Search results for the GEO ID: GSE4600  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM102825 | GPL570 |
|
UD rep 1
|
SH-SY5Y neuronal cells
|
SH-SY5Y neuroblastoma cells obtained from ATCC.
UD -Undifferentiated cells (before PMA addition).
|
Gene expression data from experimental treatment UD = Undifferentiated SH-SY5Y cells, i.e. before PMA induced differentiation (UD).
|
| Sample_geo_accession | GSM102825
| | Sample_status | Public on Jun 15 2006
| | Sample_submission_date | Apr 03 2006
| | Sample_last_update_date | May 11 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | SH-SY5Y human neuroblastoma cells (ATCC) were grown in complete minimal essential media (MEM) with 15% fetal calf serum in a large tissue culture flasks until 70-80% confluency. Differentiation was induced by adding 16 nM PMA resulting in neuronal phenotype. 12 h prior to PMA addition, transfect the cells with methylated oligonucleotide MeCP2 decoy (MD),which blocks the the binding of MeCP2 to the endogenous sites. Transfection with control decoy is also performed (CD).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriZol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microgram total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 1 microgram of biotinylated cRNA were hybridized on GeneChip Human HG U133 plus 2.0 array for 16 hr at 45C in a GeneChip hybridization oven 640. GeneChips were washed and stained in the GeneChip Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix 3000 GeneChip scanner.
| | Sample_data_processing | The data were analyzed with dChip analysis software available at http://biosun1.harvard.edu/complab/dchip/. With Invariant set normalization and Model based expression analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sailaja,,Peddada
| | Sample_contact_laboratory | LaSalle Lab
| | Sample_contact_department | Medical Microbiology and Immunology
| | Sample_contact_institute | University of California, Davis
| | Sample_contact_address | 3426 Tupper Hall, One Shields Avenue
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95616
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM102nnn/GSM102825/suppl/GSM102825.CEL.gz
| | Sample_series_id | GSE4600
| | Sample_data_row_count | 54613
| | |
|
GSM102842 | GPL570 |
|
UD rep 2
|
SH-SY5Y neuronal cells
|
SH-SY5Y neuroblastoma cells obtained from ATCC.
UD -Undifferentiated cells (before PMA addition).
|
Gene expression data from experimental treatment UD = Undifferentiated SH-SY5Y cells, i.e. before PMA induced differentiation (UD).
|
| Sample_geo_accession | GSM102842
| | Sample_status | Public on Jun 15 2006
| | Sample_submission_date | Apr 03 2006
| | Sample_last_update_date | May 11 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | SH-SY5Y human neuroblastoma cells (ATCC) were grown in complete minimal essential media (MEM) with 15% fetal calf serum in a large tissue culture flasks until 70-80% confluency. Differentiation was induced by adding 16 nM PMA resulting in neuronal phenotype. 12 h prior to PMA addition, transfect the cells with methylated oligonucleotide MeCP2 decoy (MD),which blocks the the binding of MeCP2 to the endogenous sites. Transfection with control decoy is also performed (CD).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriZol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microgram total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 1 microgram of biotinylated cRNA were hybridized on GeneChip Human HG U133 plus 2.0 array for 16 hr at 45C in a GeneChip hybridization oven 640. GeneChips were washed and stained in the GeneChip Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix 3000 GeneChip scanner.
| | Sample_data_processing | The data were analyzed with dChip analysis software available at http://biosun1.harvard.edu/complab/dchip/. With Invariant set normalization and Model based expression analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sailaja,,Peddada
| | Sample_contact_laboratory | LaSalle Lab
| | Sample_contact_department | Medical Microbiology and Immunology
| | Sample_contact_institute | University of California, Davis
| | Sample_contact_address | 3426 Tupper Hall, One Shields Avenue
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95616
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM102nnn/GSM102842/suppl/GSM102842.CEL.gz
| | Sample_series_id | GSE4600
| | Sample_data_row_count | 54613
| | |
|
GSM102870 | GPL570 |
|
UD rep 3
|
SH-SY5Y neuronal cells
|
SH-SY5Y neuroblastoma cells obtained from ATCC.
