title: GSM4503990: MEF #1 (ATAC-seq); Mus musculus; ATAC-seq
library_construction_protocol: ATAC-seq and analysis. A total of 50,000 cells were washed once with cold PBS and re-suspended in 50 μl lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2, 0.1% IGEPAL CA-630). The suspension was then centrifuged at 500 g for 10 minutes at 4°C, followed by addition of 50 μl transposition reaction mix of TruePrep DNA Library Prep Kit (Vazyme, TD502). Samples were then incubated at 37°C for 30 minutes. Transposition reactions were cleaned up using a MinElute PCR Purification Kit (QIAGEN, 28004). ATAC-seq libraries were subjected to five cycles for pre-amplification and amplified by PCR for an appropriate number of cycles. The amplified libraries were purified with a QIAquick PCR Purification Kit (QIAGEN, 28104). Library concentration was measured using VAHTSTM Library Quantification Kit (Vazyme, NQ101). Libraries were sequenced by Vazyme Co., Ltd, China. All sequencing data were mapped onto the mm10 mouse genome assembly using bowtie2 (–very-sensitive). Low quality mapped reads were removed using samtools (view –q 30) and only unique reads mapping to a single genomic location and strand were kept. We removed mitochondrial sequences using 'grep –v 'chrM'. Standard Illumina protocols
attributes.tag: GEO Accession
attributes.value: GSM4503990