Result

Search results for the GEO ID: GSE18648

(Click on the check boxes provided under "Select for analysis", to initiate grouping)

(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down)

GSM ID

GPL ID

Select for analysis

Title

Source name

Description

Characteristics

GSM463362

GPL1261

Untreated-1

Sclerotome in micromass culture, untreated.

agent: none

Untreated-1

Sample_geo_accession	GSM463362
Sample_status	Public on Apr 09 2010
Sample_submission_date	Oct 20 2009
Sample_last_update_date	Apr 09 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After overnight culture, cells were treated with or without 5ng/ml of TGFß1 or 50ng/ml BMP4 (R&D Systems) for 8 hours.
Sample_growth_protocol_ch1	Sclerotome cultures were set up using a method similar to that used for limb micromass cultures. Briefly, after removal of the notochord, sclerotome ventral to the neural tube was isolated from E11.5 day mouse embryos. Mesenchymal cells were dissociated into a single cell suspension with incubation in 1mg/ml collagenase D at 37 °C for 30 minutes and reconstituted at a density of 1 X 107 cells / ml. Twenty microliters of cell suspension was dropped into each well of a 24 well plate. After a pre-incubation time of 1 h at 37°C to allow cells to attach, the cultures were then flooded with F-12:DMEM (3:2) containing 10 % FBS, 50 µg/ml ascorbic acid, 10 mM ß-glycerolphosphate, 2 mM glutamine, antibiotics with or without 5ng/ml of TGFß1 or 50ng/ml BMP4 (R&D Systems). Cultures were incubated at 37 °C in CO2 incubator.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from the cells in culture using the standard Trizol method. RNA was Dnase treated and then tested using RT-PCR to assure there was no DNA contamination in the samples.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). Briefly, 50ng of total RNA from each sample was used in a two cycle cDNA amplification protocol using T7-linked oligo dT primers as per the manufacturer’s instructions. After the first round of cDNA synthesis an in vitro transcription step was utilized to amplify the RNA following which a second round of cDNA synthesis was performed. Subsequently, cRNA was generated and biotin was incorporated into the cRNA strand by standard methods (Affymetrix) followed by cRNA fragmentation, and preparation of hybridization cocktail.
Sample_hyb_protocol	The arrays were hybridized overnight at 45oC, and then washed, stained, and scanned the next day. Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).
Sample_scan_protocol	Gene expression levels were extracted using AGCC (Affymetrix GeneChip Command Console). Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).
Sample_data_processing	The data was analyzed with Genesprings using the default settings. The summarized probeset was generated using RMA summarization algorithm. Quantile normalization was used. Baseline transformation to median was used.
Sample_platform_id	GPL1261
Sample_contact_name	Rosa,,Serra
Sample_contact_email	rserra@uab.edu
Sample_contact_phone	205-934-0842
Sample_contact_laboratory	Serra
Sample_contact_department	Cell Biology
Sample_contact_institute	University of Alabama at Birmingham
Sample_contact_address	1918 University Blvd. 660 MCLM
Sample_contact_city	Birmingham
Sample_contact_state	AL
Sample_contact_zip/postal_code	35294-0005
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463362/suppl/GSM463362.CEL.gz
Sample_series_id	GSE18648
Sample_series_id	GSE18649
Sample_data_row_count	45101

GSM463363

GPL1261

Untreated-2

Sclerotome in micromass culture, untreated.

