Bulk RNASeq Data from mouse spleens
Description
We obtained bulk RNA sequencing data from from spleens in mouse. We performed flow cytometry-based cell sorting on mouse spleens and conducted bulk sequencing on the sorted cells. CD160- and CD160+ CD8+ T cells flow sorted from mouse spleens are named as PN and PP.
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Steps to reproduce
We obtained bulk RNA sequencing data from from spleens in mouse. We performed flow cytometry-based cell sorting on mouse spleens and conducted bulk sequencing on the sorted cells. Total RNA was extracted from relative intestine tissues using Trizol reagent. Approximately 5ug RNA was selected to remove ribosomal RNA following the instruction of Ribo-Zero Gold rRNA Removal Kit. Then the libraries were constructed through dissection, reverse transcription, amplification. And finally, 2×150bp paired-end sequencing was performed on an Illumina Novaseq 6000. To prepare data for downstream analysis, FastQC (v0.12.1) was used to assess the quality of raw sequencing data, and fastp software (v0.23.4) was applied to remove low-quality reads and any residual adapter sequences. The high-quality reads were aligned to human genome reference GRCm38 (mm10) using the STAR algorithm (v2.7.10b). ResQC (v5.0.3) is applied to assess the quality of alignment results using various alignment metrics, including coverage, mapping quality, and distribution of mapped reads. Then, FeatureCount (v2.0.6) was utilized to extract the feature count matrix from alignments. We used edgeR (v3.40.2) for normalization and multidimensional scaling.
Institutions
- Harbin Medical University