Search results for the GEO ID: GSE18309  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM457169 | GPL570 |
|
PBMC mRNA from Alzheimer's disease patient 1
|
peripheral blood mononuclear cells, Alzheimer's disease patient
|
cell type: peripheral blood mononuclear cells (PBMCs)
disease status: Alzheimer's disease patient
race/ethnicity: Taiwanese
patient id(s): LE110, LE114
|
This chip contains 47,000 transcripts and variants, including 38,500 well-characterized human genes.
|
| Sample_geo_accession | GSM457169
| | Sample_status | Public on Nov 30 2009
| | Sample_submission_date | Sep 28 2009
| | Sample_last_update_date | Oct 30 2009
| | 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 was extracted using Trizol reagent (Invitrogen), according to the manufacturer's instructions. Briefly, the leukocyte pellet was lysed with 1-2 mL Trizol, and then 0.2 mL chloroform was added. Following centrifugation, the total RNA was precipitated from the aqueous phase by mixing with isopropyl alcohol. The RNA was pelleted by centrifugation; the pellet was washed with 75% ethanol, and centrifuged again. The RNA pellet was dried and dissolved in RNase-free water. RNA quality was determined using the RNA 6000 Pico LabChip kit and the Agilent 2100 bio-analyzer (Agilent Technologies Inc., USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Trizol-purified RNA was quantified using a NanoDrop spectrophotometer (Rockland, DE, USA). RNA integrity was verified with a BioAnalyzer 2100 (Agilent, Palo Alto, CA, USA). High quality RNA (RIN>7) was transcribed into cDNA with a double reverse transcriptase-PCR technique, and in vitro transcription was performed to generate biotin-labeled cRNA for subsequent hybridization on HG-U133 Plus2 GeneChips® (Affymetrix, CA, USA).
| | Sample_hyb_protocol | The biotin labeled cRNA product (20 µg) was purified with a sample cleanup module (Qiagen) and samples were fragmented with the fragmentation buffer from Affymetrix at 94°C for 35 minutes. Fragmented and labeled targets (together with hybridization and oligo B2 controls) were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays at 45°C for 16 hours. Washing and staining of the arrays were performed on the Affymetrix fluidics station using the EukGE-WS2v5_450 protocol.
| | Sample_scan_protocol | Imaging of the arrays and signal quantification were performed with the Affymetrix GeneChip Scanner 3000 and GeneChip Operating Software.
| | Sample_data_processing | Gene expression analysis software was used for data analyses of differential expression profiles and RMA was used for normalization (GeneSpring GX software, version 7.3, Agilent Technologies, USA).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kuang-Den,,Chen
| | Sample_contact_email | dennis8857@gmail.com
| | Sample_contact_phone | 886-7-7317123
| | Sample_contact_fax | 886-7-7336856
| | Sample_contact_department | Translational Research Center in Biomedical Sicences
| | Sample_contact_institute | Chang Gung Memorial Hospital Kaohsiung
| | Sample_contact_address | 123, Ta-Pei Rd., Niao-Sung Hsiang
| | Sample_contact_city | Kaohsiung Hsien
| | Sample_contact_zip/postal_code | 83342
| | Sample_contact_country | Taiwan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM457nnn/GSM457169/suppl/GSM457169.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM457nnn/GSM457169/suppl/GSM457169.CHP.gz
| | Sample_series_id | GSE18309
| | Sample_data_row_count | 54675
| | |
|
GSM457170 | GPL570 |
|
PBMC mRNA from Alzheimer's disease patient 2
|
peripheral blood mononuclear cells, Alzheimer's disease patient
|
cell type: peripheral blood mononuclear cells (PBMCs)
disease status: Alzheimer's disease patient
race/ethnicity: Taiwanese
patient id(s): LE086
|
This chip contains 47,000 transcripts and variants, including 38,500 well-characterized human genes.
