Search results for the GEO ID: GSE7624  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM162903 | GPL570 |
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Trasnsformed Lymphocytes Unaffected Twin Pair 3 (DCBD3.2)(TP10)
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Trasnsformed Lymphocytes Unaffected (Unaffected pateint of MZ twin pair 3)
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Sample ID:TP10
Twin Pair ID:DCBD3.2
Clinical Status:Control
Age of Onset:-
Age at interview & blood sampling:35
Current Age (2007):38
Sex: Female
Medication at interview (duration) :None
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| Sample_geo_accession | GSM162903
| | Sample_status | Public on Mar 31 2007
| | Sample_submission_date | Feb 14 2007
| | Sample_last_update_date | Mar 04 2008
| | 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 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | botin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM162nnn/GSM162903/suppl/GSM162903.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM162nnn/GSM162903/suppl/GSM162903.CHP.gz
| | Sample_series_id | GSE7036
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
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GSM181371 | GPL570 |
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LCL Discordant twin pair 1 (DCE1.1) (TP11)
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Discordant twin pair 1 (Affected pateint of MZ twin pair DCE1)
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Sample ID:TP11
Twin Pair ID:DCE1.1
Clinical Status:Late onset IGE
Age of Onset:-28
Age at interview & blood sampling:39
Current Age (2007):41
Sex: MALE
Medication at blood sampling : Epilim
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| Sample_geo_accession | GSM181371
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181371/suppl/GSM181371.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181371/suppl/GSM181371.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
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GSM181372 | GPL570 |
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LCL Discordant twin pair 1 (DCE1.2) (TP12)
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Discordant twin pair 1 (Unsffected pateint of MZ twin pair DCE1)
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Sample ID: TP12
Twin Pair ID:DCE1.2
Clinical Status:Unaffected
Age of Onset:- N/A
Age at interview & blood sampling:39
Current Age (2007):41
Sex: MALE
Medication at blood sampling : Nil
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| Sample_geo_accession | GSM181372
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181372/suppl/GSM181372.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181372/suppl/GSM181372.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
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GSM181373 | GPL570 |
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LCL Discordant twin pair 2 (DCE2.1)(TP19)
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Discordant twin pair 2 (Affected pateint of MZ twin pair DCE2)
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Sample ID: TP19
Twin Pair ID:DCE2.1
Clinical Status:Childhood Absence Epilepsy + Febrile Seizures
Age of Onset:-4
Age at interview & blood sampling:42
Current Age (2007):45
Sex: FEMALE
Medication at blood sampling : None
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| Sample_geo_accession | GSM181373
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181373/suppl/GSM181373.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181373/suppl/GSM181373.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
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GSM181374 | GPL570 |
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LCL Discordant twin pair 2 (DCE2.2)(TP20)
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Discordant twin pair 2 (Unaffected pateint of MZ twin pair DCE2)
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Sample ID: TP20
Twin Pair ID:DCE2.2
Clinical Status:Unaffected
Age of Onset:- N/A
Age at interview & blood sampling:42
Current Age (2007):45
Sex: FEMALE
Medication at blood sampling : None
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| Sample_geo_accession | GSM181374
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181374/suppl/GSM181374.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181374/suppl/GSM181374.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM181375 | GPL570 |
