Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression profiles of primary LN3 T-ALL cells and wild-type T-lineage cells from the thymus and spleen

ABSTRACT: Gene expression profiles of primary LN3 T-ALL cells and wild-type T-lineage cells from the thymus and spleen

PROVIDER: PRJNA631158 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11731900_1.fastq.gz	Fastqsanger.gz
	SRR11731900_2.fastq.gz	Fastqsanger.gz
	SRR11731901_1.fastq.gz	Fastqsanger.gz
	SRR11731901_2.fastq.gz	Fastqsanger.gz
	SRR11731902_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

Gene expression profiles of primary LN3 T-ALL cells and wild-type T-lineage cells from the thymus and spleen

Project description:T cell acute lymphoblastic leukemia (T-ALL) develops spontaneously in the thymus of LN3 mice and infiltrates secondary organs, including spleen. We found leukemia-associated myeloid cells from the spleens of overtly sick LN3 mice significantly support survival of splenic T-ALL cells, but not tumor-free splenic CD8+ T cells, in vitro. To determine gene signatures induced in T-ALL cells by tumor-supportive myeloid cells, but not induced in wild-type T cells, we transcriptionally profiled primary LN3 T-ALL cells from leukemic mice and T-lineage cells from tumor-free mice, isolated from thymuses and spleens, via RNA-sequencing.

2020-07-22 | GSE150096 | GEO

RNA-seq of wild-type iNKT1 cells from thymus, liver and spleen

Project description:The goal of this study was to compare the gene expression program of iNKT1 cells in the thymus, liver and spleen. To identify iNKT1 cells we created Tbx21Cre bacterial artifical chromosome transgenic mice with a Rosa26-floxed-stop-YFP reporter. We examined gene expression by RNA-sequencing in sorted iNKT1 cells (CD1d-Tet-PBS57+ YFP+) from the thymus, liver and spleen. Reads were aligned to the mm10 reference genome using Tophat v 2.1.0. Reads were assigned to genes using the htseq-count tool from HTSeq v 0.6.1 and gene annotations from Ensembl release 78. Differential expression was calculated across 3 independent replicates by EdgeR. We found that iNKT1 cells from all tissues had very similar gene expression programs but that there were subtle difference in each tissue that may have relevance for survival and function in these tissues.

2022-10-15 | GSE215338 | GEO

RNA-seq of wild-type iNKT1 cells from thymus, liver and spleen

Project description:RNA-seq of wild-type iNKT1 cells from thymus, liver and spleen

| PRJNA889806 | ENA

Proteomic characterization for thymus and spleen in immuno-suppressed mice with 10-hydroxydec-2-enoic acid treatment

Project description:In order to elucidate the molecular basis of 10-hydroxydec-2-enoic acid regulating immunity, immuno-suppressed mice were generated by cyclophosphamide induction, then treated by 10-HDA, and the proteomes of the thymus and spleen, the immuno-organs, were characterized with a mass spectrometry-based strategy.

2019-12-29 | PXD016902 |

Single-cell immune profiling reveals thymus-seeding populations, T cell commitment, and multi-lineage development in the human thymus

Project description:Development of T lymphocytes in the thymus has been widely studied in mice, but our insights into human T cell development are scarce. Using a combination of single-cell techniques and functional assays, we report deep immune profiling of human T cell development, with a focus on the initial development stages of pre-lineage commitment. We identified three thymus-seeding progenitor populations that also have a counterpart in the bone marrow. We found that the human thymus physiologically supports development of monocytes, DCs, NK cells, and limited development of B lymphocytes. These insights are important to monitor and guide regenerative therapies after hematopoietic stem cell transplantation.

