library_construction_protocol: Total RNA from the cell lines (MDA-MB-468-RR shctrl and shHNRNPL-1) were extracted using a NucleoSpin RNA kit (740955.50 Macherey-Nagel). IMCR-seq libraries are prepared as follows: A total of 4 tubes were taken and each tube contained: 500ng of total RNA (max 6uL), 2 uL 100 uM random N6 (NEB #S1230S), and 2 uL ddH2O. The tubes were incubated at 72°C for 5 minutes then cooled down to 4°C with 0.1°C/s ramp. Each tube was then taken and the following were added to reach a total volume of 40 uL: 8 ul 5X Induro Buffer, 4.8 ul MgCl2 (NEB B9021S: 25 mM), 2 ul 10 mM dNTPs, 2 ul Induro RT (NEB M0681: 200 units/ul), and 13.2 ul ddH2O. The tubes were incubated at: 23°C for 10 minutes, 30°C for 5 minutes, warmed up to 55°C with 0.1°C/sec ramp, 55°C for 1 hour, and 95°C for 1 minute to heat inactivate the RT. All four tubes were collected for a total volume of 160 uL and then mixed with 40 uL water and 200 uL AMPure beads (A63880, Beckman Coulter). The tubes were put on a rotator for 10 minutes. The tubes were placed on a magnetic rack to remove the liquid on the magnet and then resuspended in 300 uL 10mM Tris-HCl pH:8.0, with 72 uL Mg500PEG5 solution (500mM MgCl and 5% PEG8000 in 10mM Tris-HCl pH:8.0). The tubes were on the rotator for 30 minutes, placed on magnetic rack to remove the liquid, washed with fresh 80% EtOH and eluted the cDNA in 33 uL water. A 5uL aliquot of the cDNA was taken and mixed with 5 ul 10X Phi29 Buffer, 5 ul 10mM dNTPs, 2.5 ul 1mM Exo-resistant N6 primers (SO181 Thermo Scientific), 2 ul phi29 (M0269 NEB), and 30.5 ul ddH2O. This was done for a total of 6 tubes and all of them were incubated at 30°C for 6 hours. All tubes were combined together along with 15 ul NEBuffer 2 (B7002S NEB), 100 uL ddH2O, and 75 uL T7 Endonuclease I (M0302S NEB). The tube is incubated at 37°C for 1 hour. 500 uL of AMPure beads will be added to the mixture and incubated on the rotator for 10 minutes. The liquid is removed by placing the tube on the magnetic stand and the beads are mixed with 300 ul 10mM Tris-HCl pH:8.0 and 72 ul Mg500PEG5 solution (500mM MgCl and 5% PEG8000 in 10mM Tris-HCl pH:8.0). The tube is placed on the rotator for 30 minutes. Lastly the liquid is removed with the magnetic stand, beads are washed with fresh 80% EtOH twice, and finally eluted in 60ul water. 1.5ug of DNA from IMCR-seq was used for library preparation using Nanopore ligation sequencing kit (SQK-LSK114) according to the manufacturer's protocol, with the following specific alterations.. During library preparation, pipetting of DNA samples was avoided to minimize shearing of long DNA. Incubation time for all steps was extended by 5-10 minutes. For last Ampure clean-up set, 100uL was used. Long Fragment Buffer was used twice to wash. And all elutions were done at 55C. All libraries were sequenced on R10 flow cell on MinION for 24 hours with a minimum read cutoff of 1 kilobase.