|
| Status |
Public on Aug 01, 2013 |
| Title |
Uninfected |
| Sample type |
SRA |
| |
|
| Source name |
Uninfected
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Primary human epidermal melanocytes (neonatal)
|
| Treatment protocol |
No treatment other then lentiviral infection
|
| Growth protocol |
Cells were infected with respective lentiviruses and RNA was isolated 2 weeks post infection when cells were confirmed fully senescent
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using RNA easy mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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 Genome Analyzer IIx |
| |
|
| Description |
RNA-Seq of Uninfected primary human melanocytes
|
| Data processing |
Basecalls performed using CASAVA 1.6
Sequenced reads were mapped to hg18 whole genome using tophat 1.2.0 with parameters –solexa1.3-quals, -p 7, -r 160, -G Homo_sapiens.NCBI36.54.gtf
Aligned reads normalised by library size (number of fragments) converted to bigWig format
Genome_build: hg18
Supplementary_files_format_and_content: bigWig files represent pileups of the reads at each base. bigWig files were normalised by library size and represent the number of reads at a given genomic location per million mapped reads and generated using UCSC wigToBigWig
|
| |
|
| Submission date |
May 09, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter D. Adams |
| Organization name |
University of Glasgow, Beatson Institute for Cancer Research
|
| Street address |
Switchback Rd, Bearsden
|
| City |
Glasgow |
| ZIP/Postal code |
G61 1BD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE46805 |
Expression data from Uninfected and BRAF600V induced melanocytes |
| GSE46818 |
Wnt-signaling potentiates nevogenesis. |
|
| Relations |
| BioSample |
SAMN02141836 |
| SRA |
SRX276896 |
| Named Annotation |
GSM1138580_Uninfected.accepted_hits.bigWig |
