Result

Search results for the GEO ID: GSE14007

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM351704

GPL1261

MOUSE_RZ_01

mouse 1 RZ

Mouse tibias

Resting Zone of mouse tibias' glowth plate.

Sample_geo_accession	GSM351704
Sample_status	Public on Dec 23 2008
Sample_submission_date	Dec 17 2008
Sample_last_update_date	Dec 22 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The mice were sacrificed by cervical dislocation under deep anesthesia and both tibias were harvested immediately, embedded in OCT compound, frozen in liquid nitrogen and stored at –80°C.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Each segment of growth plate (RZ, PZ, MZ, and HZ) was harvested separately using the Application Solutions Laser Microdissection System (Leica Microsystems, Bannockburn, IL). Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNAs were labeled according to the Affymetrix-provided protocol: Eukaryotic Small Sample Target Labeling Assay Version II. To improve quality and yield of cRNA, the protocol was modified as described below. Total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (InvitrogenTM). The oligonucleotide used for priming was 5’-ggccagtgaattgtaatacgactcactatagggaggcgg-(dT)24-3’ (Affymetrix). In vitro transcription (IVT) was performed on cDNA using the MEGAscript T7 kit (Ambion). The amplified cRNA was purified following the RNeasy Micro Protocol (Qiagen). Approximately 3ug of purified antisense RNA was obtained from each sample, and 200ng of antisense RNA from each sample was used in the following experiment. Following IVT, the antisense RNA product was reverse-transcribed, using random primers (Invitrogen) that filled in the T7 ends. After second strand synthesis with T7-Oligo (dT) promoter primer, double-stranded cDNA was purified using the Qiagen PCR purification kit. Second round IVT for cRNA amplification was then carried out using the MEGAscript T7 kit (Ambion). This time, during IVT, a fixed concentration of Biotin-16-UTP and Biotin-11-CTP was incorporated into the cRNA products. The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
Sample_hyb_protocol	10 micrograms of fragmented cRNA were hybridised (45 degrees Celsius, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.
Sample_scan_protocol	Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.
Sample_data_processing	Affymetrix Microarray Suite v5.0 with target intensity=100
Sample_platform_id	GPL1261
Sample_contact_name	Shuichi,,Tsutsumi
Sample_contact_email	shuichi@genome.rcast.u-tokyo.ac.jp
Sample_contact_phone	+81-3-5452-5352
Sample_contact_laboratory	Genome Science Div.
Sample_contact_institute	The University of Tokyo
Sample_contact_address	4-6-1
Sample_contact_city	Komaba
Sample_contact_zip/postal_code	153-8904
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351704/suppl/GSM351704.CEL.gz
Sample_series_id	GSE14007
Sample_data_row_count	45101

GSM351705

GPL1261

MOUSE_RZ_02

mouse 2 RZ

Mouse tibias

Resting Zone of mouse tibias' glowth plate.

Sample_geo_accession	GSM351705
Sample_status	Public on Dec 23 2008
Sample_submission_date	Dec 17 2008
Sample_last_update_date	Dec 22 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The mice were sacrificed by cervical dislocation under deep anesthesia and both tibias were harvested immediately, embedded in OCT compound, frozen in liquid nitrogen and stored at –80°C.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Each segment of growth plate (RZ, PZ, MZ, and HZ) was harvested separately using the Application Solutions Laser Microdissection System (Leica Microsystems, Bannockburn, IL). Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNAs were labeled according to the Affymetrix-provided protocol: Eukaryotic Small Sample Target Labeling Assay Version II. To improve quality and yield of cRNA, the protocol was modified as described below. Total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (InvitrogenTM). The oligonucleotide used for priming was 5’-ggccagtgaattgtaatacgactcactatagggaggcgg-(dT)24-3’ (Affymetrix). In vitro transcription (IVT) was performed on cDNA using the MEGAscript T7 kit (Ambion). The amplified cRNA was purified following the RNeasy Micro Protocol (Qiagen). Approximately 3ug of purified antisense RNA was obtained from each sample, and 200ng of antisense RNA from each sample was used in the following experiment. Following IVT, the antisense RNA product was reverse-transcribed, using random primers (Invitrogen) that filled in the T7 ends. After second strand synthesis with T7-Oligo (dT) promoter primer, double-stranded cDNA was purified using the Qiagen PCR purification kit. Second round IVT for cRNA amplification was then carried out using the MEGAscript T7 kit (Ambion). This time, during IVT, a fixed concentration of Biotin-16-UTP and Biotin-11-CTP was incorporated into the cRNA products. The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
Sample_hyb_protocol	10 micrograms of fragmented cRNA were hybridised (45 degrees Celsius, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.
Sample_scan_protocol	Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.
Sample_data_processing	Affymetrix Microarray Suite v5.0 with target intensity=100
Sample_platform_id	GPL1261
Sample_contact_name	Shuichi,,Tsutsumi
Sample_contact_email	shuichi@genome.rcast.u-tokyo.ac.jp
Sample_contact_phone	+81-3-5452-5352
Sample_contact_laboratory	Genome Science Div.
Sample_contact_institute	The University of Tokyo
Sample_contact_address	4-6-1
Sample_contact_city	Komaba
Sample_contact_zip/postal_code	153-8904
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351705/suppl/GSM351705.CEL.gz
Sample_series_id	GSE14007
Sample_data_row_count	45101

