Search results for the GEO ID: GSE33769  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM833438 | GPL570 |
|
fibroblast_patient_1_A
|
human fibroblast, Q10 deficient patient 1, rep. 1
|
age: 12-year-old
gender: girl
clinical phenotype: (1) ataxia and cerebellar atrophy, (2) decreased mitochondrial enzimatic activities in complex I+III and complex II+III, and (3) CoQ concentration in muscle was decreased.
treatment: After 16 months of CoQ supplementation, the patient is now able to walk unaided and cerebellar signs have disappeared.
|
|
| Sample_geo_accession | GSM833438
| | Sample_status | Public on Apr 05 2013
| | Sample_submission_date | Nov 16 2011
| | Sample_last_update_date | Apr 05 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were homogenized in 1 ml of Tripure Isolation Reagent (Roche) and RNA was extracted with chloroform and precipitated with 2-propanol by centrifugation at 12000 g for 10 min at 4ºC. After washing with 75% EtOH, RNA was resuspended in DEPC-treated water and treated with deoxiribonuclease I (Sigma) for removal of possible DNA contamination. Afterwards, RNA was cleaned using the RNeasy® MinElute™ Cleanup kit (Qiagen), its concentration and purity were checked spectrophotometrically and its quality was verified electrophoretically. RNA was stored at –20 ºC in RNase-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A cRNA probe was synthesized and fragmented from each RNA sample using Affymetrix protocols and kits provided by Qiagen.
| | Sample_hyb_protocol | Each cRNA probe was hybridized to independent GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix).
| | Sample_hyb_protocol | Hybridization was performed overnight in the GeneChip Hybridization
| | Sample_hyb_protocol | Oven 640 at 45ºC with shaking at 60 rpm; washes and staining of
| | Sample_hyb_protocol | the probe were performed in the GeneChip fluidics station using
| | Sample_hyb_protocol | buffers and protocols provided by the manufacturer.
| | Sample_hyb_protocol | The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_scan_protocol | High-quality scan of the arrays was performed with the GeneChip Scanner 3000. The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_data_processing | Data extraction, cell intensity calculation and computational analysis were performed using GCOS and Expression Console Release Software from Affymetrix. The signal value was obtained using MAS5 and RMA algorithms at linear scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daniel Jose,,Moreno Fernandez-Ayala
| | Sample_contact_email | dmorfer@upo.es
| | Sample_contact_laboratory | CABD/CSIC-UPO
| | Sample_contact_institute | Universidad Pablo de Olavide
| | Sample_contact_address | Carretera de Utrera, Km. 1
| | Sample_contact_city | Sevilla
| | Sample_contact_zip/postal_code | 41013
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833438/suppl/GSM833438_UBIGENES1A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833438/suppl/GSM833438_UBIGENES1A.mas5.CHP.gz
| | Sample_series_id | GSE33769
| | Sample_series_id | GSE33941
| | Sample_data_row_count | 54675
| | |
|
GSM833441 | GPL570 |
|
fibroblast_patient_1_B
|
human fibroblast, Q10 deficient patient 1, rep. 2
|
age: 12-year-old
gender: girl
clinical phenotype: (1) ataxia and cerebellar atrophy, (2) decreased mitochondrial enzimatic activities in complex I+III and complex II+III, and (3) CoQ concentration in muscle was decreased.
treatment: After 16 months of CoQ supplementation, the patient is now able to walk unaided and cerebellar signs have disappeared.
|
|
| Sample_geo_accession | GSM833441
| | Sample_status | Public on Apr 05 2013
| | Sample_submission_date | Nov 16 2011
| | Sample_last_update_date | Apr 05 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were homogenized in 1 ml of Tripure Isolation Reagent (Roche) and RNA was extracted with chloroform and precipitated with 2-propanol by centrifugation at 12000 g for 10 min at 4ºC. After washing with 75% EtOH, RNA was resuspended in DEPC-treated water and treated with deoxiribonuclease I (Sigma) for removal of possible DNA contamination. Afterwards, RNA was cleaned using the RNeasy® MinElute™ Cleanup kit (Qiagen), its concentration and purity were checked spectrophotometrically and its quality was verified electrophoretically. RNA was stored at –20 ºC in RNase-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A cRNA probe was synthesized and fragmented from each RNA sample using Affymetrix protocols and kits provided by Qiagen.
| | Sample_hyb_protocol | Each cRNA probe was hybridized to independent GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix).
| | Sample_hyb_protocol | Hybridization was performed overnight in the GeneChip Hybridization
| | Sample_hyb_protocol | Oven 640 at 45ºC with shaking at 60 rpm; washes and staining of
| | Sample_hyb_protocol | the probe were performed in the GeneChip fluidics station using
| | Sample_hyb_protocol | buffers and protocols provided by the manufacturer.
