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

Description

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

Source

Raw data was downloaded from the UCSC Genome Browser via URL: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhNsome
Input file format: BAM

Samples

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

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

Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, Johnson SM, Snyder M, Batzoglou S, Sidow A
Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Res. 2012 Sep;22(9):1735-47. doi: 10.1101/gr.136366.111. 22955985
GEO series GSE35586: Nucleosome Position by MNase-seq from ENCODE/Stanford/BYU

Last update: 1 Oct 2018