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Sample GSM4504154

Query DataSets for GSM4504154

Status

Public on Apr 29, 2020

Title

aHSC rep2

Sample type

SRA

Source name

primary hepatic stellate cells

Organism

Mus musculus

Characteristics

strain: C57BL/6
cell type: hepatic stellate cells isolated from mouse with CCl4-induced liver fibrosis

Extracted molecule

total RNA

Extraction protocol

Hepatic stellate cells were isolated from control and CCl4-treated mice, The total RNA was immediately isolated from the cells using Trizol Reagent (Invitrogen, Waltham, MA) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using the standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

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 mm10 whole genome using Hisat2 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (FPKM) 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.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

Submission date

Apr 28, 2020

Last update date

Apr 29, 2020

Contact name

Chen Qu

E-mail(s)

[email protected]

Organization name

Jinan University

Street address

#601 West Huangpu Road