Buenrostro 2013, ATAC-seq profiling of open chromatin, DNA-binding proteins and nucleosome position.


First description of an assay for transposase-accessible chromatin using sequencing (ATAC-seq), based on direct in vitro transposition of sequencing adaptors into native chromatin. It is performed on two cell lines (GM12878 and CD4+), with 500 or 50.000 cells as input and 3 time points (day 1 to 3). Short fragments (less that 100bp) are used to profile open chromatin regions whereas large fragments (180-247bp) are used to profile mononucleosomes.



From H. sapiens (Feb 2009 GRCh37/hg19).

DNase FAIRE data:

Filename Description Feature GEO-ID
1 CD4+_day1.oriented.sga CD4+|ATACseq|Day1|all ATACseq GSM1155964, GSM1155965
2 CD4+_day1_long.centered.sga CD4+|ATACseq|Day1|long ATACseq GSM1155964, GSM1155965
3 CD4+_day2.oriented.sga CD4+|ATACseq|Day2|all ATACseq GSM1155966, GSM1155967
4 CD4+_day2_long.centered.sga CD4+|ATACseq|Day2|long ATACseq GSM1155966, GSM1155967
5 CD4+_day3.oriented.sga CD4+|ATACseq|Day3|all ATACseq GSM1155968, GSM1155969
6 CD4+_day3_long.centered.sga CD4+|ATACseq|Day3|long ATACseq GSM1155968, GSM1155969
7 GM12878_500.oriented.sga GM12878|ATACseq|500|all ATACseq GSM1155961, GSM1155962, GSM1155963
8 GM12878_500_long.centered.sga GM12878|ATACseq|500|long ATACseq GSM1155961, GSM1155962, GSM1155963
9 GM12878_50K.oriented.sga GM12878|ATACseq|50K|short ATACseq GSM1155957, GSM1155958, GSM1155959, GSM1155960
10 GM12878_50K_long.centered.sga GM12878|ATACseq|50K|long ATACseq GSM1155957, GSM1155958, GSM1155959, GSM1155960

Notes on samples nomenclature:

Following description in the paper, for each samples we derived two types of reads (samples named 'short' and 'long'):

The final files include data pulled from several replicates. Files for long fragments are un-oriented whereas oriented files include all ATAC-seq cut coordinates.

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie v1.2.2 SAM files were then converted into bam using samtools v1.9 and to bed using bamToBed v2.27.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.5).


Last update: 19 Aug 2019