UD -Undifferentiated cells (before PMA addition).
|
Gene expression data from experimental treatment UD = Undifferentiated SH-SY5Y cells, i.e. before PMA induced differentiation (UD).
|
| Sample_geo_accession | GSM102870
| | Sample_status | Public on Jun 15 2006
| | Sample_submission_date | Apr 03 2006
| | Sample_last_update_date | May 11 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | SH-SY5Y human neuroblastoma cells (ATCC) were grown in complete minimal essential media (MEM) with 15% fetal calf serum in a large tissue culture flasks until 70-80% confluency. Differentiation was induced by adding 16 nM PMA resulting in neuronal phenotype. 12 h prior to PMA addition, transfect the cells with methylated oligonucleotide MeCP2 decoy (MD),which blocks the the binding of MeCP2 to the endogenous sites. Transfection with control decoy is also performed (CD).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriZol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microgram total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 1 microgram of biotinylated cRNA were hybridized on GeneChip Human HG U133 plus 2.0 array for 16 hr at 45C in a GeneChip hybridization oven 640. GeneChips were washed and stained in the GeneChip Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix 3000 GeneChip scanner.
| | Sample_data_processing | The data were analyzed with dChip analysis software available at http://biosun1.harvard.edu/complab/dchip/. With Invariant set normalization and Model based expression analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sailaja,,Peddada
| | Sample_contact_laboratory | LaSalle Lab
| | Sample_contact_department | Medical Microbiology and Immunology
| | Sample_contact_institute | University of California, Davis
| | Sample_contact_address | 3426 Tupper Hall, One Shields Avenue
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95616
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM102nnn/GSM102870/suppl/GSM102870.CEL.gz
| | Sample_series_id | GSE4600
| | Sample_data_row_count | 54613
| | |
|
GSM102875 | GPL570 |
|
UT rep 1
|
SH-SY5Y neuronal cells
|
SH-SY5Y neuroblastoma cells obtained from ATCC.
48h after PMA addition
|
Gene expression data from experimental treatment D-UT = 48h after PMA induced differentiated SH-SY5Y cells.
|
| Sample_geo_accession | GSM102875
| | Sample_status | Public on Jun 15 2006
| | Sample_submission_date | Apr 03 2006
| | Sample_last_update_date | May 11 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | SH-SY5Y human neuroblastoma cells (ATCC) were grown in complete minimal essential media (MEM) with 15% fetal calf serum in a large tissue culture flasks until 70-80% confluency. Differentiation was induced by adding 16 nM PMA resulting in neuronal phenotype. 12 h prior to PMA addition, transfect the cells with methylated oligonucleotide MeCP2 decoy (MD),which blocks the the binding of MeCP2 to the endogenous sites. Transfection with control decoy is also performed (CD).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriZol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microgram total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 1 microgram of biotinylated cRNA were hybridized on GeneChip Human HG U133 plus 2.0 array for 16 hr at 45C in a GeneChip hybridization oven 640. GeneChips were washed and stained in the GeneChip Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix 3000 GeneChip scanner.
| | Sample_data_processing | The data were analyzed with dChip analysis software available at http://biosun1.harvard.edu/complab/dchip/. With Invariant set normalization and Model based expression analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sailaja,,Peddada
| | Sample_contact_laboratory | LaSalle Lab
| | Sample_contact_department | Medical Microbiology and Immunology
| | Sample_contact_institute | University of California, Davis
| | Sample_contact_address | 3426 Tupper Hall, One Shields Avenue
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95616
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM102nnn/GSM102875/suppl/GSM102875.CEL.gz
| | Sample_series_id | GSE4600
| | Sample_data_row_count | 54613
| | |
|
GSM102876 | GPL570 |
|
UT rep 2
|
SH-SY5Y neuronal cells
|
SH-SY5Y neuroblastoma cells obtained from ATCC.
48h after PMA addition
|
Gene expression data from experimental treatment D-UT = 48h after PMA induced differentiated SH-SY5Y cells.
|
| Sample_geo_accession | GSM102876
| | Sample_status | Public on Jun 15 2006
| | Sample_submission_date | Apr 03 2006
| | Sample_last_update_date | May 11 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | SH-SY5Y human neuroblastoma cells (ATCC) were grown in complete minimal essential media (MEM) with 15% fetal calf serum in a large tissue culture flasks until 70-80% confluency. Differentiation was induced by adding 16 nM PMA resulting in neuronal phenotype. 12 h prior to PMA addition, transfect the cells with methylated oligonucleotide MeCP2 decoy (MD),which blocks the the binding of MeCP2 to the endogenous sites. Transfection with control decoy is also performed (CD).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriZol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microgram total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 1 microgram of biotinylated cRNA were hybridized on GeneChip Human HG U133 plus 2.0 array for 16 hr at 45C in a GeneChip hybridization oven 640. GeneChips were washed and stained in the GeneChip Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix 3000 GeneChip scanner.
| | Sample_data_processing | The data were analyzed with dChip analysis software available at http://biosun1.harvard.edu/complab/dchip/. With Invariant set normalization and Model based expression analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sailaja,,Peddada
| | Sample_contact_laboratory | LaSalle Lab
| | Sample_contact_department | Medical Microbiology and Immunology
| | Sample_contact_institute | University of California, Davis
| | Sample_contact_address | 3426 Tupper Hall, One Shields Avenue
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95616
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM102nnn/GSM102876/suppl/GSM102876.CEL.gz
| | Sample_series_id | GSE4600
| | Sample_data_row_count | 54613
| | |
|
GSM102877 | GPL570 |
|
UT rep 3
|
SH-SY5Y neuronal cells
|
SH-SY5Y neuroblastoma cells obtained from ATCC.
