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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
E-mail(s) bjames@sanfordburnham.org
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
Relations
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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