Result

Search results for the GEO ID: GSE21710

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM541677

GPL1261

INS1_con_rep1

control

time: 0 h agent: control cell type: osteoblast genotype: IGF-1 null

n/a

Sample_geo_accession	GSM541677
Sample_status	Public on May 07 2010
Sample_submission_date	May 06 2010
Sample_last_update_date	May 07 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The cells were serum starved and then treated with 10nM insulin for 6, 12, or 24hr.
Sample_growth_protocol_ch1	IGF-1 receptor lacking osteoblasts were cultured to confluency.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions. Purity and integrity of the isolated RNA was confirmed by BioAnalyzer (Agilent)
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The labeling of the RNA was done as per the manufacturers instructions (Affymetrix, Santa Clara, CA). Briefly, One microgram of total RNA was reverse transcribed using an oligo dT-T7 primer under standard conditions. The resulting first strand cDNA was incubated with RNAse H, E. coli DNA ligase, and E. coli DNA polymerase, dNTPs and buffer to produce second-stranded cDNA. The cDNA was purified using spin columns following the manufacturer’s instructions (Qiagen). The purified cDNA was then used in an in vitro transcription assay to produce the target biotin labeled cRNA for hybridization using the 3’ IVT kit from Affymetrix following the manufacturer’s instructions. The cRNA was purified using a spin column following the kit’s instructions (Qiagen), and fragmented prior to hybridization onto the GeneChips.
Sample_hyb_protocol	Hybridization of the GeneChips was carried out in the following the manufacturer’s protocol. Briefly, the fragmented biotin labeled cRNA was mixed with 0.05nM control oligonucleotide B2, 20X Eukaryotic hybridization controls (bioB, bioC, bioD, cre), 0.1 mg/mL herring sperm DNA, 0.5 mg/mL BSA, 2X hybridization buffer (1X 100mM MES/1M NaCl/20mM EDTA/0.01% Tween-20) and 10% DMSO. The hybridization cocktail was incubated at 99oC for 5 minutes to denature the herring sperm DNA and any secondary structure on the cRNA. The cocktail was then equilibrated to 45oC for 5 minutes prior to addition to the GeneChip. Hybridiztion was carried out in the Affymetrix Hybridization Oven 640 at 45oC with rotation at 60rpm for 16 hours. Following the hybridization step the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 following Fluidics Protocol Mini_euk2v3 as recommended by the manufacturer for this Chip type. The GeneChips were first washed in a non-stringent wash buffer of 6X SSPE/0.01% Tween-20 followed by stringent wash with 100mM MES/0.1M NaCl/0.01% Tween-20. The first staining of the GeneChips was done in 2X stain buffer (1X 100mM MES/1M NaCl/0.05% Tween-20), 2mg/mL BSA, and 0.01 mg/mL Streptavidin Phycoerythrin (SAPE). The GeneChips were washed in non-stringent wash buffer. A second stain comprised of 2X staining buffer, 2mg/mL BSA, 0.1mg/mL Goat IgG, and 0.003mg/mL of biotinylated antibody was conducted immediately followed by a third stain comprised of the SAPE solution (see above). Finally, the GeneChips were washed in non-stringent wash buffer prior to scanning.
Sample_scan_protocol	Scanning of the GeneChips was done using the Affymetrix 3000 7G scanner as described by the manufacturer. The Fluidics station and Scanner were controlled using Affymetrix GeneChip Command Console (AGCC).
Sample_data_processing	RMA via ArrayAssist Enterprise (Agilent, CA)
Sample_platform_id	GPL1261
Sample_contact_name	Dongquan,,Chen
Sample_contact_email	dongquan@uab.edu
Sample_contact_phone	2059757131
Sample_contact_laboratory	Preventive Medicine
Sample_contact_department	Medicine
Sample_contact_institute	Univ of Alabama at Birmingham
Sample_contact_address	1717 11th Ave South
Sample_contact_city	Birmingham
Sample_contact_state	AL
Sample_contact_zip/postal_code	35294
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM541nnn/GSM541677/suppl/GSM541677_INS-1_430_2.0.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM541nnn/GSM541677/suppl/GSM541677_INS-1_430_2.0.CHP.gz
Sample_series_id	GSE21710
Sample_data_row_count	45101

