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RNA Sequencing of Tgd17 progenitors

ABSTRACT: RNA Sequencing of Tgd17 progenitors

PROVIDER: PRJNA487340 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7740910.fastq.gz	Fastqsanger.gz
	SRR7740920.fastq.gz	Fastqsanger.gz
	SRR7740911.fastq.gz	Fastqsanger.gz
	SRR7740921.fastq.gz	Fastqsanger.gz
	SRR7740912.fastq.gz	Fastqsanger.gz

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RNA Sequencing of Tgd17 progenitors

Project description:Tgd17 cells are critical immune effector cells that exit the thymus committed to peripheral IL-17 responses, but whether the development of cells into this lineage is pre-programmed or driven by instructive TCR signals is unresolved. Using newly generated reporter mice for a gene necessary for Tgd17 cell development, Sox13, we identified progenitor cells (known as DN1d cells) that expressed high levels of Sox13 prior to expression of the TCR. To interrogate whether DN1d cells could be a candidate Tgd17-biased progenitor, whole transcriptome RNA sequencing was performed on these progenitors as well as canonical T cell progenitors thought to generate all T cell subsets and the proposed progeny Tgd17 cells. The data demonstrated that DN1d cells most closely resemble Tgd17 cells at a transcriptome level, while canonical T cell progenitors were very different from both DN1d cells and Tgd17 cells. Further studies demonstrated that DN1d cells generated Tgd17 cells in developmental assays, and that the transcriptional signature of DN1d cells is established and maintained independently of TCR expression or signaling but is instead dependent on HMG transcription factors SOX13 and TCF1. Thus, T cell lineage identity can be pre-programmed at the progenitor level and is not necessarily specified by specific TCR signals.

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Single-cell RT-PCR analysis of Tgd17 progenitors

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Restriction of innate Tgd17 cell plasticity by an AP-1 regulatory axis [CUT&Run]

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Single-cell RT-PCR analysis of Tgd17 progenitors

Project description:The indicated thymic progenitor population was sorted via FACS and then loaded into a Fluidigm C1 small cell capture chip for single-cell capture, lysis, reverse transcription, and preamplification. Preamplified products were analyzed on a BioMark HD with EvaGreen chemistry. The genes analyzed were selected based on bulk RNA sequencing data and/or prior publications, including genes relevant for gamma/delta T cells and T cell progenitors. B6=C57BL/6J, Rag=B6.Rag1-/-, Tcrd=B6.Tcrd-/-, DN1d=Live/TCRd-/Lin-/CD44+/CD25-/CD24+/cKit-, DN2=Live/TCRd-/Lin-/CD44+/CD25+/cKit+, cKit-=Live/TCRd-/Lin-/CD44+/CD25-/cKit-. Lin=CD3/CD8/CD11b/CD11c/CD19/Gr-1/NK1.1/TCRb/Ter-119 Sample naming nomenclature is as follows: MouseLine_CellPopoulation_DateCaptured_CaptureChamber_CellNumberInChamber

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