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LCL Discordant twin pair 3 (DCE3.1)(TP29)
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Discordant twin pair 3 (Affected pateint of MZ twin pair DCE3)
|
Sample ID: TP29
Twin Pair ID:DCE3.1
Clinical Status: Childhood Absence Epilepsy
Age of Onset:-5
Age at interview & blood sampling:23
Current Age (2007):26
Sex: MALE
Medication at blood sampling : Epilim
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| Sample_geo_accession | GSM181375
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181375/suppl/GSM181375.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181375/suppl/GSM181375.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM181376 | GPL570 |
|
LCL Discordant twin pair 3 (DCE3.2)(TP30)
|
Discordant twin pair 3 (Unaffected pateint of MZ twin pair DCE3)
|
Sample ID: TP30
Twin Pair ID:DCE3.2
Clinical Status: Unaffected
Age of Onset:-N/A
Age at interview & blood sampling:23
Current Age (2007):26
Sex: MALE
Medication at blood sampling : None
|
-
|
| Sample_geo_accession | GSM181376
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181376/suppl/GSM181376.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181376/suppl/GSM181376.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM181377 | GPL570 |
|
LCL Discordant twin pair 4 (DCE4.1)(TP33)
|
Discordant twin pair 4 (Affected pateint of MZ twin pair DCE4)
|
Sample ID: TP33
Twin Pair ID:DCE4.1
Clinical Status: Childhood Absence Epilepsy
Age of Onset:-7
Age at interview & blood sampling:26
Current Age (2007):29
Sex: MALE
Medication at blood sampling : Epilim
|
-
|
| Sample_geo_accession | GSM181377
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181377/suppl/GSM181377.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181377/suppl/GSM181377.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM181378 | GPL570 |
|
LCL Discordant twin pair 4 (DCE4.2)(TP34)
|
Discordant twin pair 4 (Affected pateint of MZ twin pair DCE4)
|
Sample ID: TP34
Twin Pair ID: DCE4.2
Clinical Status: Unaffected
Age of Onset:-N/A
Age at interview & blood sampling: 26
Current Age (2007):29
Sex: MALE
Medication at blood sampling : None
|
-
|
| Sample_geo_accession | GSM181378
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181378/suppl/GSM181378.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181378/suppl/GSM181378.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM181379 | GPL570 |
|
LCL Discordant twin pair 5 (DCE5.1)(TP37)
|
Discordant twin pair 5 (Affected patient of MZ twin pair DCE5)
|
Sample ID: TP37
Twin Pair ID: DCE5.1
Clinical Status: Juvenile Absence Epilepsy + Febrile Seizures
Age of Onset:-13
Age at interview & blood sampling: 27
Current Age (2007):30
Sex: FEMALE
Medication at blood sampling : Epilim
|
-
|
| Sample_geo_accession | GSM181379
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181379/suppl/GSM181379.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181379/suppl/GSM181379.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM181380 | GPL570 |
|
LCL Discordant twin pair 5 (DCE5.2)(TP38)
|
Discordant twin pair 5 (Unaffected patient of MZ twin pair DCE5)
|
Sample ID: TP38
Twin Pair ID: DCE5.2
Clinical Status: Unaffected
Age of Onset:- N/A
Age at interview & blood sampling: 27
Current Age (2007):30
Sex: FEMALE
Medication at blood sampling : None
|
-
|
| Sample_geo_accession | GSM181380
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181380/suppl/GSM181380.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181380/suppl/GSM181380.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM181381 | GPL570 |
|
LCL Concordant for Epilepsy twin pair 1 (CCE1.1)(TP21)
|
Concordant for Epilepsy twin pair 1 (Affected patient of MZ twin pair CCE1)
|
Sample ID: TP21
Twin Pair ID: CCE1.1
Clinical Status: Childhood Absence Epilepsy
Age of Onset:-5
Age at interview & blood sampling: 22
Current Age (2007):25
Sex: FEMALE
Medication at blood sampling : Epilim
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-
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| Sample_geo_accession | GSM181381
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181381/suppl/GSM181381.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181381/suppl/GSM181381.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