GSM351706

GPL1261

MOUSE_PZ_01

mouse 1 PZ

Mouse tibias

Proliferating Zone of mouse tibias' glowth plate.

Sample_geo_accession	GSM351706
Sample_status	Public on Dec 23 2008
Sample_submission_date	Dec 17 2008
Sample_last_update_date	Dec 22 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The mice were sacrificed by cervical dislocation under deep anesthesia and both tibias were harvested immediately, embedded in OCT compound, frozen in liquid nitrogen and stored at –80°C.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Each segment of growth plate (RZ, PZ, MZ, and HZ) was harvested separately using the Application Solutions Laser Microdissection System (Leica Microsystems, Bannockburn, IL). Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNAs were labeled according to the Affymetrix-provided protocol: Eukaryotic Small Sample Target Labeling Assay Version II. To improve quality and yield of cRNA, the protocol was modified as described below. Total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (InvitrogenTM). The oligonucleotide used for priming was 5’-ggccagtgaattgtaatacgactcactatagggaggcgg-(dT)24-3’ (Affymetrix). In vitro transcription (IVT) was performed on cDNA using the MEGAscript T7 kit (Ambion). The amplified cRNA was purified following the RNeasy Micro Protocol (Qiagen). Approximately 3ug of purified antisense RNA was obtained from each sample, and 200ng of antisense RNA from each sample was used in the following experiment. Following IVT, the antisense RNA product was reverse-transcribed, using random primers (Invitrogen) that filled in the T7 ends. After second strand synthesis with T7-Oligo (dT) promoter primer, double-stranded cDNA was purified using the Qiagen PCR purification kit. Second round IVT for cRNA amplification was then carried out using the MEGAscript T7 kit (Ambion). This time, during IVT, a fixed concentration of Biotin-16-UTP and Biotin-11-CTP was incorporated into the cRNA products. The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
Sample_hyb_protocol	10 micrograms of fragmented cRNA were hybridised (45 degrees Celsius, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.
Sample_scan_protocol	Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.
Sample_data_processing	Affymetrix Microarray Suite v5.0 with target intensity=100
Sample_platform_id	GPL1261
Sample_contact_name	Shuichi,,Tsutsumi
Sample_contact_email	shuichi@genome.rcast.u-tokyo.ac.jp
Sample_contact_phone	+81-3-5452-5352
Sample_contact_laboratory	Genome Science Div.
Sample_contact_institute	The University of Tokyo
Sample_contact_address	4-6-1
Sample_contact_city	Komaba
Sample_contact_zip/postal_code	153-8904
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351706/suppl/GSM351706.CEL.gz
Sample_series_id	GSE14007
Sample_data_row_count	45101

GSM351707

GPL1261

MOUSE_PZ_02

mouse 2 PZ

Mouse tibias

Proliferating Zone of mouse tibias' glowth plate.

