GSE169470
RNA-sequencing Analysis (RNA-seq),Genome-wide Maps of Chromatin State (ChIP-seq) and Assay for Transposase Accessible Chromatin with High-throughput Sequencing (ATAC-seq) in BMDMs or Raw 264.7 cell lines.
For RNA-seq,mRNA profiles of Bone marrow derived macrophages(BMDMs) of wild-type(WT) and Zmynd8 knockout(Zmynd8 cKO),p65 KO + p65,p65 KO + K122R in Raw264.7 cells,Zmynd8 KO + Zmynd8,Zmynd8 KO + D/E-A in Raw264.7 cells were generated from GUANGZHOU RIBOBIO,using Illumina Hiseq.The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays.For ChIP-seq,BMDMs or Raw264.7 cells (about 1x107 cells) were fixed with 1% methanol-free formaldehyde at room temperature for 10 min, followed by quenching with 125mM glycine,and chromatin immunoprecipitated DNA was send to Novogene,using Nova-PE150.The FASTQ data were mapped to the mouse genome (mm10) using Bowtie, and significant enrichments were identified by MACS2.0 using Broad Peak mode with p-value =1*10 -5, FDR = 0.01 as a cutoff to call peaks from the aligned results.For ATAC-seq,BMDMs were send to Shanghai Da Che Biotechnology Company,and the FASTQ data were mapped to the mouse genome (mm10) using Bowtie, and significant enrichments were identified by MACS2.0  using Broad Peak mode with p-value =1*10 -5, FDR = 0.01 as a cutoff to call peaks from the aligned results. Overall design: mRNA profiles of Bone marrow derived macrophages(BMDMs) of wild-type(WT) and Zmynd8 knockout(Zmynd8 cKO),p65 KO + p65,p65 KO + K122R in Raw264.7 cells,Zmynd8 KO +Zmynd8,Zmynd8 KO + D/E-A in Raw264.7 cells .For ChIP-seq,examination of ZMYND8 ,LSD1,H3K4me1 binding peaks in BMDMs,and ZMYND8 binding peaks in p65 KO,p65 KO + p65,p65 KO +K122R Raw264.7 cells ,Zmynd8 KO,Zmynd8 KO + Zmynd8,Zmynd8 KO + D/E-A Raw264.7 cells.