license:openrail region:us
PRJEB3289
https://www.ebi.ac.uk/ena/browser/view/PRJEB3289
Data that has been generated by HT-SELEX experiments (see Jolma et al. 2010. PMID: 20378718 for description of method) that has been now used to generate transcription factor binding specificity models for most of the high confidence human transcription factors. Sequence data is composed of reads generated with Illumina Genome Analyzer IIX and HiSeq2000 instruments. Samples are composed of single read sequencing of synthetic DNA fragments with a fixed length randomized region or samples derived from such a initial library by selection with a sequence specific DNA binding protein. Originally multiple samples with different "barcode" tag sequences were run on the same Illumina sequencing lane but the released files have been already de-multiplexed, and the constant regions and "barcodes" of each sequence have been cut out of the sequencing reads to facilitate the use of data. Some of the files are composed of reads from multiple different sequencing lanes and due to this each of the names of the individual reads have been edited to show the flowcell and lane that was used to generate it. Barcodes and oligonucleotide designs are indicated in the names of individual entries. Depending of the selection ligand design, the sequences in each of these fastq-files are either 14, 20, 30 or 40 bases long and had different flanking regions in both sides of the sequence. Each run entry is named in either of the following ways: Example 1) "BCL6B_DBD_AC_TGCGGG20NGA_1", where name is composed of following fields ProteinName_CloneType_Batch_BarcodeDesign_SelectionCycle. This experiment used barcode ligand TGCGGG20NGA, where both of the variable flanking constant regions are indicated as they were on the original sequence-reads. This ligand has been selected for one round of HT-SELEX using recombinant protein that contained the DNA binding domain of human transcription factor BCL6B. It also tells that the experiment was performed on batch of experiments named as "AC". Example 2) 0_TGCGGG20NGA_0 where name is composed of (zero)_BarcodeDesign_(zero) These sequences have been generated  from sequencing of the initial non-selected pool. Same initial pools have been used in multiple experiments that were  on different batches, thus for example this background sequence pool is the shared background for all of the following  samples. BCL6B_DBD_AC_TGCGGG20NGA_1, ZNF784_full_AE_TGCGGG20NGA_3, DLX6_DBD_Y_TGCGGG20NGA_4 and MSX2_DBD_W_TGCGGG20NGA_2
@article{jolma2010multiplexed,
  title={Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities},
  author={Jolma, Arttu and Kivioja, Teemu and Toivonen, Jarkko and Cheng, Lu and Wei, Gonghong and Enge, Martin and   Taipale, Mikko and Vaquerizas, Juan M and Yan, Jian and Sillanp{\"a}{\"a}, Mikko J and others},
  journal={Genome research},
  volume={20},
  number={6},
  pages={861--873},
  year={2010},
  publisher={Cold Spring Harbor Lab}
}
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license: openrail
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