agent: none

Untreated-2

Sample_geo_accession	GSM463363
Sample_status	Public on Apr 09 2010
Sample_submission_date	Oct 20 2009
Sample_last_update_date	Apr 09 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After overnight culture, cells were treated with or without 5ng/ml of TGFß1 or 50ng/ml BMP4 (R&D Systems) for 8 hours.
Sample_growth_protocol_ch1	Sclerotome cultures were set up using a method similar to that used for limb micromass cultures. Briefly, after removal of the notochord, sclerotome ventral to the neural tube was isolated from E11.5 day mouse embryos. Mesenchymal cells were dissociated into a single cell suspension with incubation in 1mg/ml collagenase D at 37 °C for 30 minutes and reconstituted at a density of 1 X 107 cells / ml. Twenty microliters of cell suspension was dropped into each well of a 24 well plate. After a pre-incubation time of 1 h at 37°C to allow cells to attach, the cultures were then flooded with F-12:DMEM (3:2) containing 10 % FBS, 50 µg/ml ascorbic acid, 10 mM ß-glycerolphosphate, 2 mM glutamine, antibiotics with or without 5ng/ml of TGFß1 or 50ng/ml BMP4 (R&D Systems). Cultures were incubated at 37 °C in CO2 incubator.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from the cells in culture using the standard Trizol method. RNA was Dnase treated and then tested using RT-PCR to assure there was no DNA contamination in the samples.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). Briefly, 50ng of total RNA from each sample was used in a two cycle cDNA amplification protocol using T7-linked oligo dT primers as per the manufacturer’s instructions. After the first round of cDNA synthesis an in vitro transcription step was utilized to amplify the RNA following which a second round of cDNA synthesis was performed. Subsequently, cRNA was generated and biotin was incorporated into the cRNA strand by standard methods (Affymetrix) followed by cRNA fragmentation, and preparation of hybridization cocktail.
Sample_hyb_protocol	The arrays were hybridized overnight at 45oC, and then washed, stained, and scanned the next day. Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).
Sample_scan_protocol	Gene expression levels were extracted using AGCC (Affymetrix GeneChip Command Console). Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).
Sample_data_processing	The data was analyzed with Genesprings using the default settings. The summarized probeset was generated using RMA summarization algorithm. Quantile normalization was used. Baseline transformation to median was used.
Sample_platform_id	GPL1261
Sample_contact_name	Rosa,,Serra
Sample_contact_email	rserra@uab.edu
Sample_contact_phone	205-934-0842
Sample_contact_laboratory	Serra
Sample_contact_department	Cell Biology
Sample_contact_institute	University of Alabama at Birmingham
Sample_contact_address	1918 University Blvd. 660 MCLM
Sample_contact_city	Birmingham
Sample_contact_state	AL
Sample_contact_zip/postal_code	35294-0005
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463363/suppl/GSM463363.CEL.gz
Sample_series_id	GSE18648
Sample_series_id	GSE18649
Sample_data_row_count	45101

GSM463364

GPL1261

Untreated-3

Sclerotome in micromass culture, untreated.

agent: none

Untreated-3

Sample_geo_accession	GSM463364
Sample_status	Public on Apr 09 2010
Sample_submission_date	Oct 20 2009
Sample_last_update_date	Apr 09 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After overnight culture, cells were treated with or without 5ng/ml of TGFß1 or 50ng/ml BMP4 (R&D Systems) for 8 hours.
Sample_growth_protocol_ch1	Sclerotome cultures were set up using a method similar to that used for limb micromass cultures. Briefly, after removal of the notochord, sclerotome ventral to the neural tube was isolated from E11.5 day mouse embryos. Mesenchymal cells were dissociated into a single cell suspension with incubation in 1mg/ml collagenase D at 37 °C for 30 minutes and reconstituted at a density of 1 X 107 cells / ml. Twenty microliters of cell suspension was dropped into each well of a 24 well plate. After a pre-incubation time of 1 h at 37°C to allow cells to attach, the cultures were then flooded with F-12:DMEM (3:2) containing 10 % FBS, 50 µg/ml ascorbic acid, 10 mM ß-glycerolphosphate, 2 mM glutamine, antibiotics with or without 5ng/ml of TGFß1 or 50ng/ml BMP4 (R&D Systems). Cultures were incubated at 37 °C in CO2 incubator.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from the cells in culture using the standard Trizol method. RNA was Dnase treated and then tested using RT-PCR to assure there was no DNA contamination in the samples.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). Briefly, 50ng of total RNA from each sample was used in a two cycle cDNA amplification protocol using T7-linked oligo dT primers as per the manufacturer’s instructions. After the first round of cDNA synthesis an in vitro transcription step was utilized to amplify the RNA following which a second round of cDNA synthesis was performed. Subsequently, cRNA was generated and biotin was incorporated into the cRNA strand by standard methods (Affymetrix) followed by cRNA fragmentation, and preparation of hybridization cocktail.
Sample_hyb_protocol	The arrays were hybridized overnight at 45oC, and then washed, stained, and scanned the next day. Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).
Sample_scan_protocol	Gene expression levels were extracted using AGCC (Affymetrix GeneChip Command Console). Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).
Sample_data_processing	The data was analyzed with Genesprings using the default settings. The summarized probeset was generated using RMA summarization algorithm. Quantile normalization was used. Baseline transformation to median was used.
Sample_platform_id	GPL1261
Sample_contact_name	Rosa,,Serra
Sample_contact_email	rserra@uab.edu
Sample_contact_phone	205-934-0842
Sample_contact_laboratory	Serra
Sample_contact_department	Cell Biology
Sample_contact_institute	University of Alabama at Birmingham
Sample_contact_address	1918 University Blvd. 660 MCLM
Sample_contact_city	Birmingham
Sample_contact_state	AL
Sample_contact_zip/postal_code	35294-0005
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463364/suppl/GSM463364.CEL.gz
Sample_series_id	GSE18648
Sample_series_id	GSE18649
Sample_data_row_count	45101

