Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Others
Cell type
3T3 fibroblasts
NA
NA

Attributes by original data submitter

Sample

source_name
mouse fibroblasts
tissue source
embryo
cell line
3T3
cell type
mouse embryo fibroblast cell line
genotype/variation
Rela wt
passages
15-20

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Cells were trypsinized and washed with PBS. Counting of cells was performed with MOXI Z Mini Automated Cell Counter Kit (Orflo) and 50.000 cells were used for ATAC Library preparation using Tn5 Transposase form Nextera DNA Sample Preparation Kit (Illumina). Cell pellet was resuspended in 50µl PBS annd mixed with 25µl TD-Buffer, 2.5µl Tn5, 0.5µl 10% NP-40 and 22µl water. Cell/Tn5 mixture was incubeated at 37°C for 30min with occasional snap mixing. Transposase treatment was followed by 30min incubation at 50°C together with 500mM EDTA pH8.0 for optimal recovery of digested DNA fragments. For neutralisation of EDTA 100µl of 50mM MgCl2 was added followed by purification of the DNA fragments by MinElute PCR Purification Kit (Qiagen). Aplification of Library together with Indexing was performed as described elswere (Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. (2013) Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang & William J Greenleaf. Nature Methods. doi:10.1038/nmeth.2688). Libraries were mixed in equimolar ratios and sequenced on NextSeq500 platform using V2 chemistry.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
16760223
Reads aligned (%)
98.4
Duplicates removed (%)
46.5
Number of peaks
8172 (qval < 1E-05)

mm9

Number of total reads
16760223
Reads aligned (%)
98.3
Duplicates removed (%)
46.6
Number of peaks
8139 (qval < 1E-05)

Base call quality data from DBCLS SRA