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

Description

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.

Source

Samples

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:

Technical Notes

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).

References

Last update: 11 Sep 2017