| | Sample_hyb_protocol | The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_scan_protocol | High-quality scan of the arrays was performed with the GeneChip Scanner 3000. The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_data_processing | Data extraction, cell intensity calculation and computational analysis were performed using GCOS and Expression Console Release Software from Affymetrix. The signal value was obtained using MAS5 and RMA algorithms at linear scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daniel Jose,,Moreno Fernandez-Ayala
| | Sample_contact_email | dmorfer@upo.es
| | Sample_contact_laboratory | CABD/CSIC-UPO
| | Sample_contact_institute | Universidad Pablo de Olavide
| | Sample_contact_address | Carretera de Utrera, Km. 1
| | Sample_contact_city | Sevilla
| | Sample_contact_zip/postal_code | 41013
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833441/suppl/GSM833441_UBIGENES1B.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833441/suppl/GSM833441_UBIGENES1B.mas5.CHP.gz
| | Sample_series_id | GSE33769
| | Sample_series_id | GSE33941
| | Sample_data_row_count | 54675
| | |
|
GSM833444 | GPL570 |
|
fibroblast_patient_1_C
|
human fibroblast, Q10 deficient patient 1, rep. 3
|
age: 12-year-old
gender: girl
clinical phenotype: (1) ataxia and cerebellar atrophy, (2) decreased mitochondrial enzimatic activities in complex I+III and complex II+III, and (3) CoQ concentration in muscle was decreased.
treatment: After 16 months of CoQ supplementation, the patient is now able to walk unaided and cerebellar signs have disappeared.
|
reference: Artuch, R. et al. Cerebellar ataxia with coenzyme Q10 deficiency: diagnosis and follow-up after coenzyme Q10 supplementation. J Neurol Sci 246, 153-8 (2006). PubMed ID: 16677673
|
| Sample_geo_accession | GSM833444
| | Sample_status | Public on Apr 05 2013
| | Sample_submission_date | Nov 16 2011
| | Sample_last_update_date | Apr 05 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were homogenized in 1 ml of Tripure Isolation Reagent (Roche) and RNA was extracted with chloroform and precipitated with 2-propanol by centrifugation at 12000 g for 10 min at 4ºC. After washing with 75% EtOH, RNA was resuspended in DEPC-treated water and treated with deoxiribonuclease I (Sigma) for removal of possible DNA contamination. Afterwards, RNA was cleaned using the RNeasy® MinElute™ Cleanup kit (Qiagen), its concentration and purity were checked spectrophotometrically and its quality was verified electrophoretically. RNA was stored at –20 ºC in RNase-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A cRNA probe was synthesized and fragmented from each RNA sample using Affymetrix protocols and kits provided by Qiagen.
| | Sample_hyb_protocol | Each cRNA probe was hybridized to independent GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix).
| | Sample_hyb_protocol | Hybridization was performed overnight in the GeneChip Hybridization
| | Sample_hyb_protocol | Oven 640 at 45ºC with shaking at 60 rpm; washes and staining of
| | Sample_hyb_protocol | the probe were performed in the GeneChip fluidics station using
| | Sample_hyb_protocol | buffers and protocols provided by the manufacturer.
| | Sample_hyb_protocol | The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_scan_protocol | High-quality scan of the arrays was performed with the GeneChip Scanner 3000. The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_data_processing | Data extraction, cell intensity calculation and computational analysis were performed using GCOS and Expression Console Release Software from Affymetrix. The signal value was obtained using MAS5 and RMA algorithms at linear scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daniel Jose,,Moreno Fernandez-Ayala
| | Sample_contact_email | dmorfer@upo.es
| | Sample_contact_laboratory | CABD/CSIC-UPO
| | Sample_contact_institute | Universidad Pablo de Olavide
| | Sample_contact_address | Carretera de Utrera, Km. 1
| | Sample_contact_city | Sevilla
| | Sample_contact_zip/postal_code | 41013
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833444/suppl/GSM833444_UBIGENES1C.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833444/suppl/GSM833444_UBIGENES1C.mas5.CHP.gz
| | Sample_series_id | GSE33769
| | Sample_series_id | GSE33941
| | Sample_data_row_count | 54675
| | |
|
GSM833478 | GPL570 |
|
control_fibroblast_A
|
human fibroblast, neonatal, rep. 1
|
cell type: Human dermal fibroblast (primary culture of cells) obtained from healthy voluntiers.
age: neonatal
|
|
| Sample_geo_accession | GSM833478
| | Sample_status | Public on Apr 05 2013
| | Sample_submission_date | Nov 16 2011
| | Sample_last_update_date | Apr 05 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were homogenized in 1 ml of Tripure Isolation Reagent (Roche) and RNA was extracted with chloroform and precipitated with 2-propanol by centrifugation at 12000 g for 10 min at 4ºC. After washing with 75% EtOH, RNA was resuspended in DEPC-treated water and treated with deoxiribonuclease I (Sigma) for removal of possible DNA contamination. Afterwards, RNA was cleaned using the RNeasy® MinElute™ Cleanup kit (Qiagen), its concentration and purity were checked spectrophotometrically and its quality was verified electrophoretically. RNA was stored at –20 ºC in RNase-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A cRNA probe was synthesized and fragmented from each RNA sample using Affymetrix protocols and kits provided by Qiagen.
| | Sample_hyb_protocol | Each cRNA probe was hybridized to independent GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix).
| | Sample_hyb_protocol | Hybridization was performed overnight in the GeneChip Hybridization
| | Sample_hyb_protocol | Oven 640 at 45ºC with shaking at 60 rpm; washes and staining of
| | Sample_hyb_protocol | the probe were performed in the GeneChip fluidics station using
| | Sample_hyb_protocol | buffers and protocols provided by the manufacturer.
