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| Status |
Public on Apr 01, 2015 |
| Title |
WT_321_St |
| Sample type |
SRA |
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| Source name |
WT_striatum
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| Organism |
Mus musculus |
| Characteristics |
strain background: CBA x C57BL/6 (50% CBA and 50% C57BL6)
genotype/variation: WT
tissue: striatum
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| Treatment protocol |
Total RNA was extracted using TRI Reagent (Molecular research center) and the Precellys lysing system (Precellys).
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| 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
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| Submission date |
Jul 18, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Karine Merienne |
| E-mail(s) |
merienne@igbmc.fr
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| Organization name |
IGBMC
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| Street address |
1 rue Laurent Fries
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| City |
ILLKIRCH |
| ZIP/Postal code |
67404 |
| Country |
France |
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| 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 |
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| Relations |
| BioSample |
SAMN02927242 |
| SRA |
SRX657182 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1439581_MAY-04_uniq_normcoverage.bedGraph.gz |
358.8 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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