Valouev 2011, Determinants of nucleosome organization in primary human cells

Description

Genome binding/occupancy profiling by high throughput sequencing of MNase trated chromatin of several samples that include: nucleosome-bound DNA isolated from primary human CD4+ T-cells, nucleosome bound-DNA isolated from primary human CD8+ T-cells, nucleosome-bound DNA isolated from primary human granulocytes, nucleosome-bound DNA isoalted from in vitro reconstitution of nucleosomes with human genomic DNA, control DNA generated by micrococcal nuclease treatment of human genomic DNA,

Source

Files downloaded from GEO: GSE25133

Input file format: SRA

Samples

ChIP-seq data from Human Mar. 2006 (NCBI36/hg18) Assembly

Filename Description Feature GEO-ID
1 cd4NucleosomeCores.sga CD4+ T-cell nucleosome cores|All rep MNase -
2 cd8NucleosomeCores.sga CD8+ T-cell nucleosome cores|All rep MNase -
3 granulocyteNucleosomeCores.sga Granulocyte nucleosome cores|All rep MNase -
4 reconstitutedNucleosomeCores.sga In vitro reconstituted nucleosome cores|All rep MNase -
5 GSM678037.sga CD4+ T-cell nucleosome cores|rep 1 MNase GSM678037
6 GSM678038.sga CD4+ T-cell nucleosome cores|rep 2 MNase GSM678038
7 GSM678039.sga CD4+ T-cell nucleosome cores|rep 3 MNase GSM678039
8 GSM678040.sga CD4+ T-cell nucleosome cores|rep 4 MNase GSM678040
9 GSM678041.sga CD8+ T-cell nucleosome cores|rep 1 MNase GSM678041
10 GSM678042.sga CD8+ T-cell nucleosome cores|rep 2 MNase GSM678042
11 GSM678043.sga CD8+ T-cell nucleosome cores|rep 3 MNase GSM678043
12 GSM678044.sga CD8+ T-cell nucleosome cores|rep 4 MNase GSM678044
13 GSM678045.sga Granulocyte nucleosome cores|rep 1 MNase GSM678045
14 GSM678046.sga Granulocyte nucleosome cores|rep 2 MNase GSM678046
15 GSM678047.sga Granulocyte nucleosome cores|rep 3 MNase GSM678047
16 GSM678048.sga Granulocyte nucleosome cores|rep 4 MNase GSM678048
17 GSM678049.sga Granulocyte nucleosome cores|rep 5 MNase GSM678049
18 GSM678050.sga Granulocyte nucleosome cores|rep 6 MNase GSM678050
19 GSM678051.sga Granulocyte nucleosome cores|rep 7 MNase GSM678051
20 GSM678052.sga Granulocyte nucleosome cores|rep 8 MNase GSM678052
21 GSM678053.sga Granulocyte nucleosome cores|rep 9 MNase GSM678053
22 GSM678054.sga Granulocyte nucleosome cores|rep 10 MNase GSM678054
23 GSM678055.sga In vitro reconstituted nucleosome cores|rep 1 MNase GSM678055
24 GSM678056.sga In vitro reconstituted nucleosome cores|rep 2 MNase GSM678056
25 GSM678057.sga In vitro reconstituted nucleosome cores|rep 3 MNase GSM678057
26 GSM678058.sga In vitro reconstituted nucleosome cores|rep 4 MNase GSM678058
27 GSM678059.sga In vitro reconstituted nucleosome cores|rep 5 MNase GSM678059
28 GSM678060.sga In vitro reconstituted nucleosome cores|rep 6 MNase GSM678060
29 GSM678061.sga MNase treated control genomic DNA|rep 1 MNase GSM678061
30 GSM678062.sga MNase treated control genomic DNA|rep 2 MNase GSM678062
31 GSM678063.sga MNase treated control genomic DNA|rep 3 MNase GSM678063

Technical Notes

Raw tag sequences were mapped to the genome using bowtie . SAM files were then transformed into SGA format using in-house software.

References

  1. Valouev A, Johnson SM, Boyd SD, Smith CL et al.
    Determinants of nucleosome organization in primary human cells. Nature 2011 May 22;474(7352):516-20. PMID: 21602827