|
| 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.
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| 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.
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| 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 |
| |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (13)
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| Relations |
| BioProject |
PRJNA385810 |
| SRA |
SRP106628 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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