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Sample GSM4826980

Query DataSets for GSM4826980

Status

Public on Oct 13, 2020

Title

RNA-seq of nucleus after 6h of LPS treatment rep 3

Sample type

SRA

Source name

nucleoplasm

Organism

Mus musculus

Characteristics

cell line: Raw264.7 cells
antibody: None
treatment: LPS 6h

Treatment protocol

LPS 80 ng/ml for 0, 2, 6, 12, or 15 h

Extracted molecule

total RNA

Extraction protocol

Cytoplasm, nucleoplasm, and nucleoli were extracted from LPS-stimulated macrophages as previously described (http://www.lamondlab.com/f5nucleolarprotocol.htm). RNAs were purifed using RiboEx reagent and cleaned up using RNeasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

RNA-seq paired-end reads were mapped to UCSC mm10 Mus musculus genome using Tophat2
Exon-regions and intron-regions (GTF files) were identified using GenomicFeature R-package
The expression level of each gene was quantified as TPM using StringTie tool v2.1.3
RIP-seq paired-end reads were mapped to UCSC mm10 Mus musculus genome using Tophat2
The FPKM values of each gene (exon and intron, respectively) was quantified using StringTie tool v2.1.3
Genome_build: UCSC mm10 Mus musculus genome
Supplementary_files_format_and_content: tpm_all.200603.3.xlsx contains TPM values of each sample for exon and intron, respectively.

Submission date

Oct 09, 2020

Last update date

Oct 13, 2020

Contact name

Boyoun Park

E-mail(s)

bypark@yonsei.ac.kr

Organization name

Yonsei University

Department

Systems biology