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

Files downloaded from SRA database: http://www.ncbi.nlm.nih.gov/sra?term=SRP028538 and http://www.ncbi.nlm.nih.gov/sra?term=SRP028537
Input file format: SRA

Samples

From Pombe 2004 (spo2) Assembly

MNase samples:

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

Technical Notes

Raw data was downloaded from the SRA database (ID SRP028537 and SRP028538) and mapped to spo2 genome using Bowtie aligner. The resulting SAM files were converted to BED using SAMtools and BEDtools. Final conversion to SGA files was done using ChIP-Seq.

References

DeGennaro CM, Alver BH, Marguerat S, Stepanova E et al. 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. PMID: 24100010

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