Gaffney 2012, Controls of nucleosome positioning in the human genome.


Paired-end sequenceing of MNase-treated chromatin of seven lymphoblastoid cell lines. Two of the cell lines have been also single-end sequenced for comparison.



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

DNase FAIRE data:

Filename Description Feature GEO-ID
1 GSM907783.sga GM18507 - MNase-seq MNase GSM907783
2 GSM907784.sga GM18508 - MNase-seq MNase GSM907784
3 GSM907786.sga GM18516 - MNase-seq MNase GSM907786
4 GSM907788.sga GM18522 - MNase-seq MNase GSM907788
5 GSM907789.sga GM19193 - MNase-seq MNase GSM907789
6 GSM907790.sga GM19238 - MNase-seq MNase GSM907790
7 GSM907791.sga GM19239 - MNase-seq MNase GSM907791
8 allSamples147.sga All Paired-end samples - 147bp fragments MNase GSM907791
9 GSM907783_147.sga GM18507 - 147bp fragments MNase GSM907783
10 GSM907784_147.sga GM18508 - 147bp fragments MNase GSM907784
11 GSM907786_147.sga GM18516 - 147bp fragments MNase GSM907786
12 GSM907788_147.sga GM18522 - 147bp fragments MNase GSM907788
13 GSM907789_147.sga GM19193 - 147bp fragments MNase GSM907789
14 GSM907790_147.sga GM19238 - 147bp fragments MNase GSM907790
15 GSM907791_147.sga GM19239 - 147bp fragments MNase GSM907791
16 GSM907785.sga GM18516 - MNase-seq - Single-end MNase GSM907785
17 GSM907787.sga GM18522 - MNase-seq - Single-end MNase GSM907787

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie v0.12.8. SAM files were then converted into bam using samtools v0.1.14 and to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using (ChIP-Seq v. 1.5.3).


Last update: 1 Oct 2018