GSM541678

GPL1261

INS2_6h_rep1

6hr, treated

time: 6 h agent: insulin cell type: osteoblast genotype: IGF-1 null

n/a

Sample_geo_accession	GSM541678
Sample_status	Public on May 07 2010
Sample_submission_date	May 06 2010
Sample_last_update_date	May 07 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The cells were serum starved and then treated with 10nM insulin for 6, 12, or 24hr.
Sample_growth_protocol_ch1	IGF-1 receptor lacking osteoblasts were cultured to confluency.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions. Purity and integrity of the isolated RNA was confirmed by BioAnalyzer (Agilent)
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The labeling of the RNA was done as per the manufacturers instructions (Affymetrix, Santa Clara, CA). Briefly, One microgram of total RNA was reverse transcribed using an oligo dT-T7 primer under standard conditions. The resulting first strand cDNA was incubated with RNAse H, E. coli DNA ligase, and E. coli DNA polymerase, dNTPs and buffer to produce second-stranded cDNA. The cDNA was purified using spin columns following the manufacturer’s instructions (Qiagen). The purified cDNA was then used in an in vitro transcription assay to produce the target biotin labeled cRNA for hybridization using the 3’ IVT kit from Affymetrix following the manufacturer’s instructions. The cRNA was purified using a spin column following the kit’s instructions (Qiagen), and fragmented prior to hybridization onto the GeneChips.
Sample_hyb_protocol	Hybridization of the GeneChips was carried out in the following the manufacturer’s protocol. Briefly, the fragmented biotin labeled cRNA was mixed with 0.05nM control oligonucleotide B2, 20X Eukaryotic hybridization controls (bioB, bioC, bioD, cre), 0.1 mg/mL herring sperm DNA, 0.5 mg/mL BSA, 2X hybridization buffer (1X 100mM MES/1M NaCl/20mM EDTA/0.01% Tween-20) and 10% DMSO. The hybridization cocktail was incubated at 99oC for 5 minutes to denature the herring sperm DNA and any secondary structure on the cRNA. The cocktail was then equilibrated to 45oC for 5 minutes prior to addition to the GeneChip. Hybridiztion was carried out in the Affymetrix Hybridization Oven 640 at 45oC with rotation at 60rpm for 16 hours. Following the hybridization step the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 following Fluidics Protocol Mini_euk2v3 as recommended by the manufacturer for this Chip type. The GeneChips were first washed in a non-stringent wash buffer of 6X SSPE/0.01% Tween-20 followed by stringent wash with 100mM MES/0.1M NaCl/0.01% Tween-20. The first staining of the GeneChips was done in 2X stain buffer (1X 100mM MES/1M NaCl/0.05% Tween-20), 2mg/mL BSA, and 0.01 mg/mL Streptavidin Phycoerythrin (SAPE). The GeneChips were washed in non-stringent wash buffer. A second stain comprised of 2X staining buffer, 2mg/mL BSA, 0.1mg/mL Goat IgG, and 0.003mg/mL of biotinylated antibody was conducted immediately followed by a third stain comprised of the SAPE solution (see above). Finally, the GeneChips were washed in non-stringent wash buffer prior to scanning.
Sample_scan_protocol	Scanning of the GeneChips was done using the Affymetrix 3000 7G scanner as described by the manufacturer. The Fluidics station and Scanner were controlled using Affymetrix GeneChip Command Console (AGCC).
Sample_data_processing	RMA via ArrayAssist Enterprise (Agilent, CA)
Sample_platform_id	GPL1261
Sample_contact_name	Dongquan,,Chen
Sample_contact_email	dongquan@uab.edu
Sample_contact_phone	2059757131
Sample_contact_laboratory	Preventive Medicine
Sample_contact_department	Medicine
Sample_contact_institute	Univ of Alabama at Birmingham
Sample_contact_address	1717 11th Ave South
Sample_contact_city	Birmingham
Sample_contact_state	AL
Sample_contact_zip/postal_code	35294
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM541nnn/GSM541678/suppl/GSM541678_INS-2_430_2.0.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM541nnn/GSM541678/suppl/GSM541678_INS-2_430_2.0.CHP.gz
Sample_series_id	GSE21710
Sample_data_row_count	45101