Sample_geo_accession	GSM351707
Sample_status	Public on Dec 23 2008
Sample_submission_date	Dec 17 2008
Sample_last_update_date	Dec 22 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The mice were sacrificed by cervical dislocation under deep anesthesia and both tibias were harvested immediately, embedded in OCT compound, frozen in liquid nitrogen and stored at –80°C.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Each segment of growth plate (RZ, PZ, MZ, and HZ) was harvested separately using the Application Solutions Laser Microdissection System (Leica Microsystems, Bannockburn, IL). Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNAs were labeled according to the Affymetrix-provided protocol: Eukaryotic Small Sample Target Labeling Assay Version II. To improve quality and yield of cRNA, the protocol was modified as described below. Total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (InvitrogenTM). The oligonucleotide used for priming was 5’-ggccagtgaattgtaatacgactcactatagggaggcgg-(dT)24-3’ (Affymetrix). In vitro transcription (IVT) was performed on cDNA using the MEGAscript T7 kit (Ambion). The amplified cRNA was purified following the RNeasy Micro Protocol (Qiagen). Approximately 3ug of purified antisense RNA was obtained from each sample, and 200ng of antisense RNA from each sample was used in the following experiment. Following IVT, the antisense RNA product was reverse-transcribed, using random primers (Invitrogen) that filled in the T7 ends. After second strand synthesis with T7-Oligo (dT) promoter primer, double-stranded cDNA was purified using the Qiagen PCR purification kit. Second round IVT for cRNA amplification was then carried out using the MEGAscript T7 kit (Ambion). This time, during IVT, a fixed concentration of Biotin-16-UTP and Biotin-11-CTP was incorporated into the cRNA products. The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
Sample_hyb_protocol	10 micrograms of fragmented cRNA were hybridised (45 degrees Celsius, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.
Sample_scan_protocol	Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.
Sample_data_processing	Affymetrix Microarray Suite v5.0 with target intensity=100
Sample_platform_id	GPL1261
Sample_contact_name	Shuichi,,Tsutsumi
Sample_contact_email	shuichi@genome.rcast.u-tokyo.ac.jp
Sample_contact_phone	+81-3-5452-5352
Sample_contact_laboratory	Genome Science Div.
Sample_contact_institute	The University of Tokyo
Sample_contact_address	4-6-1
Sample_contact_city	Komaba
Sample_contact_zip/postal_code	153-8904
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351707/suppl/GSM351707.CEL.gz
Sample_series_id	GSE14007
Sample_data_row_count	45101

GSM351708

GPL1261

MOUSE_MZ_01

mouse 1 MZ

Mouse tibias

Maturing Zone of mouse tibias' glowth plate.

Sample_geo_accession	GSM351708
Sample_status	Public on Dec 23 2008
Sample_submission_date	Dec 17 2008
Sample_last_update_date	Dec 22 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The mice were sacrificed by cervical dislocation under deep anesthesia and both tibias were harvested immediately, embedded in OCT compound, frozen in liquid nitrogen and stored at –80°C.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Each segment of growth plate (RZ, PZ, MZ, and HZ) was harvested separately using the Application Solutions Laser Microdissection System (Leica Microsystems, Bannockburn, IL). Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNAs were labeled according to the Affymetrix-provided protocol: Eukaryotic Small Sample Target Labeling Assay Version II. To improve quality and yield of cRNA, the protocol was modified as described below. Total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (InvitrogenTM). The oligonucleotide used for priming was 5’-ggccagtgaattgtaatacgactcactatagggaggcgg-(dT)24-3’ (Affymetrix). In vitro transcription (IVT) was performed on cDNA using the MEGAscript T7 kit (Ambion). The amplified cRNA was purified following the RNeasy Micro Protocol (Qiagen). Approximately 3ug of purified antisense RNA was obtained from each sample, and 200ng of antisense RNA from each sample was used in the following experiment. Following IVT, the antisense RNA product was reverse-transcribed, using random primers (Invitrogen) that filled in the T7 ends. After second strand synthesis with T7-Oligo (dT) promoter primer, double-stranded cDNA was purified using the Qiagen PCR purification kit. Second round IVT for cRNA amplification was then carried out using the MEGAscript T7 kit (Ambion). This time, during IVT, a fixed concentration of Biotin-16-UTP and Biotin-11-CTP was incorporated into the cRNA products. The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
Sample_hyb_protocol	10 micrograms of fragmented cRNA were hybridised (45 degrees Celsius, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.
Sample_scan_protocol	Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.
Sample_data_processing	Affymetrix Microarray Suite v5.0 with target intensity=100
Sample_platform_id	GPL1261
Sample_contact_name	Shuichi,,Tsutsumi
Sample_contact_email	shuichi@genome.rcast.u-tokyo.ac.jp
Sample_contact_phone	+81-3-5452-5352
Sample_contact_laboratory	Genome Science Div.
Sample_contact_institute	The University of Tokyo
Sample_contact_address	4-6-1
Sample_contact_city	Komaba
Sample_contact_zip/postal_code	153-8904
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351708/suppl/GSM351708.CEL.gz
Sample_series_id	GSE14007
Sample_data_row_count	45101

