Search results for the GEO ID: GSE38091  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM934469 | GPL570 |
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CD34+ cells in liquid culture
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Cord Blood CD34+ cells
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tissue: Cord Blood
cell type: CD34+ cells
culture condition: liquid culture
time: 3 days
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CD34+ cells in liquid culture
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| Sample_geo_accession | GSM934469
| | Sample_status | Public on May 10 2013
| | Sample_submission_date | May 21 2012
| | Sample_last_update_date | May 10 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 24h after isolation, CD34+ cells were seeded directly onto semiconfluent OB monolayers at a final density of 7x103 cell/cm2 in 6-well plates. Cultures were maintained for 2 weeks in medium consisting of a 1:1 mix of IMDM and DMEM/F12 (Dulbecco's Modified Eagle Medium: Nutrient Mixture F-12, both Celbio, Italy) supplemented with 20% FBS (Lonza, Italy), SCF 5ng/mL, FLT3LG 5ng/mL, TPO 2ng/mL, IL-3 1ng/mL and IL-6 1ng/mL (all R&D Systems, Minneapolis, MN, USA), streptomicin 100μg/mL, penicillin 100 μg/mL e L-glutamine 2mM (all purchased from Celbio, Italy). In order to better assess erythroid and megakaryocytic differentiation, cells were cultured in serum free medium consisting of a 1:1 mix of of IMDM and DMEM/F12 supplemented with 20% BIT (StemCell Technologies, Vancouver, Canada), SCF 5ng/mL, FLT3LG 5ng/mL, TPO 1ng/mL, IL-6 1ng/mL (all R&D Systems, Minneapolis, MN, USA), streptomicin 100μg/mL, penicillin 100 μg/mL e L-glutamine 2mM (all Celbio, Italy). Cells were harvested by trypsinization and vigorous pipetting on days 3, 7, 10 and 14 of co-culture.
| | Sample_growth_protocol_ch1 | Human CD34+ cells were purified from umbilical cord blood (UCB) samples, collected after normal deliveries, according to the institutional guidelines for discarded material, as previously described (Salati S. Stem Cells 2008). After purification, CD34+ cells were seeded in 24-well plates at 5x105 cells/mL in Iscove’s modified Dulbecco’s medium (IMDM) (GIBCO, Grand Island, NY, USA) containing 20% Human Serum (Bio-Whittaker, Walkersville, MD, USA), SCF (50 ng/ml), FLT3LG (50 ng/ml), TPO (20ng/ml), IL-6 (10 ng/ml) and IL-3 (10 ng/ml) (all from R&D Systems, Minneapolis, MN, USA). Human osteoblasts (OBs) were directly isolated from the trabecular bone harvested from the inner portion of the tibia plateau of 16 patients undergoing total knee replacement for osteoarthritis (mean ± SD age 70 ± 8.2 years) as previously reported (Lisignoli G., J Cell Physiol. 2006). The bone chips were fed with medium twice a week. After 2 weeks, they were removed and the OBs were allowed to grow until confluent and analyzed at the first and second passages.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was extracted after 48 hours of treatment from 0.3x106 cells of each sample using RNeasy Micro kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard 3’IVT Express Kit protocol from 500ng of total RNA. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Fragmented cRNA was hybridized for 16 hr at 45C on Affymetrix HGU-133Plus2 arrays. GeneChips were washed and stained using Hybridization, Wash, and Stain Kit for 3’IVT Arrays.
| | Sample_scan_protocol | GeneChip were scanned using GeneChip Scanner 3000 7G System.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm (MAS5) was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 300.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM934nnn/GSM934469/suppl/GSM934469_CD34+_CTR_plus_2.CEL.gz
| | Sample_series_id | GSE38091
| | Sample_data_row_count | 54675
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GSM934470 | GPL570 |
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CD34+ cells cultured with Osteoblasts
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Cord Blood CD34+ cells
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tissue: Cord Blood
cell type: CD34+ cells
culture condition: co-cultured with osteoblasts
time: 3 days
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CD34+ cells co-cultured with osteoblasts
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| Sample_geo_accession | GSM934470
| | Sample_status | Public on May 10 2013
| | Sample_submission_date | May 21 2012
| | Sample_last_update_date | May 10 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 24h after isolation, CD34+ cells were seeded directly onto semiconfluent OB monolayers at a final density of 7x103 cell/cm2 in 6-well plates. Cultures were maintained for 2 weeks in medium consisting of a 1:1 mix of IMDM and DMEM/F12 (Dulbecco's Modified Eagle Medium: Nutrient Mixture F-12, both Celbio, Italy) supplemented with 20% FBS (Lonza, Italy), SCF 5ng/mL, FLT3LG 5ng/mL, TPO 2ng/mL, IL-3 1ng/mL and IL-6 1ng/mL (all R&D Systems, Minneapolis, MN, USA), streptomicin 100μg/mL, penicillin 100 μg/mL e L-glutamine 2mM (all purchased from Celbio, Italy). In order to better assess erythroid and megakaryocytic differentiation, cells were cultured in serum free medium consisting of a 1:1 mix of of IMDM and DMEM/F12 supplemented with 20% BIT (StemCell Technologies, Vancouver, Canada), SCF 5ng/mL, FLT3LG 5ng/mL, TPO 1ng/mL, IL-6 1ng/mL (all R&D Systems, Minneapolis, MN, USA), streptomicin 100μg/mL, penicillin 100 μg/mL e L-glutamine 2mM (all Celbio, Italy). Cells were harvested by trypsinization and vigorous pipetting on days 3, 7, 10 and 14 of co-culture.
