Search results for the GEO ID: GSE18934  |
(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 |
GSM469125 | GPL570 |
|
Blood_1
|
Human fetal material, 9-14 weeks, from legal abortions.
|
developmental stage: 9-14 week old fetus
cell type: mesenchymal stem cells
tissue: blood
|
Human mesenchymal stem cells circulate in 1st and early 2nd trimester fetal blood, but not in adults. Like other fetal cell types they cross the placenta, and can be found in maternal organs decades later.
To determine potential ligands in human fetal mesenchymal stem cells not present in maternal blood, the gene expression of 1st trimester human fetal bone marrow, liver and blood derived mesenchymal stem cells will be compared to blood mononuclear cells from pregnant women using a Affymetrix human gene array system.
|
| Sample_geo_accession | GSM469125
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Queen Charlotte's & Chelsea Hospital Hammersmith Campus (anonymous donors).
| | Sample_growth_protocol_ch1 | Human fetal mesenchymal stem cells were isolated from 3 sources (fetal blood, bone marrow and liver, from 9-14 week old fetuses), all from different individuals at legal abortion after informed consent from the patients. Procedures were approved by Hammersmith and Queen Charlotte’s Research Ethics Committee.
| | Sample_growth_protocol_ch1 | Fetal liver was disintegrated by passage through a 100 μm nylon filter and fetal bone marrow was prepared by flushing long bones with 25-gauge needles. Single cells were suspended in DMEM-High Glucose supplemented with 10% fetal calf serum and 2 mmol/l L-glutamine and 50 IU/ml penicillin/streptomycin. Cells were plated at 1.8x104 cells/cm2 in 10 cm Petri dishes and maintained at 37oC in a humidified environment containing 5% CO2. After 3 days, the non-adherent cells were removed and the medium replaced. The medium was changed every three to four days thereafter. At sub-confluence (70%), cells were detached using 0.05% trypsin and 0.53 mM EDTA and replated at a density of 4x103 cells/cm2. Cells were counted and thereafter snap frozen in 80ºC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen RNeasy Kit. Isolated RNA was analysed with Agilent 2100 Bioanalyzer to verify sample integrity and quantify total RNA yield.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.
| | Sample_hyb_protocol | Hybridization was performed at the Microarray Centre, MRC at Imperial College, London, UK according to the manufacturers protocols.
| | Sample_scan_protocol | Scanning was performed according to the manufacturer's recommended protocols with Agilent Probe Array Scan.
| | Sample_data_processing | Raw data was analysed with the MAS5 method using Affymetrix GeneChip Operating Software (GCOS).
| | Sample_data_processing | Data were further analysed as follows: (i) the mean expression ratio and p value was calculated for each transcript, (ii) all transcripts that scored as present in all fetal mesenchymal stem cells absent in all maternal peripheral blood lymphocytes were selected, (iii) these transcripts were then filtered for molecules involved in cell surface linked signal transduction and antigen presentation and (iv) transcripts with a mean expression ratio of >300 were further analysed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Cecilia ,,Götherström
| | Sample_contact_email | cecilia.gotherstrom@ki.se
| | Sample_contact_laboratory | Division for Clinical Immunology, F79
| | Sample_contact_department | Department for Laboratory Medicine
| | Sample_contact_institute | Karolinska Institutet
| | Sample_contact_address | Karolinska University Hospital Huddinge
| | Sample_contact_city | Stockholm
| | Sample_contact_zip/postal_code | 14186
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469125/suppl/GSM469125.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469125/suppl/GSM469125.CHP.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE18934
| | Sample_data_row_count | 54675
| | |
|
GSM469126 | GPL570 |
|
Blood_3
|
Human fetal material, 9-14 weeks, from legal abortions.
|
developmental stage: 9-14 week old fetus
cell type: mesenchymal stem cells
tissue: blood
|
Human mesenchymal stem cells circulate in 1st and early 2nd trimester fetal blood, but not in adults. Like other fetal cell types they cross the placenta, and can be found in maternal organs decades later.
To determine potential ligands in human fetal mesenchymal stem cells not present in maternal blood, the gene expression of 1st trimester human fetal bone marrow, liver and blood derived mesenchymal stem cells will be compared to blood mononuclear cells from pregnant women using a Affymetrix human gene array system.
|
| Sample_geo_accession | GSM469126
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Queen Charlotte's & Chelsea Hospital Hammersmith Campus (anonymous donors).
| | Sample_growth_protocol_ch1 | Human fetal mesenchymal stem cells were isolated from 3 sources (fetal blood, bone marrow and liver, from 9-14 week old fetuses), all from different individuals at legal abortion after informed consent from the patients. Procedures were approved by Hammersmith and Queen Charlotte’s Research Ethics Committee.
