Histones and nulceosomes maps in WT and spt6 fission yeasts.

Description

This serie is focused on elucidating the role of the nucleosome remodelling protein Spt6 in chromatin reorganisation (MNase; histones H2B and H3, histone modifications H3K36me3 and H3K4me3), Pol-II activity (RNA Pol-II complex proteins Ctr9 and Rpb1) and other chromatin remodelling proteins (histone lysine methyltransferase Set2 and heterochromatin assembly factor Swd1).

Source

Samples

From S. pombe (Aug 2015 ASM294v2/spo2).

DNase FAIRE data:

Filename Description Feature GEO-ID
1 GSM1201968.sga WT|100Uml||rep 1 MNase-seq GSM1201968
2 GSM1201969.sga WT|100Uml||rep 2 MNase-seq GSM1201969
3 GSM1201970.sga WT|150Uml||rep 1 MNase-seq GSM1201970
4 GSM1201971.sga WT|150Uml||rep 2 MNase-seq GSM1201971
5 GSM1201972.sga spt6|100Uml||rep 1 MNase-seq GSM1201972
6 GSM1201973.sga spt6|100Uml||rep 2 MNase-seq GSM1201973
7 GSM1201974.sga spt6|150Uml||rep 1 MNase-seq GSM1201974
8 GSM1201975.sga spt6|150Uml||rep 2 MNase-seq GSM1201975

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM1201980.sga WT|Ctr9-myc||rep 1 Ctr9-myc GSM1201980
2 GSM1201981.sga WT|Ctr9-myc||rep 2 Ctr9-myc GSM1201981
3 GSM1201982.sga WT|Ctr9-myc||rep 3 Ctr9-myc GSM1201982
4 GSM1201983.sga WT|H2B||rep 1 H2B GSM1201983
5 GSM1201984.sga WT|H2B||rep 2 H2B GSM1201984
6 GSM1201985.sga WT|H2B||rep 3 H2B GSM1201985
7 GSM1201986.sga WT|H3K36me3||rep 2 H3K36me3 GSM1201986
8 GSM1201987.sga WT|H3K36me3||rep 3 H3K36me3 GSM1201987
9 GSM1201988.sga WT|H3K4me3||rep 2 H3K4me3 GSM1201988
10 GSM1201989.sga WT|H3K4me3||rep 3 H3K4me3 GSM1201989
11 GSM1201990.sga WT|H3||rep 2 H3 GSM1201990
12 GSM1201991.sga WT|H3||rep 3 H3 GSM1201991
13 GSM1202003.sga WT|Rpb1||rep 1 Rpb1 GSM1202003
14 GSM1202004.sga WT|Rpb1||rep 2 Rpb1 GSM1202004
15 GSM1202005.sga WT|Set2-myc||rep 1 Set2-myc GSM1202005
16 GSM1202006.sga WT|Set2-myc||rep 2 Set2-myc GSM1202006
17 GSM1202007.sga WT|Spt6-HA||rep 1 Spt6-HA GSM1202007
18 GSM1202008.sga WT|Spt6-HA||rep 2 Spt6-HA GSM1202008
19 GSM1202009.sga WT|Swd1-myc||rep 1 Swd1-myc GSM1202009
20 GSM1202010.sga WT|Swd1-myc|rep 3 Swd1-myc GSM1202010
21 GSM1202011.sga spt6-1|Ctr9-myc||rep 1 Ctr9-myc GSM1202011
22 GSM1202012.sga spt6-1|Ctr9-myc||rep 2 Ctr9-myc GSM1202012
23 GSM1202013.sga spt6-1|Ctr9-myc||rep 3 Ctr9-myc GSM1202013
24 GSM1202014.sga spt6-1|H2B||rep 1 H2B GSM1202014
25 GSM1202015.sga spt6-1|H2B||rep 2 H2B GSM1202015
26 GSM1202016.sga spt6-1|H2B||rep 3 H2B GSM1202016
27 GSM1202017.sga spt6-1|H3K4me3||rep 2 H3K4me3 GSM1202017
28 GSM1202018.sga spt6-1|H3K4me3||rep 3 H3K4me3 GSM1202018
29 GSM1202019.sga spt6-1|H3||rep 2 H3 GSM1202019
30 GSM1202020.sga spt6-1|H3||rep 3 H3 GSM1202020
31 GSM1202031.sga spt6-1|Rpb1||rep 1 Rpb1 GSM1202031
32 GSM1202032.sga spt6-1|Rpb1||rep 2 Rpb1 GSM1202032
33 GSM1202033.sga spt6-1|Set2-myc||rep 1 Set2-myc GSM1202033
34 GSM1202034.sga spt6-1|Set2-myc||rep 2 Set2-myc GSM1202034
35 GSM1202035.sga spt6-1|Swd1-myc||rep 1 Swd1-myc GSM1202035
36 GSM1202036.sga spt6-1|Swd1-myc||rep 3 Swd1-myc GSM1202036
37 GSM1201992.sga WT|Input|Ctr9-myc|rep 1 Input GSM1201992
38 GSM1201993.sga WT|Input|Ctr9-myc|rep 2 Input GSM1201993
39 GSM1201994.sga WT|Input|Ctr9-myc|rep 3 Input GSM1201994
40 GSM1201995.sga WT|Input||rep 1 Input GSM1201995
41 GSM1201996.sga WT|Input||rep 2 Input GSM1201996
42 GSM1201997.sga WT|Input||rep 3 Input GSM1201997
43 GSM1201998.sga WT|Input|Set2-myc|rep 1 Input GSM1201998
44 GSM1201999.sga WT|Input|Set2-myc|rep 2 Input GSM1201999
45 GSM1202000.sga WT|Input|Spt6HA|rep 1 Input GSM1202000
46 GSM1202001.sga WT|Input|Swd1-Myc|rep 1 Input GSM1202001
47 GSM1202002.sga WT|Input|Swd1-Myc|rep 3 Input GSM1202002
48 GSM1202021.sga spt6-1|Input|Ctr9-myc|rep 1 Input GSM1202021
49 GSM1202022.sga spt6-1|Input|Ctr9-myc|rep 2 Input GSM1202022
50 GSM1202023.sga spt6-1|Input|Ctr9-myc|rep 3 Input GSM1202023
51 GSM1202024.sga spt6-1|Input||rep 1 Input GSM1202024
52 GSM1202025.sga spt6-1|Input||rep 2 Input GSM1202025
53 GSM1202026.sga spt6-1|Input||rep 3 Input GSM1202026
54 GSM1202027.sga spt6-1|Input|Set2-myc|rep 1 Input GSM1202027
55 GSM1202028.sga spt6-1|Input|Set2-myc|rep 2 Input GSM1202028
56 GSM1202029.sga spt6-1|Input|Swd1-Myc|rep 1 Input GSM1202029
57 GSM1202030.sga spt6-1|Input|Swd1-Myc|rep 3 Input GSM1202030

Technical Notes

Raw data was downloaded from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to spo2 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 bed2sga.pl (ChIP-Seq v. 1.5.3).

References

Last update: 26 Sep 2017