| | Sample_growth_protocol_ch1 | Human CD34+ cells were purified from umbilical cord blood (UCB) samples, collected after normal deliveries, according to the institutional guidelines for discarded material, as previously described (Salati S. Stem Cells 2008). After purification, CD34+ cells were seeded in 24-well plates at 5x105 cells/mL in Iscove’s modified Dulbecco’s medium (IMDM) (GIBCO, Grand Island, NY, USA) containing 20% Human Serum (Bio-Whittaker, Walkersville, MD, USA), SCF (50 ng/ml), FLT3LG (50 ng/ml), TPO (20ng/ml), IL-6 (10 ng/ml) and IL-3 (10 ng/ml) (all from R&D Systems, Minneapolis, MN, USA). Human osteoblasts (OBs) were directly isolated from the trabecular bone harvested from the inner portion of the tibia plateau of 16 patients undergoing total knee replacement for osteoarthritis (mean ± SD age 70 ± 8.2 years) as previously reported (Lisignoli G., J Cell Physiol. 2006). The bone chips were fed with medium twice a week. After 2 weeks, they were removed and the OBs were allowed to grow until confluent and analyzed at the first and second passages.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was extracted after 48 hours of treatment from 0.3x106 cells of each sample using RNeasy Micro kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard 3’IVT Express Kit protocol from 500ng of total RNA. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Fragmented cRNA was hybridized for 16 hr at 45C on Affymetrix HGU-133Plus2 arrays. GeneChips were washed and stained using Hybridization, Wash, and Stain Kit for 3’IVT Arrays.
| | Sample_scan_protocol | GeneChip were scanned using GeneChip Scanner 3000 7G System.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm (MAS5) was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 300.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM934nnn/GSM934470/suppl/GSM934470_CD34+_COCULTURE_plus_2.CEL.gz
| | Sample_series_id | GSE38091
| | Sample_data_row_count | 54675
| | |
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GSM934471 | GPL570 |
|
Osteoblasts
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Human Osteoblasts from trabecular bone
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tissue: trabecular bone
cell type: Osteoblasts
culture condition: normal culture conditions
time: 3 days
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Osteoblasts maintaned in normal culture conditions
|
| Sample_geo_accession | GSM934471
| | Sample_status | Public on May 10 2013
| | Sample_submission_date | May 21 2012
| | Sample_last_update_date | May 10 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 24h after isolation, CD34+ cells were seeded directly onto semiconfluent OB monolayers at a final density of 7x103 cell/cm2 in 6-well plates. Cultures were maintained for 2 weeks in medium consisting of a 1:1 mix of IMDM and DMEM/F12 (Dulbecco's Modified Eagle Medium: Nutrient Mixture F-12, both Celbio, Italy) supplemented with 20% FBS (Lonza, Italy), SCF 5ng/mL, FLT3LG 5ng/mL, TPO 2ng/mL, IL-3 1ng/mL and IL-6 1ng/mL (all R&D Systems, Minneapolis, MN, USA), streptomicin 100μg/mL, penicillin 100 μg/mL e L-glutamine 2mM (all purchased from Celbio, Italy). In order to better assess erythroid and megakaryocytic differentiation, cells were cultured in serum free medium consisting of a 1:1 mix of of IMDM and DMEM/F12 supplemented with 20% BIT (StemCell Technologies, Vancouver, Canada), SCF 5ng/mL, FLT3LG 5ng/mL, TPO 1ng/mL, IL-6 1ng/mL (all R&D Systems, Minneapolis, MN, USA), streptomicin 100μg/mL, penicillin 100 μg/mL e L-glutamine 2mM (all Celbio, Italy). Cells were harvested by trypsinization and vigorous pipetting on days 3, 7, 10 and 14 of co-culture.
