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Sample GSM7908624

Query DataSets for GSM7908624

Status

Public on May 01, 2024

Title

NC_3

Sample type

SRA

Source name

liver

Organism

Mus musculus

Characteristics

tissue: liver
mouse: Diet-induced obese mice
treatment: NC control

Extracted molecule

total RNA

Extraction protocol

RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

Submission date

Nov 19, 2023

Last update date

May 01, 2024

Contact name

Huichen Song

E-mail(s)

DG1830025@smail.nju.edu.cn

Phone

15150516380

Organization name

Nanjing university