48h after PMA addition
|
Gene expression data from experimental treatment D-UT = 48h after PMA induced differentiated SH-SY5Y cells.
|
| Sample_geo_accession | GSM102877
| | Sample_status | Public on Jun 15 2006
| | Sample_submission_date | Apr 03 2006
| | Sample_last_update_date | May 11 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | SH-SY5Y human neuroblastoma cells (ATCC) were grown in complete minimal essential media (MEM) with 15% fetal calf serum in a large tissue culture flasks until 70-80% confluency. Differentiation was induced by adding 16 nM PMA resulting in neuronal phenotype. 12 h prior to PMA addition, transfect the cells with methylated oligonucleotide MeCP2 decoy (MD),which blocks the the binding of MeCP2 to the endogenous sites. Transfection with control decoy is also performed (CD).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriZol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microgram total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 1 microgram of biotinylated cRNA were hybridized on GeneChip Human HG U133 plus 2.0 array for 16 hr at 45C in a GeneChip hybridization oven 640. GeneChips were washed and stained in the GeneChip Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix 3000 GeneChip scanner.
| | Sample_data_processing | The data were analyzed with dChip analysis software available at http://biosun1.harvard.edu/complab/dchip/. With Invariant set normalization and Model based expression analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sailaja,,Peddada
| | Sample_contact_laboratory | LaSalle Lab
| | Sample_contact_department | Medical Microbiology and Immunology
| | Sample_contact_institute | University of California, Davis
| | Sample_contact_address | 3426 Tupper Hall, One Shields Avenue
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95616
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM102nnn/GSM102877/suppl/GSM102877.CEL.gz
| | Sample_series_id | GSE4600
| | Sample_data_row_count | 54613
| | |
|
GSM102878 | GPL570 |
|
MD rep 1
|
SH-SY5Y neuronal cells
|
SH-SY5Y neuroblastoma cells obtained from ATCC.
differentiated and MeCP2 decoy transfected SH-SY5Y cells
|
Gene expression data from experimental treatment D-MD = differentiated and MeCP2 decoy transfected cells.
|
| Sample_geo_accession | GSM102878
| | Sample_status | Public on Jun 15 2006
| | Sample_submission_date | Apr 03 2006
| | Sample_last_update_date | May 11 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | SH-SY5Y human neuroblastoma cells (ATCC) were grown in complete minimal essential media (MEM) with 15% fetal calf serum in a large tissue culture flasks until 70-80% confluency. Differentiation was induced by adding 16 nM PMA resulting in neuronal phenotype. 12 h prior to PMA addition, transfect the cells with methylated oligonucleotide MeCP2 decoy (MD),which blocks the the binding of MeCP2 to the endogenous sites. Transfection with control decoy is also performed (CD).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriZol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microgram total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 1 microgram of biotinylated cRNA were hybridized on GeneChip Human HG U133 plus 2.0 array for 16 hr at 45C in a GeneChip hybridization oven 640. GeneChips were washed and stained in the GeneChip Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix 3000 GeneChip scanner.
| | Sample_data_processing | The data were analyzed with dChip analysis software available at http://biosun1.harvard.edu/complab/dchip/. With Invariant set normalization and Model based expression analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sailaja,,Peddada
| | Sample_contact_laboratory | LaSalle Lab
| | Sample_contact_department | Medical Microbiology and Immunology
| | Sample_contact_institute | University of California, Davis
| | Sample_contact_address | 3426 Tupper Hall, One Shields Avenue
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95616
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM102nnn/GSM102878/suppl/GSM102878.CEL.gz
| | Sample_series_id | GSE4600
| | Sample_data_row_count | 54613
| | |
|
GSM102879 | GPL570 |
|
MD rep 2
|
SH-SY5Y neuronal cells
|
SH-SY5Y neuroblastoma cells obtained from ATCC.
differentiated and MeCP2 decoy transfected SH-SY5Y cells
|
Gene expression data from experimental treatment D-MD = differentiated and MeCP2 decoy transfected cells.
