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Sample GSM6752797

Query DataSets for GSM6752797

Status

Public on Jun 28, 2023

Title

Liver_TAA, IgG, Abcom

Sample type

SRA

Source name

Liver

Organism

Mus musculus

Characteristics

tissue: Liver
rip antibody: IgG (Abcam, #ab172730)
treatment: 8-week thioacetamide i.p.

Extracted molecule

total RNA

Extraction protocol

RNA extracted using Trizol by following manufacturer’s instruction (Invitrogen)
rRNAs were removed from the immunoprecipitated RNA and input RNA samples by using Ribo-Zero™ rRNA Removal Kit (Illumina, San Diego, CA, USA). RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

Library strategy

RIP-Seq

Library source

transcriptomic

Library selection

other

Instrument model

Illumina HiSeq 4000

Data processing

Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse circRNAs, LncRNAs and mRNAs.
The high quality reads were aligned to the reference genome/transcriptome with STAR software (v2.5.1b) and circRNAs were detected and identified with DCC software (v0.4.4). edgeR software (v3.16.5) was used to normalized the data and perform differentially expressed circRNA analysis.
Assembly: mm10
Supplementary files format and content: Matrix table with circRNA reads for each sample

Submission date

Nov 22, 2022

Last update date

Jun 28, 2023

Contact name

shuaijie qian

E-mail(s)

qsjbxh1997@outlook.com

Phone

13540675514

Organization name

West China Hospital, Sichuan University