Search results for the GEO ID: GSE35003  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM860168 | GPL1261 |
|
Control 1
|
Control
|
background strain: C57BL/6
cell type: Proliferative zone chondrocytes
genotype/variation: wild-type
|
|
| Sample_geo_accession | GSM860168
| | Sample_status | Public on Jan 02 2013
| | Sample_submission_date | Jan 11 2012
| | Sample_last_update_date | Jan 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Comparison of control and Col2aCre;Ift88fl/fl proliferative zone chondrocytes.
| | Sample_growth_protocol_ch1 | Mouse, 7 day post-natal.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Hindlimbs from postnatal day 7 mice were dissected and embedded in OCT, and stored at -80 ºC. 40 μm sections were cut and mounted on Superfrost Plus slides (Fischer). Sections were dehydrated immediately in 70 %, 90 %, 100 % EtOH, followed by xylene. The sections were air-dried. Proliferative zone chondrocytes were cut out from proximal tibia and distal femur using an 18 gauge needle, and collected in a tube containing 100 μl of lysis buffer from RNAqueous®-Micro Kit (Ambion, AM1931). The RNA isolation procedure was followed by the protocol for LCM (laser capture micro-dissection) samples in the manufacturer’s manual.
| | 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 | Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). The arrays were hybridized overnight at 45oC, and then washed, stained, and scanned the next day.
| | Sample_scan_protocol | Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). Gene expression levels were extracted using AGCC (Affymetrix GeneChip Command Console).
| | 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/GSM860nnn/GSM860168/suppl/GSM860168_RS-723wildtype.CEL.gz
| | Sample_series_id | GSE35003
| | Sample_data_row_count | 45101
| | |
|
GSM860169 | GPL1261 |
|
Control 2
|
Control
|
background strain: C57BL/6
cell type: Proliferative zone chondrocytes
genotype/variation: wild-type
|
|
| Sample_geo_accession | GSM860169
| | Sample_status | Public on Jan 02 2013
| | Sample_submission_date | Jan 11 2012
| | Sample_last_update_date | Jan 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Comparison of control and Col2aCre;Ift88fl/fl proliferative zone chondrocytes.
| | Sample_growth_protocol_ch1 | Mouse, 7 day post-natal.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Hindlimbs from postnatal day 7 mice were dissected and embedded in OCT, and stored at -80 ºC. 40 μm sections were cut and mounted on Superfrost Plus slides (Fischer). Sections were dehydrated immediately in 70 %, 90 %, 100 % EtOH, followed by xylene. The sections were air-dried. Proliferative zone chondrocytes were cut out from proximal tibia and distal femur using an 18 gauge needle, and collected in a tube containing 100 μl of lysis buffer from RNAqueous®-Micro Kit (Ambion, AM1931). The RNA isolation procedure was followed by the protocol for LCM (laser capture micro-dissection) samples in the manufacturer’s manual.
| | 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 | Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). The arrays were hybridized overnight at 45oC, and then washed, stained, and scanned the next day.
| | Sample_scan_protocol | Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). Gene expression levels were extracted using AGCC (Affymetrix GeneChip Command Console).
| | 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/GSM860nnn/GSM860169/suppl/GSM860169_RS-815wildtype.CEL.gz
| | Sample_series_id | GSE35003
| | Sample_data_row_count | 45101
| | |
|
GSM860170 | GPL1261 |
|
Cilia-deleted 1
|
Cilia mutant
|
background strain: C57BL/6
cell type: Proliferative zone chondrocytes
genotype/variation: Ift88-deleted
|
|
| Sample_geo_accession | GSM860170
| | Sample_status | Public on Jan 02 2013
| | Sample_submission_date | Jan 11 2012
| | Sample_last_update_date | Jan 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Comparison of control and Col2aCre;Ift88fl/fl proliferative zone chondrocytes.
| | Sample_growth_protocol_ch1 | Mouse, 7 day post-natal.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Hindlimbs from postnatal day 7 mice were dissected and embedded in OCT, and stored at -80 ºC. 40 μm sections were cut and mounted on Superfrost Plus slides (Fischer). Sections were dehydrated immediately in 70 %, 90 %, 100 % EtOH, followed by xylene. The sections were air-dried. Proliferative zone chondrocytes were cut out from proximal tibia and distal femur using an 18 gauge needle, and collected in a tube containing 100 μl of lysis buffer from RNAqueous®-Micro Kit (Ambion, AM1931). The RNA isolation procedure was followed by the protocol for LCM (laser capture micro-dissection) samples in the manufacturer’s manual.
| | 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 | Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). The arrays were hybridized overnight at 45oC, and then washed, stained, and scanned the next day.
| | Sample_scan_protocol | Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). Gene expression levels were extracted using AGCC (Affymetrix GeneChip Command Console).
| | 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/GSM860nnn/GSM860170/suppl/GSM860170_RS-544mutant.CEL.gz
| | Sample_series_id | GSE35003
| | Sample_data_row_count | 45101
| | |
|
GSM860171 | GPL1261 |
|
Cilia-deleted 2
|
Cilia mutant
|
background strain: C57BL/6
cell type: Proliferative zone chondrocytes
genotype/variation: Ift88-deleted
|
|
| Sample_geo_accession | GSM860171
| | Sample_status | Public on Jan 02 2013
| | Sample_submission_date | Jan 11 2012
| | Sample_last_update_date | Jan 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Comparison of control and Col2aCre;Ift88fl/fl proliferative zone chondrocytes.
| | Sample_growth_protocol_ch1 | Mouse, 7 day post-natal.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Hindlimbs from postnatal day 7 mice were dissected and embedded in OCT, and stored at -80 ºC. 40 μm sections were cut and mounted on Superfrost Plus slides (Fischer). Sections were dehydrated immediately in 70 %, 90 %, 100 % EtOH, followed by xylene. The sections were air-dried. Proliferative zone chondrocytes were cut out from proximal tibia and distal femur using an 18 gauge needle, and collected in a tube containing 100 μl of lysis buffer from RNAqueous®-Micro Kit (Ambion, AM1931). The RNA isolation procedure was followed by the protocol for LCM (laser capture micro-dissection) samples in the manufacturer’s manual.
| | 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 | Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). The arrays were hybridized overnight at 45oC, and then washed, stained, and scanned the next day.
| | Sample_scan_protocol | Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). Gene expression levels were extracted using AGCC (Affymetrix GeneChip Command Console).
| | 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/GSM860nnn/GSM860171/suppl/GSM860171_RS-545mutant.CEL.gz
| | Sample_series_id | GSE35003
| | Sample_data_row_count | 45101
| | |
|
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