| | Sample_growth_protocol_ch1 |
| | Sample_growth_protocol_ch1 | Fetal liver was disintegrated by passage through a 100 μm nylon filter and fetal bone marrow was prepared by flushing long bones with 25-gauge needles. Single cells were suspended in DMEM-High Glucose supplemented with 10% fetal calf serum and 2 mmol/l L-glutamine and 50 IU/ml penicillin/streptomycin. Cells were plated at 1.8x104 cells/cm2 in 10 cm Petri dishes and maintained at 37oC in a humidified environment containing 5% CO2. After 3 days, the non-adherent cells were removed and the medium replaced. The medium was changed every three to four days thereafter. At sub-confluence (70%), cells were detached using 0.05% trypsin and 0.53 mM EDTA and replated at a density of 4x103 cells/cm2. Cells were counted and thereafter snap frozen in 80ºC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen RNeasy Kit. Isolated RNA was analysed with Agilent 2100 Bioanalyzer to verify sample integrity and quantify total RNA yield.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.
| | Sample_hyb_protocol | Hybridization was performed at the Microarray Centre, MRC at Imperial College, London, UK according to the manufacturers protocols.
| | Sample_scan_protocol | Scanning was performed according to the manufacturer's recommended protocols with Agilent Probe Array Scan.
| | Sample_data_processing | Raw data was analysed with the MAS5 method using Affymetrix GeneChip Operating Software (GCOS).
| | Sample_data_processing |
| | Sample_data_processing | Data were further analysed as follows: (i) the mean expression ratio and p value was calculated for each transcript, (ii) all transcripts that scored as present in all fetal mesenchymal stem cells absent in all maternal peripheral blood lymphocytes were selected, (iii) these transcripts were then filtered for molecules involved in cell surface linked signal transduction and antigen presentation and (iv) transcripts with a mean expression ratio of >300 were further analysed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Cecilia ,,Götherström
| | Sample_contact_email | cecilia.gotherstrom@ki.se
| | Sample_contact_laboratory | Division for Clinical Immunology, F79
| | Sample_contact_department | Department for Laboratory Medicine
| | Sample_contact_institute | Karolinska Institutet
| | Sample_contact_address | Karolinska University Hospital Huddinge
| | Sample_contact_city | Stockholm
| | Sample_contact_zip/postal_code | 14186
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469126/suppl/GSM469126.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469126/suppl/GSM469126.CHP.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE18934
| | Sample_data_row_count | 54675
| | |
|
GSM469127 | GPL570 |
|
Bone Marrow_1
|
Human fetal material, 9-14 weeks, from legal abortions.
|
developmental stage: 9-14 week old fetus
cell type: mesenchymal stem cells
tissue: bone marrow
|
Human mesenchymal stem cells circulate in 1st and early 2nd trimester fetal blood, but not in adults. Like other fetal cell types they cross the placenta, and can be found in maternal organs decades later.
To determine potential ligands in human fetal mesenchymal stem cells not present in maternal blood, the gene expression of 1st trimester human fetal bone marrow, liver and blood derived mesenchymal stem cells will be compared to blood mononuclear cells from pregnant women using a Affymetrix human gene array system.
|
| Sample_geo_accession | GSM469127
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Queen Charlotte's & Chelsea Hospital Hammersmith Campus (anonymous donors).
| | Sample_growth_protocol_ch1 | Human fetal mesenchymal stem cells were isolated from 3 sources (fetal blood, bone marrow and liver, from 9-14 week old fetuses), all from different individuals at legal abortion after informed consent from the patients. Procedures were approved by Hammersmith and Queen Charlotte’s Research Ethics Committee.
| | Sample_growth_protocol_ch1 |
| | Sample_growth_protocol_ch1 | Fetal liver was disintegrated by passage through a 100 μm nylon filter and fetal bone marrow was prepared by flushing long bones with 25-gauge needles. Single cells were suspended in DMEM-High Glucose supplemented with 10% fetal calf serum and 2 mmol/l L-glutamine and 50 IU/ml penicillin/streptomycin. Cells were plated at 1.8x104 cells/cm2 in 10 cm Petri dishes and maintained at 37oC in a humidified environment containing 5% CO2. After 3 days, the non-adherent cells were removed and the medium replaced. The medium was changed every three to four days thereafter. At sub-confluence (70%), cells were detached using 0.05% trypsin and 0.53 mM EDTA and replated at a density of 4x103 cells/cm2. Cells were counted and thereafter snap frozen in 80ºC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen RNeasy Kit. Isolated RNA was analysed with Agilent 2100 Bioanalyzer to verify sample integrity and quantify total RNA yield.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.
| | Sample_hyb_protocol | Hybridization was performed at the Microarray Centre, MRC at Imperial College, London, UK according to the manufacturers protocols.
| | Sample_scan_protocol | Scanning was performed according to the manufacturer's recommended protocols with Agilent Probe Array Scan.
| | Sample_data_processing | Raw data was analysed with the MAS5 method using Affymetrix GeneChip Operating Software (GCOS).
