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Sample GSM1424870 Query DataSets for GSM1424870
Status Public on Nov 02, 2015
Title Sham_rep1
Sample type SRA
 
Source name nervous system
Organism Rattus norvegicus
Characteristics strain: Sprague-Dawley
tissue: Dorsal root ganglion (DRG)
treatment: Control, right side
Extracted molecule total RNA
Extraction protocol DRGs were removed, flash frozen on dry ice, andtotal RNA wasextracted using either Trizol reagent(Life Technologies) or RNeasy (Qiagen). Illumina TruSeq Stranded Total RNA with Ribo-zero Gold kits (RS-122-2301 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 2500
 
Description Control, right side
Data processing Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to the rn4 genome assembly using TopHat 2.0.9 with these parameters: -p 28 --b2-fast -G /UCSC/rn4/Annotation/Genes/genes.gtf --segment-length 20
Fragments Per Kilobase of exon per Megabase of library size (FPKM) and DE genes were calculated using cuffdiff v 2.1.1 with default parameters
Genome_build: rn4
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
 
Submission date Jul 02, 2014
Last update date May 15, 2019
Contact name matteo cesaroni
Organization name Temple University
Street address 3307 N. Broad S, Rm 220, PAHB
City Philadelphia
State/province PA
ZIP/Postal code 19140
Country USA
 
Platform ID GPL18694
Series (1)
GSE59043 G9a is essential for epigenetic silencing of K+ channel genes in acute-to-chronic pain transition
Relations
BioSample SAMN02900656
SRA SRX644927

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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