| | Sample_growth_protocol_ch1 | Human CD34+ cells were purified from umbilical cord blood (UCB) samples, collected after normal deliveries, according to the institutional guidelines for discarded material, as previously described (Salati S. Stem Cells 2008). After purification, CD34+ cells were seeded in 24-well plates at 5x105 cells/mL in Iscove’s modified Dulbecco’s medium (IMDM) (GIBCO, Grand Island, NY, USA) containing 20% Human Serum (Bio-Whittaker, Walkersville, MD, USA), SCF (50 ng/ml), FLT3LG (50 ng/ml), TPO (20ng/ml), IL-6 (10 ng/ml) and IL-3 (10 ng/ml) (all from R&D Systems, Minneapolis, MN, USA). Human osteoblasts (OBs) were directly isolated from the trabecular bone harvested from the inner portion of the tibia plateau of 16 patients undergoing total knee replacement for osteoarthritis (mean ± SD age 70 ± 8.2 years) as previously reported (Lisignoli G., J Cell Physiol. 2006). The bone chips were fed with medium twice a week. After 2 weeks, they were removed and the OBs were allowed to grow until confluent and analyzed at the first and second passages.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was extracted after 48 hours of treatment from 0.3x106 cells of each sample using RNeasy Micro kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard 3’IVT Express Kit protocol from 500ng of total RNA. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Fragmented cRNA was hybridized for 16 hr at 45C on Affymetrix HGU-133Plus2 arrays. GeneChips were washed and stained using Hybridization, Wash, and Stain Kit for 3’IVT Arrays.
| | Sample_scan_protocol | GeneChip were scanned using GeneChip Scanner 3000 7G System.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm (MAS5) was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 300.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM934nnn/GSM934471/suppl/GSM934471_OB_CTR_plus_2.CEL.gz
| | Sample_series_id | GSE38091
| | Sample_data_row_count | 54675
| | |
|
GSM934472 | GPL570 |
|
Osteoblasts cultured with CD34+ cells
|
Human Osteoblasts from trabecular bone
|
tissue: trabecular bone
cell type: Osteoblasts
culture condition: co-cultured with CD34+ cells
time: 3 days
|
Osteoblasts co-cultured with CD34+ cells
|
| Sample_geo_accession | GSM934472
| | Sample_status | Public on May 10 2013
| | Sample_submission_date | May 21 2012
| | Sample_last_update_date | May 10 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 24h after isolation, CD34+ cells were seeded directly onto semiconfluent OB monolayers at a final density of 7x103 cell/cm2 in 6-well plates. Cultures were maintained for 2 weeks in medium consisting of a 1:1 mix of IMDM and DMEM/F12 (Dulbecco's Modified Eagle Medium: Nutrient Mixture F-12, both Celbio, Italy) supplemented with 20% FBS (Lonza, Italy), SCF 5ng/mL, FLT3LG 5ng/mL, TPO 2ng/mL, IL-3 1ng/mL and IL-6 1ng/mL (all R&D Systems, Minneapolis, MN, USA), streptomicin 100μg/mL, penicillin 100 μg/mL e L-glutamine 2mM (all purchased from Celbio, Italy). In order to better assess erythroid and megakaryocytic differentiation, cells were cultured in serum free medium consisting of a 1:1 mix of of IMDM and DMEM/F12 supplemented with 20% BIT (StemCell Technologies, Vancouver, Canada), SCF 5ng/mL, FLT3LG 5ng/mL, TPO 1ng/mL, IL-6 1ng/mL (all R&D Systems, Minneapolis, MN, USA), streptomicin 100μg/mL, penicillin 100 μg/mL e L-glutamine 2mM (all Celbio, Italy). Cells were harvested by trypsinization and vigorous pipetting on days 3, 7, 10 and 14 of co-culture.
| | Sample_growth_protocol_ch1 | Human CD34+ cells were purified from umbilical cord blood (UCB) samples, collected after normal deliveries, according to the institutional guidelines for discarded material, as previously described (Salati S. Stem Cells 2008). After purification, CD34+ cells were seeded in 24-well plates at 5x105 cells/mL in Iscove’s modified Dulbecco’s medium (IMDM) (GIBCO, Grand Island, NY, USA) containing 20% Human Serum (Bio-Whittaker, Walkersville, MD, USA), SCF (50 ng/ml), FLT3LG (50 ng/ml), TPO (20ng/ml), IL-6 (10 ng/ml) and IL-3 (10 ng/ml) (all from R&D Systems, Minneapolis, MN, USA). Human osteoblasts (OBs) were directly isolated from the trabecular bone harvested from the inner portion of the tibia plateau of 16 patients undergoing total knee replacement for osteoarthritis (mean ± SD age 70 ± 8.2 years) as previously reported (Lisignoli G., J Cell Physiol. 2006). The bone chips were fed with medium twice a week. After 2 weeks, they were removed and the OBs were allowed to grow until confluent and analyzed at the first and second passages.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was extracted after 48 hours of treatment from 0.3x106 cells of each sample using RNeasy Micro kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard 3’IVT Express Kit protocol from 500ng of total RNA. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Fragmented cRNA was hybridized for 16 hr at 45C on Affymetrix HGU-133Plus2 arrays. GeneChips were washed and stained using Hybridization, Wash, and Stain Kit for 3’IVT Arrays.
| | Sample_scan_protocol | GeneChip were scanned using GeneChip Scanner 3000 7G System.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm (MAS5) was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 300.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM934nnn/GSM934472/suppl/GSM934472_OB_COCULTURE_plus_2.CEL.gz
| | Sample_series_id | GSE38091
| | Sample_data_row_count | 54675
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