| | Sample_data_processing |
| | Sample_data_processing | Data were further analysed as follows: (i) the mean expression ratio and p value was calculated for each transcript, (ii) all transcripts that scored as present in all fetal mesenchymal stem cells absent in all maternal peripheral blood lymphocytes were selected, (iii) these transcripts were then filtered for molecules involved in cell surface linked signal transduction and antigen presentation and (iv) transcripts with a mean expression ratio of >300 were further analysed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Cecilia ,,Götherström
| | Sample_contact_email | cecilia.gotherstrom@ki.se
| | Sample_contact_laboratory | Division for Clinical Immunology, F79
| | Sample_contact_department | Department for Laboratory Medicine
| | Sample_contact_institute | Karolinska Institutet
| | Sample_contact_address | Karolinska University Hospital Huddinge
| | Sample_contact_city | Stockholm
| | Sample_contact_zip/postal_code | 14186
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469127/suppl/GSM469127.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469127/suppl/GSM469127.CHP.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE18934
| | Sample_data_row_count | 54675
| | |
|
GSM469128 | GPL570 |
|
Bone Marrow_2
|
Human fetal material, 9-14 weeks, from legal abortions.
|
developmental stage: 9-14 week old fetus
cell type: mesenchymal stem cells
tissue: bone marrow
|
Human mesenchymal stem cells circulate in 1st and early 2nd trimester fetal blood, but not in adults. Like other fetal cell types they cross the placenta, and can be found in maternal organs decades later.
To determine potential ligands in human fetal mesenchymal stem cells not present in maternal blood, the gene expression of 1st trimester human fetal bone marrow, liver and blood derived mesenchymal stem cells will be compared to blood mononuclear cells from pregnant women using a Affymetrix human gene array system.
|
| Sample_geo_accession | GSM469128
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Queen Charlotte's & Chelsea Hospital Hammersmith Campus (anonymous donors).
| | Sample_growth_protocol_ch1 | Human fetal mesenchymal stem cells were isolated from 3 sources (fetal blood, bone marrow and liver, from 9-14 week old fetuses), all from different individuals at legal abortion after informed consent from the patients. Procedures were approved by Hammersmith and Queen Charlotte’s Research Ethics Committee.
| | Sample_growth_protocol_ch1 |
| | Sample_growth_protocol_ch1 | Fetal liver was disintegrated by passage through a 100 μm nylon filter and fetal bone marrow was prepared by flushing long bones with 25-gauge needles. Single cells were suspended in DMEM-High Glucose supplemented with 10% fetal calf serum and 2 mmol/l L-glutamine and 50 IU/ml penicillin/streptomycin. Cells were plated at 1.8x104 cells/cm2 in 10 cm Petri dishes and maintained at 37oC in a humidified environment containing 5% CO2. After 3 days, the non-adherent cells were removed and the medium replaced. The medium was changed every three to four days thereafter. At sub-confluence (70%), cells were detached using 0.05% trypsin and 0.53 mM EDTA and replated at a density of 4x103 cells/cm2. Cells were counted and thereafter snap frozen in 80ºC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen RNeasy Kit. Isolated RNA was analysed with Agilent 2100 Bioanalyzer to verify sample integrity and quantify total RNA yield.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.
| | Sample_hyb_protocol | Hybridization was performed at the Microarray Centre, MRC at Imperial College, London, UK according to the manufacturers protocols.
| | Sample_scan_protocol | Scanning was performed according to the manufacturer's recommended protocols with Agilent Probe Array Scan.
| | Sample_data_processing | Raw data was analysed with the MAS5 method using Affymetrix GeneChip Operating Software (GCOS).
| | Sample_data_processing |
| | Sample_data_processing | Data were further analysed as follows: (i) the mean expression ratio and p value was calculated for each transcript, (ii) all transcripts that scored as present in all fetal mesenchymal stem cells absent in all maternal peripheral blood lymphocytes were selected, (iii) these transcripts were then filtered for molecules involved in cell surface linked signal transduction and antigen presentation and (iv) transcripts with a mean expression ratio of >300 were further analysed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Cecilia ,,Götherström
| | Sample_contact_email | cecilia.gotherstrom@ki.se
| | Sample_contact_laboratory | Division for Clinical Immunology, F79
| | Sample_contact_department | Department for Laboratory Medicine
| | Sample_contact_institute | Karolinska Institutet
| | Sample_contact_address | Karolinska University Hospital Huddinge
| | Sample_contact_city | Stockholm
| | Sample_contact_zip/postal_code | 14186
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469128/suppl/GSM469128.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469128/suppl/GSM469128.CHP.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE18934
| | Sample_data_row_count | 54675
| | |
|
GSM469129 | GPL570 |
|
Bone Marrow_3
|
Human fetal material, 9-14 weeks, from legal abortions.
|
developmental stage: 9-14 week old fetus
cell type: mesenchymal stem cells
tissue: bone marrow
|
Human mesenchymal stem cells circulate in 1st and early 2nd trimester fetal blood, but not in adults. Like other fetal cell types they cross the placenta, and can be found in maternal organs decades later.