| | Sample_hyb_protocol | The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_scan_protocol | High-quality scan of the arrays was performed with the GeneChip Scanner 3000. The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_data_processing | Data extraction, cell intensity calculation and computational analysis were performed using GCOS and Expression Console Release Software from Affymetrix. The signal value was obtained using MAS5 and RMA algorithms at linear scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daniel Jose,,Moreno Fernandez-Ayala
| | Sample_contact_email | dmorfer@upo.es
| | Sample_contact_laboratory | CABD/CSIC-UPO
| | Sample_contact_institute | Universidad Pablo de Olavide
| | Sample_contact_address | Carretera de Utrera, Km. 1
| | Sample_contact_city | Sevilla
| | Sample_contact_zip/postal_code | 41013
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833478/suppl/GSM833478_UBIGENES2A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833478/suppl/GSM833478_UBIGENES2A.mas5.CHP.gz
| | Sample_series_id | GSE33769
| | Sample_series_id | GSE33941
| | Sample_data_row_count | 54675
| | |
|
GSM833479 | GPL570 |
|
control_fibroblast_B
|
human fibroblast, neonatal, rep. 2
|
cell type: Human dermal fibroblast (primary culture of cells) obtained from healthy voluntiers.
age: neonatal
|
|
| Sample_geo_accession | GSM833479
| | Sample_status | Public on Apr 05 2013
| | Sample_submission_date | Nov 16 2011
| | Sample_last_update_date | Apr 05 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were homogenized in 1 ml of Tripure Isolation Reagent (Roche) and RNA was extracted with chloroform and precipitated with 2-propanol by centrifugation at 12000 g for 10 min at 4ºC. After washing with 75% EtOH, RNA was resuspended in DEPC-treated water and treated with deoxiribonuclease I (Sigma) for removal of possible DNA contamination. Afterwards, RNA was cleaned using the RNeasy® MinElute™ Cleanup kit (Qiagen), its concentration and purity were checked spectrophotometrically and its quality was verified electrophoretically. RNA was stored at –20 ºC in RNase-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A cRNA probe was synthesized and fragmented from each RNA sample using Affymetrix protocols and kits provided by Qiagen.
| | Sample_hyb_protocol | Each cRNA probe was hybridized to independent GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix).
| | Sample_hyb_protocol | Hybridization was performed overnight in the GeneChip Hybridization
| | Sample_hyb_protocol | Oven 640 at 45ºC with shaking at 60 rpm; washes and staining of
| | Sample_hyb_protocol | the probe were performed in the GeneChip fluidics station using
| | Sample_hyb_protocol | buffers and protocols provided by the manufacturer.
| | Sample_hyb_protocol | The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_scan_protocol | High-quality scan of the arrays was performed with the GeneChip Scanner 3000. The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_data_processing | Data extraction, cell intensity calculation and computational analysis were performed using GCOS and Expression Console Release Software from Affymetrix. The signal value was obtained using MAS5 and RMA algorithms at linear scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daniel Jose,,Moreno Fernandez-Ayala
| | Sample_contact_email | dmorfer@upo.es
| | Sample_contact_laboratory | CABD/CSIC-UPO
| | Sample_contact_institute | Universidad Pablo de Olavide
| | Sample_contact_address | Carretera de Utrera, Km. 1
| | Sample_contact_city | Sevilla
| | Sample_contact_zip/postal_code | 41013
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833479/suppl/GSM833479_UBIGENES2B.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833479/suppl/GSM833479_UBIGENES2B.mas5.CHP.gz
| | Sample_series_id | GSE33769
| | Sample_series_id | GSE33941
| | Sample_data_row_count | 54675
| | |
|
GSM833480 | GPL570 |
|
control_fibroblast_C
|
human fibroblast, neonatal, rep. 3
|
cell type: Human dermal fibroblast (primary culture of cells) obtained from healthy voluntiers.
age: neonatal
|
|
| Sample_geo_accession | GSM833480
| | Sample_status | Public on Apr 05 2013
| | Sample_submission_date | Nov 16 2011
| | Sample_last_update_date | Apr 05 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were homogenized in 1 ml of Tripure Isolation Reagent (Roche) and RNA was extracted with chloroform and precipitated with 2-propanol by centrifugation at 12000 g for 10 min at 4ºC. After washing with 75% EtOH, RNA was resuspended in DEPC-treated water and treated with deoxiribonuclease I (Sigma) for removal of possible DNA contamination. Afterwards, RNA was cleaned using the RNeasy® MinElute™ Cleanup kit (Qiagen), its concentration and purity were checked spectrophotometrically and its quality was verified electrophoretically. RNA was stored at –20 ºC in RNase-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A cRNA probe was synthesized and fragmented from each RNA sample using Affymetrix protocols and kits provided by Qiagen.
| | Sample_hyb_protocol | Each cRNA probe was hybridized to independent GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix).
| | Sample_hyb_protocol | Hybridization was performed overnight in the GeneChip Hybridization
| | Sample_hyb_protocol | Oven 640 at 45ºC with shaking at 60 rpm; washes and staining of
| | Sample_hyb_protocol | the probe were performed in the GeneChip fluidics station using
| | Sample_hyb_protocol | buffers and protocols provided by the manufacturer.
