title: Illumina HiSeq 4000 paired end sequencing; SPATIaL-seq of primary human T Follicular Helper (TFH) cells and naive CD4-positive helper T cells from tonsils of healthy volunteers
design: SPATIaL-seq of primary human T Follicular Helper (TFH) cells and naive CD4-positive helper T cells from tonsils of healthy volunteers
library_construction_protocol: Data were derived from healthy donor children's tonsils.The following cells were sorted from human tonsils: naive CD4+CD45RO- T cells (Naive) and CD4+CD45RO+CD25-CXCR5hiPD1hi follicular helper CD4+ T cells (TFH). For each of the TFH and Naive libraries, 10 million cells were harvested and fixed. The initial 3C libraries were generated following a previously published protocol (Hughes et al., Nature genetics, 2014). The DNA was digested using DpnII, then re-ligated together using T4 DNA ligase, and finally isolated by phenol/chloroform extraction. The 3C libraries were sonicated to an average size of 300bp. Agilent SureSelect library capture protocol was then applied with capture probes targeting both ends of DpnII restriction fragments that overlap promoters of protein-coding, noncoding, antisense, snRNA, miRNA, snoRNA and lincRNA transcripts, totaling 36,691 RNA baited fragments. The bait list is provided in the file baits_1frag.bed.
attributes.tag: Experimental Factor: cell type
attributes.value: CD4-positive helper T cell