|
| Status |
Public on Aug 07, 2018 |
| Title |
wtHTT-IN1 |
| 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 RNA extraction and smallRNA sequencing.
|
| 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 |
SAMN05991413 |
| SRA |
SRX2334405 |