| | Sample_hyb_protocol | The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_scan_protocol | High-quality scan of the arrays was performed with the GeneChip Scanner 3000. The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_data_processing | Data extraction, cell intensity calculation and computational analysis were performed using GCOS and Expression Console Release Software from Affymetrix. The signal value was obtained using MAS5 and RMA algorithms at linear scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daniel Jose,,Moreno Fernandez-Ayala
| | Sample_contact_email | dmorfer@upo.es
| | Sample_contact_laboratory | CABD/CSIC-UPO
| | Sample_contact_institute | Universidad Pablo de Olavide
| | Sample_contact_address | Carretera de Utrera, Km. 1
| | Sample_contact_city | Sevilla
| | Sample_contact_zip/postal_code | 41013
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833480/suppl/GSM833480_UBIGENES2C.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833480/suppl/GSM833480_UBIGENES2C.mas5.CHP.gz
| | Sample_series_id | GSE33769
| | Sample_series_id | GSE33941
| | Sample_data_row_count | 54675
| | |
|
GSM833490 | GPL570 |
|
fibroblast_patient_3_A
|
human fibroblast, Q10 deficient patient COQ2 mutant, rep. 1
|
age: 33-month-old
gender: boy
cell type: dermal fibroblasts.
clinical phenotype: (1) corticosteroid-resistant nephrotic syndrome, (2) progressive encephalomyopathy later developed, and (3) CoQ10 was decreased (muscle and fibroblasts).
treatment: Oral CoQ10 improved the neurologic picture, but do not improved the renal dysfunction.
|
reference: Salviati, L. et al. Neurology 65, 606-8 (2005)
|
| Sample_geo_accession | GSM833490
| | Sample_status | Public on Apr 05 2013
| | Sample_submission_date | Nov 16 2011
| | Sample_last_update_date | Apr 05 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were homogenized in 1 ml of Tripure Isolation Reagent (Roche) and RNA was extracted with chloroform and precipitated with 2-propanol by centrifugation at 12000 g for 10 min at 4ºC. After washing with 75% EtOH, RNA was resuspended in DEPC-treated water and treated with deoxiribonuclease I (Sigma) for removal of possible DNA contamination. Afterwards, RNA was cleaned using the RNeasy® MinElute™ Cleanup kit (Qiagen), its concentration and purity were checked spectrophotometrically and its quality was verified electrophoretically. RNA was stored at –20 ºC in RNase-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A cRNA probe was synthesized and fragmented from each RNA sample using Affymetrix protocols and kits provided by Qiagen.
| | Sample_hyb_protocol | Each cRNA probe was hybridized to independent GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix).
| | Sample_hyb_protocol | Hybridization was performed overnight in the GeneChip Hybridization
| | Sample_hyb_protocol | Oven 640 at 45ºC with shaking at 60 rpm; washes and staining of
| | Sample_hyb_protocol | the probe were performed in the GeneChip fluidics station using
| | Sample_hyb_protocol | buffers and protocols provided by the manufacturer.
| | Sample_hyb_protocol | The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_scan_protocol | High-quality scan of the arrays was performed with the GeneChip Scanner 3000. The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_data_processing | Data extraction, cell intensity calculation and computational analysis were performed using GCOS and Expression Console Release Software from Affymetrix. The signal value was obtained using MAS5 and RMA algorithms at linear scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daniel Jose,,Moreno Fernandez-Ayala
| | Sample_contact_email | dmorfer@upo.es
| | Sample_contact_laboratory | CABD/CSIC-UPO
| | Sample_contact_institute | Universidad Pablo de Olavide
| | Sample_contact_address | Carretera de Utrera, Km. 1
| | Sample_contact_city | Sevilla
| | Sample_contact_zip/postal_code | 41013
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833490/suppl/GSM833490_UBIGENES3A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833490/suppl/GSM833490_UBIGENES3A.mas5.CHP.gz
| | Sample_series_id | GSE33769
| | Sample_series_id | GSE33941
| | Sample_data_row_count | 54675
| | |
|
GSM833491 | GPL570 |
|
fibroblast_patient_3_B
|
human fibroblast, Q10 deficient patient COQ2 mutant, rep. 2
|
age: 33-month-old
gender: boy
clinical phenotype: (1) corticosteroid-resistant nephrotic syndrome, (2) progressive encephalomyopathy later developed, and (3) CoQ10 was decreased (muscle and fibroblasts).
treatment: Oral CoQ10 improved the neurologic picture, but do not improved the renal dysfunction.
|
reference: 16116126 PubMed ID
|
| Sample_geo_accession | GSM833491
| | Sample_status | Public on Apr 05 2013
| | Sample_submission_date | Nov 16 2011
| | Sample_last_update_date | Apr 05 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were homogenized in 1 ml of Tripure Isolation Reagent (Roche) and RNA was extracted with chloroform and precipitated with 2-propanol by centrifugation at 12000 g for 10 min at 4ºC. After washing with 75% EtOH, RNA was resuspended in DEPC-treated water and treated with deoxiribonuclease I (Sigma) for removal of possible DNA contamination. Afterwards, RNA was cleaned using the RNeasy® MinElute™ Cleanup kit (Qiagen), its concentration and purity were checked spectrophotometrically and its quality was verified electrophoretically. RNA was stored at –20 ºC in RNase-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A cRNA probe was synthesized and fragmented from each RNA sample using Affymetrix protocols and kits provided by Qiagen.
| | Sample_hyb_protocol | Each cRNA probe was hybridized to independent GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix).
