Myeloid cell programming in patients with non-medullary thyroid carcinoma

1 Dataset 2 Publications

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Dataset ID	Description	Technology	Samples
EGAD00001008108	This dataset contains single-cell RNA sequencing data from patients with thyroid cancer (n=7), multinodal Goiter (n=3) and healthy individuals (n=5). Mononuclear cells were taken from both the peripheral blood and the bone marrow compartments. We used a pooled single-cell design where multiple individuals were pooled in a single sample for sequencing (NextSeq 500-V2) and later demultiplexed using their genotype data. Associated metadata contains information on the phenotypes per individual, the pooling design and the linkage between the supplied files and sequenced pools. Due to limitations from EGA in uploading single-cell data, the raw fastq files were processed as follows: (i) I1/I2/R1/R2 fast files were concatenated over the different lanes. (ii) Concatenated I1 and I2 files were interleaved, as were the concatenated R1 and R2 files to generate two fastq files per pool containing all the information. To interleave the fastq files, the BBmap tool bbmap/reformat.sh was used, which can also be used to de-interleave the files.	NextSeq 500	7

Publications	Citations
Reprogramming of myeloid cells and their progenitors in patients with non-medullary thyroid carcinoma. Rabold K, Zoodsma M, Grondman I, Kuijpers Y, Bremmers M, Jaeger M, Zhang B, Hobo W, Bonenkamp HJ, de Wilt JHW, Janssen MJR, Cornelissen LAM, van Engen-van Grunsven ICH, Mulder WJM, Smit JWA, Adema GJ, Netea MG, Li Y, Xu CJ, Netea-Maier RT. Nat Commun 13: 2022 6149	10
Single-cell immune aging clocks reveal inter-individual heterogeneity during infection and vaccination. Li W, Zhang Z, Kumar S, Botey-Bataller J, Zoodsma M, Ehsani A, Zhan Q, Alaswad A, Zhou L, Grondman I, Koeken V, Yang J, Wang G, Volland S, Crişan TO, Joosten LAB, Illig T, Xu CJ, Netea MG, Li Y. Nat Aging 5: 2025 607-621	7