To determine potential ligands in human fetal mesenchymal stem cells not present in maternal blood, the gene expression of 1st trimester human fetal bone marrow, liver and blood derived mesenchymal stem cells will be compared to blood mononuclear cells from pregnant women using a Affymetrix human gene array system.
|
| Sample_geo_accession | GSM469129
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Queen Charlotte's & Chelsea Hospital Hammersmith Campus (anonymous donors).
| | Sample_growth_protocol_ch1 | Human fetal mesenchymal stem cells were isolated from 3 sources (fetal blood, bone marrow and liver, from 9-14 week old fetuses), all from different individuals at legal abortion after informed consent from the patients. Procedures were approved by Hammersmith and Queen Charlotte’s Research Ethics Committee.
| | Sample_growth_protocol_ch1 |
| | Sample_growth_protocol_ch1 | Fetal liver was disintegrated by passage through a 100 μm nylon filter and fetal bone marrow was prepared by flushing long bones with 25-gauge needles. Single cells were suspended in DMEM-High Glucose supplemented with 10% fetal calf serum and 2 mmol/l L-glutamine and 50 IU/ml penicillin/streptomycin. Cells were plated at 1.8x104 cells/cm2 in 10 cm Petri dishes and maintained at 37oC in a humidified environment containing 5% CO2. After 3 days, the non-adherent cells were removed and the medium replaced. The medium was changed every three to four days thereafter. At sub-confluence (70%), cells were detached using 0.05% trypsin and 0.53 mM EDTA and replated at a density of 4x103 cells/cm2. Cells were counted and thereafter snap frozen in 80ºC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen RNeasy Kit. Isolated RNA was analysed with Agilent 2100 Bioanalyzer to verify sample integrity and quantify total RNA yield.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.
| | Sample_hyb_protocol | Hybridization was performed at the Microarray Centre, MRC at Imperial College, London, UK according to the manufacturers protocols.
| | Sample_scan_protocol | Scanning was performed according to the manufacturer's recommended protocols with Agilent Probe Array Scan.
| | Sample_data_processing | Raw data was analysed with the MAS5 method using Affymetrix GeneChip Operating Software (GCOS).
| | Sample_data_processing |
| | Sample_data_processing | Data were further analysed as follows: (i) the mean expression ratio and p value was calculated for each transcript, (ii) all transcripts that scored as present in all fetal mesenchymal stem cells absent in all maternal peripheral blood lymphocytes were selected, (iii) these transcripts were then filtered for molecules involved in cell surface linked signal transduction and antigen presentation and (iv) transcripts with a mean expression ratio of >300 were further analysed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Cecilia ,,Götherström
| | Sample_contact_email | cecilia.gotherstrom@ki.se
| | Sample_contact_laboratory | Division for Clinical Immunology, F79
| | Sample_contact_department | Department for Laboratory Medicine
| | Sample_contact_institute | Karolinska Institutet
| | Sample_contact_address | Karolinska University Hospital Huddinge
| | Sample_contact_city | Stockholm
| | Sample_contact_zip/postal_code | 14186
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469129/suppl/GSM469129.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469129/suppl/GSM469129.CHP.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE18934
| | Sample_data_row_count | 54675
| | |
|
GSM469130 | GPL570 |
|
Liver_1
|
Human fetal material, 9-14 weeks, from legal abortions.
|
developmental stage: 9-14 week old fetus
cell type: mesenchymal stem cells
tissue: liver
|
Human mesenchymal stem cells circulate in 1st and early 2nd trimester fetal blood, but not in adults. Like other fetal cell types they cross the placenta, and can be found in maternal organs decades later.
To determine potential ligands in human fetal mesenchymal stem cells not present in maternal blood, the gene expression of 1st trimester human fetal bone marrow, liver and blood derived mesenchymal stem cells will be compared to blood mononuclear cells from pregnant women using a Affymetrix human gene array system.
|
| Sample_geo_accession | GSM469130
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Queen Charlotte's & Chelsea Hospital Hammersmith Campus (anonymous donors).
| | Sample_growth_protocol_ch1 | Human fetal mesenchymal stem cells were isolated from 3 sources (fetal blood, bone marrow and liver, from 9-14 week old fetuses), all from different individuals at legal abortion after informed consent from the patients. Procedures were approved by Hammersmith and Queen Charlotte’s Research Ethics Committee.
| | Sample_growth_protocol_ch1 |
| | Sample_growth_protocol_ch1 | Fetal liver was disintegrated by passage through a 100 μm nylon filter and fetal bone marrow was prepared by flushing long bones with 25-gauge needles. Single cells were suspended in DMEM-High Glucose supplemented with 10% fetal calf serum and 2 mmol/l L-glutamine and 50 IU/ml penicillin/streptomycin. Cells were plated at 1.8x104 cells/cm2 in 10 cm Petri dishes and maintained at 37oC in a humidified environment containing 5% CO2. After 3 days, the non-adherent cells were removed and the medium replaced. The medium was changed every three to four days thereafter. At sub-confluence (70%), cells were detached using 0.05% trypsin and 0.53 mM EDTA and replated at a density of 4x103 cells/cm2. Cells were counted and thereafter snap frozen in 80ºC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen RNeasy Kit. Isolated RNA was analysed with Agilent 2100 Bioanalyzer to verify sample integrity and quantify total RNA yield.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.
| | Sample_hyb_protocol | Hybridization was performed at the Microarray Centre, MRC at Imperial College, London, UK according to the manufacturers protocols.
| | Sample_scan_protocol | Scanning was performed according to the manufacturer's recommended protocols with Agilent Probe Array Scan.
| | Sample_data_processing | Raw data was analysed with the MAS5 method using Affymetrix GeneChip Operating Software (GCOS).
