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Series GSE98652 Query DataSets for GSE98652
Status Public on Jun 13, 2017
Title Quantitative analysis of the DNA methylation sensitivity of transcription factor complexes
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary EpiSELEX-seq method was used to characterize the binding preference of human TF complexes to methylated DNA, including BZIP proteins ATF4 and CEBPb, homeodomain TF heterodimers of HM(Meis1)-Pbx1 together with either HoxA1, HoxA5 or HoxA9 and tumor suppressor protein p53.
 
Overall design One round of EpiSELEX-seq was performed for all TFs tested as described in Kribelbauer et al. Purified TFs were incubated with a mix of methylated and unmethylated randomized 16bp (26bp for p53) DNA libraries of sequence GGTAGTGGAGG-TGGG-CCTGG-16xN/26xN-CCAGG-GAGGTGGAGTAGG for unmethylated and GGTAGTGGAGG-GCAC-CCTGG-16xN/26xN-CCAGG-GAGGTGGAGTAGG for methylated library. Bound fractions were amplified and sequenced.
 
Contributor(s) Bussemaker HJ, Mann RS, Kribelbauer JF
Citation(s) 28614722, 29409522
Submission date May 08, 2017
Last update date Aug 01, 2019
Contact name Harmen J Bussemaker
Organization name Columbia University
Department Biological Sciences
Lab Bussemaker Lab
Street address 1212 Amsterdam Avenue, MC 2441
City New York City
State/province New York
ZIP/Postal code 10027
Country USA
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (13)
GSM2607726 R1_ATF4_homo_EpiSELEX_seq
GSM2607727 R1_CEBPb_homo_EpiSELEX_seq
GSM2607728 R1_Pbx_HoxA1_EpiSELEX_seq
Relations
BioProject PRJNA385810
SRA SRP106628

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
GSE98652_ATF4_homo_hum_filtered_rel_affinity_table_LibU_vs_LibM.txt.gz 23.2 Kb (ftp)(http) TXT
GSE98652_CEBPb_homo_hum_filtered_rel_affinity_table_LibU_vs_LibM.txt.gz 23.0 Kb (ftp)(http) TXT
GSE98652_Pbx_HOXA1_hum_filtered_rel_affinity_table_LibU_vs_LibM.txt.gz 77.1 Kb (ftp)(http) TXT
GSE98652_Pbx_HOXA5_hum_filtered_rel_affinity_table_LibU_vs_LibM.txt.gz 92.1 Kb (ftp)(http) TXT
GSE98652_Pbx_HOXA9_hum_filtered_rel_affinity_table_LibU_vs_LibM.txt.gz 77.1 Kb (ftp)(http) TXT
GSE98652_Pbx_HOXA9b_hum_filtered_rel_affinity_table_LibU_vs_LibM.txt.gz 131.7 Kb (ftp)(http) TXT
GSE98652_p53_hum_minusCterm_filtered_rel_affinity_table_LibU_vs_LibM.txt.gz 76.2 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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