSM575572.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM575nnn/GSM575572/suppl/GSM575572.CHP.gz
Sample_series_id	GSE23496
Sample_data_row_count	45101

GSM575573

GPL1261

osteocytes_lactation_rep3

purifed tibiae osteocytes from lactation mice by enzyme digestions

tissue: tibiae bone genotype: CD1 wild type age: 16-18week

Sample_geo_accession	GSM575573
Sample_status	Public on Dec 31 2011
Sample_submission_date	Aug 06 2010
Sample_last_update_date	Dec 31 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Twelve-week-old, CD1 mice purchased from Charles River Laboratories Wilmington, MA were allowed to become pregnant, deliver and lactate. Litter size was adjusted to 8–13 pups to equalize suckling intensity between dams. Pups were removed on the 12th day of lactation to induce the weaning response. Age-matched, virgin CD1 mice were used as controls. Mice were sacrificed on the 12th day of lactation or the 7th day after forced weaning. Age-matched, virgin CD1 mice were used as controls.
Sample_growth_protocol_ch1	All mice were housed in standard conditions of temperature 23 ± 2°C and light-controlled environment 12-h light/12-h dark cycle, and had free access to water and pelleted food UAR rodent diet No.R03-25; UAR, Epinay/Orge. All animal experiments were approved by the University of Missouri at Kansas City IACUC committee in accordance with regulations and guidelines.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Tibiae from CD1 mice in Virgin, Lactation and Post lactation groups were processed immediately after sacrifice. Osteocyte RNA was extracted from tibia diaphyses with all surface cells such as osteoclasts and osteoblasts removed by sequential digestion. The digestion procedure generally followed the published procedure. Namely, soft tissue and periosteum were removed from the femurs. Epiphyses were cut off and bone marrows were removed by centrifuging. Diaphyses were incubated at 37°C with 0.2% type 1 collagenase Sigma/ 0.05% trypsin Sigma for 30 minutes for 3 times, and then washed with PBS. Remaining diaphyses were digested in 0.53 mM EDTA/ 0.05 % trypsin Cellgro, Mediatech,Inc, Manassas, VA at 37°C for 30 min, and then were rinsed with PBS and digested with 0.2 % collagenase/ 0.05% trypsin solution at 37°C for 30 min. Finally the remaining diaphyses are rinsed with PBS and pulverized in liquid nitrogen, and bone powder was added to Trizol reagent Invitrogen, Carlsbad, CA. Total RNA was isolated as per the Trizol manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA reversely transcribed to cDNA, subjected to T7 mediated invitro-transcription amplification and labeling
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were 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 using the GeneChip® Scanner 3000 7G with autoloader.
Sample_data_processing	The data were analyzed with Genepattern using RMA analysis with quantile normalization and background correct. After preprocess, the data were statistical analyzed with bioconductor software package using ANOVA analysis.
Sample_platform_id	GPL1261
Sample_contact_name	Lynda,F,Bonewald
Sample_contact_email	bonewaldl@umkc.edu
Sample_contact_department	Department of Oral Biology
Sample_contact_institute	School of dentistry University of Missouri-Kansas City
Sample_contact_address	650 E 25th Street
Sample_contact_city	KANSAS CITY
Sample_contact_state	MO
Sample_contact_zip/postal_code	64108
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM575nnn/GSM575573/suppl/GSM575573.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM575nnn/GSM575573/suppl/GSM575573.CHP.gz
Sample_series_id	GSE23496
Sample_data_row_count	45101

