Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell RNA-sequencing of thymic myeloid cells from Csf1rgfp/gfp (MaFIA) and Cd11cyfp/yfp mice

ABSTRACT: Single-cell RNA-sequencing of thymic myeloid cells from Csf1rgfp/gfp (MaFIA) and Cd11cyfp/yfp mice

PROVIDER: PRJNA769128 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR16229179_1.fastq.gz	Fastqsanger.gz
	SRR16229179_2.fastq.gz	Fastqsanger.gz
	SRR16229180_1.fastq.gz	Fastqsanger.gz
	SRR16229180_2.fastq.gz	Fastqsanger.gz
	SRR16229181_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Single-cell RNA-sequencing of thymic myeloid cells from Csf1rgfp/gfp (MaFIA) and Cd11cyfp/yfp mice

Project description:Purpose: The goals of this study are to identify different sub-populations of mouse thymic myeloid cells and to compare their differentially expressed genes. Methods: Single-cell mRNA libraries of EGFP-positive and YFP-positive cells from 5-weeks-old Csf1rgfp/gfp and 9-weeks-old Cd11cyfp/yfp mice were generated with Chromium X (10X Genomics), in two biological replicates, each, followed by sequencing using Illumina NovaSeq. The sequence reads that passed quality filters were aligned against Ensembl GRCm39 mouse genome assembly with GRCm39.104 annotation by STARsolo, downsampled by DropletUtils, and analyzed by SingleCellExperiment. Results: we obtained about 1 billion sequence reads per sample, except for 1 sample (MaFIA rep1), which contained reads mostly derived from mitochondria and was excluded from downstream analysis. In the other three samples, over 90% of reads had valid barcodes and reached sequencing saturation about 70%. Over 80% of reads could be mapped to mouse genome uniquely (build GRCm39). Each sample had estimated number of cells over 6,000. Downstream analysis identified different subsets of thymic macrophages and dendritic cells, along with small amount of plasmacytoid dendritic cells, T cells and B cells, all of these populations could be clearly clustered and presented on tSNE or UMAP. Conclusions: We could identify 4 populations of dendritic cells, 2 populations of macrophages and one monocyte population in the thymus. This dataset is a rich resource for exploring the diversity of thymic myeloid cells at single cell resolution.

2021-11-03 | GSE185460 | GEO

Expression data from sorted Id3-GFP hi Id2-YFP int and Id3-GFP lo Id2-YFP hi activated CD8 T cells

Project description:During an immune response, CD8 T cells fall along a gradient of memory potential, but the regulators of these fate decsisions are not well understood. We utlized Id3-GFP and Id2-YFP reporter mice to elucidate the role of Id3 and Id2 during early CD8 T cell differentiation by gene expression. Id3-GFP hi Id2-YFP int or Id3-GFP lo Id2-YFP hi OT-I cells were sorted into trizol at day 6 of VSV-OVA infection and analyzed by microarray

2011-10-06 | E-GEOD-32675 | biostudies-arrayexpress

Expression data from sorted Id3-GFP hi Id2-YFP int and Id3-GFP lo Id2-YFP hi activated CD8 T cells

2011-10-07 | GSE32675 | GEO

Gene expression profiling of perinatal or adult regulatory T cells (Tregs)

Project description:A comparative analysis of gene expression of 3 different experiments; 1. Perinate or adult-tagged GFP+YFP+ and bulk GFP+YFP- Tregs, 2. FL or BM-derived Tregs 3. Perinate or adult thymic Tregs.

