|
| Status |
Public on Feb 28, 2008 |
| Title |
LCL Discordant twin pair 2 (DCE2.1)(TP19) |
| Sample type |
RNA |
| |
|
| Source name |
Discordant twin pair 2 (Affected pateint of MZ twin pair DCE2)
|
| Organism |
Homo sapiens |
| Characteristics |
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
|
| Growth protocol |
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
|
| Extracted molecule |
total RNA |
| Extraction protocol |
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
|
| Label |
biotin
|
| Label 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.
|
| |
|
| Hybridization 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.
|
| 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.
|
| Description |
-
|
| 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
|
| |
|
| Submission date |
Apr 09, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Nicholas Matigian |
| E-mail(s) |
n.matigian@griffith.edu.au
|
| Phone |
61 7 38753660
|
| Organization name |
National Adult Stem Cell Centre
|
| Lab |
Systems Biology
|
| Street address |
170 Kessels Rd, Nathan
|
| City |
Brisbane |
| State/province |
Queensland |
| ZIP/Postal code |
4111 |
| Country |
Australia |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE7486 |
Gene expression analysis in absence epilepsy using a monozygotic twin design |
| GSE7624 |
Expression Profiles of Monozygotic Twin |
|
| Relations |
| Reanalyzed by |
GSE64985 |
| Reanalyzed by |
GSE119087 |
