GSM3099827: RNA-Seq T cells TCR 2 days; Homo sapiens; RNA-Seq
For RNA-Seq, total RNA extracted using the RNeasy Mini Kit (Qiagen). Poly(A)+ RNA was selected twice from total RNA using Dynal oligo magnetic beads (Invitrogen). Double-stranded cDNA was synthesized using SuperScript (Invitrogen) and fragmented using Bioraptor (Diagenode). Adaptors (Illumina) were ligated to the dsDNA using T4 DNA ligase (New England Biolabs) after end-repair using End-It kit (Epicentre) and dA addition. Libraries were size-selected for 250-400 bp fragments, purified using 2% E-Gel (Invitrogen), and amplified for 18 cycles by PCR with PE 1.0 and PE 2.0 primers (Illumina) and Phusion High Fidelity PCR Master Mix. For ChIP-Seq, chromatin was isolated from 10 million cells, after cross-linking with 1% methanol-free formaldehyde (Thermo Fisher Scientific). Chromatin was fragmented by sonication and subjected to immunoprecipitation with 10 µg of either mouse IgG (Santa Cruz Biotechnology, Dallas TX) or mouse monoclonal anti-ZNF341 (8B3.1) antibodies prebound to Magna ChIPTM Protein A+G Magnetic Beads (Millipore, Billerica MA). The immunoprecipitate was washed and cross-linked, and ChIP-Seq DNA libraries were then prepared with the fragmented DNA and the KAPA Hyper Prep Kit (KAPA Biosystems, Wilmington, MA)
GEO Accession
GSM3099827