Kaplan 2009, Yeast nucleosome organization on 3 media.

Description

Solexa/Illumina sequencing of in vivo and in vitro mononucleosomes. YPD: 6 biological replicates (4 non-crosslinked, 2 crosslinked); YPEthanol: 4 replicates (2 non-crosslinked, 2 crosslinked); YPGalactose: 3 replicates (2 non-crosslinked, 1 crosslinked). The YP (yeast extract, peptone) medium was used as the basal medium.
In vitro nucleosomes were generated using D. melanogaster histones and S. cerevisiae fragmented DNA.

Source

Samples

From Yeast Apr 2011 (NCBI3.1/sacCer3) Assembly.

DNase FAIRE data:

Filename Description Feature GEO-ID
1 YPD.sga YPD all Nucleosomes Nucleosome GSM351492
2 YPD_CL.sga YPD Nucleosomes crosslinked Nucleosome GSM351492
3 YPD_CL_R2.sga YPD Nucleosomes crosslinked r2 Nucleosome GSM351492
4 YPD_CL_R3.sga YPD Nucleosomes crosslinked r3 Nucleosome GSM351492
5 YPD_NOCL.sga YPD Nucleosomes non-crosslinked Nucleosome GSM351492
6 YPD_NOCL_R1.sga YPD Nucleosomes non-crosslinked r1 Nucleosome GSM351492
7 YPD_NOCL_R2.sga YPD Nucleosomes non-crosslinked r2 Nucleosome GSM351492
8 YPD_NOCL_R3.sga YPD Nucleosomes non-crosslinked r3 Nucleosome GSM351492
9 YPD_NOCL_R4.sga YPD Nucleosomes non-crosslinked r4 Nucleosome GSM351492
10 YPEtOH.sga YPEtOH all Nucleosomes Nucleosome GSM351494
11 YPEtOH_CL.sga YPEtOH Nucleosomes crosslinked Nucleosome GSM351494
12 YPEtOH_CL_R1.sga YPEtOH Nucleosomes crosslinked r1 Nucleosome GSM351494
13 YPEtOH_CL_R2.sga YPEtOH Nucleosomes crosslinked r2 Nucleosome GSM351494
14 YPEtOH_NOCL.sga YPEtOH Nucleosomes non-crosslinked Nucleosome GSM351494
15 YPEtOH_NOCL_R1.sga YPEtOH Nucleosomes non-crosslinked r1 Nucleosome GSM351494
16 YPEtOH_NOCL_R2.sga YPEtOH Nucleosomes non-crosslinked r2 Nucleosome GSM351494
17 YPGal.sga YPGal all Nucleosomes Nucleosome GSM351493
18 YPGal_CL_R1.sga YPGal Nucleosomes crosslinked Nucleosome GSM351493
19 YPGal_NOCL.sga YPGal Nucleosomes non-crosslinked Nucleosome GSM351493
20 YPGal_NOCL_R1.sga YPGal Nucleosomes non-crosslinked r1 Nucleosome GSM351493
21 YPGal_NOCL_R2.sga YPGal Nucleosomes non-crosslinked r2 Nucleosome GSM351493
22 inVitroNucleosomes.sga In vitro nucleosomes Nucleosome GSM351491

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to 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. 1.5.2).

References

Last update: 12 Apr 2016