Transcriptomics

Dataset Information

348

Single-cell RNA-seq of murine medullary thymic epithelial cells (mTECs)


ABSTRACT: The capability of T cells for discrimination between self and non-self peptides is based on rigorous negative selection of developing thymocytes by medullary thymic epithelial cells (mTECs). The mTECs purge autoreactive T cells by expression of cell-type specific genes referred to as tissue-restricted antigens (TRAs), therefore, the expression patterns of TRA genes can help understand development of mTECs and the regulatory mechanism during the development. We use single-cell RNA-sequencing to resolve patterns of TRA expression, and to elucidate how these patterns are changed during mTEC development. Thymi were collected from 2 and 4 week-old wild-type male and female mice. The mTEC suspension obtained from sorting was loaded onto the Fluidigm C1 platform using mediumsized capture chips (10-17m cells). External RNA Control Consortium (ERCC) spike-ins (Ambion, Life Technologies) were included in the lysis buffer. Reverse transcription and cDNA preamplification were performed using the SMARTer Ultra Low RNA kit (Clontech). The cDNA libraries for sequencing were prepared and libraries from 96 single cells were pooled and subsequently purified; pooled samples were sequenced on an Illumina HiSeq 2500 instrument.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Mus musculus  

SUBMITTER: Xiuwei Zhang   Tapio Lönnberg   Ricardo J Miragaia  

PROVIDER: E-MTAB-5727 | ArrayExpress | 2018-05-08

SECONDARY ACCESSION(S): ERP022822

REPOSITORIES: ArrayExpress, ENA

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