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GSM181382 | GPL570 |
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LCL Concordant for Epilepsy twin pair 1 (CCE1.2)(TP22)
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Concordant for Epilepsy twin pair 1 (Affected patient of MZ twin pair CCE1)
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Sample ID: TP22
Twin Pair ID: CCE1.2
Clinical Status: Childhood Absence Epilepsy + Febrile Seizures
Age of Onset:-5
Age at interview & blood sampling: 22
Current Age (2007):25
Sex: FEMALE
Medication at blood sampling : None
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-
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| Sample_geo_accession | GSM181382
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181382/suppl/GSM181382.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181382/suppl/GSM181382.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
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GSM181384 | GPL570 |
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LCL Concordant for Epilepsy twin pair 2 (CCE2.1)(TP31)
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Concordant for Epilepsy twin pair 1 (Affected patient of MZ twin pair CCE1)
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Sample ID: TP31
Twin Pair ID: CCE2.1
Clinical Status: Childhood Absence Epilepsy
Age of Onset:-4.5
Age at interview & blood sampling: 34
Current Age (2007): 36
Sex: FEMALE
Medication at blood sampling : None
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-
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| Sample_geo_accession | GSM181384
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181384/suppl/GSM181384.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181384/suppl/GSM181384.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM181385 | GPL570 |
|
LCL Concordant for Epilepsy twin pair 2 (CCE2.2)(TP32)
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Concordant for Epilepsy twin pair 1 (Affected patient of MZ twin pair CCE1)
|
Sample ID: TP32
Twin Pair ID: CCE2.2
Clinical Status: Childhood Absence Epilepsy
Age of Onset:-5
Age at interview & blood sampling: 34
Current Age (2007): 36
Sex: FEMALE
Medication at blood sampling : None
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-
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| Sample_geo_accession | GSM181385
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181385/suppl/GSM181385.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181385/suppl/GSM181385.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM181389 | GPL570 |
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LCL Concordant for Epilepsy twin pair 3 (CCE3.1)(TP35)
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Concordant for Epilepsy twin pair 3 (Affected patient of MZ twin pair CCE3)
|
Sample ID: TP35
Twin Pair ID: CCE3.1
Clinical Status: Childhood Absence Epilepsy
Age of Onset:-7
Age at interview & blood sampling: 57
Current Age (2007): 60
Sex: MALE
Medication at blood sampling : Epilim
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-
|
| Sample_geo_accession | GSM181389
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181389/suppl/GSM181389.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181389/suppl/GSM181389.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM181390 | GPL570 |
|
LCL Concordant for Epilepsy twin pair 3 (CCE3.2)(TP36)
|
Concordant for Epilepsy twin pair 3 (Affected patient of MZ twin pair CCE3)
|
Sample ID: TP36
Twin Pair ID: CCE3.2
Clinical Status: Childhood Absence Epilepsy
Age of Onset:-7
Age at interview & blood sampling: 57
Current Age (2007): 60
Sex: MALE
Medication at blood sampling : None
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-
|
| Sample_geo_accession | GSM181390
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181390/suppl/GSM181390.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181390/suppl/GSM181390.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM181391 | GPL570 |
|
LCL Concordant for Epilepsy twin pair 4 (CCE4.1)(TP39)
|
Concordant for Epilepsy twin pair 4 (Affected patient of MZ twin pair CCE4)
|
Sample ID: TP39
Twin Pair ID: CCE4.1
Clinical Status: Childhood Absence Epilepsy
Age of Onset:-11.5
Age at interview & blood sampling: 31
Current Age (2007): 34
Sex: MALE
Medication at blood sampling : Epilim & Lamictal
|
-
|
| Sample_geo_accession | GSM181391