2015-02-27 | GSE66332 | GEO

YFP+PDGFRa+ and YFP+PDGFRa– stromal cells isolated from the small intestine of LTBRfloxedPDGFRa/YFP mice

Project description:YFP+PDGFRa+ and YFP+PDGFRa– stromal cells isolated from the small intestine of LTBRfloxedPDGFRa/YFP mice

| PRJNA824320 | ENA

RNA-seq of Tgfbr2-deficient thymic iNKT1 cells

Project description:The goal of this study was to identify genes that are regulated by TGF-b-signaling in thymic iNKT1 cells. To specifically target Tgfbr2 deletion to iNKT1 cells we created Tbx21Cre bacterial artifical chromosome transgenic mice with a Rosa26-floxed-stop-YFP reporter and floxed alleles of Tgfbr2 . We examined gene expression by RNA-sequencing in sorted iNKT1 cells (CD1d-Tet-PBS57+ YFP+) from Ctrl (Tbx21Cre; Rosa26-YFP+) and cKO (Tbx21Cre; Rosa26-YFP+; Tgfbr2F/F) mice. Reads were aligned to the mm10 reference genome using STAR v2.5.2. 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 TGF-b was required for normal numbers of iNKT1 cells and induced a classic TGF-b gene program in thymic iNKT1 cells but did not regulate expression of Tbx21 (T-bet).

2022-10-13 | GSE215128 | GEO

Differential expression of Hdc-GFP+/hiCD11b+Gr1lo vs Hdc-GFP+/hiCD11b+Gr1hi myeloid cells from mouse bone marrow

Project description:Bone marrow Hdc-GFP+/hiCD11b+Gr1lo vs Hdc-GFP+/hiCD11b+Gr1hi myeloid cells were isolated from bones from histidine decarboxylase (Hdc) green fluorescent protein (Hdc-GFP) mice. Hdc-GFP+/hiCD11b+Gr1hi cells and Hdc-GFP+/hiCD11b+Gr1/lo cells were sorted by combinations of GFP and myeloid cell surface markers CD11b and Gr1 and their differential mRNA expression compared with Affymetrix microarrays.

2019-04-01 | GSE80143 | GEO

RNAseq of renal dendritic cells from adult Clec9a-Cre Rosa-YFP mice

Project description:We use bulk RNA sequencing of sorted cells to characterize the gene expression profiles of renal dendritic cell (DC) subsets, cDC1 and cDC2, as well as MHCII+CD64+ F4/80hi and MHCII+CD64+ CD11bhi cells. Splenic DCs and red pulp macrophages serve as reference populations for a macrophage-like or DC-like phenotype. By sorting YFP+/YFP- F4/80hi or YFP+/YFP- CD11bhi cells from Clec9a-Cre Rosa-YFP mice we aim to reveal transcriptional differences between YFP-labelled and unlabelled cells. We showed that F4/80hi cells resemble macrophages on a transcriptional level, despite their DC origin, and that renal CD11bhi cells are a transcriptionally unique subset. However, we were not able to reveal differences between YFP+ and YFP- populations.

2020-01-31 | GSE131751 | GEO

YFP+ and YFP– stromal cells isolated from the small intestine of LTBRYFP mice

Project description:YFP+ and YFP– stromal cells isolated from the small intestine of LTBRYFP mice

| PRJNA824321 | ENA

RNA-Seq of mouse genotypes Ptf1a^YFP/+ and Ptf1a^YFP/YFP

Project description:This experiment used RNA-Seq technology to explore gene expression in mouse Ptf1a^YFP/+ [het] FACS sorted cells at E11.5 (early pancreatic Multipotent Progenitor Cells) and E15.5 (nascent acinar cells) as well as in Ptf1a^YFP/YFP [null] at E11.5 (delayed early MPC). 376 selected genes identified as differentially expressed between early pancreatic MPC and nascent acinar cells or between early pancreatic and delayed early MPCs have then been examined by Taqman Low Density Arrays (TLDAs) with Real Time RT-PCR for each 1-day time point from E10.5 to E15. 5 in Ptf1a^YFP/+ [het] and for E10.5 and E11.5 in Ptf1aYFP/YFP [null] . Finally, 94 genes identified in the first phase of TLDAs (including 2 endogenous control, Gapdh and 18S) were analyzed in a second TLDA phase for each 1-day time point from E10.5 to -E18.5 in Ptf1a^YFP/+ [het] and for E11.5 in Ptf1aYFP/YFP [null] with biological replicates (n>=3) for each time point.

2014-11-15 | E-MTAB-449 | biostudies-arrayexpress

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