Raw counts for scientific article: "A protocol for low-input RNA-sequencing of patients with febrile neutropenia captures relevant immunological information" Victoria Probst*1, Lotte Møller Smedegaard*2, Arman Simonyan1, Yuliu Guo1, Olga Østrup1, Kia Hee Schultz Dungu2, Nadja Hawwa Vissing2, Ulrikka Nygaard2 and Frederik Otzen Bagger1 *Shared first authorship Data description: The raw counts are from 88 samples of 22 patients with leukaemia and suspected infection sequenced by a low-input protocol (Takara SMART-seq HT) (96% succeeded) and 15 of these were also processed by the standard protocol (Truseq). CLI.CSV: Raw counts of control samples processed using a low input RNA sequencing protocol. 15 samples processed by the low-input protocol. CRNA.CSV: Raw counts of control samples processed using a standard RNA sequencing protocol. 15 samples processed by the standard protocol. FEB.CSV: Raw gene counts from patients. 88 samples processed by the low input protocol. 4 samples failed sequencing.