GSM575574

GPL1261

osteocytes_postlactation_rep1

purifed tibiae osteocytes from virgin by enzyme digestions

tissue: tibiae bone genotype: CD1 wild type age: 16-18week

Sample_geo_accession	GSM575574
Sample_status	Public on Dec 31 2011
Sample_submission_date	Aug 06 2010
Sample_last_update_date	Dec 31 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Twelve-week-old, CD1 mice purchased from Charles River Laboratories Wilmington, MA were allowed to become pregnant, deliver and lactate. Litter size was adjusted to 8–13 pups to equalize suckling intensity between dams. Pups were removed on the 12th day of lactation to induce the weaning response. Age-matched, virgin CD1 mice were used as controls. Mice were sacrificed on the 12th day of lactation or the 7th day after forced weaning. Age-matched, virgin CD1 mice were used as controls.
Sample_growth_protocol_ch1	All mice were housed in standard conditions of temperature 23 ± 2°C and light-controlled environment 12-h light/12-h dark cycle, and had free access to water and pelleted food UAR rodent diet No.R03-25; UAR, Epinay/Orge. All animal experiments were approved by the University of Missouri at Kansas City IACUC committee in accordance with regulations and guidelines.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Tibiae from CD1 mice in Virgin, Lactation and Post lactation groups were processed immediately after sacrifice. Osteocyte RNA was extracted from tibia diaphyses with all surface cells such as osteoclasts and osteoblasts removed by sequential digestion. The digestion procedure generally followed the published procedure. Namely, soft tissue and periosteum were removed from the femurs. Epiphyses were cut off and bone marrows were removed by centrifuging. Diaphyses were incubated at 37°C with 0.2% type 1 collagenase Sigma/ 0.05% trypsin Sigma for 30 minutes for 3 times, and then washed with PBS. Remaining diaphyses were digested in 0.53 mM EDTA/ 0.05 % trypsin Cellgro, Mediatech,Inc, Manassas, VA at 37°C for 30 min, and then were rinsed with PBS and digested with 0.2 % collagenase/ 0.05% trypsin solution at 37°C for 30 min. Finally the remaining diaphyses are rinsed with PBS and pulverized in liquid nitrogen, and bone powder was added to Trizol reagent Invitrogen, Carlsbad, CA. Total RNA was isolated as per the Trizol manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA reversely transcribed to cDNA, subjected to T7 mediated invitro-transcription amplification and labeling
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were 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 using the GeneChip® Scanner 3000 7G with autoloader.
Sample_data_processing	The data were analyzed with Genepattern using RMA analysis with quantile normalization and background correct. After preprocess, the data were statistical analyzed with bioconductor software package using ANOVA analysis.
Sample_platform_id	GPL1261
Sample_contact_name	Lynda,F,Bonewald
Sample_contact_email	bonewaldl@umkc.edu
Sample_contact_department	Department of Oral Biology
Sample_contact_institute	School of dentistry University of Missouri-Kansas City
Sample_contact_address	650 E 25th Street
Sample_contact_city	KANSAS CITY
Sample_contact_state	MO
Sample_contact_zip/postal_code	64108
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM575nnn/GSM575574/suppl/GSM575574.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM575nnn/GSM575574/suppl/GSM575574.CHP.gz
Sample_series_id	GSE23496
Sample_data_row_count	45101

GSM575575

GPL1261

osteocytes_postlactation_rep2

purifed tibiae osteocytes from virgin by enzyme digestions

tissue: tibiae bone genotype: CD1 wild type age: 16-18week

Sample_geo_accession	GSM575575
Sample_status	Public on Dec 31 2011
Sample_submission_date	Aug 06 2010
Sample_last_update_date	Dec 31 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Twelve-week-old, CD1 mice purchased from Charles River Laboratories Wilmington, MA were allowed to become pregnant, deliver and lactate. Litter size was adjusted to 8–13 pups to equalize suckling intensity between dams. Pups were removed on the 12th day of lactation to induce the weaning response. Age-matched, virgin CD1 mice were used as controls. Mice were sacrificed on the 12th day of lactation or the 7th day after forced weaning. Age-matched, virgin CD1 mice were used as controls.
Sample_growth_protocol_ch1	All mice were housed in standard conditions of temperature 23 ± 2°C and light-controlled environment 12-h light/12-h dark cycle, and had free access to water and pelleted food UAR rodent diet No.R03-25; UAR, Epinay/Orge. All animal experiments were approved by the University of Missouri at Kansas City IACUC committee in accordance with regulations and guidelines.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Tibiae from CD1 mice in Virgin, Lactation and Post lactation groups were processed immediately after sacrifice. Osteocyte RNA was extracted from tibia diaphyses with all surface cells such as osteoclasts and osteoblasts removed by sequential digestion. The digestion procedure generally followed the published procedure. Namely, soft tissue and periosteum were removed from the femurs. Epiphyses were cut off and bone marrows were removed by centrifuging. Diaphyses were incubated at 37°C with 0.2% type 1 collagenase Sigma/ 0.05% trypsin Sigma for 30 minutes for 3 times, and then washed with PBS. Remaining diaphyses were digested in 0.53 mM EDTA/ 0.05 % trypsin Cellgro, Mediatech,Inc, Manassas, VA at 37°C for 30 min, and then were rinsed with PBS and digested with 0.2 % collagenase/ 0.05% trypsin solution at 37°C for 30 min. Finally the remaining diaphyses are rinsed with PBS and pulverized in liquid nitrogen, and bone powder was added to Trizol reagent Invitrogen, Carlsbad, CA. Total RNA was isolated as per the Trizol manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA reversely transcribed to cDNA, subjected to T7 mediated invitro-transcription amplification and labeling
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were 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 using the GeneChip® Scanner 3000 7G with autoloader.
Sample_data_processing	The data were analyzed with Genepattern using RMA analysis with quantile normalization and background correct. After preprocess, the data were statistical analyzed with bioconductor software package using ANOVA analysis.
Sample_platform_id	GPL1261
Sample_contact_name	Lynda,F,Bonewald
Sample_contact_email	bonewaldl@umkc.edu
Sample_contact_department	Department of Oral Biology
Sample_contact_institute	School of dentistry University of Missouri-Kansas City
Sample_contact_address	650 E 25th Street
Sample_contact_city	KANSAS CITY
Sample_contact_state	MO
Sample_contact_zip/postal_code	64108
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM575nnn/GSM575575/suppl/GSM575575.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM575nnn/GSM575575/suppl/GSM575575.CHP.gz
Sample_series_id	GSE23496
Sample_data_row_count	45101