| | Sample_hyb_protocol | Hybridization was performed overnight in the GeneChip Hybridization
| | Sample_hyb_protocol | Oven 640 at 45ºC with shaking at 60 rpm; washes and staining of
| | Sample_hyb_protocol | the probe were performed in the GeneChip fluidics station using
| | Sample_hyb_protocol | buffers and protocols provided by the manufacturer.
| | Sample_hyb_protocol | The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_scan_protocol | High-quality scan of the arrays was performed with the GeneChip Scanner 3000. The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_data_processing | Data extraction, cell intensity calculation and computational analysis were performed using GCOS and Expression Console Release Software from Affymetrix. The signal value was obtained using MAS5 and RMA algorithms at linear scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daniel Jose,,Moreno Fernandez-Ayala
| | Sample_contact_email | dmorfer@upo.es
| | Sample_contact_laboratory | CABD/CSIC-UPO
| | Sample_contact_institute | Universidad Pablo de Olavide
| | Sample_contact_address | Carretera de Utrera, Km. 1
| | Sample_contact_city | Sevilla
| | Sample_contact_zip/postal_code | 41013
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833491/suppl/GSM833491_UBIGENES3B.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833491/suppl/GSM833491_UBIGENES3B.mas5.CHP.gz
| | Sample_series_id | GSE33769
| | Sample_series_id | GSE33941
| | Sample_data_row_count | 54675
| | |
|
GSM833492 | GPL570 |
|
fibroblast_patient_3_C
|
human fibroblast, Q10 deficient patient COQ2 mutant, rep. 3
|
age: 33-month-old
gender: boy
clinical phenotype: (1) corticosteroid-resistant nephrotic syndrome, (2) progressive encephalomyopathy later developed, and (3) CoQ10 was decreased (muscle and fibroblasts)
treatment: Oral CoQ10 improved the neurologic picture, but do not improved the renal dysfunction.
|
reference: 16116126 PubMed ID
|
| Sample_geo_accession | GSM833492
| | Sample_status | Public on Apr 05 2013
| | Sample_submission_date | Nov 16 2011
| | Sample_last_update_date | Apr 05 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were homogenized in 1 ml of Tripure Isolation Reagent (Roche) and RNA was extracted with chloroform and precipitated with 2-propanol by centrifugation at 12000 g for 10 min at 4ºC. After washing with 75% EtOH, RNA was resuspended in DEPC-treated water and treated with deoxiribonuclease I (Sigma) for removal of possible DNA contamination. Afterwards, RNA was cleaned using the RNeasy® MinElute™ Cleanup kit (Qiagen), its concentration and purity were checked spectrophotometrically and its quality was verified electrophoretically. RNA was stored at –20 ºC in RNase-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A cRNA probe was synthesized and fragmented from each RNA sample using Affymetrix protocols and kits provided by Qiagen.
| | Sample_hyb_protocol | Each cRNA probe was hybridized to independent GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix).
| | Sample_hyb_protocol | Hybridization was performed overnight in the GeneChip Hybridization
| | Sample_hyb_protocol | Oven 640 at 45ºC with shaking at 60 rpm; washes and staining of
| | Sample_hyb_protocol | the probe were performed in the GeneChip fluidics station using
| | Sample_hyb_protocol | buffers and protocols provided by the manufacturer.
| | Sample_hyb_protocol | The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_scan_protocol | High-quality scan of the arrays was performed with the GeneChip Scanner 3000. The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_data_processing | Data extraction, cell intensity calculation and computational analysis were performed using GCOS and Expression Console Release Software from Affymetrix. The signal value was obtained using MAS5 and RMA algorithms at linear scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daniel Jose,,Moreno Fernandez-Ayala
| | Sample_contact_email | dmorfer@upo.es
| | Sample_contact_laboratory | CABD/CSIC-UPO
| | Sample_contact_institute | Universidad Pablo de Olavide
| | Sample_contact_address | Carretera de Utrera, Km. 1
| | Sample_contact_city | Sevilla
| | Sample_contact_zip/postal_code | 41013
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833492/suppl/GSM833492_UBIGENES3C.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833492/suppl/GSM833492_UBIGENES3C.mas5.CHP.gz
| | Sample_series_id | GSE33769
| | Sample_series_id | GSE33941
| | Sample_data_row_count | 54675
| | |
|
GSM833493 | GPL570 |
|
fibroblast_patient_5_A
|
human fibroblast, Q10 deficient patient COQ2 mutant (sister), rep. 1
|
gender: girl
|
reference: unpublished (sister of patient 3; reference 16116126 PubMed ID)
|
| Sample_geo_accession | GSM833493
| | Sample_status | Public on Apr 05 2013
| | Sample_submission_date | Nov 16 2011
| | Sample_last_update_date | Apr 05 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were homogenized in 1 ml of Tripure Isolation Reagent (Roche) and RNA was extracted with chloroform and precipitated with 2-propanol by centrifugation at 12000 g for 10 min at 4ºC. After washing with 75% EtOH, RNA was resuspended in DEPC-treated water and treated with deoxiribonuclease I (Sigma) for removal of possible DNA contamination. Afterwards, RNA was cleaned using the RNeasy® MinElute™ Cleanup kit (Qiagen), its concentration and purity were checked spectrophotometrically and its quality was verified electrophoretically. RNA was stored at –20 ºC in RNase-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A cRNA probe was synthesized and fragmented from each RNA sample using Affymetrix protocols and kits provided by Qiagen.
