title: GSM5273069: MC-MO-RS8-MC1; Mus musculus; RNA-Seq
library_construction_protocol: RNA-seq: FACS sorted cells from small pre-B and immature B cells isolated from WT, Igkdel k-mac, k-mac CXCR4fl/fl and k-mac CXCR4fl/fl mb1-cre+ mice and total RNA isolated using Trizol (15596026, Invitrogen) following the protocol described by the Immunological Genome Project (Immgen.org). RNA-seq: Libraries were generated TruSeq® Stranded mRNA Sample Prep” kit from Illumina and the associated user manual ATAC-seq: 1.2x105 small pre-B and immature B cells sorted from WT, Igkdel k-mac, k-mac CXCR4fl/fl and k-mac CXCR4fl/fl mb1-cre+ mice were used for ATAC-seq. Cells were centrifuged at 500g at 4°C for 5 minutes, washed with 1X PBS, and centrifuged again. Cells were resuspended in lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g at 4°C for 10 minutes. Pellet was resuspended in transposition reaction buffer (25ml 2x Tagment Buffer (FC-121-1030, Illumina), 2.5ml Tagment DNA Enzyme, 22.5ml nuclease free H2O) for 30 minutes at 37°C. ATAC-seq: DNA was purified with a Qiagen MinElute Kit and amplified with Nextera PCR Primers (Illumina Nextera Index Kit) and NEBNext PCR Master Mix (M0541, New England BioLabs) for 11 cycles. Amplified DNA was purified with a Qiagen PCR cleanup kit. Libraries were sequenced on a NextSeq 550 sequencer at University of Chicago Genomics Facility.