GSM575576

GPL1261

osteocytes_postlactation_rep3

purifed tibiae osteocytes from virgin by enzyme digestions

tissue: tibiae bone genotype: CD1 wild type age: 16-18week

Sample_geo_accession	GSM575576
Sample_status	Public on Dec 31 2011
Sample_submission_date	Aug 06 2010
Sample_last_update_date	Dec 31 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Twelve-week-old, CD1 mice purchased from Charles River Laboratories Wilmington, MA were allowed to become pregnant, deliver and lactate. Litter size was adjusted to 8–13 pups to equalize suckling intensity between dams. Pups were removed on the 12th day of lactation to induce the weaning response. Age-matched, virgin CD1 mice were used as controls. Mice were sacrificed on the 12th day of lactation or the 7th day after forced weaning. Age-matched, virgin CD1 mice were used as controls.
Sample_growth_protocol_ch1	All mice were housed in standard conditions of temperature 23 ± 2°C and light-controlled environment 12-h light/12-h dark cycle, and had free access to water and pelleted food UAR rodent diet No.R03-25; UAR, Epinay/Orge. All animal experiments were approved by the University of Missouri at Kansas City IACUC committee in accordance with regulations and guidelines.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Tibiae from CD1 mice in Virgin, Lactation and Post lactation groups were processed immediately after sacrifice. Osteocyte RNA was extracted from tibia diaphyses with all surface cells such as osteoclasts and osteoblasts removed by sequential digestion. The digestion procedure generally followed the published procedure. Namely, soft tissue and periosteum were removed from the femurs. Epiphyses were cut off and bone marrows were removed by centrifuging. Diaphyses were incubated at 37°C with 0.2% type 1 collagenase Sigma/ 0.05% trypsin Sigma for 30 minutes for 3 times, and then washed with PBS. Remaining diaphyses were digested in 0.53 mM EDTA/ 0.05 % trypsin Cellgro, Mediatech,Inc, Manassas, VA at 37°C for 30 min, and then were rinsed with PBS and digested with 0.2 % collagenase/ 0.05% trypsin solution at 37°C for 30 min. Finally the remaining diaphyses are rinsed with PBS and pulverized in liquid nitrogen, and bone powder was added to Trizol reagent Invitrogen, Carlsbad, CA. Total RNA was isolated as per the Trizol manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA reversely transcribed to cDNA, subjected to T7 mediated invitro-transcription amplification and labeling
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were 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 using the GeneChip® Scanner 3000 7G with autoloader.
Sample_data_processing	The data were analyzed with Genepattern using RMA analysis with quantile normalization and background correct. After preprocess, the data were statistical analyzed with bioconductor software package using ANOVA analysis.
Sample_platform_id	GPL1261
Sample_contact_name	Lynda,F,Bonewald
Sample_contact_email	bonewaldl@umkc.edu
Sample_contact_department	Department of Oral Biology
Sample_contact_institute	School of dentistry University of Missouri-Kansas City
Sample_contact_address	650 E 25th Street
Sample_contact_city	KANSAS CITY
Sample_contact_state	MO
Sample_contact_zip/postal_code	64108
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM575nnn/GSM575576/suppl/GSM575576.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM575nnn/GSM575576/suppl/GSM575576.CHP.gz
Sample_series_id	GSE23496
Sample_data_row_count	45101

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