Search results for the GEO ID: GSE33656 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM832368 | GPL1261 |
|
6-1 tibia Bl6
|
tibial articular cartilage and subchondral bone
|
gender: male
strain: C57Bl/6J
tissue: tibial articular cartilage/subchondral bone
age: 6 weeks
genotype: wild-type
|
|
Sample_geo_accession | GSM832368
| Sample_status | Public on Jan 12 2012
| Sample_submission_date | Nov 14 2011
| Sample_last_update_date | Jan 13 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_biomaterial_provider_ch1 | Rik Lories - Lab for Skeletal Development and Joint Disorders
| Sample_growth_protocol_ch1 | Snap freeze in Liquid Nitrogen
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Samples were homogenized using the Fastprep-24 tissue-homogenizer (MP Biomedicals, Solon, OH, USA) in lysing matrix A tubes and RLT lysis buffer (RNeasy Fibrous Tissue kit (Qiagen, Chatsworth, CA, USA)). Samples were kept under pre-cooled conditions using the CryoPrep Adaptor. RNA was isolated with the RNeasy Fibrous Tissue kit (Qiagen) with proteinase K and deoxyribonuclease (DNaseI) treatment.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 2 µg of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted and amplified to antisense cRNA and labeled with biotin in an in vitro transcription reaction. All steps were carried out according to the manufacturers protocol (Affymetrix).
| Sample_hyb_protocol | A mixture of purified and fragmented biotinylated cRNA and hybridisation controls (Affymetrix) was hybridised on the Affymetrix GeneChip Mouse Genome 430 2.0 Array followed by staining and washing in a GeneChip fluidics station 450 (Affymetrix) according to the manufacturer's procedures.
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip scanner 3000 (Affymetrix)
| Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.20.0) of Bioconductor.
| Sample_platform_id | GPL1261
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM832nnn/GSM832368/suppl/GSM832368.CEL.gz
| Sample_series_id | GSE33656
| Sample_data_row_count | 30618
| |
|
GSM832369 | GPL1261 |
|
6-tibia AC FRZB KO
|
tibial articular cartilage and subchondral bone
|
gender: male
strain: C57Bl/6J
tissue: tibial articular cartilage/subchondral bone
age: 6 weeks
genotype: Frzb -/-
|
|
Sample_geo_accession | GSM832369
| Sample_status | Public on Jan 12 2012
| Sample_submission_date | Nov 14 2011
| Sample_last_update_date | Jan 13 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_biomaterial_provider_ch1 | Rik Lories - Lab for skeletal development and joint disorders
| Sample_growth_protocol_ch1 | Snap freeze in Liquid Nitrogen
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Samples were homogenized using the Fastprep-24 tissue-homogenizer (MP Biomedicals, Solon, OH, USA) in lysing matrix A tubes and RLT lysis buffer (RNeasy Fibrous Tissue kit (Qiagen, Chatsworth, CA, USA)). Samples were kept under pre-cooled conditions using the CryoPrep Adaptor. RNA was isolated with the RNeasy Fibrous Tissue kit (Qiagen) with proteinase K and deoxyribonuclease (DNaseI) treatment.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 2 µg of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted and amplified to antisense cRNA and labeled with biotin in an in vitro transcription reaction. All steps were carried out according to the manufacturers protocol (Affymetrix).
| Sample_hyb_protocol | A mixture of purified and fragmented biotinylated cRNA and hybridisation controls (Affymetrix) was hybridised on the Affymetrix GeneChip Mouse Genome 430 2.0 Array followed by staining and washing in a GeneChip fluidics station 450 (Affymetrix) according to the manufacturer's procedures.
