title: GSM2830218: ATAC-seq LPL Treg Ahr KO (rep2); Mus musculus; ATAC-seq
library_construction_protocol: [RNA-seq] Lamina propria cells were isolated and sorted by flow cytometry.  Sorted Tregs were lysed in Trizol (Invitrogen), and RNA was subsequently extracted with RNAeasy Mini Kit (Qiagen).  [ATAC-seq]  Lamina propria cells were isolated and Tregs were sorted by flow cytometry. [RNA-seq] Total RNA was treated with Ribo-zero kit and RNAseq libraries were generated using kits from Illumina. Barcoded samples were pooled and sequenced over 2 lanes on an Illumina HiSeq 2500 instrument to produce 50 bp single-end reads. [ATAC-seq] Large intestinal CD4+TCRβ+YFP+ Tregs were sorted and subjected to ATAC-Seq according to a published protocol (Buenrostro et al., 2013) with a modification in the library purification step. Briefly, 5x10^4 sorted Tregs were washed once with 50 ul PBS, and then lysed in lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) on ice. Pelleted nuclei were resuspended in transposition reaction mix with Tn5 transposase (Illumina) and incubated at 37℃ for 30 min with gentle shaking. The DNA was purified with MinElute PCR Purification Kit (Qiagen) and was used as a template of PCR with 10 cycles of amplification. The library was cleaned up with 1.2x SPRIselect beads (Beckman Coulter), to exclude the small fragments, before sequencing with Illumia HiSeq 2500.
attributes.tag: GEO Accession
attributes.value: GSM2830218