GSM5269376: H3K4me2_Gfi1WT_GMP; Mus musculus; ChIP-Seq
RNA was extracted using MagMax-96 Total RNA Isolation kit (Ambion) and quality-checked with RNA 6000 Pico kit (Agilent). RNA-seq libraries were prepared from the RNA extracts using the Illumina TruSeq Stranded mRNA Kit according to the manufacturer's instructions, and sequenced using the TruSeq PE Clusterkit v3-cBot-HS on an Illumina HiSEq 2000 system. Sequencing reads were aligned to the mm10 genome using Tophat v2.0.10. Reads were processed with Samtools and then mapped to Ensembl transcripts using HTSeq. Differential expression was tested using the DESeq R package (Anders & Huber, 2010)(R Core Team 2015, http://www.r-project.org/). A genome coverage file was generated and scaled to RPM using Bedtools. ChIPs were performed on 1-20x106 sorted cells. The cells were cross-linked with 1.5mM EGS for 20 minutes and 1% formaldehyde for 8 minutes before quenching with 125mM glycine. Cells were lysed in lysis buffer and sonicated using a Covaris E220 to generate 200-600bp fragments (Lee, Johnstone, & Young, 2006). Samples were immuno-precipitated with 2-5 µg of either anti- GFI1 (AF3540, R&D systems), anti-H3K4me1 (ab8895, Abcam),  anti-H3K4me2 (ab11946; Abcam), anti-H3K4me3 (ab8580; Abcam) or anti-H3K9me2 (ab1220; Abcam). Libraries were generated according to Illumina's instructions. Libraries were sequenced on the Illumina Hi-seq 2000 following the manufacturer's protocols to obtain 50bp paired end reads. External datasets were obtained in the form of .bed files of peaks and .wig visualization tracks, aligned to the mm9 build, with the exception of LSD1, which only included the .bed peak file.