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Series GSE27381 Query DataSets for GSE27381
Status Public on Feb 18, 2011
Title Multiplexed identification of the genomic targets of DNA-binding proteins
Organism Saccharomyces cerevisiae
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Transcription factors direct gene expression, and so there is much interest in mapping their genome-wide binding locations.  Current methods do not allow for the multiplexed analysis of TF binding, and this limits their throughput. We describe a novel method for determining the genomic target genes of multiple transcription factors simultaneously. DNA-binding proteins are endowed with the ability to direct transposon insertions into the genome near to where they bind. The transposon becomes a “Calling Card” marking the visit of the DNA-binding protein to that location. A unique sequence “barcode” in the transposon matches it to the DNA-binding protein that directed its insertion. The sequences of the DNA flanking the transposon (which reveal where in the genome the transposon landed) and the barcode within the transposon (which identifies the TF that put it there) are determined by massively-parallel DNA sequencing. To demonstrate the method’s feasibility, we determined the genomic targets of eight transcription factors in a single experiment. The Calling Card method promises to significantly reduce the cost and labor needed to determine the genomic targets of many transcription factors in different environmental conditions and genetic backgrounds.
Overall design These data contain Ty5 insertion sites mapped by an Illumina GAII analyzer in the S. cerevisiae genome for the background strain without any Sir4 present (1 run), in strains expressing Sir4-tagged copies of three well-characterized TFs: Gal4, Leu3, and Gcn4 (1 run each), and a multiplex of eight Sir4-tagged TFs pooled in a single experiment (2 biological replicates), and insertions from the Thi2-Sir4 fusion expressed from its native locus in two conditions (1 run each). The format of each insertions file is [chromosome number] [position of genomic base] [direction of insertion] [number of reads at that position]. Raw sequencing data comes in two varieties. Paired-end data contains a 5 bp barcode at the beginning of read #2. Single-end data contains a 2 bp barcode on the beggining of read #1.
Contributor(s) Robi M, Mark J
Citation(s) 21471402
Submission date Feb 17, 2011
Last update date May 15, 2019
Contact name David Mayhew
Organization name GlaxoSmithKline
Department Target Sciences, Computation Biology, R&D
Street address 1250 South Collegeville Road
City Collegeville
State/province PA
ZIP/Postal code 19426
Country USA
Platforms (1)
GPL9377 Illumina Genome Analyzer II (Saccharomyces cerevisiae)
Samples (22)
GSM677083 Background Strain (Sir4 KO) Insertions
GSM677084 Positive Control Gal4 Insertions
GSM677085 Positive Control Leu3 Insertions
SRA SRP005862
BioProject PRJNA137021

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE27381_RAW.tar 2.3 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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