| | Sample_hyb_protocol | Each cRNA probe was hybridized to independent GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix).
| | Sample_hyb_protocol | Hybridization was performed overnight in the GeneChip Hybridization
| | Sample_hyb_protocol | Oven 640 at 45ºC with shaking at 60 rpm; washes and staining of
| | Sample_hyb_protocol | the probe were performed in the GeneChip fluidics station using
| | Sample_hyb_protocol | buffers and protocols provided by the manufacturer.
| | Sample_hyb_protocol | The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_scan_protocol | High-quality scan of the arrays was performed with the GeneChip Scanner 3000. The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_data_processing | Data extraction, cell intensity calculation and computational analysis were performed using GCOS and Expression Console Release Software from Affymetrix. The signal value was obtained using MAS5 and RMA algorithms at linear scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daniel Jose,,Moreno Fernandez-Ayala
| | Sample_contact_email | dmorfer@upo.es
| | Sample_contact_laboratory | CABD/CSIC-UPO
| | Sample_contact_institute | Universidad Pablo de Olavide
| | Sample_contact_address | Carretera de Utrera, Km. 1
| | Sample_contact_city | Sevilla
| | Sample_contact_zip/postal_code | 41013
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833493/suppl/GSM833493_UBIGENES5A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833493/suppl/GSM833493_UBIGENES5A.mas5.CHP.gz
| | Sample_series_id | GSE33769
| | Sample_series_id | GSE33941
| | Sample_data_row_count | 54675
| | |
|
GSM833494 | GPL570 |
|
fibroblast_patient_5_B
|
human fibroblast, Q10 deficient patient COQ2 mutant (sister), rep. 2
|
gender: girl
|
reference: unpublished (sister of patient 3; reference 16116126 PubMed ID)
|
| Sample_geo_accession | GSM833494
| | Sample_status | Public on Apr 05 2013
| | Sample_submission_date | Nov 16 2011
| | Sample_last_update_date | Apr 05 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were homogenized in 1 ml of Tripure Isolation Reagent (Roche) and RNA was extracted with chloroform and precipitated with 2-propanol by centrifugation at 12000 g for 10 min at 4ºC. After washing with 75% EtOH, RNA was resuspended in DEPC-treated water and treated with deoxiribonuclease I (Sigma) for removal of possible DNA contamination. Afterwards, RNA was cleaned using the RNeasy® MinElute™ Cleanup kit (Qiagen), its concentration and purity were checked spectrophotometrically and its quality was verified electrophoretically. RNA was stored at –20 ºC in RNase-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A cRNA probe was synthesized and fragmented from each RNA sample using Affymetrix protocols and kits provided by Qiagen.
| | Sample_hyb_protocol | Each cRNA probe was hybridized to independent GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix).
| | Sample_hyb_protocol | Hybridization was performed overnight in the GeneChip Hybridization
| | Sample_hyb_protocol | Oven 640 at 45ºC with shaking at 60 rpm; washes and staining of
| | Sample_hyb_protocol | the probe were performed in the GeneChip fluidics station using
| | Sample_hyb_protocol | buffers and protocols provided by the manufacturer.
| | Sample_hyb_protocol | The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_scan_protocol | High-quality scan of the arrays was performed with the GeneChip Scanner 3000. The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_data_processing | Data extraction, cell intensity calculation and computational analysis were performed using GCOS and Expression Console Release Software from Affymetrix. The signal value was obtained using MAS5 and RMA algorithms at linear scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daniel Jose,,Moreno Fernandez-Ayala
| | Sample_contact_email | dmorfer@upo.es
| | Sample_contact_laboratory | CABD/CSIC-UPO
| | Sample_contact_institute | Universidad Pablo de Olavide
| | Sample_contact_address | Carretera de Utrera, Km. 1
| | Sample_contact_city | Sevilla
| | Sample_contact_zip/postal_code | 41013
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833494/suppl/GSM833494_UBIGENES5B.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833494/suppl/GSM833494_UBIGENES5B.mas5.CHP.gz
| | Sample_series_id | GSE33769
| | Sample_series_id | GSE33941
| | Sample_data_row_count | 54675
| | |
|
GSM833495 | GPL570 |
|
fibroblast_patient_5_C
|
human fibroblast, Q10 deficient patient COQ2 mutant (sister), rep. 3
|
gender: girl
|
reference: unpublished (sister of patient 3; reference 16116126 PubMed ID)
|
| Sample_geo_accession | GSM833495
| | Sample_status | Public on Apr 05 2013
| | Sample_submission_date | Nov 16 2011
| | Sample_last_update_date | Apr 05 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were homogenized in 1 ml of Tripure Isolation Reagent (Roche) and RNA was extracted with chloroform and precipitated with 2-propanol by centrifugation at 12000 g for 10 min at 4ºC. After washing with 75% EtOH, RNA was resuspended in DEPC-treated water and treated with deoxiribonuclease I (Sigma) for removal of possible DNA contamination. Afterwards, RNA was cleaned using the RNeasy® MinElute™ Cleanup kit (Qiagen), its concentration and purity were checked spectrophotometrically and its quality was verified electrophoretically. RNA was stored at –20 ºC in RNase-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A cRNA probe was synthesized and fragmented from each RNA sample using Affymetrix protocols and kits provided by Qiagen.
