Search results for the GEO ID: GSE38680 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM947461 | GPL570 |
|
Biceps_Control_1
|
Biceps muscle, Control patient
|
tissue: Biceps muscle
patient: C.b.1
diagnosis: Control
treatment: None
treatment time (rhgaa): --
gender: M
age at baseline: 1y 2m
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947461
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947461/suppl/GSM947461_H0013501.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947462 | GPL570 |
|
Biceps_Control_2
|
Biceps muscle, Control patient
|
tissue: Biceps muscle
patient: C.b.2
diagnosis: Control
treatment: None
treatment time (rhgaa): --
gender: M
age at baseline: 1y 11m
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947462
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947462/suppl/GSM947462_H0013502.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947463 | GPL570 |
|
Biceps_Control_3
|
Biceps muscle, Control patient
|
tissue: Biceps muscle
patient: C.b.3
diagnosis: Control
treatment: None
treatment time (rhgaa): --
gender: M
age at baseline: 2y 1m
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947463
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947463/suppl/GSM947463_H0013504.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947464 | GPL570 |
|
Biceps_Control_4
|
Biceps muscle, Control patient
|
tissue: Biceps muscle
patient: C.b.4
diagnosis: Control
treatment: None
treatment time (rhgaa): --
gender: M
age at baseline: 2m
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947464
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947464/suppl/GSM947464_H0013505.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947465 | GPL570 |
|
Biceps_Control_5
|
Biceps muscle, Control patient
|
tissue: Biceps muscle
patient: C.b.5
diagnosis: Control
treatment: None
treatment time (rhgaa): --
gender: F
age at baseline: 2y
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947465
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947465/suppl/GSM947465_H0013506.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947466 | GPL570 |
|
Biceps_Control_6
|
Biceps muscle, Control patient
|
tissue: Biceps muscle
patient: C.b.6
diagnosis: Control
treatment: None
treatment time (rhgaa): --
gender: F
age at baseline: 2y
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947466
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947466/suppl/GSM947466_H0013507.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947467 | GPL570 |
|
Biceps_Control_7
|
Biceps muscle, Control patient
|
tissue: Biceps muscle
patient: C.b.7
diagnosis: Control
treatment: None
treatment time (rhgaa): --
gender: F
age at baseline: 2y 3m
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947467
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947467/suppl/GSM947467_H0013508.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947468 | GPL570 |
|
Biceps_Control_8
|
Biceps muscle, Control patient
|
tissue: Biceps muscle
patient: C.b.8
diagnosis: Control
treatment: None
treatment time (rhgaa): --
gender: F
age at baseline: 1y 9m
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947468
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947468/suppl/GSM947468_H0013509.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947469 | GPL570 |
|
Biceps_Control_9
|
Biceps muscle, Control patient
|
tissue: Biceps muscle
patient: C.b.9
diagnosis: Control
treatment: None
treatment time (rhgaa): --
gender: F
age at baseline: 2y 11m
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947469
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947469/suppl/GSM947469_H0013510.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947470 | GPL570 |
|
Biceps_Control_10
|
Biceps muscle, Control patient
|
tissue: Biceps muscle
patient: C.b.10.MELAS
diagnosis: Control
treatment: None
treatment time (rhgaa): --
gender: M
age at baseline: 2y 9m
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947470
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947470/suppl/GSM947470_H0013503.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947471 | GPL570 |
|
Biceps_Pompe_1
|
Biceps muscle, Pompe patient
|
tissue: Biceps muscle
patient: P.b.1
diagnosis: Pompe
treatment: None
treatment time (rhgaa): --
gender: M
age at baseline: 7m
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947471
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947471/suppl/GSM947471_H0013492.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947472 | GPL570 |
|
Biceps_Pompe_2
|
Biceps muscle, Pompe patient
|
tissue: Biceps muscle
patient: P.b.2
diagnosis: Pompe
treatment: None
treatment time (rhgaa): --
gender: M
age at baseline: 4m
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947472
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947472/suppl/GSM947472_H0013493.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947473 | GPL570 |
