Near-saturation Akata and Mutu I cell cultures were diluted with equal volumes of fresh RPMI 1640 (with 10% FBS and 0.5% pen/strep) one day before induction. To induce reactivation, cells were pelleted and resuspended at a concentration of 106 cells/ml in fresh RPMI 1640 (with 10% FBS and 0.5% pen/strep) plus either 10μg/ml anti-human IgG (Sigma-Aldrich, catalog no. I2136) (for Akata cells) or 10 μg/ml anti-human IgM (Sigma-Aldrich, catalog no. I0759) (for Mutu cells). For Pacific Biosciences Iso-Seq, cells were harvested at 20 and 24 h post-induction, for Illumina RNA-Seq, cells were harvested at 0 min, 5 min, 30 min, 1 h, 2 h, 4 h, 8 h, 24 h and 48 h post-induction and for deepCAGE, cells were harvested at 24 h post-induction. For qRT-PCR, cells were harvested at 0 and 24 h (Akata) or 0 and 48 h (Mutu).
Iso seq
Manufactured by Illumina
Iso-Seq is a long-read sequencing technology developed by Illumina. It enables the generation of full-length transcript sequences, providing comprehensive information about isoform diversity and expression levels within a sample.
Automatically generated - may contain errors
2 protocols using iso seq
1
Epstein-Barr Virus Reactivation Assay
2
Whole genome sequencing of Ceratopteris richardii
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We sequenced Ceratopteris richardii genotype Hn-n using a range of sequencing technologies, including single-molecule real-time long-read sequencing from Pacific Biosciences (PacBio), chromosome conformation capture using HiC sequencing, Illumina short-read sequencing, bisulfite sequencing, PacBio Iso-Seq and RNA-seq (Supplementary Table 4 ). High molecular mass DNA was isolated from fresh leaf tissue at the Arizona Genomics Institute. Sequencing reads were collected using Illumina and PacBio platforms. Illumina and PacBio reads were sequenced at the Department of Energy Joint Genome Institute in Walnut Creek, CA, USA and the HudsonAlpha Institute for Biotechnology in Huntsville, AL, USA. Illumina reads were sequenced using the Illumina NovaSeq platform, and the PacBio reads were sequenced using the SEQUEL platform. Before assembly, Illumina fragment reads were screened for PhiX contamination. Reads composed of >95% simple sequences were removed. Illumina reads <50 bp after trimming for adaptor and quality (q < 20) were removed. The final read set consists of 2,438,428,350 reads for a total of 47.27× of high-quality Illumina bases. For the PacBio sequencing, a total of 93 PB chemistry 2.1 chips (10-h movie time) was sequenced with a sequence yield of 777.1 Gb, with a total coverage of 69.02× (Supplementary Table 5 ).
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