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Sample GSM2108310 Query DataSets for GSM2108310
Status Public on Apr 29, 2016
Title siSV5-1
Sample type SRA
Source name H3A cells
Organism Homo sapiens
Characteristics tissue: human melanocytes
sirna: siATF2SV5
Extracted molecule total RNA
Extraction protocol Total RNA from tumors was extracted using TRIzol (Ambion, CA, USA). Total RNA from cell lines was extracted using a total RNA miniprep kit (Sigma-Aldrich)
Protocol outlined in Ion AmpliSeq Transcriptome Human Gene Expression Kit from ThermoFisher Scientific
Ampliseq RNA-Seq
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
Data processing basecalling from AmpliSeq Platform
data pre-processing (5' trimming or low qulaity filter?)
two step alignment integrated with Tophat2 and Bowtie2
count reads (HT-Seq v0.6.0)
read count normalization by edgeR v3.8.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM and raw count values for each Sample.
Submission date Apr 04, 2016
Last update date May 15, 2019
Contact name brian james
Organization name Sanford Burnham
Street address 10901 North Torrey Pines Road
City San Diego
ZIP/Postal code 92037
Country USA
Platform ID GPL17303
Series (2)
GSE79917 Transcriptionally inactive ATF2 variant drives melanomagenesis [Seq]
GSE81014 Transcriptionally inactive ATF2 variant drives melanomagenesis
BioSample SAMN04606402
SRA SRX1678605

Supplementary file Size Download File type/resource
GSM2108310_siSV5-1-RPM.txt.gz 392.0 Kb (ftp)(http) TXT
GSM2108310_siSV5-1-rawcount.txt.gz 371.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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