GSM463365

GPL1261

BMP-1

Sclerotome in micromass culture, BMP treated.

agent: BMP

BMP-1

Sample_geo_accession	GSM463365
Sample_status	Public on Apr 09 2010
Sample_submission_date	Oct 20 2009
Sample_last_update_date	Apr 09 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After overnight culture, cells were treated with or without 5ng/ml of TGFß1 or 50ng/ml BMP4 (R&D Systems) for 8 hours.
Sample_growth_protocol_ch1	Sclerotome cultures were set up using a method similar to that used for limb micromass cultures. Briefly, after removal of the notochord, sclerotome ventral to the neural tube was isolated from E11.5 day mouse embryos. Mesenchymal cells were dissociated into a single cell suspension with incubation in 1mg/ml collagenase D at 37 °C for 30 minutes and reconstituted at a density of 1 X 107 cells / ml. Twenty microliters of cell suspension was dropped into each well of a 24 well plate. After a pre-incubation time of 1 h at 37°C to allow cells to attach, the cultures were then flooded with F-12:DMEM (3:2) containing 10 % FBS, 50 µg/ml ascorbic acid, 10 mM ß-glycerolphosphate, 2 mM glutamine, antibiotics with or without 5ng/ml of TGFß1 or 50ng/ml BMP4 (R&D Systems). Cultures were incubated at 37 °C in CO2 incubator.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from the cells in culture using the standard Trizol method. RNA was Dnase treated and then tested using RT-PCR to assure there was no DNA contamination in the samples.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). Briefly, 50ng of total RNA from each sample was used in a two cycle cDNA amplification protocol using T7-linked oligo dT primers as per the manufacturer’s instructions. After the first round of cDNA synthesis an in vitro transcription step was utilized to amplify the RNA following which a second round of cDNA synthesis was performed. Subsequently, cRNA was generated and biotin was incorporated into the cRNA strand by standard methods (Affymetrix) followed by cRNA fragmentation, and preparation of hybridization cocktail.
Sample_hyb_protocol	The arrays were hybridized overnight at 45oC, and then washed, stained, and scanned the next day. Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).
Sample_scan_protocol	Gene expression levels were extracted using AGCC (Affymetrix GeneChip Command Console). Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).
Sample_data_processing	The data was analyzed with Genesprings using the default settings. The summarized probeset was generated using RMA summarization algorithm. Quantile normalization was used. Baseline transformation to median was used.
Sample_platform_id	GPL1261
Sample_contact_name	Rosa,,Serra
Sample_contact_email	rserra@uab.edu
Sample_contact_phone	205-934-0842
Sample_contact_laboratory	Serra
Sample_contact_department	Cell Biology
Sample_contact_institute	University of Alabama at Birmingham
Sample_contact_address	1918 University Blvd. 660 MCLM
Sample_contact_city	Birmingham
Sample_contact_state	AL
Sample_contact_zip/postal_code	35294-0005
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463365/suppl/GSM463365.CEL.gz
Sample_series_id	GSE18648
Sample_series_id	GSE18649
Sample_data_row_count	45101

