GSM4503996: OSKMD5 FLAG #2 (ATAC-seq); Mus musculus; ATAC-seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
ATAC-Seq
Antigen
ATAC-Seq
Cell type
Cell type Class
Embryonic fibroblast
Cell type
MEF
Tissue
Embryonic Fibroblast
Lineage
primaryCells
Description
Mouse Embryonic Fibroblast
Attributes by original data submitter
Sample
source_name
Mouse MEFs, OSKM day 5
day
5
transfection
OSKM retroiviral transfection
overexpression
FLAG
knockout
Wildtype
presumed cell type
Intermediate pluripotent reprogrammed cells
strain
C57BL/6J-OG2
Sequenced DNA Library
library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
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