| | Sample_data_processing |
| | Sample_data_processing | Data were further analysed as follows: (i) the mean expression ratio and p value was calculated for each transcript, (ii) all transcripts that scored as present in all fetal mesenchymal stem cells absent in all maternal peripheral blood lymphocytes were selected, (iii) these transcripts were then filtered for molecules involved in cell surface linked signal transduction and antigen presentation and (iv) transcripts with a mean expression ratio of >300 were further analysed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Cecilia ,,Götherström
| | Sample_contact_email | cecilia.gotherstrom@ki.se
| | Sample_contact_laboratory | Division for Clinical Immunology, F79
| | Sample_contact_department | Department for Laboratory Medicine
| | Sample_contact_institute | Karolinska Institutet
| | Sample_contact_address | Karolinska University Hospital Huddinge
| | Sample_contact_city | Stockholm
| | Sample_contact_zip/postal_code | 14186
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469130/suppl/GSM469130.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469130/suppl/GSM469130.CHP.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE18934
| | Sample_data_row_count | 54675
| | |
|
GSM469131 | GPL570 |
|
Liver_2
|
Human fetal material, 9-14 weeks, from legal abortions.
|
developmental stage: 9-14 week old fetus
cell type: mesenchymal stem cells
tissue: liver
|
Human mesenchymal stem cells circulate in 1st and early 2nd trimester fetal blood, but not in adults. Like other fetal cell types they cross the placenta, and can be found in maternal organs decades later.
To determine potential ligands in human fetal mesenchymal stem cells not present in maternal blood, the gene expression of 1st trimester human fetal bone marrow, liver and blood derived mesenchymal stem cells will be compared to blood mononuclear cells from pregnant women using a Affymetrix human gene array system.
|
| Sample_geo_accession | GSM469131
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Queen Charlotte's & Chelsea Hospital Hammersmith Campus (anonymous donors).
| | Sample_growth_protocol_ch1 | Human fetal mesenchymal stem cells were isolated from 3 sources (fetal blood, bone marrow and liver, from 9-14 week old fetuses), all from different individuals at legal abortion after informed consent from the patients. Procedures were approved by Hammersmith and Queen Charlotte’s Research Ethics Committee.
| | Sample_growth_protocol_ch1 |
| | Sample_growth_protocol_ch1 | Fetal liver was disintegrated by passage through a 100 μm nylon filter and fetal bone marrow was prepared by flushing long bones with 25-gauge needles. Single cells were suspended in DMEM-High Glucose supplemented with 10% fetal calf serum and 2 mmol/l L-glutamine and 50 IU/ml penicillin/streptomycin. Cells were plated at 1.8x104 cells/cm2 in 10 cm Petri dishes and maintained at 37oC in a humidified environment containing 5% CO2. After 3 days, the non-adherent cells were removed and the medium replaced. The medium was changed every three to four days thereafter. At sub-confluence (70%), cells were detached using 0.05% trypsin and 0.53 mM EDTA and replated at a density of 4x103 cells/cm2. Cells were counted and thereafter snap frozen in 80ºC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen RNeasy Kit. Isolated RNA was analysed with Agilent 2100 Bioanalyzer to verify sample integrity and quantify total RNA yield.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.
| | Sample_hyb_protocol | Hybridization was performed at the Microarray Centre, MRC at Imperial College, London, UK according to the manufacturers protocols.
| | Sample_scan_protocol | Scanning was performed according to the manufacturer's recommended protocols with Agilent Probe Array Scan.
| | Sample_data_processing | Raw data was analysed with the MAS5 method using Affymetrix GeneChip Operating Software (GCOS).
| | Sample_data_processing |
| | Sample_data_processing | Data were further analysed as follows: (i) the mean expression ratio and p value was calculated for each transcript, (ii) all transcripts that scored as present in all fetal mesenchymal stem cells absent in all maternal peripheral blood lymphocytes were selected, (iii) these transcripts were then filtered for molecules involved in cell surface linked signal transduction and antigen presentation and (iv) transcripts with a mean expression ratio of >300 were further analysed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Cecilia ,,Götherström
| | Sample_contact_email | cecilia.gotherstrom@ki.se
| | Sample_contact_laboratory | Division for Clinical Immunology, F79
| | Sample_contact_department | Department for Laboratory Medicine
| | Sample_contact_institute | Karolinska Institutet
| | Sample_contact_address | Karolinska University Hospital Huddinge
| | Sample_contact_city | Stockholm
| | Sample_contact_zip/postal_code | 14186
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469131/suppl/GSM469131.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469131/suppl/GSM469131.CHP.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE18934
| | Sample_data_row_count | 54675
| | |
|
GSM469132 | GPL570 |
|
Liver_3
|
Human fetal material, 9-14 weeks, from legal abortions.
|
developmental stage: 9-14 week old fetus
cell type: mesenchymal stem cells
tissue: liver
|
Human mesenchymal stem cells circulate in 1st and early 2nd trimester fetal blood, but not in adults. Like other fetal cell types they cross the placenta, and can be found in maternal organs decades later.