|
Biceps_Pompe_3
|
Biceps muscle, Pompe patient
|
tissue: Biceps muscle
patient: P.b.3
diagnosis: Pompe
treatment: None
treatment time (rhgaa): --
gender: M
age at baseline: 7m
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947473
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947473/suppl/GSM947473_H0013494.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947474 | GPL570 |
|
Biceps_Pompe_4
|
Biceps muscle, Pompe patient
|
tissue: Biceps muscle
patient: P.b.4
diagnosis: Pompe
treatment: None
treatment time (rhgaa): --
gender: M
age at baseline: 10m
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947474
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947474/suppl/GSM947474_H0013495.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947475 | GPL570 |
|
Biceps_Pompe_5
|
Biceps muscle, Pompe patient
|
tissue: Biceps muscle
patient: P.b.5
diagnosis: Pompe
treatment: None
treatment time (rhgaa): --
gender: M
age at baseline: 4m
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947475
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947475/suppl/GSM947475_H0013496.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947476 | GPL570 |
|
Biceps_Pompe_6
|
Biceps muscle, Pompe patient
|
tissue: Biceps muscle
patient: P.b.6
diagnosis: Pompe
treatment: None
treatment time (rhgaa): --
gender: F
age at baseline: 4m
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947476
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947476/suppl/GSM947476_H0013497.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947477 | GPL570 |
|
Biceps_Pompe_7
|
Biceps muscle, Pompe patient
|
tissue: Biceps muscle
patient: P.b.7
diagnosis: Pompe
treatment: None
treatment time (rhgaa): --
gender: F
age at baseline: 7m
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947477
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947477/suppl/GSM947477_H0013498.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947478 | GPL570 |
|
Biceps_Pompe_8
|
Biceps muscle, Pompe patient
|
tissue: Biceps muscle
patient: P.b.8
diagnosis: Pompe
treatment: None
treatment time (rhgaa): --
gender: F
age at baseline: 1y 5m
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947478
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947478/suppl/GSM947478_H0013499.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947479 | GPL570 |
|
Biceps_Pompe_9
|
Biceps muscle, Pompe patient
|
tissue: Biceps muscle
patient: P.b.9
diagnosis: Pompe
treatment: None
treatment time (rhgaa): --
gender: F
age at baseline: 1m
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947479
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947479/suppl/GSM947479_H0013500.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947480 | GPL570 |
|
Quadriceps_Control_1
|
Quadriceps muscle, Control patient
|
tissue: Quadriceps muscle
patient: C.q.1
diagnosis: Control
treatment: None
treatment time (rhgaa): --
gender: M
age at baseline: 5y
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947480
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947480/suppl/GSM947480_H0024642.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947481 | GPL570 |
|
Quadriceps_Control_2
|
Quadriceps muscle, Control patient
|
tissue: Quadriceps muscle
patient: C.q.2
diagnosis: Control
treatment: None
treatment time (rhgaa): --
gender: M
age at baseline: 6m
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947481
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947481/suppl/GSM947481_H0024648.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947482 | GPL570 |
|
Quadriceps_Control_3
|
Quadriceps muscle, Control patient
|
tissue: Quadriceps muscle
patient: C.q.3
diagnosis: Control
treatment: None
treatment time (rhgaa): --
gender: M
age at baseline: 9y
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947482
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947482/suppl/GSM947482_H0024654.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947483 | GPL570 |
|
Quadriceps_Control_4
|
Quadriceps muscle, Control patient
|
tissue: Quadriceps muscle
patient: C.q.4
diagnosis: Control
treatment: None
treatment time (rhgaa): --
gender: F
age at baseline: 8m
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947483
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947483/suppl/GSM947483_H0024665.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947484 | GPL570 |
|
Quadriceps_Control_5
|
Quadriceps muscle, Control patient
|
tissue: Quadriceps muscle
patient: C.q.5
diagnosis: Control
treatment: None
treatment time (rhgaa): --
gender: F
age at baseline: 6m
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947484
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947484/suppl/GSM947484_H0024670.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947485 | GPL570 |