|
| Sample_geo_accession | GSM457170
| | Sample_status | Public on Nov 30 2009
| | Sample_submission_date | Sep 28 2009
| | Sample_last_update_date | Oct 30 2009
| | 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 was extracted using Trizol reagent (Invitrogen), according to the manufacturer's instructions. Briefly, the leukocyte pellet was lysed with 1-2 mL Trizol, and then 0.2 mL chloroform was added. Following centrifugation, the total RNA was precipitated from the aqueous phase by mixing with isopropyl alcohol. The RNA was pelleted by centrifugation; the pellet was washed with 75% ethanol, and centrifuged again. The RNA pellet was dried and dissolved in RNase-free water. RNA quality was determined using the RNA 6000 Pico LabChip kit and the Agilent 2100 bio-analyzer (Agilent Technologies Inc., USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Trizol-purified RNA was quantified using a NanoDrop spectrophotometer (Rockland, DE, USA). RNA integrity was verified with a BioAnalyzer 2100 (Agilent, Palo Alto, CA, USA). High quality RNA (RIN>7) was transcribed into cDNA with a double reverse transcriptase-PCR technique, and in vitro transcription was performed to generate biotin-labeled cRNA for subsequent hybridization on HG-U133 Plus2 GeneChips® (Affymetrix, CA, USA).
| | Sample_hyb_protocol | The biotin labeled cRNA product (20 µg) was purified with a sample cleanup module (Qiagen) and samples were fragmented with the fragmentation buffer from Affymetrix at 94°C for 35 minutes. Fragmented and labeled targets (together with hybridization and oligo B2 controls) were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays at 45°C for 16 hours. Washing and staining of the arrays were performed on the Affymetrix fluidics station using the EukGE-WS2v5_450 protocol.
| | Sample_scan_protocol | Imaging of the arrays and signal quantification were performed with the Affymetrix GeneChip Scanner 3000 and GeneChip Operating Software.
| | Sample_data_processing | Gene expression analysis software was used for data analyses of differential expression profiles and RMA was used for normalization (GeneSpring GX software, version 7.3, Agilent Technologies, USA).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kuang-Den,,Chen
| | Sample_contact_email | dennis8857@gmail.com
| | Sample_contact_phone | 886-7-7317123
| | Sample_contact_fax | 886-7-7336856
| | Sample_contact_department | Translational Research Center in Biomedical Sicences
| | Sample_contact_institute | Chang Gung Memorial Hospital Kaohsiung
| | Sample_contact_address | 123, Ta-Pei Rd., Niao-Sung Hsiang
| | Sample_contact_city | Kaohsiung Hsien
| | Sample_contact_zip/postal_code | 83342
| | Sample_contact_country | Taiwan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM457nnn/GSM457170/suppl/GSM457170.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM457nnn/GSM457170/suppl/GSM457170.CHP.gz
| | Sample_series_id | GSE18309
| | Sample_data_row_count | 54675
| | |
|
GSM457171 | GPL570 |
|
PBMC mRNA from Alzheimer's disease patient 3
|
peripheral blood mononuclear cells, Alzheimer's disease patient
|
cell type: peripheral blood mononuclear cells (PBMCs)
disease status: Alzheimer's disease patient
race/ethnicity: Taiwanese
patient id(s): LE102
|
This chip contains 47,000 transcripts and variants, including 38,500 well-characterized human genes.
|
| Sample_geo_accession | GSM457171
| | Sample_status | Public on Nov 30 2009
| | Sample_submission_date | Sep 29 2009
| | Sample_last_update_date | Oct 30 2009
| | 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 was extracted using Trizol reagent (Invitrogen), according to the manufacturer's instructions. Briefly, the leukocyte pellet was lysed with 1-2 mL Trizol, and then 0.2 mL chloroform was added. Following centrifugation, the total RNA was precipitated from the aqueous phase by mixing with isopropyl alcohol. The RNA was pelleted by centrifugation; the pellet was washed with 75% ethanol, and centrifuged again. The RNA pellet was dried and dissolved in RNase-free water. RNA quality was determined using the RNA 6000 Pico LabChip kit and the Agilent 2100 bio-analyzer (Agilent Technologies Inc., USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Trizol-purified RNA was quantified using a NanoDrop spectrophotometer (Rockland, DE, USA). RNA integrity was verified with a BioAnalyzer 2100 (Agilent, Palo Alto, CA, USA). High quality RNA (RIN>7) was transcribed into cDNA with a double reverse transcriptase-PCR technique, and in vitro transcription was performed to generate biotin-labeled cRNA for subsequent hybridization on HG-U133 Plus2 GeneChips® (Affymetrix, CA, USA).
