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Sample GSM1439582 Query DataSets for GSM1439582
Status Public on Apr 01, 2015
Title R6_1_323_St
Sample type SRA
 
Source name R6_1_striatum
Organism Mus musculus
Characteristics strain background: CBA x C57BL/6 (50% CBA and 50% C57BL6)
genotype/variation: R6/1; transgenic for exon 1 of the HD gene carrying CAG expansion (115)
tissue: striatum
Treatment protocol Total RNA was extracted using TRI Reagent (Molecular research center) and the Precellys lysing system (Precellys).
Extracted molecule total RNA
Extraction protocol RNA-seq libraries of template molecules suitable for strand specific high throughput DNA sequencing were created using “TruSeq Stranded Total RNA with Ribo-Zero Gold Prep Kit” (# RS-122-2301, Illumina). Briefly, starting with 1 µg of total RNA, the first step involved the removal of cytoplasmic and mitochondrial ribosomal RNA (rRNA) using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the RNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72°C). Then surplus PCR primers were removed by purification using AMPure XP beads (Agencourt Biosciences Corporation). Final cDNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Base calling : Image analysis and base calling were performed using RTA 1.17.21.3 and CASAVA 1.8.2
Alignment : Reads were mapped to mm9 assembly of mouse genome using Tophat v1.4.1
Quantification : Gene expression was quantified using HTSeq v0.5.4p3 and annotations from Ensembl release 67
Normalization : Data normalization was performed with DESeq2 v1.0.19 Bioconductor package
Genome_build: mm9
Supplementary_files_format_and_content: The processed data file is a tabulated text with the following columns : Ensembl gene id, Gene name and one column for each sample containing the normalized read counts. BedGraph files were computed on unique reads (tophat v1.4.1) and normalized using the size factors calculated with DESeq2 v1.0.19 Bioconductor package
 
Submission date Jul 18, 2014
Last update date May 15, 2019
Contact name Karine Merienne
E-mail(s) merienne@igbmc.fr
Organization name IGBMC
Street address 1 rue Laurent Fries
City ILLKIRCH
ZIP/Postal code 67404
Country France
 
Platform ID GPL13112
Series (2)
GSE59571 Striatal genes regulated by super-enhancers and displaying low paused RNAPII are preferentially down-regulated in Huntington’s disease [RNA-seq]
GSE59572 Striatal genes regulated by super-enhancers and displaying low paused RNAPII are preferentially down-regulated in Huntington's disease
Relations
BioSample SAMN02927243
SRA SRX657183

Supplementary file Size Download File type/resource
GSM1439582_MAY-05_uniq_normcoverage.bedGraph.gz 509.9 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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