Kaplan 2009, Yeast nucleosome organization on 3 media.

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.

• Raw data was downloaded from: ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP001/SRP001116 and ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP001/SRP001117
• Input file format: SRA
• Download date: 12-04-2016

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

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

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).

• Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, Segal E
  The DNA-encoded nucleosome organization of a eukaryotic genome. Nature. 2009 Mar 19;458(7236):362-6. doi: 10.1038/nature07667. Epub 2008 Dec 17. 19092803
• GEO series GSE13622: The DNA-Encoded Nucleosome Organization of a Eukaryotic Genome