| | Sample_hyb_protocol | The biotin labeled cRNA product (20 µg) was purified with a sample cleanup module (Qiagen) and samples were fragmented with the fragmentation buffer from Affymetrix at 94°C for 35 minutes. Fragmented and labeled targets (together with hybridization and oligo B2 controls) were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays at 45°C for 16 hours. Washing and staining of the arrays were performed on the Affymetrix fluidics station using the EukGE-WS2v5_450 protocol.
| | Sample_scan_protocol | Imaging of the arrays and signal quantification were performed with the Affymetrix GeneChip Scanner 3000 and GeneChip Operating Software.
| | Sample_data_processing | Gene expression analysis software was used for data analyses of differential expression profiles and RMA was used for normalization (GeneSpring GX software, version 7.3, Agilent Technologies, USA).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kuang-Den,,Chen
| | Sample_contact_email | dennis8857@gmail.com
| | Sample_contact_phone | 886-7-7317123
| | Sample_contact_fax | 886-7-7336856
| | Sample_contact_department | Translational Research Center in Biomedical Sicences
| | Sample_contact_institute | Chang Gung Memorial Hospital Kaohsiung
| | Sample_contact_address | 123, Ta-Pei Rd., Niao-Sung Hsiang
| | Sample_contact_city | Kaohsiung Hsien
| | Sample_contact_zip/postal_code | 83342
| | Sample_contact_country | Taiwan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM457nnn/GSM457171/suppl/GSM457171.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM457nnn/GSM457171/suppl/GSM457171.CHP.gz
| | Sample_series_id | GSE18309
| | Sample_data_row_count | 54675
| | |
|
GSM457172 | GPL570 |
|
PBMC mRNA from mild cognitive impairment (MCI) patient 1
|
peripheral blood mononuclear cells, MCI patient
|
cell type: peripheral blood mononuclear cells (PBMCs)
disease status: mild cognitive impairment (MCI) patient
race/ethnicity: Taiwanese
patient id(s): LE038, LE046, LE049
|
This chip contains 47,000 transcripts and variants, including 38,500 well-characterized human genes.
|
| Sample_geo_accession | GSM457172
| | Sample_status | Public on Nov 30 2009
| | Sample_submission_date | Sep 29 2009
| | Sample_last_update_date | Oct 30 2009
| | 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 was extracted using Trizol reagent (Invitrogen), according to the manufacturer's instructions. Briefly, the leukocyte pellet was lysed with 1-2 mL Trizol, and then 0.2 mL chloroform was added. Following centrifugation, the total RNA was precipitated from the aqueous phase by mixing with isopropyl alcohol. The RNA was pelleted by centrifugation; the pellet was washed with 75% ethanol, and centrifuged again. The RNA pellet was dried and dissolved in RNase-free water. RNA quality was determined using the RNA 6000 Pico LabChip kit and the Agilent 2100 bio-analyzer (Agilent Technologies Inc., USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Trizol-purified RNA was quantified using a NanoDrop spectrophotometer (Rockland, DE, USA). RNA integrity was verified with a BioAnalyzer 2100 (Agilent, Palo Alto, CA, USA). High quality RNA (RIN>7) was transcribed into cDNA with a double reverse transcriptase-PCR technique, and in vitro transcription was performed to generate biotin-labeled cRNA for subsequent hybridization on HG-U133 Plus2 GeneChips® (Affymetrix, CA, USA).
| | Sample_hyb_protocol | The biotin labeled cRNA product (20 µg) was purified with a sample cleanup module (Qiagen) and samples were fragmented with the fragmentation buffer from Affymetrix at 94°C for 35 minutes. Fragmented and labeled targets (together with hybridization and oligo B2 controls) were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays at 45°C for 16 hours. Washing and staining of the arrays were performed on the Affymetrix fluidics station using the EukGE-WS2v5_450 protocol.
| | Sample_scan_protocol | Imaging of the arrays and signal quantification were performed with the Affymetrix GeneChip Scanner 3000 and GeneChip Operating Software.
