Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell RNA-seq analysis of mouse tracheal epithelial cells from wild-type and Tppp3 knockout mice

ABSTRACT: Single-cell RNA-seq was performed on tracheal epithelial cells from wild-type and Tppp3 knockout mice using the 10x Genomics Chromium Single Cell 3′ v3 platform. Seven major epithelial cell types were identified, and no novel cell type was detected in Tppp3 KO trachea. Expression of cilia-related genes (Mcidas, Foxj1, Myb, Ccno, Rfx2, Rfx3) showed no significant changes, suggesting that differentiation of tracheal ciliated cells was not affected by Tppp3 loss.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER: Takafumi Sakai

PROVIDER: E-MTAB-16187 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single cell RNA-seq to resolve heterogeneity in a cardiac differentiation timecourse

Project description:Differentiation of HES3 hESCs using BMP4, Activin A and CHIR99021. 5 timepoints of sample collection (day 3-12). Differentiations were started sequentially and collected and processed on the same day. Sample1 = day 3 + day3.75 (50:50 mix); Sample2 = day 4.75; Sample3 = day 5.75; Sample 4 = day 12.

2025-01-31 | E-MTAB-14249 | biostudies-arrayexpress

Clonal hematopoiesis activates pro-calcific pathways in macrophages and promotes aortic valve stenosis

Project description:PBMCs of patients with AVS having TET2 mutations versus those with no known CHIP mutations were utilized for scRNA-seq

2025-10-22 | E-MTAB-15820 | biostudies-arrayexpress

Haematopoietic stem and progenitor cells are present in healthy gingiva tissue

Project description:Haematopoietic stem cells reside in the bone marrow where they generate the effector cells that drive immune responses. However, in response to inflammation some haematopoietic stem and progenitor cells (HSPC) are recruited to tissue sites and undergo extramedullary haematopoiesis. Contrasting this paradigm here we show, with single cell sequencing, residence and differentiation of HSPC in healthy gingiva, a key oral barrier, in the absence of overt inflammation.

2021-02-23 | E-MTAB-10050 | biostudies-arrayexpress

Single-cell RNA-Sequencing of testis tissue from 3 mouse species and their immediate crosses

Project description:We performed an inter-species comparison of murine spermatogenesis using the inbred strains C57B6J, CAST/EiJ and CAROLI/EiJ to investigate the cell type-specific evolution of gene expression levels among closely related species. We also used F1 crosses of C57B6J and CAST/EiJ to investigate context-specific regulatory effects on gene expression in cis and trans by measuring allele-specific expression (Goncalves et al. 2012; Wittkopp et al. 2021). To this end, single-cell RNA-Sequencing data was generated from dissociated testicular tissue in each mouse strain using the 10x Genomics scRNA-Seq platform.

2023-12-11 | E-MTAB-11602 | biostudies-arrayexpress

scRNAseq of four syngeneic human melanoma cell lines (two replicate per cell line) to study mechanisms of resistance to the BRAF inhibitor vemurafenib

Project description:Three cell lines were derived from the A375 human melanoma (harbouring the BRAF v600e mutation; ATCC) after treatment with vemurafenib during a period of 4-5 weeks in the absence (MAPKi-resist Rep1/Rep2) or presence of the fatty acid oxidation inhibitors etomoxir (Etomoxir Rep1/Rep2) or ranolazine (Ranolazine Rep1/Rep2).

2023-06-20 | E-MTAB-12412 | biostudies-arrayexpress

Charting the age-altered thymic epithelial cell differentiation by lineage tracing from a beta 5-t expressing TEC progenitor

Project description:TEC progenitors that express beta 5-t contribute to both the cortical and medullary TEC compartments. Our initial experiments across ageing thymi identified a population of potential progenitor TECs which expanded with age, and appears to be a progenitor population for mTEC. These lineage tracing experiments are designed to chart the altered differentiation and senescence of mTEC progenitors with age.

2020-09-14 | E-MTAB-8737 | biostudies-arrayexpress

Clonally expanded EOMES+ Tr1-like cells in primary and metastatic tumors associate with disease progression

Project description:We performed single-cell transcriptome analysis with the 10X Genomic Chromium platform of CD4+ T cells infiltrating human primary and metastatic colorectal cancer (CRC) and non-small-cell lung cancer (NSCLC). Datasets derive from fresh samples collected and immediately processed by cell sorting and single-cell isolation 10X protocol. A total number of 10000 cells per sample was analyzed by scRNA-seq.

2021-04-28 | E-MTAB-7006 | biostudies-arrayexpress

Single-cell RNA-sequencing of cells from spinal cord central canal region of young adult and aged mice

Project description:The spinal cord neural stem cell potential is contained within the ependymal cells lining the central canal. This neural stem cell potential is known to decline with age in the mouse. Here, we microdissected and dissociated into single cells the central canal region from the spinal cord of 4 young adult (3-to-4-month old) and 4 aged (18-to-19-month old) C57BL/6J mice to profile the transcriptomes of cells in and around the central canal using 10x Genomics technology.

2022-12-13 | E-MTAB-11561 | biostudies-arrayexpress

Single-cell RNAseq of α-PD-1 relapsing YUMM2.1 tumours subsequently treated with PARP14i in vivo

Project description:PD-1 signalling blockade is highly effective at restoring immune surveillance and treating melanoma. However, redundant immune homeostatic mechanisms driven by chronic IFNγ signalling can lead to ongoing immune evasion and acquired resistance. PARP14 mediates IFNγ-driven resistance, and prolongs responsiveness to PD-1 blockade in preclinical models. Here we present a single cell RNAseq of immune cells from α-PD-1 relapsing mouse tumours, following subsequent PARP14i treatments alone and in combination with α-PD-1. Our findings highlight a robust PARP14i gene signature associated with improved patient survival, suggesting its potential to enhance PD-1 blockade efficacy.

2025-01-27 | E-MTAB-14471 | biostudies-arrayexpress

Single-Cell and Spatial Transcriptomic Profiling Reveals Distinct Tumor Microenvironment Dynamics in Cervical Adenocarcinoma and Squamous Cell Carcinoma

Project description:The 5’ single-cell library was prepared strictly following the manufacturer's instructions (User Guide CG000733, 10x Genomics) using the Chromium GEM-X Single Cell 5' Kit v3 (cat# PN-1000701).

2025-11-07 | E-MTAB-15983 | 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