Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

High throughput quantitative whole transcriptome analysis of CC10- B4+ and Krt5-CreERT2 - labeled distal lung cells

ABSTRACT: We used microfluidic single cell RNA-seq on adult isolated CC10-CreERT2 (negative) integrin beta4(pos) cells lung epithelial cells in order to determine the transcriptional profile of this putative progenitor population. CC10-CreERT2 / tdTomato (negative) integrin beta4(pos) cells were isolated by FACS, as were Krt5-CreERT2 / tdTomato (positive) cells. These cells were pooled and loaded onto the Fluidigm C1 device.

ORGANISM(S): Mus musculus

SUBMITTER: Andrew Vaughan

PROVIDER: E-GEOD-61300 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

High throughput quantitative whole transcriptome analysis of CC10- B4+ and Krt5-CreERT2 - labeled distal lung cells

Project description:We used microfluidic single cell RNA-seq on adult isolated CC10-CreERT2 (negative) integrin beta4(pos) cells lung epithelial cells in order to determine the transcriptional profile of this putative progenitor population.

2014-11-17 | GSE61300 | GEO

Transcription profiling of human MDA-MB-435 breast carcinoma cell line transfected with the integrin beta4 subunit revealsIntegrin alpha6-beta4 control the expression of genes associated with cell motility, invasion and metastasis

Project description:The objective of this study was to determine the gene expression changes mediated by the alpha6beta4 integrin using MDA-MB-435 breast carcinoma cell line under normal culturing conditions (10% FCS in DMEM). Experiment Overall Design: Comparison of clones of MDA-MB-435 cells transfected with the integrin beta4 subunit (which results in cell surface expression of the integrin apha6beta4 integrin; clones 3A7 and 5B3) to those transfected with vector (mock; 6D2 and 6D7) only.

2009-01-13 | E-GEOD-11466 | biostudies-arrayexpress

Characterizing the gene expression profile of Prox1+ intestinal adenoma organoid cells

Project description:We isolated and selected intestinal adenoma organoids from Apcmin/+; Rosa26LSL-TdTomato; Prox1-CreERT2 mice. After the selection procedure without growth factors, we induced CreERT2 activity and the transcription of tdTomato to label Prox1+ cells by 300 nM 4-hydroxytamoxifen for 16h. tdTomato+ (Prox1+) and tdTomato- cells (enriched for Prox1- cells) were FACS sorted and total RNA was isolated.

2018-08-21 | GSE117981 | GEO

Single Cell Transcriptional Profile of brain endothelial cells from nine different brain regions in adult mice

Project description:tdTomato+ endothelial cells from different brain regions of healthy adult Rosa-tdTomato; VE-Cadherin-CreERT2 mice

2021-01-26 | GSE165457 | GEO

RNA sequencing data of microglia isolated from brains of WT, Hexb-tdTomato, Hexb-CreERT2 and Hexb-KO mice. {Reporter]

Project description:RNA sequencing of FACS sorted microglia isolated from brain tissue of WT, Hexb-tdTomato, Hexb-CreERT2 and Hexb-KO mice was performed to test for potential differences in gene expression caused by the knock-in of tdTomato and CreERT2 into the Hexb locus.

2020-05-25 | GSE148412 | GEO

RNA sequencing data of microglia isolated from brains of WT, Hexb-tdTomato, Hexb-CreERT2 and Hexb-KO mice. [Hexb-KO]

2020-05-25 | GSE148411 | GEO

RNA sequencing data of microglia isolated from brains of WT, Hexb-tdTomato, Hexb-CreERT2 and Hexb-KO mice. [Cre]

2020-05-25 | GSE148410 | GEO

A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche - Visium

Project description:Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).

2022-01-06 | E-MTAB-11640 | biostudies-arrayexpress

Transcriptome analysis of hepatocellular carcinoma and adjacent non-tumor liver tissues [I]

Project description:Integrin alpha 6 (ITGA6) forms integrin receptors with either integrin β1 (ITGB1) or integrin beta 4 (ITGB4). To study its expression and regulatory functions in hepatocellular carcinoma (HCC) progression, whole transcriptome RNA sequencing in paired HCC tumor and adjacent non-tumor liver tissue samples from ten local Hispanic patients was performed. The average expression of ITGA6 was found increased by over 3.5-fold in HCC tumor tissues in comparison with their adjacent non-tumor tissues. The study indicates integrin alpha6-beta4 complex as a potential therapeutic target for treating patients in HCC.

2022-05-18 | GSE202853 | GEO

Smartseq3 Single-cell RNA-seq analysis of acutely FACS-purified tdTomato+ astrocyte derived cells from aged injured mice in vivo

Project description:To investigate the mechanisms that underlie astrocyte dedifferentiation, we performed single cell RNA sequencing analysis of tdTomato+ astrocyte derived cells approx 1 year after stab-wound injury. 2-3 month old GFAP-CreERT2;p53flox/flox;LSL-tdTomato (p53Gfap-icKO) mice were subjected to intracortical endoxifen injection to enable deletion of p53 gene and simultaneous expression of tdTomato for fate-mapping specifically in astrocytes (GFAP+) in the context of a stab-wound injury. GFAP-CreERT2;p53wt/wt;LSL-tdTomato (p53Gfapwt/wt) mice were used as control whereby p53 remains fate-mapped tdTomato+ astrocytes remain p53 wildtype after endoxifen injection. Approx 10-12 months after injury, mice were sacrificed and the peri-wound region was dissected. Mice of the same genotypes were pooled (3 p53Gfap-icKO and 2 p53Gfapwt/wt) and digested using the Miltenyi Adult brain dissociation kit. Single cell suspension was FACS sorted for tdTomato+ cells into 384 well plates and then Smartseq3 libraries were generated.

2023-02-23 | GSE220479 | 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