| | Sample_data_processing | Gene expression analysis software was used for data analyses of differential expression profiles and RMA was used for normalization (GeneSpring GX software, version 7.3, Agilent Technologies, USA).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kuang-Den,,Chen
| | Sample_contact_email | dennis8857@gmail.com
| | Sample_contact_phone | 886-7-7317123
| | Sample_contact_fax | 886-7-7336856
| | Sample_contact_department | Translational Research Center in Biomedical Sicences
| | Sample_contact_institute | Chang Gung Memorial Hospital Kaohsiung
| | Sample_contact_address | 123, Ta-Pei Rd., Niao-Sung Hsiang
| | Sample_contact_city | Kaohsiung Hsien
| | Sample_contact_zip/postal_code | 83342
| | Sample_contact_country | Taiwan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM457nnn/GSM457172/suppl/GSM457172.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM457nnn/GSM457172/suppl/GSM457172.CHP.gz
| | Sample_series_id | GSE18309
| | Sample_data_row_count | 54675
| | |
|
GSM457173 | GPL570 |
|
PBMC mRNA from mild cognitive impairment (MCI) patient 2
|
peripheral blood mononuclear cells, MCI patient
|
cell type: peripheral blood mononuclear cells (PBMCs)
disease status: mild cognitive impairment (MCI) patient
race/ethnicity: Taiwanese
patient id(s): LE085
|
This chip contains 47,000 transcripts and variants, including 38,500 well-characterized human genes.
|
| Sample_geo_accession | GSM457173
| | Sample_status | Public on Nov 30 2009
| | Sample_submission_date | Sep 29 2009
| | Sample_last_update_date | Oct 30 2009
| | 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 was extracted using Trizol reagent (Invitrogen), according to the manufacturer's instructions. Briefly, the leukocyte pellet was lysed with 1-2 mL Trizol, and then 0.2 mL chloroform was added. Following centrifugation, the total RNA was precipitated from the aqueous phase by mixing with isopropyl alcohol. The RNA was pelleted by centrifugation; the pellet was washed with 75% ethanol, and centrifuged again. The RNA pellet was dried and dissolved in RNase-free water. RNA quality was determined using the RNA 6000 Pico LabChip kit and the Agilent 2100 bio-analyzer (Agilent Technologies Inc., USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Trizol-purified RNA was quantified using a NanoDrop spectrophotometer (Rockland, DE, USA). RNA integrity was verified with a BioAnalyzer 2100 (Agilent, Palo Alto, CA, USA). High quality RNA (RIN>7) was transcribed into cDNA with a double reverse transcriptase-PCR technique, and in vitro transcription was performed to generate biotin-labeled cRNA for subsequent hybridization on HG-U133 Plus2 GeneChips® (Affymetrix, CA, USA).
| | Sample_hyb_protocol | The biotin labeled cRNA product (20 µg) was purified with a sample cleanup module (Qiagen) and samples were fragmented with the fragmentation buffer from Affymetrix at 94°C for 35 minutes. Fragmented and labeled targets (together with hybridization and oligo B2 controls) were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays at 45°C for 16 hours. Washing and staining of the arrays were performed on the Affymetrix fluidics station using the EukGE-WS2v5_450 protocol.
| | Sample_scan_protocol | Imaging of the arrays and signal quantification were performed with the Affymetrix GeneChip Scanner 3000 and GeneChip Operating Software.
| | Sample_data_processing | Gene expression analysis software was used for data analyses of differential expression profiles and RMA was used for normalization (GeneSpring GX software, version 7.3, Agilent Technologies, USA).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kuang-Den,,Chen
| | Sample_contact_email | dennis8857@gmail.com
| | Sample_contact_phone | 886-7-7317123
| | Sample_contact_fax | 886-7-7336856
| | Sample_contact_department | Translational Research Center in Biomedical Sicences
| | Sample_contact_institute | Chang Gung Memorial Hospital Kaohsiung
| | Sample_contact_address | 123, Ta-Pei Rd., Niao-Sung Hsiang
| | Sample_contact_city | Kaohsiung Hsien
| | Sample_contact_zip/postal_code | 83342
| | Sample_contact_country | Taiwan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM457nnn/GSM457173/suppl/GSM457173.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM457nnn/GSM457173/suppl/GSM457173.CHP.gz
| | Sample_series_id | GSE18309
| | Sample_data_row_count | 54675
| | |
|
GSM457174 | GPL570 |
|
PBMC mRNA from mild cognitive impairment (MCI) patient 3
|
peripheral blood mononuclear cells, MCI patient
|
cell type: peripheral blood mononuclear cells (PBMCs)
disease status: mild cognitive impairment (MCI) patient
race/ethnicity: Taiwanese
patient id(s): LE106
|
This chip contains 47,000 transcripts and variants, including 38,500 well-characterized human genes.
