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Sample GSM7921564

Query DataSets for GSM7921564

Status

Public on Dec 01, 2024

Title

casrx_ms_rep2

Sample type

SRA

Source name

striatum

Organism

Mus musculus

Characteristics

tissue: striatum
disease state: hd
treatment: casrx

Extracted molecule

polyA RNA

Extraction protocol

Total RNAs from striatum of mice, and striatum of pigs were extracted using the Trizol method (Thermo Fisher Scientific, MA, USA).
Sequencing libraries were generated using the SEQUMED ® MustSeq ® 3'mRNA DEG kit（Sequmed，China）.The first step is to capture polyA mRNA with polyT primer and reverse transcript it to form DNA-RNA heterozygous chain. The primer consists of oligo-dT, a sample barcode, a unique and the Illumina-compatible 5ʹ adaptor. Then RNA is removed, the sample is purified with 1X magnetic beads.After the RNA removal,the random primer is used for two-chain synthesis,and the P5 and P7 adaptor that are suitable for the Illumina platform are used for PCR amplification.At last, PCR products were purified 250bp-1000bp fragments for sequencing library.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

rawcount_ms.txt

Data processing

Raw data (raw reads) of fastq format were firstly processed through Trimmomatic v0.39[2]. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-A and low quality reads from raw data. FastQC v0.11.9[3] software was used to perform quality control on raw data and clean data respectively. Q20, Q30 and GC content were calculated through in-house python scripts. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from Ensembl website directly. Index of the reference genome was built using Hisat2 v2.2.1[4] and clean reads were aligned to the reference genome using Hisat2 v2.2.1 to generate a .sam or .bam files containing the alignments.
The gene expression level quantification was performed separately for each sample using the featureCounts v2.0.1[5] software in the subRead package, and the reads count of each gene was obtained with the parameter "-t exon -g gene_id -s 1". Then results of all samples were combined to obtain the expression matrix of all samples. The RPM (Reads per million mapped reads) of each gene was based on the reads count mapped to this gene and sequencing depth.
Assembly: Sus_scrofa.Sscrofa11.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

Submission date

Nov 28, 2023

Last update date

Dec 01, 2024

Contact name

yizhi chen

E-mail(s)

[email protected]

Organization name

Jinan university

Department

Guangdong-Hong Kong-Macau Institute of CNS Regeneration