GSM463366

GPL1261

BMP-2

Sclerotome in micromass culture, BMP treated.

agent: BMP

BMP-2

Sample_geo_accession	GSM463366
Sample_status	Public on Apr 09 2010
Sample_submission_date	Oct 20 2009
Sample_last_update_date	Apr 09 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After overnight culture, cells were treated with or without 5ng/ml of TGFß1 or 50ng/ml BMP4 (R&D Systems) for 8 hours.
Sample_growth_protocol_ch1	Sclerotome cultures were set up using a method similar to that used for limb micromass cultures. Briefly, after removal of the notochord, sclerotome ventral to the neural tube was isolated from E11.5 day mouse embryos. Mesenchymal cells were dissociated into a single cell suspension with incubation in 1mg/ml collagenase D at 37 °C for 30 minutes and reconstituted at a density of 1 X 107 cells / ml. Twenty microliters of cell suspension was dropped into each well of a 24 well plate. After a pre-incubation time of 1 h at 37°C to allow cells to attach, the cultures were then flooded with F-12:DMEM (3:2) containing 10 % FBS, 50 µg/ml ascorbic acid, 10 mM ß-glycerolphosphate, 2 mM glutamine, antibiotics with or without 5ng/ml of TGFß1 or 50ng/ml BMP4 (R&D Systems). Cultures were incubated at 37 °C in CO2 incubator.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from the cells in culture using the standard Trizol method. RNA was Dnase treated and then tested using RT-PCR to assure there was no DNA contamination in the samples.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). Briefly, 50ng of total RNA from each sample was used in a two cycle cDNA amplification protocol using T7-linked oligo dT primers as per the manufacturer’s instructions. After the first round of cDNA synthesis an in vitro transcription step was utilized to amplify the RNA following which a second round of cDNA synthesis was performed. Subsequently, cRNA was generated and biotin was incorporated into the cRNA strand by standard methods (Affymetrix) followed by cRNA fragmentation, and preparation of hybridization cocktail.
Sample_hyb_protocol	The arrays were hybridized overnight at 45oC, and then washed, stained, and scanned the next day. Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).
Sample_scan_protocol	Gene expression levels were extracted using AGCC (Affymetrix GeneChip Command Console). Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).
Sample_data_processing	The data was analyzed with Genesprings using the default settings. The summarized probeset was generated using RMA summarization algorithm. Quantile normalization was used. Baseline transformation to median was used.
Sample_platform_id	GPL1261
Sample_contact_name	Rosa,,Serra
Sample_contact_email	rserra@uab.edu
Sample_contact_phone	205-934-0842
Sample_contact_laboratory	Serra
Sample_contact_department	Cell Biology
Sample_contact_institute	University of Alabama at Birmingham
Sample_contact_address	1918 University Blvd. 660 MCLM
Sample_contact_city	Birmingham
Sample_contact_state	AL
Sample_contact_zip/postal_code	35294-0005
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463366/suppl/GSM463366.CEL.gz
Sample_series_id	GSE18648
Sample_series_id	GSE18649
Sample_data_row_count	45101

GSM463367

GPL1261

BMP-3

Sclerotome in micromass culture, BMP treated.

