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Sample GSM2581131 Query DataSets for GSM2581131
Status Public on Jan 17, 2018
Title Sample_1964
Sample type SRA
 
Source name WD_LPS
Organism Mus musculus
Characteristics cell type: GMP
genotype: Ldlr-/-
stimulation: LPS
diet: WD
batch: batch2
Treatment protocol Mice were intravenously injected with PBS (vehicle control) or E.coli derived ultrapure LPS (0111:B4; 10ug/ mouse) six hours prior to sacrifice
Extracted molecule total RNA
Extraction protocol For RNA-sequencing 10.000-50.000 sorted HSPCs , CMPs and GMPs were collected immediately in Trizol containing b-mercaptoethanol. RNA was extracted using the RNeasy Micro RNA Isolation kit (Quiagen)
Library preparation for subsequent RNA-sequencing analysis was performed using the TruSeq. RNA Library Prep Kitv2 (Illumina) following manufacturer’s protocol instructions
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing Illumina Casava1.81 software used for basecalling.
Sequenced reads were demultiplexed, then aligned with Hisat2 (v2.0.6) against the mm10 reference genome
Gene and transcript information was extracted with Partek Genomics Suite (v6.6). Annotated data was normalized using statistical software R (v3.0.2) including DESeq2 package. Normalized read counts lower than 1 were set to the floor value 1.Genes were defined as expressed with normalized RNA-seq values ≥ 10.
Genome_build: mm10
Supplementary_files_format_and_content: Processed DeSeq2 normalized RNA-seq tag counts annotated to the mm10 reference transcriptome
 
Submission date Apr 18, 2017
Last update date May 15, 2019
Contact name Joachim Schultze
E-mail(s) j.schultze@uni-bonn.de
Organization name LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)
Department Genomics and Immunoregulation
Street address Carl-Troll-Strasse 31
City Bonn
State/province NRW
ZIP/Postal code 53115
Country Germany
 
Platform ID GPL18480
Series (2)
GSE97925 Western diet triggers NLRP3-dependent persistent functional reprogramming of myeloid cells [RNA-Seq]
GSE97926 Western diet triggers NLRP3-dependent persistent functional reprogramming of myeloid cells
Relations
BioSample SAMN06761680
SRA SRX2742575

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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