|
Status |
Public on Apr 29, 2021 |
Title |
CTRL-C3_Replicate_2 |
Sample type |
RNA |
|
|
Source name |
Lymphoblastoid Cell Line from Control Healthy Individual. Age- and Sex-matched Control for AOA2-P3.
|
Organism |
Homo sapiens |
Characteristics |
cell type: Lymphoblastoid Cell Line transformed by Epstein-Barr Virus morphology: Lymphoblast genotype: Normal
|
Treatment protocol |
Cells were harvested by trypsinization followed by two washes with ice-cold PBS.
|
Growth protocol |
Lymphoblastoid cell lines (LCLs) from control and AOA2 patients were cultured in RPMI 1640 medium (ThermoFisher) containing 20% FBS (Sigma-Aldrich), 1% Penicillin/Streptomycin (P/S; Sigma-Aldrich), 2 mM L-glutamine (ThermoFisher) and 1% Non-Essential Amino Acids (ThermoFisher). All LCLs were grown at 37°C and in a humidified atmosphere containing 5% CO2.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from cultured human and mouse cells using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including an on-column DNase treatment to eliminate any contaminating genomic DNA.
|
Label |
Biotin
|
Label protocol |
RNA samples were amplified and biotin labeled using the WT-Ovation Pico target prep v1.0 protocol, which was derived from the NuGEN WT-Ovation Pico RNA Amplification system and the NuGEN FL-Ovation cDNA Biotin Module v2.
|
|
|
Hybridization protocol |
All fragmented and biotin labeled cDNA samples were hybridized to Affymetrix GeneChip Human Gene 1.0 ST microarrays for 16 hr at 45C. Arrays were washed using the Affymetrix Fluidics Station 450 according to the manufacturer’s recommendations.
|
Scan protocol |
Scanning was performed using the Affymetrix GeneChip 3000 7G scanner with autoloader running Affymetrix GeneChip Command Console (AGCC) software.
|
Description |
Gene expression data from CTRL-C3
|
Data processing |
Affymetrix gene expression data was analyzed using Bioconductor 2.5 running on R version 2.10.0. Probeset expression measures were calculated using RMA with the oligo package.
|
|
|
Submission date |
Jan 14, 2020 |
Last update date |
Apr 29, 2021 |
Contact name |
Steve West |
E-mail(s) |
stephen.west@crick.ac.uk
|
Organization name |
The Francis Crick Institute
|
Street address |
1 Midland Road
|
City |
London |
ZIP/Postal code |
NW1 1AT |
Country |
United Kingdom |
|
|
Platform ID |
GPL6244 |
Series (2) |
GSE143574 |
Integrated Genome and Transcriptome Analyses Reveal the Mechanism of Genome Instability in Ataxia with Oculomotor Apraxia 2 |
GSE143680 |
Integrated Genome and Transcriptome Analyses Reveal the Mechanism of Genome Instability in Ataxia with Oculomotor Apraxia 2. |
|