agent: BMP

BMP-3

Sample_geo_accession	GSM463367
Sample_status	Public on Apr 09 2010
Sample_submission_date	Oct 20 2009
Sample_last_update_date	Apr 09 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After overnight culture, cells were treated with or without 5ng/ml of TGFß1 or 50ng/ml BMP4 (R&D Systems) for 8 hours.
Sample_growth_protocol_ch1	Sclerotome cultures were set up using a method similar to that used for limb micromass cultures. Briefly, after removal of the notochord, sclerotome ventral to the neural tube was isolated from E11.5 day mouse embryos. Mesenchymal cells were dissociated into a single cell suspension with incubation in 1mg/ml collagenase D at 37 °C for 30 minutes and reconstituted at a density of 1 X 107 cells / ml. Twenty microliters of cell suspension was dropped into each well of a 24 well plate. After a pre-incubation time of 1 h at 37°C to allow cells to attach, the cultures were then flooded with F-12:DMEM (3:2) containing 10 % FBS, 50 µg/ml ascorbic acid, 10 mM ß-glycerolphosphate, 2 mM glutamine, antibiotics with or without 5ng/ml of TGFß1 or 50ng/ml BMP4 (R&D Systems). Cultures were incubated at 37 °C in CO2 incubator.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from the cells in culture using the standard Trizol method. RNA was Dnase treated and then tested using RT-PCR to assure there was no DNA contamination in the samples.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). Briefly, 50ng of total RNA from each sample was used in a two cycle cDNA amplification protocol using T7-linked oligo dT primers as per the manufacturer’s instructions. After the first round of cDNA synthesis an in vitro transcription step was utilized to amplify the RNA following which a second round of cDNA synthesis was performed. Subsequently, cRNA was generated and biotin was incorporated into the cRNA strand by standard methods (Affymetrix) followed by cRNA fragmentation, and preparation of hybridization cocktail.
Sample_hyb_protocol	The arrays were hybridized overnight at 45oC, and then washed, stained, and scanned the next day. Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).
Sample_scan_protocol	Gene expression levels were extracted using AGCC (Affymetrix GeneChip Command Console). Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).
Sample_data_processing	The data was analyzed with Genesprings using the default settings. The summarized probeset was generated using RMA summarization algorithm. Quantile normalization was used. Baseline transformation to median was used.
Sample_platform_id	GPL1261
Sample_contact_name	Rosa,,Serra
Sample_contact_email	rserra@uab.edu
Sample_contact_phone	205-934-0842
Sample_contact_laboratory	Serra
Sample_contact_department	Cell Biology
Sample_contact_institute	University of Alabama at Birmingham
Sample_contact_address	1918 University Blvd. 660 MCLM
Sample_contact_city	Birmingham
Sample_contact_state	AL
Sample_contact_zip/postal_code	35294-0005
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463367/suppl/GSM463367.CEL.gz
Sample_series_id	GSE18648
Sample_series_id	GSE18649
Sample_data_row_count	45101

GSM463368

GPL1261

TGFb-1

Sclerotome in micromass culture, TGFb treated.

