Kasinathan 2014, High-resolution mapping of Abf1 and Reb1 on native chromatin.

Description of a new profiling technique, ORGANIC (Occupied Regions of Genomes from Affinity-purified Naturally Isolated Chromatin), with two TFs examples (Abf1 and Reb1). Reb1 ORGANIC profiling was performed at three different salt (NaCl) concentrations (80, 150, and 600 mM) and Abf1 ORGANIC profiling was done at two different salt concentrations (80 and 600 mM) to achieve varying levels of stringency. Two additional Sono-seq samples (chromatin sonication followed by sequencing) are also present.

• Raw data was downloaded from: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45672
• Input file format: BED
• Download date: 24-11-2017

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

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM1111706.sga	W1588-4C|Reb1|80mM	Reb1	GSM1111706
2	GSM1111707.sga	W1588-4C|Reb1|80mM|ctrl	Reb1	GSM1111707
3	GSM1111708.sga	W1588-4C|Reb1|150mM	Reb1	GSM1111708
4	GSM1111709.sga	W1588-4C|Reb1|150mM|ctrl	Reb1	GSM1111709
5	GSM1111710.sga	W1588-4C|Reb1|600mM|Rep 1	Reb1	GSM1111710
6	GSM1111711.sga	W1588-4C|Reb1|600mM|Rep 1 ctrl	Reb1	GSM1111711
7	GSM1111712.sga	W1588-4C|Reb1|600mM|Rep 2	Reb1	GSM1111712
8	GSM1111713.sga	W1588-4C|Reb1|600mM|Rep 2 ctrl	Reb1	GSM1111713
9	GSM1111714.sga	W1588-4C|Abf1|80mM	Abf1	GSM1111714
10	GSM1111715.sga	W1588-4C|Abf1|80mM|ctrl	Abf1	GSM1111715
11	GSM1111716.sga	W1588-4C|Abf1|600mM|Rep 1	Abf1	GSM1111716
12	GSM1111717.sga	W1588-4C|Abf1|600mM|Rep 1 ctrl	Abf1	GSM1111717
13	GSM1111718.sga	W1588-4C|Abf1|600mM|Rep 2	Abf1	GSM1111718
14	GSM1111719.sga	W1588-4C|Abf1|600mM|Rep 2 ctrl	Abf1	GSM1111719
15	GSM1111726.sga	W1588-4C S2|Reb1|150mM|Rep 1	Reb1	GSM1111726
16	GSM1111727.sga	W1588-4C S2|Reb1|150mM|Rep 1 ctrl	Reb1	GSM1111727
17	GSM1111728.sga	W1588-4C S2|Reb1|150mM|Rep 2	Reb1	GSM1111728
18	GSM1111729.sga	W1588-4C S2|Reb1|150mM|Rep 2 ctrl	Reb1	GSM1111729

:

	Filename	Description	Feature	GEO-ID
1	GSM1111720.sga	W1588-4C|sonoication||Rep 1	nucl	GSM1111720
2	GSM1111721.sga	W1588-4C|sonoication||Rep 2	nucl	GSM1111721

BED to SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.3).

• Kasinathan S, Orsi GA, Zentner GE, Ahmad K, Henikoff S
  High-resolution mapping of transcription factor binding sites on native chromatin. Nat Methods. 2014 Feb;11(2):203-9. doi: 10.1038/nmeth.2766. Epub 2013 Dec 15. 24336359
• GEO series GSE45672: High-resolution mapping of transcription factor binding sites on native chromatin