|
| Sample_geo_accession | GSM102879
| | Sample_status | Public on Jun 15 2006
| | Sample_submission_date | Apr 03 2006
| | Sample_last_update_date | May 11 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | SH-SY5Y human neuroblastoma cells (ATCC) were grown in complete minimal essential media (MEM) with 15% fetal calf serum in a large tissue culture flasks until 70-80% confluency. Differentiation was induced by adding 16 nM PMA resulting in neuronal phenotype. 12 h prior to PMA addition, transfect the cells with methylated oligonucleotide MeCP2 decoy (MD),which blocks the the binding of MeCP2 to the endogenous sites. Transfection with control decoy is also performed (CD).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriZol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microgram total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 1 microgram of biotinylated cRNA were hybridized on GeneChip Human HG U133 plus 2.0 array for 16 hr at 45C in a GeneChip hybridization oven 640. GeneChips were washed and stained in the GeneChip Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix 3000 GeneChip scanner.
| | Sample_data_processing | The data were analyzed with dChip analysis software available at http://biosun1.harvard.edu/complab/dchip/. With Invariant set normalization and Model based expression analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sailaja,,Peddada
| | Sample_contact_laboratory | LaSalle Lab
| | Sample_contact_department | Medical Microbiology and Immunology
| | Sample_contact_institute | University of California, Davis
| | Sample_contact_address | 3426 Tupper Hall, One Shields Avenue
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95616
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM102nnn/GSM102879/suppl/GSM102879.CEL.gz
| | Sample_series_id | GSE4600
| | Sample_data_row_count | 54613
| | |
|
GSM102880 | GPL570 |
|
MD rep 3
|
SH-SY5Y neuronal cells
|
SH-SY5Y neuroblastoma cells obtained from ATCC.
differentiated and MeCP2 decoy transfected SH-SY5Y cells
|
Gene expression data from experimental treatment D-MD = differentiated and MeCP2 decoy transfected cells.
|
| Sample_geo_accession | GSM102880
| | Sample_status | Public on Jun 15 2006
| | Sample_submission_date | Apr 03 2006
| | Sample_last_update_date | May 11 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | SH-SY5Y human neuroblastoma cells (ATCC) were grown in complete minimal essential media (MEM) with 15% fetal calf serum in a large tissue culture flasks until 70-80% confluency. Differentiation was induced by adding 16 nM PMA resulting in neuronal phenotype. 12 h prior to PMA addition, transfect the cells with methylated oligonucleotide MeCP2 decoy (MD),which blocks the the binding of MeCP2 to the endogenous sites. Transfection with control decoy is also performed (CD).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriZol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microgram total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 1 microgram of biotinylated cRNA were hybridized on GeneChip Human HG U133 plus 2.0 array for 16 hr at 45C in a GeneChip hybridization oven 640. GeneChips were washed and stained in the GeneChip Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix 3000 GeneChip scanner.
| | Sample_data_processing | The data were analyzed with dChip analysis software available at http://biosun1.harvard.edu/complab/dchip/. With Invariant set normalization and Model based expression analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sailaja,,Peddada
| | Sample_contact_laboratory | LaSalle Lab
| | Sample_contact_department | Medical Microbiology and Immunology
| | Sample_contact_institute | University of California, Davis
| | Sample_contact_address | 3426 Tupper Hall, One Shields Avenue
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95616
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM102nnn/GSM102880/suppl/GSM102880.CEL.gz
| | Sample_series_id | GSE4600
| | Sample_data_row_count | 54613
| | |
|
GSM102881 | GPL570 |
|
CD rep 1
|
SH-SY5Y neuronal cells
|
SH-SY5Y neuroblastoma cells obtained from ATCC.
differentiated and control decoy transfected SH-SY5Y cells
|
Gene expression data from experimental treatment D-CD = Differentiated and control decoy transfected cells.
|
| Sample_geo_accession | GSM102881
| | Sample_status | Public on Jun 15 2006
| | Sample_submission_date | Apr 03 2006
| | Sample_last_update_date | May 11 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | SH-SY5Y human neuroblastoma cells (ATCC) were grown in complete minimal essential media (MEM) with 15% fetal calf serum in a large tissue culture flasks until 70-80% confluency. Differentiation was induced by adding 16 nM PMA resulting in neuronal phenotype. 12 h prior to PMA addition, transfect the cells with methylated oligonucleotide MeCP2 decoy (MD),which blocks the the binding of MeCP2 to the endogenous sites. Transfection with control decoy is also performed (CD).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriZol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microgram total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 1 microgram of biotinylated cRNA were hybridized on GeneChip Human HG U133 plus 2.0 array for 16 hr at 45C in a GeneChip hybridization oven 640. GeneChips were washed and stained in the GeneChip Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix 3000 GeneChip scanner.