agent: TGFb

TGFb-1

Sample_geo_accession	GSM463368
Sample_status	Public on Apr 09 2010
Sample_submission_date	Oct 20 2009
Sample_last_update_date	Apr 09 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After overnight culture, cells were treated with or without 5ng/ml of TGFß1 or 50ng/ml BMP4 (R&D Systems) for 8 hours.
Sample_growth_protocol_ch1	Sclerotome cultures were set up using a method similar to that used for limb micromass cultures. Briefly, after removal of the notochord, sclerotome ventral to the neural tube was isolated from E11.5 day mouse embryos. Mesenchymal cells were dissociated into a single cell suspension with incubation in 1mg/ml collagenase D at 37 °C for 30 minutes and reconstituted at a density of 1 X 107 cells / ml. Twenty microliters of cell suspension was dropped into each well of a 24 well plate. After a pre-incubation time of 1 h at 37°C to allow cells to attach, the cultures were then flooded with F-12:DMEM (3:2) containing 10 % FBS, 50 µg/ml ascorbic acid, 10 mM ß-glycerolphosphate, 2 mM glutamine, antibiotics with or without 5ng/ml of TGFß1 or 50ng/ml BMP4 (R&D Systems). Cultures were incubated at 37 °C in CO2 incubator.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from the cells in culture using the standard Trizol method. RNA was Dnase treated and then tested using RT-PCR to assure there was no DNA contamination in the samples.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). Briefly, 50ng of total RNA from each sample was used in a two cycle cDNA amplification protocol using T7-linked oligo dT primers as per the manufacturer’s instructions. After the first round of cDNA synthesis an in vitro transcription step was utilized to amplify the RNA following which a second round of cDNA synthesis was performed. Subsequently, cRNA was generated and biotin was incorporated into the cRNA strand by standard methods (Affymetrix) followed by cRNA fragmentation, and preparation of hybridization cocktail.
Sample_hyb_protocol	The arrays were hybridized overnight at 45oC, and then washed, stained, and scanned the next day. Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).
Sample_scan_protocol	Gene expression levels were extracted using AGCC (Affymetrix GeneChip Command Console). Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).
Sample_data_processing	The data was analyzed with Genesprings using the default settings. The summarized probeset was generated using RMA summarization algorithm. Quantile normalization was used. Baseline transformation to median was used.
Sample_platform_id	GPL1261
Sample_contact_name	Rosa,,Serra
Sample_contact_email	rserra@uab.edu
Sample_contact_phone	205-934-0842
Sample_contact_laboratory	Serra
Sample_contact_department	Cell Biology
Sample_contact_institute	University of Alabama at Birmingham
Sample_contact_address	1918 University Blvd. 660 MCLM
Sample_contact_city	Birmingham
Sample_contact_state	AL
Sample_contact_zip/postal_code	35294-0005
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463368/suppl/GSM463368.CEL.gz
Sample_series_id	GSE18648
Sample_series_id	GSE18649
Sample_data_row_count	45101

GSM463369

GPL1261

TGFb-2

Sclerotome in micromass culture, TGFb treated.

agent: TGFb

TGFb-2

Sample_geo_accession	GSM463369
Sample_status	Public on Apr 09 2010
Sample_submission_date	Oct 20 2009
Sample_last_update_date	Apr 09 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After overnight culture, cells were treated with or without 5ng/ml of TGFß1 or 50ng/ml BMP4 (R&D Systems) for 8 hours.
Sample_growth_protocol_ch1	Sclerotome cultures were set up using a method similar to that used for limb micromass cultures. Briefly, after removal of the notochord, sclerotome ventral to the neural tube was isolated from E11.5 day mouse embryos. Mesenchymal cells were dissociated into a single cell suspension with incubation in 1mg/ml collagenase D at 37 °C for 30 minutes and reconstituted at a density of 1 X 107 cells / ml. Twenty microliters of cell suspension was dropped into each well of a 24 well plate. After a pre-incubation time of 1 h at 37°C to allow cells to attach, the cultures were then flooded with F-12:DMEM (3:2) containing 10 % FBS, 50 µg/ml ascorbic acid, 10 mM ß-glycerolphosphate, 2 mM glutamine, antibiotics with or without 5ng/ml of TGFß1 or 50ng/ml BMP4 (R&D Systems). Cultures were incubated at 37 °C in CO2 incubator.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from the cells in culture using the standard Trizol method. RNA was Dnase treated and then tested using RT-PCR to assure there was no DNA contamination in the samples.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). Briefly, 50ng of total RNA from each sample was used in a two cycle cDNA amplification protocol using T7-linked oligo dT primers as per the manufacturer’s instructions. After the first round of cDNA synthesis an in vitro transcription step was utilized to amplify the RNA following which a second round of cDNA synthesis was performed. Subsequently, cRNA was generated and biotin was incorporated into the cRNA strand by standard methods (Affymetrix) followed by cRNA fragmentation, and preparation of hybridization cocktail.
Sample_hyb_protocol	The arrays were hybridized overnight at 45oC, and then washed, stained, and scanned the next day. Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).
Sample_scan_protocol	Gene expression levels were extracted using AGCC (Affymetrix GeneChip Command Console). Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).
Sample_data_processing	The data was analyzed with Genesprings using the default settings. The summarized probeset was generated using RMA summarization algorithm. Quantile normalization was used. Baseline transformation to median was used.
Sample_platform_id	GPL1261
Sample_contact_name	Rosa,,Serra
Sample_contact_email	rserra@uab.edu
Sample_contact_phone	205-934-0842
Sample_contact_laboratory	Serra
Sample_contact_department	Cell Biology
Sample_contact_institute	University of Alabama at Birmingham
Sample_contact_address	1918 University Blvd. 660 MCLM
Sample_contact_city	Birmingham
Sample_contact_state	AL
Sample_contact_zip/postal_code	35294-0005
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463369/suppl/GSM463369.CEL.gz
Sample_series_id	GSE18648
Sample_series_id	GSE18649
Sample_data_row_count	45101

