Example Datasets¶
To test all the functionalities present in HiTIPS, we have uploaded several datasets to the BioImage Archive, under accession number S-BIAD1043. These datasets were also used for the Preprint, and a more detailed explanation of the results can be found in the paper.
The full description of the datasets can be found on its BioImage Archive page as well as in the Preprint. However, we provide a brief description of the data here.
There are three subfolders within this dataset that correspond to figures 3, 4, and 5 in the Preprint:
Fig. 3: 3D maximally projected images of HCT116-RAD21-AID cells stained with DNA FISH probes targeted to the 5’ and 3’ boundaries of the EGFR TAD, respectively.
Fig. 4: Images of reverse-transfected HCT116-Cas9 cells with siRNA oligos against the NCAPH2 gene, or a scrambled negative siRNA control in 384-well plates. Cells were fixed and stained with DAPI for nuclei segmentation and with a CENPC-specific antibody to visualize centromeres. Stained cells were then imaged in 3D and maximally projected.
Fig. 5: This folder includes nine subfolders of human bronchial epithelial cell lines (HBEC3-KT) with a monoallelic insertion of an MS2 array in the intron of the model genes. To enable visualization of the nascent RNA, the viral MS2 capsid protein (MCP) fused to GFP, and an NLS (nuclear localization signal) tag were stably introduced into the cells using lentiviral expression vectors.