To determine potential ligands in human fetal mesenchymal stem cells not present in maternal blood, the gene expression of 1st trimester human fetal bone marrow, liver and blood derived mesenchymal stem cells will be compared to blood mononuclear cells from pregnant women using a Affymetrix human gene array system.
|
| Sample_geo_accession | GSM469132
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Queen Charlotte's & Chelsea Hospital Hammersmith Campus (anonymous donors).
| | Sample_growth_protocol_ch1 | Human fetal mesenchymal stem cells were isolated from 3 sources (fetal blood, bone marrow and liver, from 9-14 week old fetuses), all from different individuals at legal abortion after informed consent from the patients. Procedures were approved by Hammersmith and Queen Charlotte’s Research Ethics Committee.
| | Sample_growth_protocol_ch1 |
| | Sample_growth_protocol_ch1 | Fetal liver was disintegrated by passage through a 100 μm nylon filter and fetal bone marrow was prepared by flushing long bones with 25-gauge needles. Single cells were suspended in DMEM-High Glucose supplemented with 10% fetal calf serum and 2 mmol/l L-glutamine and 50 IU/ml penicillin/streptomycin. Cells were plated at 1.8x104 cells/cm2 in 10 cm Petri dishes and maintained at 37oC in a humidified environment containing 5% CO2. After 3 days, the non-adherent cells were removed and the medium replaced. The medium was changed every three to four days thereafter. At sub-confluence (70%), cells were detached using 0.05% trypsin and 0.53 mM EDTA and replated at a density of 4x103 cells/cm2. Cells were counted and thereafter snap frozen in 80ºC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen RNeasy Kit. Isolated RNA was analysed with Agilent 2100 Bioanalyzer to verify sample integrity and quantify total RNA yield.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.
| | Sample_hyb_protocol | Hybridization was performed at the Microarray Centre, MRC at Imperial College, London, UK according to the manufacturers protocols.
| | Sample_scan_protocol | Scanning was performed according to the manufacturer's recommended protocols with Agilent Probe Array Scan.
| | Sample_data_processing | Raw data was analysed with the MAS5 method using Affymetrix GeneChip Operating Software (GCOS).
| | Sample_data_processing |
| | Sample_data_processing | Data were further analysed as follows: (i) the mean expression ratio and p value was calculated for each transcript, (ii) all transcripts that scored as present in all fetal mesenchymal stem cells absent in all maternal peripheral blood lymphocytes were selected, (iii) these transcripts were then filtered for molecules involved in cell surface linked signal transduction and antigen presentation and (iv) transcripts with a mean expression ratio of >300 were further analysed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Cecilia ,,Götherström
| | Sample_contact_email | cecilia.gotherstrom@ki.se
| | Sample_contact_laboratory | Division for Clinical Immunology, F79
| | Sample_contact_department | Department for Laboratory Medicine
| | Sample_contact_institute | Karolinska Institutet
| | Sample_contact_address | Karolinska University Hospital Huddinge
| | Sample_contact_city | Stockholm
| | Sample_contact_zip/postal_code | 14186
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469132/suppl/GSM469132.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469132/suppl/GSM469132.CHP.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE18934
| | Sample_data_row_count | 54675
| | |
|
GSM469133 | GPL570 |
|
Peripheral blood lymphocytes_1
|
Maternal Peripheral blood lymphocytes
|
developmental stage: pregnant (maternal)
gender: female
cell type: Peripheral blood lymphocytes
|
Human mesenchymal stem cells circulate in 1st and early 2nd trimester fetal blood, but not in adults. Like other fetal cell types they cross the placenta, and can be found in maternal organs decades later.
To determine potential ligands in human fetal mesenchymal stem cells not present in maternal blood, the gene expression of 1st trimester human fetal bone marrow, liver and blood derived mesenchymal stem cells will be compared to blood mononuclear cells from pregnant women using a Affymetrix human gene array system.
|
| Sample_geo_accession | GSM469133
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Queen Charlotte's & Chelsea Hospital Hammersmith Campus (anonymous donors).
| | Sample_growth_protocol_ch1 | Peripheral blood from three pregnant women (gestational weeks 12+0, 12+0 and 13+1) with continuing pregnancies were taken. Adult maternal peripheral blood lymphocytes were prepared by centrifuging peripheral blood layered on a Ficoll gradient at 500g for 20 minutes at room temperature. The interphase was collected, washed twice in phosphate buffer saline by centrifugation and then re-suspended in PBS. Mononuclear cells were counted and the cell pellets snap frozen in 80ºC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen RNeasy Kit. Isolated RNA was analysed with Agilent 2100 Bioanalyzer to verify sample integrity and quantify total RNA yield.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.
| | Sample_hyb_protocol | Hybridization was performed at the Microarray Centre, MRC at Imperial College, London, UK according to the manufacturers protocols.
| | Sample_scan_protocol | Scanning was performed according to the manufacturer's recommended protocols with Agilent Probe Array Scan.
| | Sample_data_processing | Raw data was analysed with the MAS5 method using Affymetrix GeneChip Operating Software (GCOS).