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181391/suppl/GSM181391.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181391/suppl/GSM181391.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM181392 | GPL570 |
|
LCL Concordant for Epilepsy twin pair 4 (CCE4.2)(TP40)
|
Concordant for Epilepsy twin pair 4 (Affected patient of MZ twin pair CCE4)
|
Sample ID: TP40
Twin Pair ID: CCE4.2
Clinical Status: Childhood Absence Epilepsy
Age of Onset:-10.5
Age at interview & blood sampling: 31
Current Age (2007): 34
Sex: MALE
Medication at blood sampling : Epilim
|
-
|
| Sample_geo_accession | GSM181392
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181392/suppl/GSM181392.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181392/suppl/GSM181392.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM181395 | GPL570 |
|
LCL Unaffected MZ twin pair 1 (CCN1.1)(TP13)
|
Unaffected MZ twin pair 1 (Unaffected patient of MZ twin pair CCN1)
|
Sample ID: TP13
Twin Pair ID: CCN1.1
Clinical Status: Unaffected
Age of Onset:-N/A
Age at interview & blood sampling: 37
Current Age (2007): 40
Sex: MALE
Medication at blood sampling : None
**Note this sample has a Biological replicate- Blood was taken from this patient on two separate occasions and two different transformed lymphocytes were arrayed. The matching sample is CCN1.1R**
|
-
|
| Sample_geo_accession | GSM181395
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181395/suppl/GSM181395.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181395/suppl/GSM181395.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM181396 | GPL570 |
|
LCL Unaffected MZ twin pair 1 (CCN1.2)(TP14)
|
Unaffected MZ twin pair 1 (Unaffected patient of MZ twin pair CCN1)
|
Sample ID: TP14
Twin Pair ID: CCN1.2
Clinical Status: Unaffected
Age of Onset:-N/A
Age at interview & blood sampling: 37
Current Age (2007): 40
Sex: MALE
Medication at blood sampling : None
**Note this sample has a Biological replicate- Blood was taken from this patient on two separate occasions and two different transformed lymphocytes were arrayed. The matching sample is CCN1.2R**
|
-
|
| Sample_geo_accession | GSM181396
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181396/suppl/GSM181396.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181396/suppl/GSM181396.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM181399 | GPL570 |
|
LCL Unaffected MZ twin pair 1 (CCN1.1R)(TP15)
|
Unaffected MZ twin pair 1 Repeat (Unaffected patient of MZ twin pair CCN1)
|
Sample ID: TP15
Twin Pair ID: CCN1.1R
Clinical Status: Unaffected
Age of Onset:-N/A
Age at interview & blood sampling: 37
Current Age (2007): 40
Sex: MALE
Medication at blood sampling : None
**Note this sample has a Biological replicate- Blood was taken from this patient on two separate occasions and two different transformed lymphocytes were arrayed. The matching sample is CCN1.1**
|
-
|
| Sample_geo_accession | GSM181399
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181399/suppl/GSM181399.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181399/suppl/GSM181399.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM181400 | GPL570 |
|
LCL Unaffected MZ twin pair 1 (CCN1.2R)(TP16)
|
Unaffected MZ twin pair 1 Repeat (Unaffected patient of MZ twin pair CCN1)
|
Sample ID: TP16
Twin Pair ID: CCN1.2R
Clinical Status: Unaffected
Age of Onset:-N/A
Age at interview & blood sampling: 37
Current Age (2007): 40
Sex: MALE
Medication at blood sampling : None
**Note this sample has a Biological replicate- Blood was taken from this patient on two separate occasions and two different transformed lymphocytes were arrayed. The matching sample is CCN1.2**
|
-
|
| Sample_geo_accession | GSM181400
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181400/suppl/GSM181400.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181400/suppl/GSM181400.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM181405 | GPL570 |
|
LCL Unaffected MZ twin pair 2 (CCN2.1)(TP17)
|
Unaffected MZ twin pair 2 (Unaffected patient of MZ twin pair CCN2)
|
Sample ID: TP17
Twin Pair ID: CCN2.1
Clinical Status: Unaffected
Age of Onset:-N/A
Age at interview & blood sampling: 27
Current Age (2007): 30
Sex: MALE
Medication at blood sampling : None
|
-
|
| Sample_geo_accession | GSM181405
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181405/suppl/GSM181405.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181405/suppl/GSM181405.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM181406 | GPL570 |