|
Quadriceps_Control_6
|
Quadriceps muscle, Control patient
|
tissue: Quadriceps muscle
patient: C.q.6
diagnosis: Control
treatment: None
treatment time (rhgaa): --
gender: M
age at baseline: 5m
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947485
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947485/suppl/GSM947485_H0024674.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947486 | GPL570 |
|
Quadriceps_Control_7
|
Quadriceps muscle, Control patient
|
tissue: Quadriceps muscle
patient: C.q.7
diagnosis: Control
treatment: None
treatment time (rhgaa): --
gender: F
age at baseline: 6m
motor status (52 weeks treatment): --
change in glycogen content (52 weeks treatment): --
response: --
|
|
Sample_geo_accession | GSM947486
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947486/suppl/GSM947486_H0024677.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947487 | GPL570 |
|
Quadriceps_Pompe_1_00wks
|
Quadriceps muscle, Pompe patient, 0 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.1
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 00 Weeks
gender: M
age at baseline: 5m
motor status (52 weeks treatment): No gains
change in glycogen content (52 weeks treatment): Increased
response: Poor Clinical Outcome
|
|
Sample_geo_accession | GSM947487
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947487/suppl/GSM947487_H0024651.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947488 | GPL570 |
|
Quadriceps_Pompe_1_12wks
|
Quadriceps muscle, Pompe patient, 12 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.1
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 12 Weeks
gender: M
age at baseline: 5m
motor status (52 weeks treatment): No gains
change in glycogen content (52 weeks treatment): Increased
response: Poor Clinical Outcome
|
|
Sample_geo_accession | GSM947488
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947488/suppl/GSM947488_H0024667.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947489 | GPL570 |
|
Quadriceps_Pompe_1_52wks
|
Quadriceps muscle, Pompe patient, 52 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.1
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 52 Weeks
gender: M
age at baseline: 5m
motor status (52 weeks treatment): No gains
change in glycogen content (52 weeks treatment): Increased
response: Poor Clinical Outcome
|
|
Sample_geo_accession | GSM947489
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947489/suppl/GSM947489_H0024673.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947490 | GPL570 |
|
Quadriceps_Pompe_2_00wks
|
Quadriceps muscle, Pompe patient, 0 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.2
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 00 Weeks
gender: M
age at baseline: 7m
motor status (52 weeks treatment): Walking
change in glycogen content (52 weeks treatment): Stable
response: Positive Clinical Outcome
|
|
Sample_geo_accession | GSM947490
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947490/suppl/GSM947490_H0024664.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947491 | GPL570 |
|
Quadriceps_Pompe_2_12wks
|
Quadriceps muscle, Pompe patient, 12 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.2
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 12 Weeks
gender: M
age at baseline: 7m
motor status (52 weeks treatment): Walking
change in glycogen content (52 weeks treatment): Stable
response: Positive Clinical Outcome
|
|
Sample_geo_accession | GSM947491
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947491/suppl/GSM947491_H0024657.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947492 | GPL570 |
|
Quadriceps_Pompe_2_52wks
|
Quadriceps muscle, Pompe patient, 52 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.2
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 52 Weeks
gender: M
age at baseline: 7m
motor status (52 weeks treatment): Walking
change in glycogen content (52 weeks treatment): Stable
response: Positive Clinical Outcome
|
|
Sample_geo_accession | GSM947492
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947492/suppl/GSM947492_H0024652.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947493 | GPL570 |
|
Quadriceps_Pompe_3_00wks
|
Quadriceps muscle, Pompe patient, 0 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.3
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 00 Weeks
gender: F
age at baseline: 5.7m
motor status (52 weeks treatment): No gains
change in glycogen content (52 weeks treatment): Decreased
response: Poor Clinical Outcome
|
|
Sample_geo_accession | GSM947493
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947493/suppl/GSM947493_H0024653.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947494 | GPL570 |
|
Quadriceps_Pompe_3_12wks
|
Quadriceps muscle, Pompe patient, 12 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.3
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 12 Weeks