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip scanner 3000 (Affymetrix)
| Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.20.0) of Bioconductor.
| Sample_platform_id | GPL1261
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM832nnn/GSM832369/suppl/GSM832369.CEL.gz
| Sample_series_id | GSE33656
| Sample_data_row_count | 30618
| |
|
GSM832370 | GPL1261 |
|
8-1 tibia Bl6
|
tibial articular cartilage and subchondral bone
|
gender: male
strain: C57Bl/6J
tissue: tibial articular cartilage/subchondral bone
age: 6 weeks
genotype: wild-type
|
|
Sample_geo_accession | GSM832370
| Sample_status | Public on Jan 12 2012
| Sample_submission_date | Nov 14 2011
| Sample_last_update_date | Jan 13 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_biomaterial_provider_ch1 | Rik Lories - Lab for skeletal development and joint disorders
| Sample_growth_protocol_ch1 | Snap freeze in Liquid Nitrogen
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Samples were homogenized using the Fastprep-24 tissue-homogenizer (MP Biomedicals, Solon, OH, USA) in lysing matrix A tubes and RLT lysis buffer (RNeasy Fibrous Tissue kit (Qiagen, Chatsworth, CA, USA)). Samples were kept under pre-cooled conditions using the CryoPrep Adaptor. RNA was isolated with the RNeasy Fibrous Tissue kit (Qiagen) with proteinase K and deoxyribonuclease (DNaseI) treatment.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 2 µg of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted and amplified to antisense cRNA and labeled with biotin in an in vitro transcription reaction. All steps were carried out according to the manufacturers protocol (Affymetrix).
| Sample_hyb_protocol | A mixture of purified and fragmented biotinylated cRNA and hybridisation controls (Affymetrix) was hybridised on the Affymetrix GeneChip Mouse Genome 430 2.0 Array followed by staining and washing in a GeneChip fluidics station 450 (Affymetrix) according to the manufacturer's procedures.
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip scanner 3000 (Affymetrix)
| Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.20.0) of Bioconductor.
| Sample_platform_id | GPL1261
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM832nnn/GSM832370/suppl/GSM832370.CEL.gz
| Sample_series_id | GSE33656
| Sample_data_row_count | 30618
| |
|
GSM832371 | GPL1261 |
|
14-tibia AC FRZB KO
|
tibial articular cartilage and subchondral bone
|
gender: male
strain: C57Bl/6J
tissue: tibial articular cartilage/subchondral bone
age: 6 weeks
genotype: Frzb -/-
|
|
Sample_geo_accession | GSM832371
| Sample_status | Public on Jan 12 2012
| Sample_submission_date | Nov 14 2011
| Sample_last_update_date | Jan 13 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_biomaterial_provider_ch1 | Rik Lories - Lab for skeletal development and joint disorders
| Sample_growth_protocol_ch1 | Snap freeze in Liquid Nitrogen
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Samples were homogenized using the Fastprep-24 tissue-homogenizer (MP Biomedicals, Solon, OH, USA) in lysing matrix A tubes and RLT lysis buffer (RNeasy Fibrous Tissue kit (Qiagen, Chatsworth, CA, USA)). Samples were kept under pre-cooled conditions using the CryoPrep Adaptor. RNA was isolated with the RNeasy Fibrous Tissue kit (Qiagen) with proteinase K and deoxyribonuclease (DNaseI) treatment.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 2 µg of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted and amplified to antisense cRNA and labeled with biotin in an in vitro transcription reaction. All steps were carried out according to the manufacturers protocol (Affymetrix).
| Sample_hyb_protocol | A mixture of purified and fragmented biotinylated cRNA and hybridisation controls (Affymetrix) was hybridised on the Affymetrix GeneChip Mouse Genome 430 2.0 Array followed by staining and washing in a GeneChip fluidics station 450 (Affymetrix) according to the manufacturer's procedures.
