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Sample GSM1138580 Query DataSets for GSM1138580
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.
BioSample SAMN02141836
SRA SRX276896
Named Annotation GSM1138580_Uninfected.accepted_hits.bigWig

Supplementary file Size Download File type/resource
GSM1138580_Uninfected.accepted_hits.bigWig 106.3 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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