|
| Status |
Public on Jun 07, 2016 |
| Title |
Rab7 deltaMG rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Microglia
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57bl6
tissue: brain
age: 3 months
|
| Treatment protocol |
Mice were untreated
|
| Growth protocol |
Mice were housed under standard conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mouse brains were triturated according to manufacturer protocols and microglial cells MACS purified (Mylteni), eluted cells were flash frozen, total RNA was extracted and frozen at -80 until usage
Total RNA was subjected to amplification using Ovation RNA-Seq System V2 (NuGEN). 1 μg of cDNA was used as input for Ion Xpress™ Plus Fragment Library Kit (ThermoFisher Scientific) to generate barcoded libraries.
RNA Seq Library Preparation using Ion Xpress Plus Fragment System using IonXpress Barcodes
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
total RNA from MACS isolated cells
|
| Data processing |
Raw reads were sorted based on barcodes and were subjected to quality analysis using FASTQC
The sequences were aligned to the genome of Mus musculus (GRCm38/Mm10) using the TMAP aligner with default parameters
The reads mapping to unique locations were quantified using RefSeq Gene Annotations(v73) into genes
Genome_build: Mus musculus (GRCm38/Mm10)
Supplementary_files_format_and_content: tab-delimited text files include normalised read counts for each Sample and Gene Symbol
|
| |
|
| Submission date |
May 09, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Moritz J Rossner |
| E-mail(s) |
moritz.rossner@med.uni-muenchen.de
|
| Organization name |
Lud.-Max.-University
|
| Department |
Psychiatry
|
| Lab |
Molecular Neurobiology
|
| Street address |
Nussbaumstr. 7
|
| City |
Munich |
| ZIP/Postal code |
80336 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18635 |
| Series (1) |
| GSE81230 |
RNAseq of microglia from Rab7 Mutants & Control and Wild-Type mice |
|
| Relations |
| BioSample |
SAMN04962314 |
| SRA |
SRX1750581 |
