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.

• Raw data was downloaded from: SRA
• Input file format: SRA
• Download date: 13-8-2019

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'):

• Short: contain only fragments shorter than 100bp
• Long: contain only fragment between 180 and 247bp (mononucleosomes)

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.

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).

• Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ
  Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods. 2013 Dec;10(12):1213-8. doi: 10.1038/nmeth.2688. Epub 2013 Oct 6. 24097267
• GEO series GSE47753: Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position