gender: F
age at baseline: 5.7m
motor status (52 weeks treatment): No gains
change in glycogen content (52 weeks treatment): Decreased
response: Poor Clinical Outcome
|
|
Sample_geo_accession | GSM947494
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947494/suppl/GSM947494_H0024645.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947495 | GPL570 |
|
Quadriceps_Pompe_3_52wks
|
Quadriceps muscle, Pompe patient, 52 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.3
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 52 Weeks
gender: F
age at baseline: 5.7m
motor status (52 weeks treatment): No gains
change in glycogen content (52 weeks treatment): Decreased
response: Poor Clinical Outcome
|
|
Sample_geo_accession | GSM947495
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947495/suppl/GSM947495_H0024663.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947496 | GPL570 |
|
Quadriceps_Pompe_4_00wks
|
Quadriceps muscle, Pompe patient, 0 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.4
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 00 Weeks
gender: M
age at baseline: 5.9m
motor status (52 weeks treatment): No gains
change in glycogen content (52 weeks treatment): Increased
response: Poor Clinical Outcome
|
|
Sample_geo_accession | GSM947496
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947496/suppl/GSM947496_H0024676.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947497 | GPL570 |
|
Quadriceps_Pompe_4_12wks
|
Quadriceps muscle, Pompe patient, 12 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.4
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 12 Weeks
gender: M
age at baseline: 5.9m
motor status (52 weeks treatment): No gains
change in glycogen content (52 weeks treatment): Increased
response: Poor Clinical Outcome
|
|
Sample_geo_accession | GSM947497
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947497/suppl/GSM947497_H0024650.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947498 | GPL570 |
|
Quadriceps_Pompe_4_52wks
|
Quadriceps muscle, Pompe patient, 52 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.4
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 52 Weeks
gender: M
age at baseline: 5.9m
motor status (52 weeks treatment): No gains
change in glycogen content (52 weeks treatment): Increased
response: Poor Clinical Outcome
|
|
Sample_geo_accession | GSM947498
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947498/suppl/GSM947498_H0024679.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947499 | GPL570 |
|
Quadriceps_Pompe_5_00wks
|
Quadriceps muscle, Pompe patient, 0 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.5
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 00 Weeks
gender: M
age at baseline: 6.9m
motor status (52 weeks treatment): Walking
change in glycogen content (52 weeks treatment): Decreased
response: Positive Clinical Outcome
|
|
Sample_geo_accession | GSM947499
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947499/suppl/GSM947499_H0024662.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947500 | GPL570 |
|
Quadriceps_Pompe_5_12wks
|
Quadriceps muscle, Pompe patient, 12 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.5
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 12 Weeks
gender: M
age at baseline: 6.9m
motor status (52 weeks treatment): Walking
change in glycogen content (52 weeks treatment): Decreased
response: Positive Clinical Outcome
|
|
Sample_geo_accession | GSM947500
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947500/suppl/GSM947500_H0024678.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947501 | GPL570 |
|
Quadriceps_Pompe_5_52wks
|
Quadriceps muscle, Pompe patient, 52 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.5
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 52 Weeks
gender: M
age at baseline: 6.9m
motor status (52 weeks treatment): Walking
change in glycogen content (52 weeks treatment): Decreased
response: Positive Clinical Outcome
|
|
Sample_geo_accession | GSM947501
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947501/suppl/GSM947501_H0024658.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947502 | GPL570 |
|
Quadriceps_Pompe_6_00wks
|
Quadriceps muscle, Pompe patient, 0 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.6
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 00 Weeks
gender: M
age at baseline: 4.3m
motor status (52 weeks treatment): Walking
change in glycogen content (52 weeks treatment): Decreased
response: Positive Clinical Outcome
|
|
Sample_geo_accession | GSM947502
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947502/suppl/GSM947502_H0024669.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947503 | GPL570 |
|
Quadriceps_Pompe_6_12wks
|
Quadriceps muscle, Pompe patient, 12 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.6
