|
| Status |
Public on Nov 01, 2011 |
| Title |
Patient 3 [RNA-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
Lymphoblastoid cell line
|
| Organism |
Homo sapiens |
| Characteristics |
individual: Patient 3
cell line: Lymphoblastoid cell line
disease state: UPF3B mutation
|
| Treatment protocol |
No treatment
|
| Growth protocol |
The Epstein-Barr virus (EBV) immortalized B- cell lines (B-LCL) used in this study were established from peripheral blood lymphocytes of patients and controls. Once established the LCL cell lines were cultured in RPMI 1640 (Sigma) supplemented with 10% FCS, 2mM L-Glutamine, 0.017mg/ml benzylpenicillin and grown at 37 0 C with 5% CO2
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from lymphoblastoid cell lines using Trizol (Inivtrogen) and RNeasy mini-kit (QIAGNE). PolyA+ RNA was purified from total RNA using oligo-dT magnetic beads. RT-PCR was performed to make cDNA with random primers. All outlined steps are part of the mRNA-seq 8 sample preparation kit (cat# RS-100-0801, Illumina) and were performed by Geneworks (Australia). ds-cDNA was sequenced using Illumina Genome Analyzer II as recommended my manufacturer, and was also performed by Geneworks (Australia).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
The first and last 14 bases of all reads were trimmed to improve alignment and error rate. Reads were aligned to the human genome HG19, splice junctions database, mitochondrion DNA and rRNA. Splice junctions were built from exon annotation which comprises of 45 bases on each side of the exon-exon junction (see supplementary file 'Splice_Sites_45.fa.txt' on Series GSE27199 record). If the exon is less than 45 bp, the whole exon is included. Reads were mapped using ELAND (Illumina). Mapped reads with more than 2 mismatches were excluded from downstream analysis.
Description of *_HG19_Aligned.txt file:
1. Machine
2. Run number
3. Lane
4. Tile
5. X coordinate of cluster
6. Y coordinate of cluster
7. Index value (0 for a non-indexed run)
8. Read number (1 or 2 for paired-read analysis, 0 for single read analysis)
9. Read sequence
10. Quality string--In sym,bolic ASCII format (ASCII character code = quality value +64)
11. Match chromosome
12. Match contig
13. Match position--Always with respect to forward strand, number starts at 1
14. Match strand
15. Match descriptor--Concise description of alignment (Number denotes a run of matching bases, letter denotes substitution of a nucleotide)
16. Single read alignment score
|
| |
|
| Submission date |
Feb 09, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Jozef Gecz |
| Organization name |
SA Pathology
|
| Department |
Genetics Medicine
|
| Lab |
Neurogenetics
|
| Street address |
72 King William Rd
|
| City |
North Adelaide |
| State/province |
South Australia |
| ZIP/Postal code |
5006 |
| Country |
Australia |
| |
|
| Platform ID |
GPL9115 |
| Series (3) |
| GSE27125 |
Genome-wide consequences of compromised NMD and their relavence for variable clinical phenotype of patients with UPF3B mutations [mRNA profiling] |
| GSE27199 |
Genome-wide consequences of compromised NMD and their relavence for variable clinical phenotype of patients with UPF3B mutations [RNA-seq] |
| GSE27433 |
Genome-wide consequences of compromised NMD and their relavence for variable clinical phenotype of patients with UPF3B mutations |
|
| Relations |
| SRA |
SRX044550 |
| BioSample |
SAMN00216495 |