|
| Sample_geo_accession | GSM457174
| | Sample_status | Public on Nov 30 2009
| | Sample_submission_date | Sep 29 2009
| | Sample_last_update_date | Oct 30 2009
| | 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 was extracted using Trizol reagent (Invitrogen), according to the manufacturer's instructions. Briefly, the leukocyte pellet was lysed with 1-2 mL Trizol, and then 0.2 mL chloroform was added. Following centrifugation, the total RNA was precipitated from the aqueous phase by mixing with isopropyl alcohol. The RNA was pelleted by centrifugation; the pellet was washed with 75% ethanol, and centrifuged again. The RNA pellet was dried and dissolved in RNase-free water. RNA quality was determined using the RNA 6000 Pico LabChip kit and the Agilent 2100 bio-analyzer (Agilent Technologies Inc., USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Trizol-purified RNA was quantified using a NanoDrop spectrophotometer (Rockland, DE, USA). RNA integrity was verified with a BioAnalyzer 2100 (Agilent, Palo Alto, CA, USA). High quality RNA (RIN>7) was transcribed into cDNA with a double reverse transcriptase-PCR technique, and in vitro transcription was performed to generate biotin-labeled cRNA for subsequent hybridization on HG-U133 Plus2 GeneChips® (Affymetrix, CA, USA).
| | Sample_hyb_protocol | The biotin labeled cRNA product (20 µg) was purified with a sample cleanup module (Qiagen) and samples were fragmented with the fragmentation buffer from Affymetrix at 94°C for 35 minutes. Fragmented and labeled targets (together with hybridization and oligo B2 controls) were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays at 45°C for 16 hours. Washing and staining of the arrays were performed on the Affymetrix fluidics station using the EukGE-WS2v5_450 protocol.
| | Sample_scan_protocol | Imaging of the arrays and signal quantification were performed with the Affymetrix GeneChip Scanner 3000 and GeneChip Operating Software.
| | Sample_data_processing | Gene expression analysis software was used for data analyses of differential expression profiles and RMA was used for normalization (GeneSpring GX software, version 7.3, Agilent Technologies, USA).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kuang-Den,,Chen
| | Sample_contact_email | dennis8857@gmail.com
| | Sample_contact_phone | 886-7-7317123
| | Sample_contact_fax | 886-7-7336856
| | Sample_contact_department | Translational Research Center in Biomedical Sicences
| | Sample_contact_institute | Chang Gung Memorial Hospital Kaohsiung
| | Sample_contact_address | 123, Ta-Pei Rd., Niao-Sung Hsiang
| | Sample_contact_city | Kaohsiung Hsien
| | Sample_contact_zip/postal_code | 83342
| | Sample_contact_country | Taiwan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM457nnn/GSM457174/suppl/GSM457174.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM457nnn/GSM457174/suppl/GSM457174.CHP.gz
| | Sample_series_id | GSE18309
| | Sample_data_row_count | 54675
| | |
|
GSM457175 | GPL570 |
|
PBMC mRNA from Normal elder individual 1
|
peripheral blood mononuclear cells, Normal elder individual
|
cell type: peripheral blood mononuclear cells (PBMCs)
disease status: Normal elder individual
Taiwanese
patient id(s): LE039, LE045
|
This chip contains 47,000 transcripts and variants, including 38,500 well-characterized human genes.
|
| Sample_geo_accession | GSM457175
| | Sample_status | Public on Nov 30 2009
| | Sample_submission_date | Sep 29 2009
| | Sample_last_update_date | Oct 30 2009
| | 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 was extracted using Trizol reagent (Invitrogen), according to the manufacturer's instructions. Briefly, the leukocyte pellet was lysed with 1-2 mL Trizol, and then 0.2 mL chloroform was added. Following centrifugation, the total RNA was precipitated from the aqueous phase by mixing with isopropyl alcohol. The RNA was pelleted by centrifugation; the pellet was washed with 75% ethanol, and centrifuged again. The RNA pellet was dried and dissolved in RNase-free water. RNA quality was determined using the RNA 6000 Pico LabChip kit and the Agilent 2100 bio-analyzer (Agilent Technologies Inc., USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Trizol-purified RNA was quantified using a NanoDrop spectrophotometer (Rockland, DE, USA). RNA integrity was verified with a BioAnalyzer 2100 (Agilent, Palo Alto, CA, USA). High quality RNA (RIN>7) was transcribed into cDNA with a double reverse transcriptase-PCR technique, and in vitro transcription was performed to generate biotin-labeled cRNA for subsequent hybridization on HG-U133 Plus2 GeneChips® (Affymetrix, CA, USA).