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 12 Weeks
gender: M
age at baseline: 4.3m
motor status (52 weeks treatment): Walking
change in glycogen content (52 weeks treatment): Decreased
response: Positive Clinical Outcome
|
|
Sample_geo_accession | GSM947503
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947503/suppl/GSM947503_H0024675.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947504 | GPL570 |
|
Quadriceps_Pompe_6_52wks
|
Quadriceps muscle, Pompe patient, 52 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.6
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 52 Weeks
gender: M
age at baseline: 4.3m
motor status (52 weeks treatment): Walking
change in glycogen content (52 weeks treatment): Decreased
response: Positive Clinical Outcome
|
|
Sample_geo_accession | GSM947504
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947504/suppl/GSM947504_H0024649.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947505 | GPL570 |
|
Quadriceps_Pompe_7_00wks
|
Quadriceps muscle, Pompe patient, 0 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.7
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 00 Weeks
gender: F
age at baseline: 5.3m
motor status (52 weeks treatment): Walking
change in glycogen content (52 weeks treatment): Decreased
response: Positive Clinical Outcome
|
|
Sample_geo_accession | GSM947505
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947505/suppl/GSM947505_H0024680.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947506 | GPL570 |
|
Quadriceps_Pompe_7_12wks
|
Quadriceps muscle, Pompe patient, 12 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.7
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 12 Weeks
gender: F
age at baseline: 5.3m
motor status (52 weeks treatment): Walking
change in glycogen content (52 weeks treatment): Decreased
response: Positive Clinical Outcome
|
|
Sample_geo_accession | GSM947506
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947506/suppl/GSM947506_H0024666.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947507 | GPL570 |
|
Quadriceps_Pompe_7_52wks
|
Quadriceps muscle, Pompe patient, 52 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.7
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 52 Weeks
gender: F
age at baseline: 5.3m
motor status (52 weeks treatment): Walking
change in glycogen content (52 weeks treatment): Decreased
response: Positive Clinical Outcome
|
|
Sample_geo_accession | GSM947507
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947507/suppl/GSM947507_H0024641.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947508 | GPL570 |
|
Quadriceps_Pompe_8_00wks
|
Quadriceps muscle, Pompe patient, 0 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.8
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 00 Weeks
gender: M
age at baseline: 6.4m
motor status (52 weeks treatment): Standing
change in glycogen content (52 weeks treatment): Decreased
response: Positive Clinical Outcome
|
|
Sample_geo_accession | GSM947508
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947508/suppl/GSM947508_H0024644.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947509 | GPL570 |
|
Quadriceps_Pompe_8_12wks
|
Quadriceps muscle, Pompe patient, 12 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.8
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 12 Weeks
gender: M
age at baseline: 6.4m
motor status (52 weeks treatment): Standing
change in glycogen content (52 weeks treatment): Decreased
response: Positive Clinical Outcome
|
|
Sample_geo_accession | GSM947509
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947509/suppl/GSM947509_H0024668.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947510 | GPL570 |
|
Quadriceps_Pompe_8_52wks
|
Quadriceps muscle, Pompe patient, 52 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.8
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 52 Weeks
gender: M
age at baseline: 6.4m
motor status (52 weeks treatment): Standing
change in glycogen content (52 weeks treatment): Decreased
response: Positive Clinical Outcome
|
|
Sample_geo_accession | GSM947510
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947510/suppl/GSM947510_H0024672.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947511 | GPL570 |
|
Quadriceps_Pompe_9_00wks
|
Quadriceps muscle, Pompe patient, 0 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.9
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 00 Weeks
gender: F
age at baseline: 1.2m
motor status (52 weeks treatment): Walking
change in glycogen content (52 weeks treatment): Decreased
response: Positive Clinical Outcome
|
|
Sample_geo_accession | GSM947511
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947511/suppl/GSM947511_H0024656.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947512 | GPL570 |
|
Quadriceps_Pompe_9_12wks
|
