Hi-C data from the filamentous fungus Podospora anserina
Hi-C experiments were performed in duplicate, using nuclei purified from wild-type fungal mycelium.  Preparation of crosslinked nuclei: Frozen fixed mycelium was ground manually into powder using a mortar and pestle with liquid nitrogen and placed on ice with 600 µL of HiC buffer (Tris-HCl pH8 15 mM, KCl 5 mM, NaCl 15 mM, MgCl2 3 mM, Igepal CA-630 0.2 %, Roche mini EDTA-free protease inhibitor cocktail cOmplete™ Protease inhibitor Cocktail 1X (Roche®) in 1.5 mL Diagenode microtubes. After eight cycles of gentle sonication (mode “low” – 15s ON/30s OFF) on a Bioruptor Standard waterbath Sonicator (Diagenode), samples were filtered on Sefar Nitex (100 µm) by centrifugating 10 min at 4,700g and 4°C. Pellets were then carefully resuspended in one mL of nuclei buffer (Tris-HCl pH8 15 mM, sucrose 250 mM, KCl 5 mM, MgCl2 1 mM, glycerol 40 %, PMSF 1 mM, Roche mini EDTA-free protease inhibitor cocktail (cOmplete™ Protease inhibitor Cocktail 1X (Roche®) and centrifuged at 7,000g for 5 min and 4°C. After a final wash with 0.5 mL of nuclei buffer, nuclei pellets were collected and stored at -80°C until in situ HiC sample preparation.   In situ HiC, library construction and Illumina sequencing: HiC samples were generated using the Arima-HiC kit (Arima Genomics, Carlsbad, United States) according to supplier recommendations. Hi-C libraries were created using KAPA Library Amplification Kit with Primer Mix (Roche sequencing, United states). Hi-C libraries were sequenced on Illumina NextSeq2000 (GenomEast platform, a member of the 'France Génomique' consortium (ANR-10-INBS-0009)), producing 2x100 bp paired-end reads. Analysis were performed for two biological replicates
Hi-C experiments were performed in duplicate, using nuclei purified from wild-type fungal mycelium.  Preparation of crosslinked nuclei: Frozen fixed mycelium was ground manually into powder using a mortar and pestle with liquid nitrogen and placed on ice with 600 µL of HiC buffer (Tris-HCl pH8 15 mM, KCl 5 mM, NaCl 15 mM, MgCl2 3 mM, Igepal CA-630 0.2 %, Roche mini EDTA-free protease inhibitor cocktail cOmplete™ Protease inhibitor Cocktail 1X (Roche®) in 1.5 mL Diagenode microtubes. After eight cycles of gentle sonication (mode “low” – 15s ON/30s OFF) on a Bioruptor Standard waterbath Sonicator (Diagenode), samples were filtered on Sefar Nitex (100 µm) by centrifugating 10 min at 4,700g and 4°C. Pellets were then carefully resuspended in one mL of nuclei buffer (Tris-HCl pH8 15 mM, sucrose 250 mM, KCl 5 mM, MgCl2 1 mM, glycerol 40 %, PMSF 1 mM, Roche mini EDTA-free protease inhibitor cocktail (cOmplete™ Protease inhibitor Cocktail 1X (Roche®) and centrifuged at 7,000g for 5 min and 4°C. After a final wash with 0.5 mL of nuclei buffer, nuclei pellets were collected and stored at -80°C until in situ HiC sample preparation.   In situ HiC, library construction and Illumina sequencing: HiC samples were generated using the Arima-HiC kit (Arima Genomics, Carlsbad, United States) according to supplier recommendations. Hi-C libraries were created using KAPA Library Amplification Kit with Primer Mix (Roche sequencing, United states). Hi-C libraries were sequenced on Illumina NextSeq2000 (GenomEast platform, a member of the 'France Génomique' consortium (ANR-10-INBS-0009)), producing 2x100 bp paired-end reads. Analysis were performed for two biological replicates
Universite Paris-Saclay