title: GSM8148115: SPF 2X CYTOKINE_2 [RNA-Seq]; Mus musculus; ATAC-seq
library_construction_protocol: N/A Sorted cells were lysed and RNA isolated using the Qiagen RNeasy Micro kit (Qiagen, #74004) with on-column DNase I digestion (Qiagen, #79254). RNA was suspended in 10 µL of nuclease free water at 0.5-1 ng/µL and sequenced using SMARTSeq279 at the Broad Institute Technology Labs and the Broad Genomics Platform. Processed RNA-seq data was filtered by removing genes with low read counts. Read counts were normalized using TMM normalization and CPM (counts per million) were calculated to create a matrix of normalized expression values. The fastq files of each RNA-seq data sample were aligned to the Mus musculus GRCm38 transcriptome using Kallisto (v0.46.1), and the same software was used to quantify the alignment results. Differential expression analysis was conducted using DESeq2, and the log2 fold change was adjusted using apeGLM for downstream analysis. Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described (Trombetta et al 2014).