DeGennaro 2013, Histone and nucleosome maps in WT and spt6 fission yeasts.

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).

• Raw data was downloaded from: SRP028538 and SRP028537
• Input file format: SRA
• Download date: 26-9-2017

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

• DeGennaro CM, Alver BH, Marguerat S, Stepanova E, Davis CP, Bähler J, Park PJ, Winston F
  Spt6 regulates intragenic and antisense transcription, nucleosome positioning, and histone modifications genome-wide in fission yeast. Mol Cell Biol. 2013 Dec;33(24):4779-92. doi: 10.1128/MCB.01068-13. Epub 2013 Oct 7. 24100010