| | Sample_hyb_protocol | The biotin labeled cRNA product (20 µg) was purified with a sample cleanup module (Qiagen) and samples were fragmented with the fragmentation buffer from Affymetrix at 94°C for 35 minutes. Fragmented and labeled targets (together with hybridization and oligo B2 controls) were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays at 45°C for 16 hours. Washing and staining of the arrays were performed on the Affymetrix fluidics station using the EukGE-WS2v5_450 protocol.
| | Sample_scan_protocol | Imaging of the arrays and signal quantification were performed with the Affymetrix GeneChip Scanner 3000 and GeneChip Operating Software.
| | Sample_data_processing | Gene expression analysis software was used for data analyses of differential expression profiles and RMA was used for normalization (GeneSpring GX software, version 7.3, Agilent Technologies, USA).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kuang-Den,,Chen
| | Sample_contact_email | dennis8857@gmail.com
| | Sample_contact_phone | 886-7-7317123
| | Sample_contact_fax | 886-7-7336856
| | Sample_contact_department | Translational Research Center in Biomedical Sicences
| | Sample_contact_institute | Chang Gung Memorial Hospital Kaohsiung
| | Sample_contact_address | 123, Ta-Pei Rd., Niao-Sung Hsiang
| | Sample_contact_city | Kaohsiung Hsien
| | Sample_contact_zip/postal_code | 83342
| | Sample_contact_country | Taiwan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM457nnn/GSM457175/suppl/GSM457175.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM457nnn/GSM457175/suppl/GSM457175.CHP.gz
| | Sample_series_id | GSE18309
| | Sample_data_row_count | 54675
| | |
|
GSM457176 | GPL570 |
|
PBMC mRNA from Normal elder individual 2
|
peripheral blood mononuclear cells, Normal elder individual
|
cell type: peripheral blood mononuclear cells (PBMCs)
disease status: Normal elder individual
Taiwanese
patient id(s): LE078
|
This chip contains 47,000 transcripts and variants, including 38,500 well-characterized human genes.
|
| Sample_geo_accession | GSM457176
| | Sample_status | Public on Nov 30 2009
| | Sample_submission_date | Sep 29 2009
| | Sample_last_update_date | Oct 30 2009
| | 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 was extracted using Trizol reagent (Invitrogen), according to the manufacturer's instructions. Briefly, the leukocyte pellet was lysed with 1-2 mL Trizol, and then 0.2 mL chloroform was added. Following centrifugation, the total RNA was precipitated from the aqueous phase by mixing with isopropyl alcohol. The RNA was pelleted by centrifugation; the pellet was washed with 75% ethanol, and centrifuged again. The RNA pellet was dried and dissolved in RNase-free water. RNA quality was determined using the RNA 6000 Pico LabChip kit and the Agilent 2100 bio-analyzer (Agilent Technologies Inc., USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Trizol-purified RNA was quantified using a NanoDrop spectrophotometer (Rockland, DE, USA). RNA integrity was verified with a BioAnalyzer 2100 (Agilent, Palo Alto, CA, USA). High quality RNA (RIN>7) was transcribed into cDNA with a double reverse transcriptase-PCR technique, and in vitro transcription was performed to generate biotin-labeled cRNA for subsequent hybridization on HG-U133 Plus2 GeneChips® (Affymetrix, CA, USA).
| | Sample_hyb_protocol | The biotin labeled cRNA product (20 µg) was purified with a sample cleanup module (Qiagen) and samples were fragmented with the fragmentation buffer from Affymetrix at 94°C for 35 minutes. Fragmented and labeled targets (together with hybridization and oligo B2 controls) were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays at 45°C for 16 hours. Washing and staining of the arrays were performed on the Affymetrix fluidics station using the EukGE-WS2v5_450 protocol.
| | Sample_scan_protocol | Imaging of the arrays and signal quantification were performed with the Affymetrix GeneChip Scanner 3000 and GeneChip Operating Software.
