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Sample GSM2385386 Query DataSets for GSM2385386
Status Public on Aug 07, 2018
Title wtHTT-RIP1
Sample type SRA
 
Source name freshly dissected tissue
Organism Mus musculus
Characteristics strain: C57BL/6
lentiviral mediated overexpression: wtHTT
Treatment protocol Striatal tissue was harvested 3 weeks after virus injection and immediately lysed for AGO2-RIPseq.
Growth protocol All stereotactic injections into the striatum were performed as described before with minor changes (Malmevik, J. et al. Identification of the miRNA targetome in hippocampal neurons using RIP-seq. Scientific reports 5, 12609 (2015)). All mice were adult C57BL/6 females aged 9 to 10 weeks old at the time of surgery. Injections were unilateral, always on the right side of the brain with a total of 1 µl injected. The injection coordinates were: AP: +0,9 mm; ML: +/-1.8 mm; DV (from dura): -2.7 mm.
Extracted molecule total RNA
Extraction protocol smallRNA was extracted using the miRNeasy Mini kit from Qiagen
NEBNext Multiplex Small RNA Library Prep Set for Illumina
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 3000
 
Description Striatal tissue collected 3 weeks after unilateral injection of AAV-wtHTT
Data processing Adaptor sequences were removed using cutadapt
Reads obtained from mouse tissue were mapped to the mouse genome using STAR_2.4.0j (for microRNAs 1 mismatches per 20nt were allowed)
Reads were quantified using the Rsubread package for R using miRbase annotation (miRNAs)
Genome_build: mm10 for mouse tissue
Supplementary_files_format_and_content: txt files containing abundance measurements of miRNA features from miRBase, repeats annotation from repeatMasker. Whitespace separated. Columns: [Geneid- Chr- Start- End- Strand- Length - #reads mapping to feature]
 
Submission date Nov 07, 2016
Last update date May 15, 2019
Contact name Per Brattas
Organization name Lund University
Lab Clinical Genomics
Street address Sölvegatan 17
City Lund
ZIP/Postal code 221 84
Country Sweden
 
Platform ID GPL21493
Series (1)
GSE78928 Huntingtin aggregation impairs autophagy leading to Argonaute-2 accumulation and global microRNA dysregulation
Relations
BioSample SAMN05991428
SRA SRX2334408

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

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