RNA Sequencing Analysis of Gene Expression Profiles in WT and CIC-deficient DP Thymocytes
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA727543 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14432206_1.fastq.gz | Fastqsanger.gz | |||
| SRR14432206_2.fastq.gz | Fastqsanger.gz | |||
| SRR14432207_1.fastq.gz | Fastqsanger.gz | |||
| SRR14432207_2.fastq.gz | Fastqsanger.gz | |||
| SRR14432208_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 8 |
Similar Datasets
Project description:Purpose : The goal of this study is to compare the gene expression profiles between wild-type (WT) and CIC-deficient DP thymocytes to understand the molecular mechanisms of CIC regulation of T cell development, especially in DP thymocytes. Methods : DP thymocytes (lin-CD4+CD8+TCRlo (Lineage : CD11b, CD11c, CD19, NK1.1, Gr-1, γδTCR, and TER119)) from thymus were sorted by a MoFlo-XDP (Beckman Coulter). Total RNA was extracted using RiboEX (GeneAll) according to the manufacturer's instructions. The library for mRNA sequencing was generated using the TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina) and sequencing was performed with NovaSeq 6000 (Illumina). Results : Trimmed reads were mapped to the mouse reference genome (mm10 RefSeq) with HISAT2, and the transcripts were assembled using StringTie. A total of 482 differentially expressed genes (DEGs; fold change > 2 and P-value < 0.05) were generated using edgeR. The 263 upregulated genes included known CIC target genes such as Etv1, Etv4, Etv5, Spry4, Spred1, Dusp4, and Dusp6. Conclusions : Our study represents the first comparative analysis of DP thymocytes from WT and hematopoietic lineage cell-specific Cic deficient mice. We concluded that CIC deficiency leads to impaired positive and negative selection, and TCR signaling in DP cells. The attenuation of TCR signaling is caused by derepression of CIC target genes involved in dephosphorylation of ERK.
2021-05-06 | GSE173909 | GEO
Project description:We wanted to test the role of mammalian E proteins E2A and HEB in the development of T cells. Using a conditional deletion system in which these proteins are deleted at the DP stage of T cell development, we compared DP thymocytes deficient for E2A, HEB or both to wild-type thymocytes
2010-01-16 | GSE19923 | GEO
Project description:T cell-specific deletion of PTEN induces premalignancy in CD4+ CD8+ (DP) immature T cells in the thymus, which progresses to the development of mature CD4+ T cell lymphomas in the lymph nodes and spleen. As part of a screen to identify factors that inhibit progression to malignancy, we compared miRNA expression in premalignant PTEN-deficient DP thymocytes versus wild-type controls. DP thymocytes were collected by cell sorting from three 9-week-old, premalignant T cell-specific PTEN-deficient mice (tPTEN-/-) and three littermate controls. miRNA expression was assessed relative to a reference pool generated from an equal mixture of all samples.
2014-04-12 | E-GEOD-56759 | biostudies-arrayexpress
Project description:T cell-specific deletion of PTEN induces premalignancy in CD4+ CD8+ (DP) immature T cells in the thymus, which progresses to the development of mature CD4+ T cell lymphomas in the lymph nodes and spleen. As part of a screen to identify factors that inhibit progression to malignancy, we compared miRNA expression in premalignant PTEN-deficient DP thymocytes versus wild-type controls.