2022-08-01 | GSE195812 | GEO

RNA-seq analysis of regulatory T cells in thymus, placenta, spleen and white adipose tissue of pregnant mice

Project description:In this study we performed RNA sequencing to determine and compare the transcriptome of regulatory T cells (Tregs) present in the thymus, placenta, spleen and white adipose tissue (FAT) of pregnant mice. We further assessed how the expression of the receptor Rank in the thymic medullary epithelia affects the transcriptional program of these Treg populations. For the isolation of viable and bona fide Tregs, we first generated RankWt (wild type control mice) and RankΔFoxn1 (which lack expression of Rank in the thymic epithelia) and further crossed them to mice that express GFP from the Foxp3 promoter. Neuropilin1 was used to mark the thymic origin of the Tregs. Equal numbers of Tregs (280 cells) were sorted as CD45-CD8-CD4+GFP+Neuropilin1High cells from the thymus and placenta of RankWtFoxp3GFP/GFP and RankΔFoxn1Foxp3GFP/GFP pregnant females at E17.5 (both samples from the same female; n=4 females per genotype). Thymus Tregs from non-pregnant littermate female mice for each genotype cohort were also studied. To increase robustness, the 280 placental Tregs were purified from 5 individual placentas per pregnant female (56 Tregs/placenta). Our study is the first one to determine the transcriptome of thymus and placenta Tregs during pregnancy and reveals that, partially dependent on Rank expression in the thymic epithelia, placental-resident Tregs are molecularly distinct from thymic Tregs. In a separate experiment with different pregnant mice than those used for thymus and placenta analysis, VAT Tregs (20-30 cells) and splenic Tregs (150 cells) were sorted (both samples from the same female) by using the same mouse lines (Rank Wt and RankΔFoxn1), embryological days of analysis (E17.5) and sorting strategies.

2020-10-21 | GSE97666 | GEO

Characterization of mature Tregs in the thymus

Project description:Using Foxp3.RFP Rag.GFP reporter mice, mature Tregs in the thymus were characterized by performing RNA sequencing on Rag.GFP– and Rag.GFP+ Tregs that were isolated from the thymus and Tregs isolated from the spleen

2020-07-27 | GSE153154 | GEO

Study of differential gene expression in the thymus, spleen and lymphatic nodes of susceptible and resistant mice during T. cruzi infection

Project description:This is a time course study of differential gene expression in the thymus and spleen of susceptible (Balb/c) and resistant (C57BL/6) mice during experimental Trypanosoma cruzi infection. There is a special interest in the expression of galectins, glycosyltransferases, neuraminidases and chemokines in the gene expression patterns. Mice were infected with 1000 trypomastigotes of T. cruzi strain Y i.p. Organs (thymus and spleen) were removed aseptically at days 0, 7, 14, 21 and 28 post-infection. The time points have been selected as they allow the following of the acute phase of the disease with the peak of parasitemia (between 7 and 14 days), and the chronic phase (more than 21 days post infection). RNA from at least three animals from the same data point was pooled to normalize internal variability. Total RNA was isolated as per recommended protocol and shipped to the Core E site. Samples were hybridized to the GLYCOv3 array.

2011-04-29 | E-GEOD-28921 | biostudies-arrayexpress

Study of differential gene expression in the thymus, spleen and lymphatic nodes of susceptible and resistant mice during T. cruzi infection

2011-04-29 | GSE28921 | GEO

Identification of age-related changes in gene expression and chromatin accessibility in T cells from thymus to periphery (44K)

Project description:Aging of immune system is characterized by progressive decline of physiological and cellular function of T cells. Recent studies of naïve T cells from young and old mice have identified age-related altered gene expressions but the mechanisms underlying age associated changes of naïve T cells remain poorly understood. Here we compared the transcriptome and chromatin accessibility in mature CD4 and CD8 thymocytes and in naïve CD4 and CD8 T cells of spleen between young (6-8 weeks) and old (79-121 weeks) C57Bl/6 mice. We used Agilent microarray method and identified the age-related altering gene expressions 1) only in mature CD4 and CD8 T cell from thymus, 2) shared by both thymus and spleen naïve T cells, and 3) only in naïve T cells from spleen. The shared changes include increased chemokine and chemokine receptor expressions and decreased cell cycle regulator expression. We further analyzed the chromatin basis of altered gene expression using Assaying Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) between young and old mice. We have identified age-related changes of chromatin accessibility in T cells from thymus and spleen, and some correlated changes between gene expression and chromatin accessibility. Overall, we observedmore age-related alterations of gene expression and chromatin accessibility inthymus than in spleen, suggesting some age-related changes of T cells in thymus did not retain in periphery. Together, our findings have identified tissue specific altered gene expressions and chromatin status in T cells during aging and further study of these altered genes will shed new insights into the mechanisms underlying these age-related changes.

2021-03-19 | GSE112390 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data