Allergen-specific immunotherapy modulates the balance of circulating Tfh and Tfr cells- GSE87399

RNA-sequencing of sorted memory CXCR5 high and CXCR5low T cells from cryopreserved PBMC of 5 subjects with allergy and 5 patients undergoing allergen-specific immunotherapy

The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls.RNA-Seq data was mapped against hg19 reference genome using tophat (v1.4.1., --library-type fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC genome bioinformatics site.The alignment results (sam files) were converted into bam files and sorted by using samtools.DUST scores were calculated with PRINSEQ Lite (v 0.20.3) and low-complexity reads (DUST > 4) were removed from the BAM files.Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -t exon -i gene_id).Genome_build: hg19Supplementary_files_format_and_content: [.txt] file reports raw counts of sequencing reads per gene generated by HTSeq-count

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87399