Search results for the GEO ID: GSE12396  |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM310905 | GPL96 |
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Control LXIDN transduced CD34++ cells
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CB CD34+ progenitors cells
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CD34+ hematopoietic progenitors purified from cord blood (CB).
Human CD34+ cells were purified from umbilical cord blood samples, collected after normal deliveries, according to the institutional guidelines for discarded material. Mononuclear cells were isolated by Ficoll-Hypaque (Lymphoprep; Nycomed Pharma, Oslo, Norway) gradient separation, washed twice with PBS, and then CD34+ cells separated using magnetic cell sorting procedure (EasySep Human CD34+ positive selection kit, StemCell Techonologies Inc.; Vancouver, Canada). CD34+ cell purity assessed by flow cytometry were always >95%.
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Synthesis of biotinylated cRNA targets, arrays hybridization (Mouse430_2 GeneChip, Affymetrix, Santa Clara,CA), staining and scanning were performed using Affymetrix standard protocols starting from 100 ng of total RNA.
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| Sample_geo_accession | GSM310905
| | Sample_status | Public on Aug 12 2008
| | Sample_submission_date | Aug 08 2008
| | Sample_last_update_date | Aug 11 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CD34+ hematopoietic progenitors, pre-activated for 48 hours in liquid culture, were transduced by two cycles of infection (12 h each) with viral supernatant on retronectin-coated plates (10 ug / cm2). NGFR purification of transduced cells was performed after a 48 hours post-transduction incubation using a purified mouse anti - human p75 - NGFR monoclonal antibody (MoAb) and tiny FACS-compatible magnetic nanoparticles in a column-free magnetic system [EasySepTM “Do-It-Your Self” Selection Kit (Stem cells Technologies; Vancouver, BC, Canada)] following the manufacturer guidelines.
| | Sample_growth_protocol_ch1 | Human CD34+ hematopoietic stem / progenitor cells were purified from umbilical cord blood (CB) samples and maintained in liquid culture for two weeks. During the initial 5 days of culture, necessary for retroviral transduction, these cells were seeded at a 5-10 x 10^4 / ml density in IMDM (Euroclone) containing 10% Human Serum (HS) (Biowhittaker) and early acting human hematopoietic cytokines: 50 ng/ml Stem Cell Factor (SCF) and Flt3-ligand (Flt3-l), 20 ng/ml Thrombopoietin (TPO), 10 ng/ml Interleukin-6 (IL-6) and Interleukin-3 (IL-3) (R&D Systems, Minneapolis, MN). The subsequent phase of culture was accomplished in similar conditions without TPO and in the presence of 20 % FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from the various analyzed cell populations by means of the Qiagen total RNA purification kits as recommended by the manufacturer (Qiagen, Valencia, CA). RNA integrity and concentration was then verified by the Bio-Analyzer technique
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA pools (100 ng) of LXIDN transduced CD34+ cells, obtained from three independent experiments, were converted in labelled cRNA according with the “Two cycle” protocol advised by Affymetrix. cRNA has been used to hybridise Affymetrix HG-U133A GeneChip arrays
| | Sample_hyb_protocol | Affymetrix Human HG-U133A GeneChip arrays hybridization and staining was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA).The fragmented cRNA was then hybridized to an identical lot of Affymetrix Human HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | Scaling to TGT value=90. The GeneChip-Operating-Software (GCOS) absolute analysis algorithm 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.