2014-04-12 | GSE56759 | GEO
Project description:murine DP thymocytes transcriptome
| PRJNA804863 | ENA
Project description:Notch1 signaling is an important regulator of cell fate in early stages of T cell development. Because Notch receptors can function redundantly, we sought an approach for inhibiting all endogenous Notch signaling in thymocytes. Upon ligand engagement, Notch receptors undergo two successive proteolytic cleavages, the second involving a Presenilin (PS) containing complex with -secretase activity that releases a small intracellular fragment of Notch. This activated form of Notch (NotchIC) translocates from the membrane to the nucleus, where it acts as a transcription factor, inducing the expression of multiple target genes . Since Presenilins are required for the activation of all four mammalian forms of Notch, we generated mice with deletions of both Presenilin1 and Presenilin2 genes, the only genes encoding Presenilin in the mouse genome. To target Notch inactivation specifically to developing T cells, we introduced Cd4-Cre to mediate Presenilin gene deletion in a tissue- and stage-specific manner. Direct target genes of Notch signaling are largely unknown, and are likely to be cell lineage and stage specific. Therefore in order to identify potential Notch target genes , we compared RNA of thymocytes at the CD4+CD8+ stage of development from H-2b transgenic 5CC7 TCR/ RAG2-deficient / Presenilin1flox/flox /PS2-/- mice, with and without Cd4-Cre. Thymocyte single cell suspensions were generated using 100 µm nylon mesh (PGC Scientifics). DP thymocytes were isolated from RAG2° control or PS1/2° 5CC7 TCR H2bb mice by magnetic bead separation on anti-CD4 coated microbeads (Miltenyi Biotec.). Total RNA was isolated using TRIzol according to manufacturer's instructions (Invitrogen). After quantification and checking for integrity, 1 µg of RNA was subjected to linear amplification. The resulting aRNA was labeled by reverse transcription via Cy5-dCTP incorporation and Cy3-dCTP incorporation. The fluorescent labeled probes were subsequently combined and hybridized on topic-defined PIQORTM Immunology Microarrays Mouse Antisense.
2007-09-14 | E-GEOD-6590 | biostudies-arrayexpress
Project description:Comparing the mRNA expression profiles of c-Myb deficient and c-Myb sufficient Tcra-/- DP thymocytes. Results provide insight into the role of c-Myb in the regulation of survival and differentiation during the pre-selection DP stage where c-Myb expression is abundant during T cell development. DP thymocytes were purified from four c-Myb deficient and four c-Myb sufficient mice over magnetic columns. RNA from each biological replicate was individually hybridized onto a total of eight MOE430 2.0 Chips.
2010-01-21 | E-GEOD-19528 | biostudies-arrayexpress
Project description:Comparing the mRNA expression profiles of c-Myb deficient and c-Myb sufficient Tcra-/- DP thymocytes. Results provide insight into the role of c-Myb in the regulation of survival and differentiation during the pre-selection DP stage where c-Myb expression is abundant during T cell development.
2010-01-22 | GSE19528 | GEO
Project description:Notch1 signaling is an important regulator of cell fate in early stages of T cell development. Because Notch receptors can function redundantly, we sought an approach for inhibiting all endogenous Notch signaling in thymocytes. Upon ligand engagement, Notch receptors undergo two successive proteolytic cleavages, the second involving a Presenilin (PS) containing complex with -secretase activity that releases a small intracellular fragment of Notch. This activated form of Notch (NotchIC) translocates from the membrane to the nucleus, where it acts as a transcription factor, inducing the expression of multiple target genes . Since Presenilins are required for the activation of all four mammalian forms of Notch, we generated mice with deletions of both Presenilin1 and Presenilin2 genes, the only genes encoding Presenilin in the mouse genome. To target Notch inactivation specifically to developing T cells, we introduced Cd4-Cre to mediate Presenilin gene deletion in a tissue- and stage-specific manner. Direct target genes of Notch signaling are largely unknown, and are likely to be cell lineage and stage specific. Therefore in order to identify potential Notch target genes , we compared RNA of thymocytes at the CD4+CD8+ stage of development from H-2b transgenic 5CC7 TCR/ RAG2-deficient / Presenilin1flox/flox /PS2-/- mice, with and without Cd4-Cre. Keywords: presenilin, thymocytes, mouse
2007-09-14 | GSE6590 | GEO
Project description:Review on the role of Bcl11b in thymus and periphery and impact on diseases RNA was extracted from DP thymocytes of bcl11bf/fCd4cre/tcra-/- and tcra-/- mice. Tcra-/- mice only have preselected DP thymocytes. Such mice were used to determine the role of Bcl11b before selection, considering the defective positive selection in bcl11bf/fcd4cre mice. RNA was isolated and submitted for library generation and microarray analysis to determine expression profile of bcl11b-/- preselected DP thymocytes.
2014-04-12 | E-GEOD-56714 | biostudies-arrayexpress