|
| Status |
Public on Apr 03, 2013 |
| Title |
FRDA19.UTB |
| Sample type |
SRA |
| |
|
| Source name |
primary cultured lymphocytes
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: PBMC
treatment: Un-treated control
|
| Treatment protocol |
Primary lymphocytes at cell density of 1x10^7cells/ml were treated with 10mM nicotinamide for 3 days. Culture medium with or without (untreated as control) nicotinamide was changed every 24 hours incubation.
|
| Growth protocol |
Primary lymphocytes from FRDA patients were isolated from the blood samples using Ficoll-Hypaque TM gradient (Sigma) by following the manufacturer’s protocol. Human blood samples were obtained from patients in accordance with UK Human Tissue Authority ethical guidelines. Cells were grown in RPMI 1640 (PAA) medium with 2 mM L-glutamine and 10% fetal calf serum (PAA) and supplemented with 1x penicillin/streptomycin solution (GIBCO) at 37 °C in 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. TruSeq DNA Sample Prep Kits v2 - Illumina (Cat#FC-121-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina CASAVA 1.8.2 software was used for basecalling. The reads were demultiplexed, allowing no mismatches in the index sequence.
Sequence reads were aligned to hg19 version of human genome with Tophat 1.4.1 software with parameters -p 8 and transcript annotation file supplied.
Gene based counts were obtained using HTSeq count module (version 0.5.3p9) using parameters -m intersection-nonempty --stranded=no
Differential expression analysis was then performed using DESeq Bioconductor package with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Count files were obtained using HTSeq count module (version 0.5.3p9) using parameters -m intersection-nonempty --stranded=no
|
| |
|
| Submission date |
Dec 17, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Sanjay Padmakar Khadayate |
| Organization name |
MRC London Institute of Medical Sciences
|
| Street address |
Du Cane Road
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE42960 |
The effect of nicotinamide on dysregulated genes associated with frataxin deficiency in FRDA. |
|
| Relations |
| SRA |
SRX210738 |
| BioSample |
SAMN01831457 |
