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Series GSE110653 Query DataSets for GSE110653
Status Public on Feb 15, 2018
Title Sequence variation within similar cis-elements promotes context-specific functions of two Drosophila GA-binding transcription factors (protein binding microarray data set)
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by array
Summary To more specifically define the sequence content that favors direct binding of GAF, a genomic-context protein binding microarray (gcPBM) was used to detect GST-tagged GAF binding to double stranded DNA probes using a fluorescently conjugated anti-GST secondary antibody
Overall design GPL22023 - PBM experiments were performed using a custom-designed oligonucleotide array in 4x180K format (Agilent Technologies, Inc., AMADID #037964), described in detail previously (Kuzu G, Kaye EG, Chery J, Siggers T et al. Expansion of GA Dinucleotide Repeats Increases the Density of CLAMP Binding Sites on the X-Chromosome to Promote Drosophila Dosage Compensation. PLoS Genet 2016 Jul;12(7):e1006120. PMID: 27414415). The array was converted to a double-stranded DNA array and used in PBM experiments essentially as described previously using PBS binding buffer with 50 μM zinc acetate (Berger et al., Nat Biotech, 2006 and Berger & Bulyk, Nat Protoc, 2009), except that here GST-GAF-DBD was applied to one fresh and one stripped array at a final concentration of 150 nM, and either 525 nM or 600 nM MBP, respectively. N-terminal GST-tagged protein samples were made for the protein GAF; samples were made by in vitro transcription translation (IVT). IVT reaction mixtures for the GAF construct were applied directly to the PBM microarray and incubated for 1hour. Microarray-bound protein was fluorescently labeled using Alexa488-conjugated antibodies targeting GST, and the microarray was scanned in using a standard microarray scanner. Median fluorescence intensity over eight replicate probes was reported for each unique DNA sequence on the microarray.
Contributor(s) Kaye EG, Booker M
Citation(s) 29562179
Submission date Feb 15, 2018
Last update date Mar 23, 2018
Contact name Michael Tolstorukov
Organization name Massachusetts General Hospital
Department Molecular Biology
Street address 185 Cambridge Street
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
Platforms (1)
GPL22023 Agilent-037964 mre_4x180k_design_1_1211 Protein Binding Microarray (Condensed probe version)
Samples (2)
GSM3005018 GAF Replicate 1
GSM3005019 GAF Replicate 2
This SubSeries is part of SuperSeries:
GSE110654 Sequence variation within similar cis-elements promotes context-specific functions of two Drosophila GA-binding transcription factors
BioProject PRJNA434200

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
GSE110653_RAW.tar 12.2 Mb (http)(custom) TAR (of TXT)
GSE110653_gafnromalizedvalues.xlsx 12.4 Mb (ftp)(http) XLSX
Processed data are available on Series record

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