Kubik 2015, Nucleosome architectures at promoters of protein-coding genes .

MNase-seq profiles obtained with various MNase concentrations from wild-type cells and cells depleted of different transcription factors (see "Notes on samples").
ChIP-seq against RNA polymerase II and 2 histones H2A and H3 in Saccharomyces cerevisiae cells.

• Raw data was downloaded from: SRP064008
• Input file format: SRA
• Download date: 4-9-2017

From S. cerevisiae (Apr 2011 R64/sacCer3).

DNase FAIRE data:

	Filename	Description	Feature	GEO-ID
1	GSM1891198.sga	WT|MNase 0.5U|rapamicin	MNase	GSM1891198
2	GSM1891199.sga	WT|MNase 1.0U|rapamicin	MNase	GSM1891199
3	GSM1891200.sga	WT|MNase 1.5U|rapamicin	MNase	GSM1891200
4	GSM1891201.sga	WT|MNase 2.0U|rapamicin	MNase	GSM1891201
5	GSM1891202.sga	WT|MNase 0.2U|vehicle	MNase	GSM1891202
6	GSM1891203.sga	WT|MNase 0.5U|vehicle	MNase	GSM1891203
7	GSM1891204.sga	WT|MNase 1.0U|vehicle	MNase	GSM1891204
8	GSM1891205.sga	WT|MNase 1.5U|vehicle	MNase	GSM1891205
9	GSM1891206.sga	WT|MNase 2.0U|vehicle	MNase	GSM1891206
10	GSM1891207.sga	WT|MNase 4.0U|vehicle	MNase	GSM1891207
11	GSM1891208.sga	anchor-away Rbp1|MNase 0.2U|vehicle	MNase	GSM1891208
12	GSM1891209.sga	anchor-away Rbp1|MNase 0.2U|rapamicin	MNase	GSM1891209
13	GSM1891210.sga	anchor-away Rbp1|MNase 2U|vehicle	MNase	GSM1891210
14	GSM1891211.sga	anchor-away Rbp1|MNase 2U|rapamicin	MNase	GSM1891211
15	GSM1891212.sga	anchor-away Sth1|MNase ?U|vehicle	MNase	GSM1891212
16	GSM1891213.sga	anchor-away Sth1|MNase ?U|rapamicin	MNase	GSM1891213
17	GSM1891214.sga	anchor-away Rap1|MNase 0.2U|vehicle	MNase	GSM1891214
18	GSM1891215.sga	anchor-away Rap1|MNase 1.5U|vehicle	MNase	GSM1891215
19	GSM1891216.sga	anchor-away Rap1|MNase 0.2U|rapamicin	MNase	GSM1891216
20	GSM1891217.sga	anchor-away Rap1|MNase 1.5U|rapamicin	MNase	GSM1891217
21	GSM1891218.sga	anchor-away Abf1|MNase 0.1U|vehicle	MNase	GSM1891218
22	GSM1891219.sga	anchor-away Abf1|MNase 0.1U|rapamycin	MNase	GSM1891219
23	GSM1891220.sga	anchor-away Abf1|MNase 1.5U|vehicle	MNase	GSM1891220
24	GSM1891221.sga	anchor-away Abf1|MNase 1.5U|rapamycin	MNase	GSM1891221
25	GSM1891222.sga	anchor-away Reb1|MNase 0.1U|vehicle	MNase	GSM1891222
26	GSM1891223.sga	anchor-away Reb1|MNase 0.1U|rapamycin	MNase	GSM1891223
27	GSM1891224.sga	anchor-away Reb1|MNase 0.2U|rapamycin	MNase	GSM1891224
28	GSM1891225.sga	anchor-away Reb1|MNase 0.2U|vehicle	MNase	GSM1891225

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM1891226.sga	WT|RNAPII	RNAPII	GSM1891226
2	GSM1891227.sga	WT|input	input	GSM1891227
3	GSM1891228.sga	WT|H2A|vehicle	H2A	GSM1891228
4	GSM1891229.sga	WT|H3|vehicle	H3	GSM1891229

Notes on samples :

Descriptions of the strains as provided in GEO:

• WT: HHY168 (W303 MATalpha tor1-1 fpr1::NAT RPL13A-2xFKBP12::TRP1)
• anchor-away Rbp1: HHY170 (HHY168 RPB1-FRB1-KanMX6)
• anchor-away Sth1: YSK111(HHY168 STH1-FRB1-KanMX6)
• anchor-away Rap1: YJB26 (HHY168 RAP1(1-134)-FRB1-RAP1(136-827)-KanMX6)
• anchor-away Abf1: YSK227 (HHY168 ABF1-FRB-KanMX6)
• anchor-away Reb1: YSK229 (HHY168 REB1-FRB-KanMX6)

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the Saccharomyces cerevisiae 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).

• Kubik S, Bruzzone MJ, Jacquet P, Falcone JL, Rougemont J, Shore D
  Nucleosome Stability Distinguishes Two Different Promoter Types at All Protein-Coding Genes in Yeast. Mol Cell. 2015 Nov 5;60(3):422-34. doi: 10.1016/j.molcel.2015.10.002. 26545077
• GEO series GSE73337: Two Distinct Promoter Nucleosome Architectures at Protein-Coding Genes in Yeast