GSE35586, Nucleosome Position by MNase-seq from ENCODE/Stanford/BYU

Description

Nucleosome maps (MNase-seq) from the GM12878 and K562 ENCODE cell lines.

Source

Samples

From Human Feb. 2009 (GRCh37/hg19) Assembly.

DNase FAIRE data:

Filename Description Feature GEO-ID
1 Nucleosome-GM12878.sga GM12878|Nucleosome|all (SLOW!) Nucleosome GSM920558
2 Nucleosome-K562.sga K562|Nucleosome|all (SLOW!) Nucleosome GSM920557
3 Nucleosome_Gm12878_rep1.sga Gm12878|Nucleosome|rep1 Nucleosome -
4 Nucleosome_Gm12878_rep2.sga Gm12878|Nucleosome|rep2 Nucleosome -
5 Nucleosome_Gm12878_rep3.sga Gm12878|Nucleosome|rep3 Nucleosome -
6 Nucleosome_Gm12878_rep4.sga Gm12878|Nucleosome|rep4 Nucleosome -
7 Nucleosome_Gm12878_rep5.sga Gm12878|Nucleosome|rep5 Nucleosome -
8 Nucleosome_Gm12878_rep6.sga Gm12878|Nucleosome|rep6 Nucleosome -
9 Nucleosome_Gm12878_rep7.sga Gm12878|Nucleosome|rep7 Nucleosome -
10 Nucleosome_Gm12878_rep8.sga Gm12878|Nucleosome|rep8 Nucleosome -
11 Nucleosome_Gm12878_rep9.sga Gm12878|Nucleosome|rep9 Nucleosome -
12 Nucleosome_K562_rep1.sga K562|Nucleosome|rep1 Nucleosome -
13 Nucleosome_K562_rep2.sga K562|Nucleosome|rep2 Nucleosome -
14 Nucleosome_K562_rep3.sga K562|Nucleosome|rep3 Nucleosome -
15 Nucleosome_K562_rep4.sga K562|Nucleosome|rep4 Nucleosome -
16 Nucleosome_K562_rep5.sga K562|Nucleosome|rep5 Nucleosome -
17 Nucleosome_K562_rep6.sga K562|Nucleosome|rep6 Nucleosome -
18 Nucleosome_K562_rep7.sga K562|Nucleosome|rep7 Nucleosome -
19 Nucleosome_K562_rep8.sga K562|Nucleosome|rep8 Nucleosome -
20 Nucleosome_K562_rep9.sga K562|Nucleosome|rep9 Nucleosome -
21 Nucleosome_K562_rep10.sga K562|Nucleosome|rep10 Nucleosome -
22 Nucleosome_K562_rep11.sga K562|Nucleosome|rep11 Nucleosome -

Technical replicas for each cell line were merged (samples marked as 'all').

Technical Notes

BAM files were converted to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.2).

References

Last update: 23 Feb 2016