| | Sample_hyb_protocol | Each cRNA probe was hybridized to independent GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix).
| | Sample_hyb_protocol | Hybridization was performed overnight in the GeneChip Hybridization
| | Sample_hyb_protocol | Oven 640 at 45ºC with shaking at 60 rpm; washes and staining of
| | Sample_hyb_protocol | the probe were performed in the GeneChip fluidics station using
| | Sample_hyb_protocol | buffers and protocols provided by the manufacturer.
| | Sample_hyb_protocol | The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_scan_protocol | High-quality scan of the arrays was performed with the GeneChip Scanner 3000. The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_data_processing | Data extraction, cell intensity calculation and computational analysis were performed using GCOS and Expression Console Release Software from Affymetrix. The signal value was obtained using MAS5 and RMA algorithms at linear scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daniel Jose,,Moreno Fernandez-Ayala
| | Sample_contact_email | dmorfer@upo.es
| | Sample_contact_laboratory | CABD/CSIC-UPO
| | Sample_contact_institute | Universidad Pablo de Olavide
| | Sample_contact_address | Carretera de Utrera, Km. 1
| | Sample_contact_city | Sevilla
| | Sample_contact_zip/postal_code | 41013
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833495/suppl/GSM833495_UBIGENES5C.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833495/suppl/GSM833495_UBIGENES5C.mas5.CHP.gz
| | Sample_series_id | GSE33769
| | Sample_series_id | GSE33941
| | Sample_data_row_count | 54675
| | |
|
GSM833502 | GPL570 |
|
fibroblast_patient_4_A
|
human fibroblast, Q10 deficient patient, MELAS, rep. 1
|
cell type: fibroblast
clinical phenotype: MELAS (A3243G mutation).
cell phenotype: (1) decreased mitochondrial respiratory chain enzyme activities, (2) low CoQ10 level, (3) decreased mitochondrial membrane potential, (4) increased oxidative stress and the activation of mitochondrial permeability, and (5) defective autophagosome elimination in MELAS fibroblasts.
|
|
| Sample_geo_accession | GSM833502
| | Sample_status | Public on Apr 05 2013
| | Sample_submission_date | Nov 16 2011
| | Sample_last_update_date | Apr 05 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were homogenized in 1 ml of Tripure Isolation Reagent (Roche) and RNA was extracted with chloroform and precipitated with 2-propanol by centrifugation at 12000 g for 10 min at 4ºC. After washing with 75% EtOH, RNA was resuspended in DEPC-treated water and treated with deoxiribonuclease I (Sigma) for removal of possible DNA contamination. Afterwards, RNA was cleaned using the RNeasy® MinElute™ Cleanup kit (Qiagen), its concentration and purity were checked spectrophotometrically and its quality was verified electrophoretically. RNA was stored at –20 ºC in RNase-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A cRNA probe was synthesized and fragmented from each RNA sample using Affymetrix protocols and kits provided by Qiagen.
| | Sample_hyb_protocol | Each cRNA probe was hybridized to independent GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix).
| | Sample_hyb_protocol | Hybridization was performed overnight in the GeneChip Hybridization
| | Sample_hyb_protocol | Oven 640 at 45ºC with shaking at 60 rpm; washes and staining of
| | Sample_hyb_protocol | the probe were performed in the GeneChip fluidics station using
| | Sample_hyb_protocol | buffers and protocols provided by the manufacturer.
| | Sample_hyb_protocol | The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_scan_protocol | High-quality scan of the arrays was performed with the GeneChip Scanner 3000. The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_data_processing | Data extraction, cell intensity calculation and computational analysis were performed using GCOS and Expression Console Release Software from Affymetrix. The signal value was obtained using MAS5 and RMA algorithms at linear scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daniel Jose,,Moreno Fernandez-Ayala
| | Sample_contact_email | dmorfer@upo.es
| | Sample_contact_laboratory | CABD/CSIC-UPO
| | Sample_contact_institute | Universidad Pablo de Olavide
| | Sample_contact_address | Carretera de Utrera, Km. 1
| | Sample_contact_city | Sevilla
| | Sample_contact_zip/postal_code | 41013
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833502/suppl/GSM833502_UBIGENES4A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833502/suppl/GSM833502_UBIGENES4A.mas5.CHP.gz
| | Sample_series_id | GSE33769
| | Sample_series_id | GSE33941
| | Sample_data_row_count | 54675
| | |
|
GSM833503 | GPL570 |
|
fibroblast_patient_4_B
|
human fibroblast, Q10 deficient patient, MELAS, rep. 2
|
cell type: fibroblast
clinical phenotype: MELAS (A3243G mutation).
cell phenotype: (1) decreased mitochondrial respiratory chain enzyme activities, (2) low CoQ10 level, (3) decreased mitochondrial membrane potential, (4) increased oxidative stress and the activation of mitochondrial permeability, and (5) defective autophagosome elimination in MELAS fibroblasts.
|
reference: PubMed ID #21551238 - Cotan, D. et al. Secondary coenzyme Q10 deficiency triggers mitochondria degradation by mitophagy in MELAS fibroblasts. Faseb J 25, 2669-87 (2011).