| | Sample_data_processing | The data were analyzed with dChip analysis software available at http://biosun1.harvard.edu/complab/dchip/. With Invariant set normalization and Model based expression analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sailaja,,Peddada
| | Sample_contact_laboratory | LaSalle Lab
| | Sample_contact_department | Medical Microbiology and Immunology
| | Sample_contact_institute | University of California, Davis
| | Sample_contact_address | 3426 Tupper Hall, One Shields Avenue
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95616
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM102nnn/GSM102881/suppl/GSM102881.CEL.gz
| | Sample_series_id | GSE4600
| | Sample_data_row_count | 54613
| | |
|
GSM102882 | GPL570 |
|
CD rep 2
|
SH-SY5Y neuronal cells
|
SH-SY5Y neuroblastoma cells obtained from ATCC.
differentiated and control decoy transfected SH-SY5Y cells
|
Gene expression data from experimental treatment D-CD = Differentiated and control decoy transfected cells.
|
| Sample_geo_accession | GSM102882
| | Sample_status | Public on Jun 15 2006
| | Sample_submission_date | Apr 03 2006
| | Sample_last_update_date | May 11 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | SH-SY5Y human neuroblastoma cells (ATCC) were grown in complete minimal essential media (MEM) with 15% fetal calf serum in a large tissue culture flasks until 70-80% confluency. Differentiation was induced by adding 16 nM PMA resulting in neuronal phenotype. 12 h prior to PMA addition, transfect the cells with methylated oligonucleotide MeCP2 decoy (MD),which blocks the the binding of MeCP2 to the endogenous sites. Transfection with control decoy is also performed (CD).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriZol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microgram total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 1 microgram of biotinylated cRNA were hybridized on GeneChip Human HG U133 plus 2.0 array for 16 hr at 45C in a GeneChip hybridization oven 640. GeneChips were washed and stained in the GeneChip Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix 3000 GeneChip scanner.
| | Sample_data_processing | The data were analyzed with dChip analysis software available at http://biosun1.harvard.edu/complab/dchip/. With Invariant set normalization and Model based expression analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sailaja,,Peddada
| | Sample_contact_laboratory | LaSalle Lab
| | Sample_contact_department | Medical Microbiology and Immunology
| | Sample_contact_institute | University of California, Davis
| | Sample_contact_address | 3426 Tupper Hall, One Shields Avenue
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95616
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM102nnn/GSM102882/suppl/GSM102882.CEL.gz
| | Sample_series_id | GSE4600
| | Sample_data_row_count | 54613
| | |
|
GSM102883 | GPL570 |
|
CD rep 3
|
SH-SY5Y neuronal cells
|
SH-SY5Y neuroblastoma cells obtained from ATCC.
differentiated and control decoy transfected SH-SY5Y cells
|
Gene expression data from experimental treatment D-CD = Differentiated and control decoy transfected cells.
|
| Sample_geo_accession | GSM102883
| | Sample_status | Public on Jun 15 2006
| | Sample_submission_date | Apr 03 2006
| | Sample_last_update_date | May 11 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | SH-SY5Y human neuroblastoma cells (ATCC) were grown in complete minimal essential media (MEM) with 15% fetal calf serum in a large tissue culture flasks until 70-80% confluency. Differentiation was induced by adding 16 nM PMA resulting in neuronal phenotype. 12 h prior to PMA addition, transfect the cells with methylated oligonucleotide MeCP2 decoy (MD),which blocks the the binding of MeCP2 to the endogenous sites. Transfection with control decoy is also performed (CD).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriZol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microgram total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 1 microgram of biotinylated cRNA were hybridized on GeneChip Human HG U133 plus 2.0 array for 16 hr at 45C in a GeneChip hybridization oven 640. GeneChips were washed and stained in the GeneChip Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix 3000 GeneChip scanner.
| | Sample_data_processing | The data were analyzed with dChip analysis software available at http://biosun1.harvard.edu/complab/dchip/. With Invariant set normalization and Model based expression analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sailaja,,Peddada
| | Sample_contact_laboratory | LaSalle Lab
| | Sample_contact_department | Medical Microbiology and Immunology
| | Sample_contact_institute | University of California, Davis
| | Sample_contact_address | 3426 Tupper Hall, One Shields Avenue
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95616
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM102nnn/GSM102883/suppl/GSM102883.CEL.gz
| | Sample_series_id | GSE4600
| | Sample_data_row_count | 54613
| | |
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