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Sample GSM4006444 Query DataSets for GSM4006444
Status Public on Jun 19, 2020
Title TET2_WT_LPS_302_TET2_LPS_RNA_Seq
Sample type SRA
 
Source name TET2_WT_LPS
Organism Mus musculus
Characteristics sttrain background: C57BL/6J
tet2: wild-type
Sex: M
treatment: LPS
tissue: Midbrain
replicate: Biological Sample
Treatment protocol At two months of age mice received an intraperitoneal injection of saline (PBS) or lipopolysaccharide (LPS; 5 mg/kg) and brain tissues were harvested exactly 24 hours post-injection.
Growth protocol Tet2 knock-out mice were obtained from The Jackson Laboratory (strain 023359) and maintained in a pathogen-free barrier facility and provided with food (LabDiet 5021) and water for ad libitum consumption. The vivarium was maintained under controlled temperature (21°C±1°C) and humidity (50-60%), with a 12-h diurnal cycle (lights on: 0700-1900).
Extracted molecule total RNA
Extraction protocol Mice were perfused with PBS and the midbrain was isolated and snap frozen. Midbrain tissue (25-50 mg) homogenized in TRIzol (Invitrogen) using a Precellys Lysing Kit (Bertin Technologies) with the MiniLys (Bertin). Total RNA was isolated and treated with DNase I (Qiagen), followed by a clean up using an RNeasy Mini Kit (Qiagen). The resulting RNA quantity was assessed by Nanodrop 8000 (Thermo Scientific) and quality was assessed with an Agilent RNA 6000 Nano Kit on a 2100 Bioanalyzer (Agilent Technologies).
Libraries were prepared from 500 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboseErase (v1.16) (Kapa Biosystems). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to Bioo Scientific NEXTflex Adapters (Bioo Scientific). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies), QuantiFluor® dsDNA System (Promega Corp), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). Sequencing (single-end 75 bp) was performed on an Illumina NextSeq500 sequencer.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description 24hrs LPS injection in tet2 wild-type mice
TET2_WT_LPS_302_L001
Data processing Adapter sequences were removed from fastq files using TrimGalore (v0.4.4).
The remaining sequencing reads were then aligned to the reference genome (GRCm38/mm10) and the Gencode vM20 primary assembly transcriptome indexed by STAR (v2.3.5a).
Reads per gene were counted using STAR (v2.3.5a).
Gene counts matrix was imported into R (3.5.1) and low expressed genes (counts per million <1 in all samples) were removed prior to trimmed mean of M-values normalization in EdgeR (v3.24.3).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Each ReadsPerGene.txt file contains the following information in order: gene ID, counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA, counts for the 2nd read strand aligned with RNA
 
Submission date Aug 02, 2019
Last update date Oct 19, 2023
Contact name Lee Marshall
E-mail(s) lee.marshall@vai.org
Phone 616 920 9824
Organization name Van Andel Research Institute
Department Center for Neurodegenerative Science
Lab Viviane Labrie
Street address 333 Bostwick Ave NE
City Grand Rapids
State/province MI
ZIP/Postal code 49503
Country USA
 
Platform ID GPL19057
Series (2)
GSE135334 Epigenomic analysis of Parkinson’s disease neurons identifies TET2 loss as neuroprotective [TET2_LPS_RNA_Seq]
GSE136010 Epigenomic analysis of Parkinson's disease neurons identifies TET2 loss as neuroprotective
Relations
BioSample SAMN12477098
SRA SRX6648166

Supplementary file Size Download File type/resource
GSM4006444_TET2_WT_LPS_302_ReadsPerGene.txt.gz 346.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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