| | Sample_data_processing |
| | Sample_data_processing | Data were further analysed as follows: (i) the mean expression ratio and p value was calculated for each transcript, (ii) all transcripts that scored as present in all fetal mesenchymal stem cells absent in all maternal peripheral blood lymphocytes were selected, (iii) these transcripts were then filtered for molecules involved in cell surface linked signal transduction and antigen presentation and (iv) transcripts with a mean expression ratio of >300 were further analysed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Cecilia ,,Götherström
| | Sample_contact_email | cecilia.gotherstrom@ki.se
| | Sample_contact_laboratory | Division for Clinical Immunology, F79
| | Sample_contact_department | Department for Laboratory Medicine
| | Sample_contact_institute | Karolinska Institutet
| | Sample_contact_address | Karolinska University Hospital Huddinge
| | Sample_contact_city | Stockholm
| | Sample_contact_zip/postal_code | 14186
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469133/suppl/GSM469133.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469133/suppl/GSM469133.CHP.gz
| | Sample_series_id | GSE18934
| | Sample_data_row_count | 54675
| | |
|
GSM469134 | GPL570 |
|
Peripheral blood lymphocytes_2
|
Maternal Peripheral blood lymphocytes
|
developmental stage: pregnant (maternal)
gender: female
cell type: Peripheral blood lymphocytes
|
Human mesenchymal stem cells circulate in 1st and early 2nd trimester fetal blood, but not in adults. Like other fetal cell types they cross the placenta, and can be found in maternal organs decades later.
To determine potential ligands in human fetal mesenchymal stem cells not present in maternal blood, the gene expression of 1st trimester human fetal bone marrow, liver and blood derived mesenchymal stem cells will be compared to blood mononuclear cells from pregnant women using a Affymetrix human gene array system.
|
| Sample_geo_accession | GSM469134
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Queen Charlotte's & Chelsea Hospital Hammersmith Campus (anonymous donors).
| | Sample_growth_protocol_ch1 | Peripheral blood from three pregnant women (gestational weeks 12+0, 12+0 and 13+1) with continuing pregnancies were taken. Adult maternal peripheral blood lymphocytes were prepared by centrifuging peripheral blood layered on a Ficoll gradient at 500g for 20 minutes at room temperature. The interphase was collected, washed twice in phosphate buffer saline by centrifugation and then re-suspended in PBS. Mononuclear cells were counted and the cell pellets snap frozen in 80ºC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen RNeasy Kit. Isolated RNA was analysed with Agilent 2100 Bioanalyzer to verify sample integrity and quantify total RNA yield.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.
| | Sample_hyb_protocol | Hybridization was performed at the Microarray Centre, MRC at Imperial College, London, UK according to the manufacturers protocols.
| | Sample_scan_protocol | Scanning was performed according to the manufacturer's recommended protocols with Agilent Probe Array Scan.
| | Sample_data_processing | Raw data was analysed with the MAS5 method using Affymetrix GeneChip Operating Software (GCOS).
| | Sample_data_processing |
| | Sample_data_processing | Data were further analysed as follows: (i) the mean expression ratio and p value was calculated for each transcript, (ii) all transcripts that scored as present in all fetal mesenchymal stem cells absent in all maternal peripheral blood lymphocytes were selected, (iii) these transcripts were then filtered for molecules involved in cell surface linked signal transduction and antigen presentation and (iv) transcripts with a mean expression ratio of >300 were further analysed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Cecilia ,,Götherström
| | Sample_contact_email | cecilia.gotherstrom@ki.se
| | Sample_contact_laboratory | Division for Clinical Immunology, F79
| | Sample_contact_department | Department for Laboratory Medicine
| | Sample_contact_institute | Karolinska Institutet
| | Sample_contact_address | Karolinska University Hospital Huddinge
| | Sample_contact_city | Stockholm
| | Sample_contact_zip/postal_code | 14186
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469134/suppl/GSM469134.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469134/suppl/GSM469134.CHP.gz
| | Sample_series_id | GSE18934
| | Sample_data_row_count | 54675
| | |
|
GSM469135 | GPL570 |
|
Peripheral blood lymphocytes_3
|
Maternal Peripheral blood lymphocytes
|
developmental stage: pregnant (maternal)
gender: female
cell type: Peripheral blood lymphocytes
|
Human mesenchymal stem cells circulate in 1st and early 2nd trimester fetal blood, but not in adults. Like other fetal cell types they cross the placenta, and can be found in maternal organs decades later.
To determine potential ligands in human fetal mesenchymal stem cells not present in maternal blood, the gene expression of 1st trimester human fetal bone marrow, liver and blood derived mesenchymal stem cells will be compared to blood mononuclear cells from pregnant women using a Affymetrix human gene array system.
|
| Sample_geo_accession | GSM469135
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Queen Charlotte's & Chelsea Hospital Hammersmith Campus (anonymous donors).
| | Sample_growth_protocol_ch1 | Peripheral blood from three pregnant women (gestational weeks 12+0, 12+0 and 13+1) with continuing pregnancies were taken. Adult maternal peripheral blood lymphocytes were prepared by centrifuging peripheral blood layered on a Ficoll gradient at 500g for 20 minutes at room temperature. The interphase was collected, washed twice in phosphate buffer saline by centrifugation and then re-suspended in PBS. Mononuclear cells were counted and the cell pellets snap frozen in 80ºC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen RNeasy Kit. Isolated RNA was analysed with Agilent 2100 Bioanalyzer to verify sample integrity and quantify total RNA yield.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.