GSM541679

GPL1261

INS3_12h_rep1

12hr, treated

time: 12 h agent: insulin cell type: osteoblast genotype: IGF-1 null

n/a

Sample_geo_accession	GSM541679
Sample_status	Public on May 07 2010
Sample_submission_date	May 06 2010
Sample_last_update_date	May 07 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The cells were serum starved and then treated with 10nM insulin for 6, 12, or 24hr.
Sample_growth_protocol_ch1	IGF-1 receptor lacking osteoblasts were cultured to confluency.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions. Purity and integrity of the isolated RNA was confirmed by BioAnalyzer (Agilent)
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The labeling of the RNA was done as per the manufacturers instructions (Affymetrix, Santa Clara, CA). Briefly, One microgram of total RNA was reverse transcribed using an oligo dT-T7 primer under standard conditions. The resulting first strand cDNA was incubated with RNAse H, E. coli DNA ligase, and E. coli DNA polymerase, dNTPs and buffer to produce second-stranded cDNA. The cDNA was purified using spin columns following the manufacturer’s instructions (Qiagen). The purified cDNA was then used in an in vitro transcription assay to produce the target biotin labeled cRNA for hybridization using the 3’ IVT kit from Affymetrix following the manufacturer’s instructions. The cRNA was purified using a spin column following the kit’s instructions (Qiagen), and fragmented prior to hybridization onto the GeneChips.
Sample_hyb_protocol	Hybridization of the GeneChips was carried out in the following the manufacturer’s protocol. Briefly, the fragmented biotin labeled cRNA was mixed with 0.05nM control oligonucleotide B2, 20X Eukaryotic hybridization controls (bioB, bioC, bioD, cre), 0.1 mg/mL herring sperm DNA, 0.5 mg/mL BSA, 2X hybridization buffer (1X 100mM MES/1M NaCl/20mM EDTA/0.01% Tween-20) and 10% DMSO. The hybridization cocktail was incubated at 99oC for 5 minutes to denature the herring sperm DNA and any secondary structure on the cRNA. The cocktail was then equilibrated to 45oC for 5 minutes prior to addition to the GeneChip. Hybridiztion was carried out in the Affymetrix Hybridization Oven 640 at 45oC with rotation at 60rpm for 16 hours. Following the hybridization step the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 following Fluidics Protocol Mini_euk2v3 as recommended by the manufacturer for this Chip type. The GeneChips were first washed in a non-stringent wash buffer of 6X SSPE/0.01% Tween-20 followed by stringent wash with 100mM MES/0.1M NaCl/0.01% Tween-20. The first staining of the GeneChips was done in 2X stain buffer (1X 100mM MES/1M NaCl/0.05% Tween-20), 2mg/mL BSA, and 0.01 mg/mL Streptavidin Phycoerythrin (SAPE). The GeneChips were washed in non-stringent wash buffer. A second stain comprised of 2X staining buffer, 2mg/mL BSA, 0.1mg/mL Goat IgG, and 0.003mg/mL of biotinylated antibody was conducted immediately followed by a third stain comprised of the SAPE solution (see above). Finally, the GeneChips were washed in non-stringent wash buffer prior to scanning.
Sample_scan_protocol	Scanning of the GeneChips was done using the Affymetrix 3000 7G scanner as described by the manufacturer. The Fluidics station and Scanner were controlled using Affymetrix GeneChip Command Console (AGCC).
Sample_data_processing	RMA via ArrayAssist Enterprise (Agilent, CA)
Sample_platform_id	GPL1261
Sample_contact_name	Dongquan,,Chen
Sample_contact_email	dongquan@uab.edu
Sample_contact_phone	2059757131
Sample_contact_laboratory	Preventive Medicine
Sample_contact_department	Medicine
Sample_contact_institute	Univ of Alabama at Birmingham
Sample_contact_address	1717 11th Ave South
Sample_contact_city	Birmingham
Sample_contact_state	AL
Sample_contact_zip/postal_code	35294
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM541nnn/GSM541679/suppl/GSM541679_INS-3_430_2.0.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM541nnn/GSM541679/suppl/GSM541679_INS-3_430_2.0.CHP.gz
Sample_series_id	GSE21710
Sample_data_row_count	45101