|
| Sample_geo_accession | GSM833503
| | Sample_status | Public on Apr 05 2013
| | Sample_submission_date | Nov 16 2011
| | Sample_last_update_date | Apr 05 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were homogenized in 1 ml of Tripure Isolation Reagent (Roche) and RNA was extracted with chloroform and precipitated with 2-propanol by centrifugation at 12000 g for 10 min at 4ºC. After washing with 75% EtOH, RNA was resuspended in DEPC-treated water and treated with deoxiribonuclease I (Sigma) for removal of possible DNA contamination. Afterwards, RNA was cleaned using the RNeasy® MinElute™ Cleanup kit (Qiagen), its concentration and purity were checked spectrophotometrically and its quality was verified electrophoretically. RNA was stored at –20 ºC in RNase-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A cRNA probe was synthesized and fragmented from each RNA sample using Affymetrix protocols and kits provided by Qiagen.
| | Sample_hyb_protocol | Each cRNA probe was hybridized to independent GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix).
| | Sample_hyb_protocol | Hybridization was performed overnight in the GeneChip Hybridization
| | Sample_hyb_protocol | Oven 640 at 45ºC with shaking at 60 rpm; washes and staining of
| | Sample_hyb_protocol | the probe were performed in the GeneChip fluidics station using
| | Sample_hyb_protocol | buffers and protocols provided by the manufacturer.
| | Sample_hyb_protocol | The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_scan_protocol | High-quality scan of the arrays was performed with the GeneChip Scanner 3000. The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_data_processing | Data extraction, cell intensity calculation and computational analysis were performed using GCOS and Expression Console Release Software from Affymetrix. The signal value was obtained using MAS5 and RMA algorithms at linear scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daniel Jose,,Moreno Fernandez-Ayala
| | Sample_contact_email | dmorfer@upo.es
| | Sample_contact_laboratory | CABD/CSIC-UPO
| | Sample_contact_institute | Universidad Pablo de Olavide
| | Sample_contact_address | Carretera de Utrera, Km. 1
| | Sample_contact_city | Sevilla
| | Sample_contact_zip/postal_code | 41013
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833503/suppl/GSM833503_UBIGENES4B.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833503/suppl/GSM833503_UBIGENES4B.mas5.CHP.gz
| | Sample_series_id | GSE33769
| | Sample_series_id | GSE33941
| | Sample_data_row_count | 54675
| | |
|
GSM833504 | GPL570 |
|
fibroblast_patient_4_C
|
human fibroblast, Q10 deficient patient, MELAS, rep. 3
|
cell type: fibroblast
clinical phenotype: MELAS (A3243G mutation).
cell phenotype: (1) decreased mitochondrial respiratory chain enzyme activities, (2) low CoQ10 level, (3) decreased mitochondrial membrane potential, (4) increased oxidative stress and the activation of mitochondrial permeability, and (5) defective autophagosome elimination in MELAS fibroblasts.
|
reference: PubMed ID #21551238 - Cotan, D. et al. Secondary coenzyme Q10 deficiency triggers mitochondria degradation by mitophagy in MELAS fibroblasts. Faseb J 25, 2669-87 (2011).
|
| Sample_geo_accession | GSM833504
| | Sample_status | Public on Apr 05 2013
| | Sample_submission_date | Nov 16 2011
| | Sample_last_update_date | Apr 05 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were homogenized in 1 ml of Tripure Isolation Reagent (Roche) and RNA was extracted with chloroform and precipitated with 2-propanol by centrifugation at 12000 g for 10 min at 4ºC. After washing with 75% EtOH, RNA was resuspended in DEPC-treated water and treated with deoxiribonuclease I (Sigma) for removal of possible DNA contamination. Afterwards, RNA was cleaned using the RNeasy® MinElute™ Cleanup kit (Qiagen), its concentration and purity were checked spectrophotometrically and its quality was verified electrophoretically. RNA was stored at –20 ºC in RNase-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | A cRNA probe was synthesized and fragmented from each RNA sample using Affymetrix protocols and kits provided by Qiagen.
| | Sample_hyb_protocol | Each cRNA probe was hybridized to independent GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix).
| | Sample_hyb_protocol | Hybridization was performed overnight in the GeneChip Hybridization
| | Sample_hyb_protocol | Oven 640 at 45ºC with shaking at 60 rpm; washes and staining of
| | Sample_hyb_protocol | the probe were performed in the GeneChip fluidics station using
| | Sample_hyb_protocol | buffers and protocols provided by the manufacturer.
| | Sample_hyb_protocol | The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_scan_protocol | High-quality scan of the arrays was performed with the GeneChip Scanner 3000. The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.
| | Sample_data_processing | Data extraction, cell intensity calculation and computational analysis were performed using GCOS and Expression Console Release Software from Affymetrix. The signal value was obtained using MAS5 and RMA algorithms at linear scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daniel Jose,,Moreno Fernandez-Ayala
| | Sample_contact_email | dmorfer@upo.es
| | Sample_contact_laboratory | CABD/CSIC-UPO
| | Sample_contact_institute | Universidad Pablo de Olavide
| | Sample_contact_address | Carretera de Utrera, Km. 1
| | Sample_contact_city | Sevilla
| | Sample_contact_zip/postal_code | 41013
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833504/suppl/GSM833504_UBIGENES4C.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM833nnn/GSM833504/suppl/GSM833504_UBIGENES4C.mas5.CHP.gz
| | Sample_series_id | GSE33769
| | Sample_series_id | GSE33941
| | Sample_data_row_count | 54675
| | |
|
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