Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing

BMC Genomics

Table 10 Experimental design and values for ChIP replicates and input samples

Experiment #	Experiment ID	Barcode	Sample	DNA Concentration (ng/φL)	A_260/280	Total reads	Mapped reads	% Mapping	Threshold
1	PolII_Rep1	ACGT	PolII	16.6	1.83	1110177	623328	56.15	14
2	Input_CATT	CATT	Input	51.6	1.85	2526689	1719855	68.07	Not being scored
3	Cse4_Rep1	GTAT	Cse4	12.0	1.99	2606497	1080537	41.46	81
4	Ste12_Rep1	TGCT	Ste12	11.6	1.85	2020432	1072428	53.08	42
5	Input_ACGT	ACGT	Input	66.9	1.80	4678579	2857615	61.08	Not being scored
6	Cse4_Rep2	CATT	Cse4	8.6	1.85	679315	357384	52.61	25
7	Ste12_Rep2	GTAT	Ste12	9.4	1.86	2316023	1067739	46.10	44
8	PolII_Rep2	TGCT	PolII	15.5	2.00	3991833	2561147	64.16	12
9	PolII_Rep3	ACGT	PolII	9.7	1.97	2661304	1725793	64.85	42
10	Input_NB	None	Input	60.4	1.83	2432221	1582226	65.05	Not being scored
11A*	Cse4_Rep3	None	Cse4	10.7	1.69	1168583	239580	20.50	60
11B*	Cse4_Rep3	None	Cse4	10.7	1.69	3245287	583876	17.99
12A*	Ste12_Rep3	None	Ste12	9.1	1.64	2106917	473965	22.50	39
12B*	Ste12_Rep3	None	Ste12	9.1	1.64	2668067	551040	20.65
13	PolII_Rep4	None	PolII	18.8	1.94	4649077	3151068	67.78	40
14	Input_NB	None	Input	60.4	1.83	4373256	2455181	56.14	Not being scored
15	Input_ACGT	ACGT	Input	66.9	1.80	873037	529038	60.60	5
16	Input_CATT	CATT	Input	51.6	1.85	799430	479546	59.99	5
17	Input_GTAT	GTAT	Input	34.6	1.69	1380820	850262	61.58	6
18	Input_TGCT	TGCT	Input	68.1	1.78	611123	362458	59.31	4

NB (No Barcode) indicates that standard non-barcoded Illumina adapters were used. DNA concentrations of Illumina DNA libraries and their A_260/280 ratios are given in columns 5 and 6.
Mapping values after sequencing (total sequencing reads, total mapped reads and percentage of mapped reads) are shown in columns 7, 8 and 9.
Threshold values for PeakSeq scoring algorithm are displayed in column 10.
* Sample ran twice on sequencer and reads pooled together from both lanes for scoring as a single experiment

ISSN: 1471-2164