GSM541680

GPL1261

INS4_24h_rep1

24h, treated

time: 24 h agent: insulin cell type: osteoblast genotype: IGF-1 null

n/a

Sample_geo_accession	GSM541680
Sample_status	Public on May 07 2010
Sample_submission_date	May 06 2010
Sample_last_update_date	May 07 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The cells were serum starved and then treated with 10nM insulin for 6, 12, or 24hr.
Sample_growth_protocol_ch1	IGF-1 receptor lacking osteoblasts were cultured to confluency.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions. Purity and integrity of the isolated RNA was confirmed by BioAnalyzer (Agilent)
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The labeling of the RNA was done as per the manufacturers instructions (Affymetrix, Santa Clara, CA). Briefly, One microgram of total RNA was reverse transcribed using an oligo dT-T7 primer under standard conditions. The resulting first strand cDNA was incubated with RNAse H, E. coli DNA ligase, and E. coli DNA polymerase, dNTPs and buffer to produce second-stranded cDNA. The cDNA was purified using spin columns following the manufacturer’s instructions (Qiagen). The purified cDNA was then used in an in vitro transcription assay to produce the target biotin labeled cRNA for hybridization using the 3’ IVT kit from Affymetrix following the manufacturer’s instructions. The cRNA was purified using a spin column following the kit’s instructions (Qiagen), and fragmented prior to hybridization onto the GeneChips.
Sample_hyb_protocol	Hybridization of the GeneChips was carried out in the following the manufacturer’s protocol. Briefly, the fragmented biotin labeled cRNA was mixed with 0.05nM control oligonucleotide B2, 20X Eukaryotic hybridization controls (bioB, bioC, bioD, cre), 0.1 mg/mL herring sperm DNA, 0.5 mg/mL BSA, 2X hybridization buffer (1X 100mM MES/1M NaCl/20mM EDTA/0.01% Tween-20) and 10% DMSO. The hybridization cocktail was incubated at 99oC for 5 minutes to denature the herring sperm DNA and any secondary structure on the cRNA. The cocktail was then equilibrated to 45oC for 5 minutes prior to addition to the GeneChip. Hybridiztion was carried out in the Affymetrix Hybridization Oven 640 at 45oC with rotation at 60rpm for 16 hours. Following the hybridization step the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 following Fluidics Protocol Mini_euk2v3 as recommended by the manufacturer for this Chip type. The GeneChips were first washed in a non-stringent wash buffer of 6X SSPE/0.01% Tween-20 followed by stringent wash with 100mM MES/0.1M NaCl/0.01% Tween-20. The first staining of the GeneChips was done in 2X stain buffer (1X 100mM MES/1M NaCl/0.05% Tween-20), 2mg/mL BSA, and 0.01 mg/mL Streptavidin Phycoerythrin (SAPE). The GeneChips were washed in non-stringent wash buffer. A second stain comprised of 2X staining buffer, 2mg/mL BSA, 0.1mg/mL Goat IgG, and 0.003mg/mL of biotinylated antibody was conducted immediately followed by a third stain comprised of the SAPE solution (see above). Finally, the GeneChips were washed in non-stringent wash buffer prior to scanning.
Sample_scan_protocol	Scanning of the GeneChips was done using the Affymetrix 3000 7G scanner as described by the manufacturer. The Fluidics station and Scanner were controlled using Affymetrix GeneChip Command Console (AGCC).
Sample_data_processing	RMA via ArrayAssist Enterprise (Agilent, CA)
Sample_platform_id	GPL1261
Sample_contact_name	Dongquan,,Chen
Sample_contact_email	dongquan@uab.edu
Sample_contact_phone	2059757131
Sample_contact_laboratory	Preventive Medicine
Sample_contact_department	Medicine
Sample_contact_institute	Univ of Alabama at Birmingham
Sample_contact_address	1717 11th Ave South
Sample_contact_city	Birmingham
Sample_contact_state	AL
Sample_contact_zip/postal_code	35294
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM541nnn/GSM541680/suppl/GSM541680_INS-4_430_2.0.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM541nnn/GSM541680/suppl/GSM541680_INS-4_430_2.0.CHP.gz
Sample_series_id	GSE21710
Sample_data_row_count	45101

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