Bacterial 16S and fungal ITS2 rRNA data from adult humans with lymphoma treated with CAR T-cell therapy
Stool samples (n=106) collected from NYU Langone Health adult patients with lymphoma treated with CAR T-cell therapy; bacterial DNA extraction with Qiagen PowerSoil Pro kit; samples prepared for 16S rRNA gene sequencing by the NYU Genome Technology Center using KAPA HiFi polymerase to amplify the V4 region of the 16S rRNA gene and sequenced on Illumina MiSeq using MiSeq Reagent Kit v2. Samples prepared for 16S rRNA gene sequencing were pooled equimolar and sequenced using 2 x 150bp paired-end protocol for 6 patients' samples (n=57) and 2 x 250bp for 8 patients' samples (n=49). Fungal DNA was extracted with phenol:chloroform:isoamyl alcohol (PCI). ITS2 region of the ITS region was amplified by PCR using uniquely barcoded ITS3 and ITS4. PCR reactions were performed according to the Earth Microbiome protocol. Samples were pooled equimolar and sequenced on MiSeq platform using 2x300bp paired-end protocol for all samples (n=106).