| | Sample_platform_id | GPL96
| | Sample_contact_name | CLAUDIA,,GEMELLI
| | Sample_contact_email | gemelli.claudia@unimore.it
| | Sample_contact_phone | 059 2055404
| | Sample_contact_fax | 059 2055410
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Biomedical Science
| | Sample_contact_institute | University of Modena and Reggio Emilia
| | Sample_contact_address | Via Campi 287
| | Sample_contact_city | Modena
| | Sample_contact_state | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310905/suppl/GSM310905.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310905/suppl/GSM310905.CHP.gz
| | Sample_series_id | GSE12396
| | Sample_data_row_count | 22283
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GSM311193 | GPL96 |
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LHoxA10IDN transduced CD34+ cells
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Cord Blood CD34++ hematopoeitic progenitors
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Human CD34+ cells were purified from umbilical cord blood samples, collected after normal deliveries, according to the institutional guidelines for discarded material. Mononuclear cells were isolated by Ficoll-Hypaque (Lymphoprep; Nycomed Pharma, Oslo, Norway) gradient separation, washed twice with PBS, and then CD34+ cells separated using magnetic cell sorting procedure (EasySep Human CD34+ positive selection kit, StemCell Techonologies Inc.; Vancouver, Canada). CD34+ cell purity assessed by flow cytometry were always >95%.
|
Synthesis of biotinylated cRNA targets, arrays hybridization staining and scanning were performed using Affymetrix standard protocols starting from 100 ng of total RNA.
|
| Sample_geo_accession | GSM311193
| | Sample_status | Public on Aug 12 2008
| | Sample_submission_date | Aug 09 2008
| | Sample_last_update_date | Aug 11 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CD34+ hematopoietic progenitors, pre-activated for 48 hours in liquid culture, were transduced by two cycles of infection (12 h each) with viral supernatant on retronectin-coated plates (10 ug / cm2). NGFR purification of transduced cells was performed after a 48 hours post-transduction incubation using a purified mouse anti - human p75 - NGFR monoclonal antibody (MoAb) and tiny FACS-compatible magnetic nanoparticles in a column-free magnetic system [EasySepTM “Do-It-Your Self” Selection Kit (Stem cells Technologies; Vancouver, BC, Canada)] following the manufacturer guidelines.
| | Sample_growth_protocol_ch1 | Human CD34+ hematopoietic stem / progenitor cells were purified from umbilical cord blood (CB) samples and maintained in liquid culture for two weeks. During the initial 5 days of culture, necessary for retroviral transduction, these cells were seeded at a 5-10 x 10^4 / ml density in IMDM (Euroclone) containing 10% Human Serum (HS) (Biowhittaker) and early acting human hematopoietic cytokines: 50 ng/ml Stem Cell Factor (SCF) and Flt3-ligand (Flt3-l), 20 ng/ml Thrombopoietin (TPO), 10 ng/ml Interleukin-6 (IL-6) and Interleukin-3 (IL-3) (R&D Systems, Minneapolis, MN). The subsequent phase of culture was accomplished in similar conditions without TPO and in the presence of 20 % FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from the analyzed cell population by means of the Qiagen total RNA purification kits as recommended by the manufacturer (Qiagen, Valencia, CA). RNA integrity and concentration was then verified by the Bio-Analyzer technique (Applied Biosystem, Foster City, CA, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA pools (100 ng) of LHoxA10IDN transduced CD34+ cells, obtained from three independent experiments, were converted in labelled cRNA according with the “Two cycle” protocol advised by Affymetrix. cRNA has been used to hybridise Affymetrix HG-U133A GeneChip arrays
| | Sample_hyb_protocol | Affymetrix Human HG-U133A GeneChip arrays hybridization and staining was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA).The fragmented cRNA was then hybridized to an identical lot of Affymetrix Human HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | Scaling to TGT value=90. The GeneChip-Operating-Software (GCOS) absolute analysis algorithm 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.
| | Sample_platform_id | GPL96
| | Sample_contact_name | CLAUDIA,,GEMELLI
| | Sample_contact_email | gemelli.claudia@unimore.it
| | Sample_contact_phone | 059 2055404
| | Sample_contact_fax | 059 2055410
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Biomedical Science
| | Sample_contact_institute | University of Modena and Reggio Emilia
| | Sample_contact_address | Via Campi 287
| | Sample_contact_city | Modena
| | Sample_contact_state | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311193/suppl/GSM311193.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311193/suppl/GSM311193.CHP.gz
| | Sample_series_id | GSE12396
| | Sample_data_row_count | 22283
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