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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
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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