|
LCL Unaffected MZ twin pair 2 (CCN2.2)(TP18)
|
Unaffected MZ twin pair 2 (Unaffected patient of MZ twin pair CCN2)
|
Sample ID: TP18
Twin Pair ID: CCN2.2
Clinical Status: Unaffected
Age of Onset:-N/A
Age at interview & blood sampling: 27
Current Age (2007): 30
Sex: MALE
Medication at blood sampling : None
|
-
|
| Sample_geo_accession | GSM181406
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181406/suppl/GSM181406.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181406/suppl/GSM181406.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM181409 | GPL570 |
|
LCL Unaffected MZ twin pair 3 (CCN3.1)(TP23)
|
Unaffected MZ twin pair 3 (Unaffected patient of MZ twin pair CCN3)
|
Sample ID: TP23
Twin Pair ID: CCN3.1
Clinical Status: Unaffected
Age of Onset:-N/A
Age at interview & blood sampling: 25
Current Age (2007): 28
Sex: MALE
Medication at blood sampling : None
|
-
|
| Sample_geo_accession | GSM181409
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181409/suppl/GSM181409.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181409/suppl/GSM181409.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM181410 | GPL570 |
|
LCL Unaffected MZ twin pair 3 (CCN3.2)(TP24)
|
Unaffected MZ twin pair 3 (Unaffected patient of MZ twin pair CCN3)
|
Sample ID: TP24
Twin Pair ID: CCN3.2
Clinical Status: Unaffected
Age of Onset:-N/A
Age at interview & blood sampling: 25
Current Age (2007): 28
Sex: MALE
Medication at blood sampling : None
|
-
|
| Sample_geo_accession | GSM181410
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181410/suppl/GSM181410.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181410/suppl/GSM181410.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM181412 | GPL570 |
|
LCL Unaffected MZ twin pair 4 (CCN4.1)(TP25)
|
Unaffected MZ twin pair 4 (Unaffected patient of MZ twin pair CCN4)
|
Sample ID: TP25
Twin Pair ID: CCN4.1
Clinical Status: Unaffected
Age of Onset:-N/A
Age at interview & blood sampling: 29
Current Age (2007): 32
Sex: FEMALE
Medication at blood sampling : None
|
-
|
| Sample_geo_accession | GSM181412
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 09 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181412/suppl/GSM181412.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181412/suppl/GSM181412.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM181413 | GPL570 |
|
LCL Unaffected MZ twin pair 4 (CCN4.2)(TP26)
|
Unaffected MZ twin pair 4 (Unaffected patient of MZ twin pair CCN4)
|
Sample ID: TP26
Twin Pair ID: CCN4.2
Clinical Status: Unaffected
Age of Onset:-N/A
Age at interview & blood sampling: 29
Current Age (2007): 32
Sex: FEMALE
Medication at blood sampling : None
|
-
|
| Sample_geo_accession | GSM181413
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 10 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181413/suppl/GSM181413.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181413/suppl/GSM181413.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM181416 | GPL570 |
|
LCL Unaffected MZ twin pair 5 (CCN5.1)(TP27)
|
Unaffected MZ twin pair 5 (Unaffected patient of MZ twin pair CCN5)
|
Sample ID: TP27
Twin Pair ID: CCN5.1
Clinical Status: Unaffected
Age of Onset:-N/A
Age at interview & blood sampling: 34
Current Age (2007): 37
Sex: FEMALE
Medication at blood sampling : None
|
-
|
| Sample_geo_accession | GSM181416
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 10 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181416/suppl/GSM181416.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181416/suppl/GSM181416.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM181417 | GPL570 |
|
LCL Unaffected MZ twin pair 5 (CCN5.2)(TP28)
|
Unaffected MZ twin pair 5 (Unaffected patient of MZ twin pair CCN5)
|
Sample ID: TP28
Twin Pair ID: CCN5.2
Clinical Status: Unaffected
Age of Onset:-N/A
Age at interview & blood sampling: 34
Current Age (2007): 37
Sex: FEMALE
Medication at blood sampling : None
|
-
|
| Sample_geo_accession | GSM181417
| | Sample_status | Public on Feb 28 2008
| | Sample_submission_date | Apr 10 2007
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22 LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture. RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181417/suppl/GSM181417.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM181nnn/GSM181417/suppl/GSM181417.CHP.gz