GSM463370

GPL1261

TGFb-3

Sclerotome in micromass culture, TGFb treated.

agent: TGFb

TGFb-3

Sample_geo_accession	GSM463370
Sample_status	Public on Apr 09 2010
Sample_submission_date	Oct 20 2009
Sample_last_update_date	Apr 09 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After overnight culture, cells were treated with or without 5ng/ml of TGFß1 or 50ng/ml BMP4 (R&D Systems) for 8 hours.
Sample_growth_protocol_ch1	Sclerotome cultures were set up using a method similar to that used for limb micromass cultures. Briefly, after removal of the notochord, sclerotome ventral to the neural tube was isolated from E11.5 day mouse embryos. Mesenchymal cells were dissociated into a single cell suspension with incubation in 1mg/ml collagenase D at 37 °C for 30 minutes and reconstituted at a density of 1 X 107 cells / ml. Twenty microliters of cell suspension was dropped into each well of a 24 well plate. After a pre-incubation time of 1 h at 37°C to allow cells to attach, the cultures were then flooded with F-12:DMEM (3:2) containing 10 % FBS, 50 µg/ml ascorbic acid, 10 mM ß-glycerolphosphate, 2 mM glutamine, antibiotics with or without 5ng/ml of TGFß1 or 50ng/ml BMP4 (R&D Systems). Cultures were incubated at 37 °C in CO2 incubator.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from the cells in culture using the standard Trizol method. RNA was Dnase treated and then tested using RT-PCR to assure there was no DNA contamination in the samples.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). Briefly, 50ng of total RNA from each sample was used in a two cycle cDNA amplification protocol using T7-linked oligo dT primers as per the manufacturer’s instructions. After the first round of cDNA synthesis an in vitro transcription step was utilized to amplify the RNA following which a second round of cDNA synthesis was performed. Subsequently, cRNA was generated and biotin was incorporated into the cRNA strand by standard methods (Affymetrix) followed by cRNA fragmentation, and preparation of hybridization cocktail.
Sample_hyb_protocol	The arrays were hybridized overnight at 45oC, and then washed, stained, and scanned the next day. Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).
Sample_scan_protocol	Gene expression levels were extracted using AGCC (Affymetrix GeneChip Command Console). Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).
Sample_data_processing	The data was analyzed with Genesprings using the default settings. The summarized probeset was generated using RMA summarization algorithm. Quantile normalization was used. Baseline transformation to median was used.
Sample_platform_id	GPL1261
Sample_contact_name	Rosa,,Serra
Sample_contact_email	rserra@uab.edu
Sample_contact_phone	205-934-0842
Sample_contact_laboratory	Serra
Sample_contact_department	Cell Biology
Sample_contact_institute	University of Alabama at Birmingham
Sample_contact_address	1918 University Blvd. 660 MCLM
Sample_contact_city	Birmingham
Sample_contact_state	AL
Sample_contact_zip/postal_code	35294-0005
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463370/suppl/GSM463370.CEL.gz
Sample_series_id	GSE18648
Sample_series_id	GSE18649
Sample_data_row_count	45101

Make groups for comparisons

(2 groups will be compared at a time)

Select GSMs and click on "Add groups"

Enter the group name here:

Select expression type

Transcripts profile based on;

A. Differential status (Up/Down regulation)

B. Absolute calls (Transcribed/Not-detected)

Filter results by number of probes