GSM351709

GPL1261

MOUSE_MZ_02

mouse 2 MZ

Mouse tibias

Maturing Zone of mouse tibias' glowth plate.

Sample_geo_accession	GSM351709
Sample_status	Public on Dec 23 2008
Sample_submission_date	Dec 17 2008
Sample_last_update_date	Dec 22 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The mice were sacrificed by cervical dislocation under deep anesthesia and both tibias were harvested immediately, embedded in OCT compound, frozen in liquid nitrogen and stored at –80°C.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Each segment of growth plate (RZ, PZ, MZ, and HZ) was harvested separately using the Application Solutions Laser Microdissection System (Leica Microsystems, Bannockburn, IL). Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNAs were labeled according to the Affymetrix-provided protocol: Eukaryotic Small Sample Target Labeling Assay Version II. To improve quality and yield of cRNA, the protocol was modified as described below. Total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (InvitrogenTM). The oligonucleotide used for priming was 5’-ggccagtgaattgtaatacgactcactatagggaggcgg-(dT)24-3’ (Affymetrix). In vitro transcription (IVT) was performed on cDNA using the MEGAscript T7 kit (Ambion). The amplified cRNA was purified following the RNeasy Micro Protocol (Qiagen). Approximately 3ug of purified antisense RNA was obtained from each sample, and 200ng of antisense RNA from each sample was used in the following experiment. Following IVT, the antisense RNA product was reverse-transcribed, using random primers (Invitrogen) that filled in the T7 ends. After second strand synthesis with T7-Oligo (dT) promoter primer, double-stranded cDNA was purified using the Qiagen PCR purification kit. Second round IVT for cRNA amplification was then carried out using the MEGAscript T7 kit (Ambion). This time, during IVT, a fixed concentration of Biotin-16-UTP and Biotin-11-CTP was incorporated into the cRNA products. The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
Sample_hyb_protocol	10 micrograms of fragmented cRNA were hybridised (45 degrees Celsius, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.
Sample_scan_protocol	Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.
Sample_data_processing	Affymetrix Microarray Suite v5.0 with target intensity=100
Sample_platform_id	GPL1261
Sample_contact_name	Shuichi,,Tsutsumi
Sample_contact_email	shuichi@genome.rcast.u-tokyo.ac.jp
Sample_contact_phone	+81-3-5452-5352
Sample_contact_laboratory	Genome Science Div.
Sample_contact_institute	The University of Tokyo
Sample_contact_address	4-6-1
Sample_contact_city	Komaba
Sample_contact_zip/postal_code	153-8904
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351709/suppl/GSM351709.CEL.gz
Sample_series_id	GSE14007
Sample_data_row_count	45101

GSM351710

GPL1261

MOUSE_HZ_01

mouse 1 HZ

Mouse tibias

Hypertrophic Zone of mouse tibias' glowth plate.