| | Sample_series_id | GSE7486
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM184438 | GPL570 |
|
Trasnsformed Lymphocytes Brief Psychotic Disorder Affected Twin Pair 1 (TP1)
|
Trasnsformed Lymphocytes Brief Psychotic Disorder (Affected pateint of MZ twin pair 1)
|
Sample ID:TP1
Twin Pair ID:-
Clinical Status: Brief Psychotic Disorder
Age of Onset:55
Age at interview & blood sampling:61
Current Age (2007):66
Sex: Female
Medication at interview (duration) :Thyroxine
|
-
|
| Sample_geo_accession | GSM184438
| | Sample_status | Public on Mar 30 2008
| | Sample_submission_date | Apr 26 2007
| | Sample_last_update_date | Feb 21 2008
| | 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 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM184nnn/GSM184438/suppl/GSM184438.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM184nnn/GSM184438/suppl/GSM184438.CHP.gz
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM184439 | GPL570 |
|
Trasnsformed Lymphocytes Unaffected Twin Pair 1 (TP2)
|
Trasnsformed Lymphocytes Unaffected (Unaffected pateint of MZ twin pair 1)
|
Sample ID:TP2
Twin Pair ID:-
Clinical Status: Unaffected
Age of Onset:N/A
Age at interview & blood sampling:61
Current Age (2007):66
Sex: Female
Medication at interview (duration) : thyroxine
|
-
|
| Sample_geo_accession | GSM184439
| | Sample_status | Public on Mar 30 2008
| | Sample_submission_date | Apr 26 2007
| | Sample_last_update_date | Feb 21 2008
| | 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 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM184nnn/GSM184439/suppl/GSM184439.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM184nnn/GSM184439/suppl/GSM184439.CHP.gz
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
| | |
|
GSM184442 | GPL570 |
|
Trasnsformed Lymphocytes Schizophrenia Affected discordant twin (TP3)
|
Trasnsformed Lymphocytes Schizophrenia (Affected pateint of MZ twin 2)
|
Sample ID:TP3
Twin Pair ID:-
Clinical Status: Schizophrenia
Age of Onset:21
Age at interview & blood sampling:26
Current Age (2007):31
Sex: Female
Medication at interview (duration) :Olanzapine
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| Sample_geo_accession | GSM184442
| | Sample_status | Public on Mar 30 2008
| | Sample_submission_date | Apr 26 2007
| | Sample_last_update_date | Feb 21 2008
| | 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 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM184nnn/GSM184442/suppl/GSM184442.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM184nnn/GSM184442/suppl/GSM184442.CHP.gz
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
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GSM184443 | GPL570 |
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Trasnsformed Lymphocytes Schizophrenia Affected discordant twin (TP4)
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Trasnsformed Lymphocytes Unaffected (Unaffected pateint of MZ twin 2)
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Sample ID:TP4
Twin Pair ID:-
Clinical Status: Schizophrenia
Age of Onset:N/A
Age at interview & blood sampling:26
Current Age (2007):31
Sex: Female
Medication at interview (duration) :Nil
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| Sample_geo_accession | GSM184443
| | Sample_status | Public on Mar 30 2008
| | Sample_submission_date | Apr 26 2007
| | Sample_last_update_date | Feb 21 2008
| | 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 | LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_hyb_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_scan_protocol | Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.
| | Sample_data_processing | Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nicholas,,Matigian
| | Sample_contact_email | n.matigian@griffith.edu.au
| | Sample_contact_phone | 61 7 38753660
| | Sample_contact_laboratory | Systems Biology
| | Sample_contact_institute | National Adult Stem Cell Centre
| | Sample_contact_address | 170 Kessels Rd, Nathan
| | Sample_contact_city | Brisbane
| | Sample_contact_state | Queensland
| | Sample_contact_zip/postal_code | 4111
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM184nnn/GSM184443/suppl/GSM184443.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM184nnn/GSM184443/suppl/GSM184443.CHP.gz
| | Sample_series_id | GSE7624
| | Sample_data_row_count | 54675
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