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip scanner 3000 (Affymetrix)
| Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.20.0) of Bioconductor.
| Sample_platform_id | GPL1261
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM832nnn/GSM832371/suppl/GSM832371.CEL.gz
| Sample_series_id | GSE33656
| Sample_data_row_count | 30618
| |
|
GSM832372 | GPL1261 |
|
9-1 tibia Bl6
|
tibial articular cartilage and subchondral bone
|
gender: male
strain: C57Bl/6J
tissue: tibial articular cartilage/subchondral bone
age: 6 weeks
genotype: wild-type
|
|
Sample_geo_accession | GSM832372
| Sample_status | Public on Jan 12 2012
| Sample_submission_date | Nov 14 2011
| Sample_last_update_date | Jan 13 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_biomaterial_provider_ch1 | Rik Lories - Lab for skeletal development and joint disorders
| Sample_growth_protocol_ch1 | Snap freeze in Liquid Nitrogen
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Samples were homogenized using the Fastprep-24 tissue-homogenizer (MP Biomedicals, Solon, OH, USA) in lysing matrix A tubes and RLT lysis buffer (RNeasy Fibrous Tissue kit (Qiagen, Chatsworth, CA, USA)). Samples were kept under pre-cooled conditions using the CryoPrep Adaptor. RNA was isolated with the RNeasy Fibrous Tissue kit (Qiagen) with proteinase K and deoxyribonuclease (DNaseI) treatment.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 2 µg of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted and amplified to antisense cRNA and labeled with biotin in an in vitro transcription reaction. All steps were carried out according to the manufacturers protocol (Affymetrix).
| Sample_hyb_protocol | A mixture of purified and fragmented biotinylated cRNA and hybridisation controls (Affymetrix) was hybridised on the Affymetrix GeneChip Mouse Genome 430 2.0 Array followed by staining and washing in a GeneChip fluidics station 450 (Affymetrix) according to the manufacturer's procedures.
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip scanner 3000 (Affymetrix)
| Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.20.0) of Bioconductor.
| Sample_platform_id | GPL1261
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM832nnn/GSM832372/suppl/GSM832372.CEL.gz
| Sample_series_id | GSE33656
| Sample_data_row_count | 30618
| |
|
GSM832373 | GPL1261 |
|
17-tibia AC FRZB KO
|
tibial articular cartilage and subchondral bone
|
gender: male
strain: C57Bl/6J
tissue: tibial articular cartilage/subchondral bone
age: 6 weeks
genotype: Frzb -/-
|
|
Sample_geo_accession | GSM832373
| Sample_status | Public on Jan 12 2012
| Sample_submission_date | Nov 14 2011
| Sample_last_update_date | Jan 13 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_biomaterial_provider_ch1 | Rik Lories - Lab for skeletal development and joint disorders
| Sample_growth_protocol_ch1 | Snap freeze in Liquid Nitrogen
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Samples were homogenized using the Fastprep-24 tissue-homogenizer (MP Biomedicals, Solon, OH, USA) in lysing matrix A tubes and RLT lysis buffer (RNeasy Fibrous Tissue kit (Qiagen, Chatsworth, CA, USA)). Samples were kept under pre-cooled conditions using the CryoPrep Adaptor. RNA was isolated with the RNeasy Fibrous Tissue kit (Qiagen) with proteinase K and deoxyribonuclease (DNaseI) treatment.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 2 µg of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted and amplified to antisense cRNA and labeled with biotin in an in vitro transcription reaction. All steps were carried out according to the manufacturers protocol (Affymetrix).
| Sample_hyb_protocol | A mixture of purified and fragmented biotinylated cRNA and hybridisation controls (Affymetrix) was hybridised on the Affymetrix GeneChip Mouse Genome 430 2.0 Array followed by staining and washing in a GeneChip fluidics station 450 (Affymetrix) according to the manufacturer's procedures.
| Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip scanner 3000 (Affymetrix)
| Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.20.0) of Bioconductor.
| Sample_platform_id | GPL1261
| Sample_contact_name | Joke,,Allemeersch
| Sample_contact_email | joke.allemeersch@vib.be
| Sample_contact_phone | +32(0)16 37 31 26
| Sample_contact_department | Nucleomics Core
| Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| Sample_contact_address | Herestraat 49 Box 816
| Sample_contact_city | Leuven
| Sample_contact_zip/postal_code | B-3000
| Sample_contact_country | Belgium
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM832nnn/GSM832373/suppl/GSM832373.CEL.gz
| Sample_series_id | GSE33656
| Sample_data_row_count | 30618
| |
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