| | Sample_hyb_protocol | Hybridization was performed at the Microarray Centre, MRC at Imperial College, London, UK according to the manufacturers protocols.
| | Sample_scan_protocol | Scanning was performed according to the manufacturer's recommended protocols with Agilent Probe Array Scan.
| | Sample_data_processing | Raw data was analysed with the MAS5 method using Affymetrix GeneChip Operating Software (GCOS).
| | Sample_data_processing |
| | Sample_data_processing | Data were further analysed as follows: (i) the mean expression ratio and p value was calculated for each transcript, (ii) all transcripts that scored as present in all fetal mesenchymal stem cells absent in all maternal peripheral blood lymphocytes were selected, (iii) these transcripts were then filtered for molecules involved in cell surface linked signal transduction and antigen presentation and (iv) transcripts with a mean expression ratio of >300 were further analysed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Cecilia ,,Götherström
| | Sample_contact_email | cecilia.gotherstrom@ki.se
| | Sample_contact_laboratory | Division for Clinical Immunology, F79
| | Sample_contact_department | Department for Laboratory Medicine
| | Sample_contact_institute | Karolinska Institutet
| | Sample_contact_address | Karolinska University Hospital Huddinge
| | Sample_contact_city | Stockholm
| | Sample_contact_zip/postal_code | 14186
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469135/suppl/GSM469135.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469135/suppl/GSM469135.CHP.gz
| | Sample_series_id | GSE18934
| | Sample_data_row_count | 54675
| | |
|
GSM469136 | GPL570 |
|
Blood_2
|
Human fetal material, 9-14 weeks, from legal abortions.
|
developmental stage: 9-14 week old fetus
cell type: mesenchymal stem cells
tissue: blood
|
Human mesenchymal stem cells circulate in 1st and early 2nd trimester fetal blood, but not in adults. Like other fetal cell types they cross the placenta, and can be found in maternal organs decades later.
To determine potential ligands in human fetal mesenchymal stem cells not present in maternal blood, the gene expression of 1st trimester human fetal bone marrow, liver and blood derived mesenchymal stem cells will be compared to blood mononuclear cells from pregnant women using a Affymetrix human gene array system.
|
| Sample_geo_accession | GSM469136
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Queen Charlotte's & Chelsea Hospital Hammersmith Campus (anonymous donors).
| | Sample_growth_protocol_ch1 | Human fetal mesenchymal stem cells were isolated from 3 sources (fetal blood, bone marrow and liver, from 9-14 week old fetuses), all from different individuals at legal abortion after informed consent from the patients. Procedures were approved by Hammersmith and Queen Charlotte’s Research Ethics Committee.
| | Sample_growth_protocol_ch1 |
| | Sample_growth_protocol_ch1 | Fetal liver was disintegrated by passage through a 100 μm nylon filter and fetal bone marrow was prepared by flushing long bones with 25-gauge needles. Single cells were suspended in DMEM-High Glucose supplemented with 10% fetal calf serum and 2 mmol/l L-glutamine and 50 IU/ml penicillin/streptomycin. Cells were plated at 1.8x104 cells/cm2 in 10 cm Petri dishes and maintained at 37oC in a humidified environment containing 5% CO2. After 3 days, the non-adherent cells were removed and the medium replaced. The medium was changed every three to four days thereafter. At sub-confluence (70%), cells were detached using 0.05% trypsin and 0.53 mM EDTA and replated at a density of 4x103 cells/cm2. Cells were counted and thereafter snap frozen in 80ºC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen RNeasy Kit. Isolated RNA was analysed with Agilent 2100 Bioanalyzer to verify sample integrity and quantify total RNA yield.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.
| | Sample_hyb_protocol | Hybridization was performed at the Microarray Centre, MRC at Imperial College, London, UK according to the manufacturers protocols.
| | Sample_scan_protocol | Scanning was performed according to the manufacturer's recommended protocols with Agilent Probe Array Scan.
| | Sample_data_processing | Raw data was analysed with the MAS5 method using Affymetrix GeneChip Operating Software (GCOS).
| | Sample_data_processing |
| | Sample_data_processing | Data were further analysed as follows: (i) the mean expression ratio and p value was calculated for each transcript, (ii) all transcripts that scored as present in all fetal mesenchymal stem cells absent in all maternal peripheral blood lymphocytes were selected, (iii) these transcripts were then filtered for molecules involved in cell surface linked signal transduction and antigen presentation and (iv) transcripts with a mean expression ratio of >300 were further analysed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Cecilia ,,Götherström
| | Sample_contact_email | cecilia.gotherstrom@ki.se
| | Sample_contact_laboratory | Division for Clinical Immunology, F79
| | Sample_contact_department | Department for Laboratory Medicine
| | Sample_contact_institute | Karolinska Institutet
| | Sample_contact_address | Karolinska University Hospital Huddinge
| | Sample_contact_city | Stockholm
| | Sample_contact_zip/postal_code | 14186
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469136/suppl/GSM469136.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469136/suppl/GSM469136.CHP.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE18934
| | Sample_data_row_count | 54675
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