Quadriceps muscle, Pompe patient, 12 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.9
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 12 Weeks
gender: F
age at baseline: 1.2m
motor status (52 weeks treatment): Walking
change in glycogen content (52 weeks treatment): Decreased
response: Positive Clinical Outcome
|
|
Sample_geo_accession | GSM947512
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947512/suppl/GSM947512_H0024647.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947513 | GPL570 |
|
Quadriceps_Pompe_9_52wks
|
Quadriceps muscle, Pompe patient, 52 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.9
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 52 Weeks
gender: F
age at baseline: 1.2m
motor status (52 weeks treatment): Walking
change in glycogen content (52 weeks treatment): Decreased
response: Positive Clinical Outcome
|
|
Sample_geo_accession | GSM947513
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947513/suppl/GSM947513_H0024661.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947514 | GPL570 |
|
Quadriceps_Pompe_10_00wks
|
Quadriceps muscle, Pompe patient, 0 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.10
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 00 Weeks
gender: M
age at baseline: 6.9m
motor status (52 weeks treatment): Walking
change in glycogen content (52 weeks treatment): Decreased
response: Positive Clinical Outcome
|
|
Sample_geo_accession | GSM947514
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947514/suppl/GSM947514_H0024671.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947515 | GPL570 |
|
Quadriceps_Pompe_10_12wks
|
Quadriceps muscle, Pompe patient, 12 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.10
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 12 Weeks
gender: M
age at baseline: 6.9m
motor status (52 weeks treatment): Walking
change in glycogen content (52 weeks treatment): Decreased
response: Positive Clinical Outcome
|
|
Sample_geo_accession | GSM947515
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947515/suppl/GSM947515_H0024655.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947516 | GPL570 |
|
Quadriceps_Pompe_10_52wks
|
Quadriceps muscle, Pompe patient, 52 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.10
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 52 Weeks
gender: M
age at baseline: 6.9m
motor status (52 weeks treatment): Walking
change in glycogen content (52 weeks treatment): Decreased
response: Positive Clinical Outcome
|
|
Sample_geo_accession | GSM947516
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947516/suppl/GSM947516_H0024646.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947517 | GPL570 |
|
Quadriceps_Pompe_11_00wks
|
Quadriceps muscle, Pompe patient, 0 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.11
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 00 Weeks
gender: F
age at baseline: 2.1m
motor status (52 weeks treatment): No gains
change in glycogen content (52 weeks treatment): Stable
response: Poor Clinical Outcome
|
|
Sample_geo_accession | GSM947517
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947517/suppl/GSM947517_H0024643.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
GSM947518 | GPL570 |
|
Quadriceps_Pompe_11_12wks
|
Quadriceps muscle, Pompe patient, 12 weeks rhGAA treatment
|
tissue: Quadriceps muscle
patient: P.q.11
diagnosis: Pompe
treatment: rhGAA
treatment time (rhgaa): 12 Weeks
gender: F
age at baseline: 2.1m
motor status (52 weeks treatment): No gains
change in glycogen content (52 weeks treatment): Stable
response: Poor Clinical Outcome
|
|
Sample_geo_accession | GSM947518
| Sample_status | Public on Jun 14 2012
| Sample_submission_date | Jun 13 2012
| Sample_last_update_date | Jun 14 2012
| 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 | Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions. Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)
| Sample_hyb_protocol | Following fragmentation, 2.2 ug of labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.
| Sample_scan_protocol | The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
| Sample_data_processing | The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm. RMA was run separately for biceps and quadriceps.
| Sample_platform_id | GPL570
| Sample_contact_name | Adam,T,Palermo
| Sample_contact_email | adam.palermo@genzyme.com
| Sample_contact_department | Functional Genomics
| Sample_contact_institute | Genzyme
| Sample_contact_address | 49 New York Ave
| Sample_contact_city | Framingham
| Sample_contact_state | MA
| Sample_contact_zip/postal_code | 01701
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM947nnn/GSM947518/suppl/GSM947518_H0024660.CEL.gz
| Sample_series_id | GSE38680
| Sample_data_row_count | 54675
| |
|
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