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Sample GSM4087787

Query DataSets for GSM4087787

Status

Public on Dec 31, 2019

Title

S353_1_WT_1

Sample type

SRA

Source name

WT_hippocampus

Organism

Mus musculus

Characteristics

strain background: C57Bl/6J
genotype/variation: wild type
treatment: untreated
tissue: hippocampus

Extracted molecule

total RNA

Extraction protocol

bulk RNA extracted from the whole tissue: RNA was extracted from hippocampal lysates using PicoPure RNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol.
for WT and MAVS-KO ICV-Veh and ICV-STZ mice: Total RNA library preparation and sequencing (500ng 2x125bp). RNA sequencing libraries were prepared using the KAPA Stranded RNA-Seq Kit with RiboErase (kapabiosystems) in accordance with the manufacturer’s instructions. Briefly, 500ng of total RNA was used for ribosomal depletion and fragmentation. Depleted RNA underwent first and second strand cDNA synthesis. cDNA was then adenylated, ligated to Illumina sequencing adapters, and amplified by PCR (using 9 cycles). Final libraries were evaluated using fluorescent-based assays including PicoGreen (Life Technologies) or Qubit Fluorometer (invitrogen) and Fragment Analyzer (Advanced Analytics) or BioAnalyzer (Agilent 2100), and were sequenced on an Illumina HiSeq2500 sequencer (v2 chemistry for Rapid Run) using 2 x 125bp cycles.
muMT and WT mice: Library preparation and RNAseq for WT and muMT mice were carried out as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide, the Illumina NextSeq 500 System Guide (Illumina, Inc., San Diego, CA, USA), and the KAPA Library Quantification Kit – Illumina/ABI Prism User Guide (Kapa Biosystems, Inc., Woburn, MA, USA).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Description

processed data file:
3wt-vs-2mumt-genomic-counts.csv
3wt-vs-2mumt-genomic+transposable-elements-counts.csv
S353_1_WT_1_S1

Data processing

Basecalling was performed using RTA 2.4.11
bcl files were converted to fastq using CASAVA 1.8.2
For protein coding genes, Fastq files were mapped to the Gencode mouse genome Release M21 (GRCm38.p6) using the STAR aligner v2.7.1a with standard settings.
Count tables were generated using featureCounts v1.6.2.
For Transposable elements, Fastq files were mapped to the Gencode mouse genome Release M21 (GRCm38.p6) using the STAR aligner v2.7.1a with standard settings.
Genome_build: GRCm38
Supplementary_files_format_and_content: csv files of raw counts

Submission date

Sep 20, 2019

Last update date

Dec 31, 2019

Contact name

Roman Sankowski

E-mail(s)

[email protected]

Phone

+4976127051110

Organization name

University of Freiburg Medical Center