Sample_geo_accession	GSM351710
Sample_status	Public on Dec 23 2008
Sample_submission_date	Dec 17 2008
Sample_last_update_date	Dec 22 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The mice were sacrificed by cervical dislocation under deep anesthesia and both tibias were harvested immediately, embedded in OCT compound, frozen in liquid nitrogen and stored at –80°C.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Each segment of growth plate (RZ, PZ, MZ, and HZ) was harvested separately using the Application Solutions Laser Microdissection System (Leica Microsystems, Bannockburn, IL). Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNAs were labeled according to the Affymetrix-provided protocol: Eukaryotic Small Sample Target Labeling Assay Version II. To improve quality and yield of cRNA, the protocol was modified as described below. Total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (InvitrogenTM). The oligonucleotide used for priming was 5’-ggccagtgaattgtaatacgactcactatagggaggcgg-(dT)24-3’ (Affymetrix). In vitro transcription (IVT) was performed on cDNA using the MEGAscript T7 kit (Ambion). The amplified cRNA was purified following the RNeasy Micro Protocol (Qiagen). Approximately 3ug of purified antisense RNA was obtained from each sample, and 200ng of antisense RNA from each sample was used in the following experiment. Following IVT, the antisense RNA product was reverse-transcribed, using random primers (Invitrogen) that filled in the T7 ends. After second strand synthesis with T7-Oligo (dT) promoter primer, double-stranded cDNA was purified using the Qiagen PCR purification kit. Second round IVT for cRNA amplification was then carried out using the MEGAscript T7 kit (Ambion). This time, during IVT, a fixed concentration of Biotin-16-UTP and Biotin-11-CTP was incorporated into the cRNA products. The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
Sample_hyb_protocol	10 micrograms of fragmented cRNA were hybridised (45 degrees Celsius, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.
Sample_scan_protocol	Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.
Sample_data_processing	Affymetrix Microarray Suite v5.0 with target intensity=100
Sample_platform_id	GPL1261
Sample_contact_name	Shuichi,,Tsutsumi
Sample_contact_email	shuichi@genome.rcast.u-tokyo.ac.jp
Sample_contact_phone	+81-3-5452-5352
Sample_contact_laboratory	Genome Science Div.
Sample_contact_institute	The University of Tokyo
Sample_contact_address	4-6-1
Sample_contact_city	Komaba
Sample_contact_zip/postal_code	153-8904
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351710/suppl/GSM351710.CEL.gz
Sample_series_id	GSE14007
Sample_data_row_count	45101

GSM351711

GPL1261

MOUSE_HZ_02

mouse 2 HZ

Mouse tibias

Hypertrophic Zone of mouse tibias' glowth plate.

Sample_geo_accession	GSM351711
Sample_status	Public on Dec 23 2008
Sample_submission_date	Dec 17 2008
Sample_last_update_date	Dec 22 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The mice were sacrificed by cervical dislocation under deep anesthesia and both tibias were harvested immediately, embedded in OCT compound, frozen in liquid nitrogen and stored at –80°C.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Each segment of growth plate (RZ, PZ, MZ, and HZ) was harvested separately using the Application Solutions Laser Microdissection System (Leica Microsystems, Bannockburn, IL). Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNAs were labeled according to the Affymetrix-provided protocol: Eukaryotic Small Sample Target Labeling Assay Version II. To improve quality and yield of cRNA, the protocol was modified as described below. Total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (InvitrogenTM). The oligonucleotide used for priming was 5’-ggccagtgaattgtaatacgactcactatagggaggcgg-(dT)24-3’ (Affymetrix). In vitro transcription (IVT) was performed on cDNA using the MEGAscript T7 kit (Ambion). The amplified cRNA was purified following the RNeasy Micro Protocol (Qiagen). Approximately 3ug of purified antisense RNA was obtained from each sample, and 200ng of antisense RNA from each sample was used in the following experiment. Following IVT, the antisense RNA product was reverse-transcribed, using random primers (Invitrogen) that filled in the T7 ends. After second strand synthesis with T7-Oligo (dT) promoter primer, double-stranded cDNA was purified using the Qiagen PCR purification kit. Second round IVT for cRNA amplification was then carried out using the MEGAscript T7 kit (Ambion). This time, during IVT, a fixed concentration of Biotin-16-UTP and Biotin-11-CTP was incorporated into the cRNA products. The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
Sample_hyb_protocol	10 micrograms of fragmented cRNA were hybridised (45 degrees Celsius, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.
Sample_scan_protocol	Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.
Sample_data_processing	Affymetrix Microarray Suite v5.0 with target intensity=100
Sample_platform_id	GPL1261
Sample_contact_name	Shuichi,,Tsutsumi
Sample_contact_email	shuichi@genome.rcast.u-tokyo.ac.jp
Sample_contact_phone	+81-3-5452-5352
Sample_contact_laboratory	Genome Science Div.
Sample_contact_institute	The University of Tokyo
Sample_contact_address	4-6-1
Sample_contact_city	Komaba
Sample_contact_zip/postal_code	153-8904
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351711/suppl/GSM351711.CEL.gz
Sample_series_id	GSE14007
Sample_data_row_count	45101

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