|
| Status |
Public on Jun 13, 2017 |
| Title |
R0_Pbx_HoxA5_EpiSELEX_seq |
| Sample type |
SRA |
| |
|
| Source name |
in-vitro purification
|
| Organism |
Homo sapiens |
| Characteristics |
rounds of selection: 0
variable region length: 16
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were amplified by using overhang primers targeting the GGTAGTGGAGG and GG-GAGGTGGAGTAGG parts of the library and adding the Illumina TruSEQ adapter and universal or Index primers respectively. During amplification the extracted, TF-bound DNA was split in two separate pools and Illumina primer landing sites were added from both orientations respectively (Universal-for & Index-rev or Index-for and Universal-rev). Next, Illumina-specific barcodes were added in a 5 cycles PCR to allow for multiplexing of multiple samples. In order to obtain unidirectional reads starting from the barcode end of the library, reads need to be reverse-complemented and merged with the forward reads.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Library strategy: EpiSELEX-seq
Fastq files were reverse-complemented and both forward and reverse-complement read merged into one (fastx_reverse_complement -Q33 -z ; FASTX toolkit 0.0.12;Hannon lab).
Next, fixed primer sites were trimmed using the following options: fastx_trimmer -Q33 -f 12 -l 41 –z (FASTX toolkit 0.0.12;Hannon lab).
Kmer counting and relative affinity estimates were computed using the R package bioconductor.org/packages/SELEX.
To filter for kmers that are aligned with the actual Protein:DNA interface, position-specific affinity matrices were calculated for each library and probes were scanned in a sliding-window approach in either orientation to find the optimal protein footprint. Only probes where a single offset contributed at least 95% to the overall probe affinity were retained.
Oligomer-based relative affinity tables for the unmethylated and methylated libraries were generated for the set of kmers that passed the filtering criterion.
Genome_build: randomized DNA
Supplementary_files_format_and_content: txt files contain two columns describing the relative affinity of individual kmers from the unmethylated and methylated libraries. Rownames contain the specific kmer sequences.
|
| |
|
| Submission date |
May 08, 2017 |
| Last update date |
May 15, 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 |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE98652 |
Quantitative analysis of the DNA methylation sensitivity of transcription factor complexes |
|
| Relations |
| BioSample |
SAMN06915171 |
| SRA |
SRX2789139 |
