|
| Status |
Public on Aug 15, 2019 |
| Title |
AGO2_mRNA_Control_4 |
| Sample type |
SRA |
| |
|
| Source name |
bed nuclei of stria terminalis
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6Crl
age on dissection: 8 weeks
Sex: male
csds phenotype: Control
|
| Treatment protocol |
Mice were killed by cervical dislocation between 8 am and 11 am to avoid circadian differences in gene expression, and the order was counterbalanced across experimental conditions.
|
| Growth protocol |
Mice (Charles River Laboratories, Sulzfeld, Germany) were housed in groups in a temperature and humidity controlled facility on a 12h light/dark cycle for the acclimatization period. All mice had ad libitum access to food and water throughout the experiment (except for the durations of behavioral tests). Animal procedures were approved by the Regional State Administration Agency for Southern Finland (license numbers ESAVI-3801-041003-2011 and ESAVI/2766/04.10.07/2014) and carried out in accordance to directive 2010/63/EU of the European Parliament and of the Council, and the Finnish Act on the Protection of Animals Used for Science or Educational Purposes (497/2013).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Brain regions were dissected on a sterile chilled petri dish within 7 minutes and tissue was flash-frozen in liquid N2. Total RNA was extracted with TriReagent (Molecular Research Center, Inc.) and RNA integrity was controlled with Bioanalyzer (Agilent). The rRNA was depleted with Ribozero Globin depletion Kit (Illumina, CA, USA) and fragmented using the S2 ultrasonicator (Covaris Inc., MA, USA).
Sequencing libraries were prepared with TruSeq Stranded mRNA Library Prep (Illumina; BNST AGO2 mRNA), TruSeq Stranded Total RNA (Illumina; blood cells RNA), TruSeq Small RNA Library Prep Kit (Illumina; BNST AGO2 miRNA) and NEXTflex Small RNA-Seq Kit v3 (Bioo Scientific; blood cells miRNA) library preparation kits.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Ago2 pull down
|
| Data processing |
For mRNA-seq data: Sequenced reads were trimmed for adaptors and aligned to mouse genome GRCm38/mm10 using STARv 2.5.0c with default settings. Aligned reads were annotated to gene exons with HTSeq v0.6.11 using GTF release 86 (update 2016-10), using stranded intersection-nonempty. Count matrixes were TMM and voom normalized with limma and batch adjusted with ComBat.
For miRNA-seq data: The reads were aligned to mouse reference miRNAs (miRBase v21) using miRDeep2 v0.0.7 software package and to mouse genome GRCm38 (GRCm38) using bowtie v1.1.1. The expression of mature miRNAs was quantified using miRDeep2 v0.0.7 quantifier.pl module. Count matrixes were TMM and voom normalized with limma and batch adjusted with ComBat.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log(CPM) values, normalization was done separately for each count matrix.
|
| |
|
| Submission date |
Nov 22, 2018 |
| Last update date |
Aug 15, 2019 |
| Contact name |
Iiris Hovatta |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Helsinki
|
| Department |
Department of Psychology and Logopedics
|
| Lab |
Neurogenomics
|
| Street address |
Haartmaninkatu 3
|
| City |
Helsinki |
| ZIP/Postal code |
00014 |
| Country |
Finland |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE122840 |
Gene expression analysis of mouse BNST and blood cells after chronic social defeat stress (CSDS) |
|
| Relations |
| BioSample |
SAMN10477204 |
| SRA |
SRX5060868 |