| | Sample_data_processing | Gene expression analysis software was used for data analyses of differential expression profiles and RMA was used for normalization (GeneSpring GX software, version 7.3, Agilent Technologies, USA).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kuang-Den,,Chen
| | Sample_contact_email | dennis8857@gmail.com
| | Sample_contact_phone | 886-7-7317123
| | Sample_contact_fax | 886-7-7336856
| | Sample_contact_department | Translational Research Center in Biomedical Sicences
| | Sample_contact_institute | Chang Gung Memorial Hospital Kaohsiung
| | Sample_contact_address | 123, Ta-Pei Rd., Niao-Sung Hsiang
| | Sample_contact_city | Kaohsiung Hsien
| | Sample_contact_zip/postal_code | 83342
| | Sample_contact_country | Taiwan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM457nnn/GSM457176/suppl/GSM457176.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM457nnn/GSM457176/suppl/GSM457176.CHP.gz
| | Sample_series_id | GSE18309
| | Sample_data_row_count | 54675
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GSM457177 | GPL570 |
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PBMC mRNA from Normal elder individual 3
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peripheral blood mononuclear cells, Normal elder individual
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cell type: peripheral blood mononuclear cells (PBMCs)
disease status: Normal elder individual
Taiwanese
patient id(s): LE100
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This chip contains 47,000 transcripts and variants, including 38,500 well-characterized human genes.
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| Sample_geo_accession | GSM457177
| | Sample_status | Public on Nov 30 2009
| | Sample_submission_date | Sep 29 2009
| | Sample_last_update_date | Oct 30 2009
| | 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 was extracted using Trizol reagent (Invitrogen), according to the manufacturer's instructions. Briefly, the leukocyte pellet was lysed with 1-2 mL Trizol, and then 0.2 mL chloroform was added. Following centrifugation, the total RNA was precipitated from the aqueous phase by mixing with isopropyl alcohol. The RNA was pelleted by centrifugation; the pellet was washed with 75% ethanol, and centrifuged again. The RNA pellet was dried and dissolved in RNase-free water. RNA quality was determined using the RNA 6000 Pico LabChip kit and the Agilent 2100 bio-analyzer (Agilent Technologies Inc., USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Trizol-purified RNA was quantified using a NanoDrop spectrophotometer (Rockland, DE, USA). RNA integrity was verified with a BioAnalyzer 2100 (Agilent, Palo Alto, CA, USA). High quality RNA (RIN>7) was transcribed into cDNA with a double reverse transcriptase-PCR technique, and in vitro transcription was performed to generate biotin-labeled cRNA for subsequent hybridization on HG-U133 Plus2 GeneChips® (Affymetrix, CA, USA).
| | Sample_hyb_protocol | The biotin labeled cRNA product (20 µg) was purified with a sample cleanup module (Qiagen) and samples were fragmented with the fragmentation buffer from Affymetrix at 94°C for 35 minutes. Fragmented and labeled targets (together with hybridization and oligo B2 controls) were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays at 45°C for 16 hours. Washing and staining of the arrays were performed on the Affymetrix fluidics station using the EukGE-WS2v5_450 protocol.
| | Sample_scan_protocol | Imaging of the arrays and signal quantification were performed with the Affymetrix GeneChip Scanner 3000 and GeneChip Operating Software.
| | Sample_data_processing | Gene expression analysis software was used for data analyses of differential expression profiles and RMA was used for normalization (GeneSpring GX software, version 7.3, Agilent Technologies, USA).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kuang-Den,,Chen
| | Sample_contact_email | dennis8857@gmail.com
| | Sample_contact_phone | 886-7-7317123
| | Sample_contact_fax | 886-7-7336856
| | Sample_contact_department | Translational Research Center in Biomedical Sicences
| | Sample_contact_institute | Chang Gung Memorial Hospital Kaohsiung
| | Sample_contact_address | 123, Ta-Pei Rd., Niao-Sung Hsiang
| | Sample_contact_city | Kaohsiung Hsien
| | Sample_contact_zip/postal_code | 83342
| | Sample_contact_country | Taiwan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM457nnn/GSM457177/suppl/GSM457177.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM457nnn/GSM457177/suppl/GSM457177.CHP.gz
| | Sample_series_id | GSE18309
| | Sample_data_row_count | 54675
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