Lefrancois 2009, Efficient Yeast ChIP-Seq using Multiplex Short-Read DNA Sequencing


Examination of the distribution of PolII (4 biological replicates), Cse4 (3 biological replicates) and Ste12 (3 biological replicates) using barcoded adapters and non-barcoded genomic DNA Illumina adapters. Input DNA was used as a reference sample and for scoring as well.


Files downloaded from GEO series: GSE13322
Input file format: Tab-delimited TXT


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

Filename Description Feature GEO-ID
1 GSM336333-PolII.sga PolII PolII GSM336333
2 GSM336334-Ste12.sga Ste12 Ste12 GSM336334
3 GSM336335-Cse4.sga Cse4 Cse4 GSM336335
4 GSM336336-Input.sga Input rep1 Input GSM336336
5 GSM336337-Input.sga Input rep2 Input GSM336337
6 GSM336338-Input.sga Input rep3 Input GSM336338
7 GSM336333-PolII-rep1.sga PolII rep1 PolII GSM336333
8 GSM336333-PolII-rep2.sga PolII rep2 PolII GSM336333
9 GSM336333-PolII-rep3.sga PolII rep3 PolII GSM336333
10 GSM336333-PolII-rep4.sga PolII rep4 PolII GSM336333
11 GSM336334-Ste12-rep1.sga Ste12 rep1 Ste12 GSM336334
12 GSM336334-Ste12-rep2.sga Ste12 rep2 Ste12 GSM336334
13 GSM336334-Ste12-rep3.sga Ste12 rep3 Ste12 GSM336334
14 GSM336335-Cse4-rep1.sga Cse4 rep1 Cse4 GSM336335
15 GSM336335-Cse4-rep2.sga Cse4 rep2 Cse4 GSM336335
16 GSM336335-Cse4-rep3.sga Cse4 rep3 Cse4 GSM336335
17 GSM336336-Input-ACGT.sga Input ACGT rep1 Input GSM336336
18 GSM336337-Input-ACGT.sga Input ACGT rep2 Input GSM336337
19 GSM336338-Input-ACGT.sga Input ACGT rep3 Input GSM336338
20 GSM336337-Input-CATT.sga Input CATT rep1 Input GSM336337
21 GSM336338-Input-CATT.sga Input CATT rep2 Input GSM336338
22 GSM336337-Input-GTAT.sga Input GTAT Input GSM336337
23 GSM336337-Input-TGCT.sga Input TGCT Input GSM336337
24 GSM336337-Input-NB.sga Input NB rep1 Input GSM336337
25 GSM336338-Input-NB.sga Input NB rep2 Input GSM336338

Technical Notes

The original eland results have been converted to sga using in house software and have been merged sample by sample.


  1. Lefrancois P, Euskirchen GM, Auerbach RK, Rozowsky J, Gibson T, Yellman CM, Gerstein M, Snyder M
    Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC Genomics 2009 Jan 21;10:37. PMID: 19159457

  2. GEO series GSE13322 Efficient Yeast ChIP-Seq using Multiplex Short-Read DNA Sequencing.