Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next Generation Sequencing Facilitates Quantitative Analysis of the Role of Transcriptional Factor FoxM1 in Muscle Satellte Cells

ABSTRACT: Purpose:To identify genes and the molecular pathways involved in the transcriptional factor FoxM1 regulating muscle satellite cells (SCs) in mice, we performed RNA-Sequence of SCs in qiuescent state (homeostatic condition) or activated state (48 hours-post injury). Methods: mRNA profiles of SCs in FoxM1fl/fl (floxp) and FoxM1fl/fl,Pax7Cre/+ (cKO) in quiescent state (Qfloxp or QcKO) or activated state (Afloxp or AcKO) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000. Activated state was induced by Bacl2 injection (48 hours-post injury). Results:Using an optimized data analysis workflow, we mapped about 9 million sequence reads per sample to the mouse genome (build mm10) and identified 13776 transcripts in SCs (the floxp and cKO group) with BWA workflow. Conclusions: Our results represent the first detailed analysis of SCs transcriptomes in FoxM1-knockout mice and found that FoxM1 regulated multiple mRNA pathways in SCs.

ORGANISM(S): Mus musculus

PROVIDER: GSE135486 | GEO | 2020/03/23

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

mRNA-sequencing of METTL3-deficient NK cells

Project description:Purpose: For comparing the transcript changes, we conducted mRNA-sequencing of splenic NK cells from Ncr1Cre-Mettl3fl/fl (cKO) and Mettl3fl/fl (WT) mice. Method: Firstly, The splenic NK cells (CD45.2+CD3-NK1.1+NKp46+) are purified via Fluorescence activated Cell Sorting (FACS), then frozen in -80 °C ultra-low temperature refrigerator, followed by High-throughput sequencing, in three replicates, using Illumina Hiseq 1500 platform. Result: Using standard data process workflow, we found the differentailly expressed genes in NK cells from Ncr1Cre-Mettl3fl/fl (cKO) mice, compared with those from Mettl3fl/fl (WT) mice.

2021-07-20 | GSE180053 | GEO

RNA-seq analysis of transcriptomes of Noc4L deficient and the Nco4L sufficient Treg cells

Project description:To gain in depth transcriptional information about the Noc4L deficient and Noc4L sufficient Tregs, we performed RNA-seq analysis to compare the transcriptomes of Noc4L deficient (CD4+GFP+CD62Lhigh, cKO) and Noc4L sufficient (CD4+GFP+CD62Lhigh, Het) Tregs activated in vitro with Dynabeads for 48 hours or 72 hours. We found ~25 unique genes with differential expression between the Noc4L deficient and Noc4L sufficient Treg cells when activated for 48 hours in vitro. And ~100 unique genes with differential expression between the Noc4L deficient and Noc4L sufficient Treg cells when activated for 72 hours in vitro in two times experiment.

2018-07-04 | GSE116572 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of the Role of nuclear protein DEK in hematopoietic stem cells [RNA-seq]

Project description:Purpose:To identify genes and the molecular pathways involved in the DEK regulating hematopoietic stem cells (HSC) in mice, we performed RNA-Sequence of HSC freshly sorted from mice. Methods: mRNA profiles of HSC in Dekfl/fl (floxp) and Dekfl/fl,Tie2-Cre (cKO) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000. Results:Using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the mouse genome (build mm10) and identified 33299 transcripts in HSC (the floxp and cKO group) with BWA workflow. Conclusions: Our results represent the first detailed analysis of HSC transcriptomes in Dek-knockout mice and found that DEK regulated multiple mRNA pathways in HSC.

2021-02-22 | GSE166431 | GEO

FoxM1 is essential for quiescence and maintenance of hematopoietic stem cell

Project description:FoxM1, a mammalian Forkhead Box M1 protein, is known as a typical proliferation-associated transcription factor that regulates of G1/S and G2/M transition in the proliferating cells. However, the in vivo function of FoxM1 in adult stem cells remains unknown. Here, we found that FoxM1 is highly expressed in hematopoietic stem cells (HSCs) and is essential for maintaining quiescence and self-renewal of HSCs in vivo. FoxM1-deficient mice developed leukopenia, thrombocytopenia and neutropenia with an approximately 6-fold decrease in HSC pool size, which is associated with a failure of G0 cell cycle regulation and increased cell cycling in HSCs. FoxM1 absence did not affect lineage commitment of HSCs and progenitors. However, FoxM1 loss significantly reduced the repopulating capacity and self-renewal of long-term HSC in a cell-autonomous manner. Mechanistically, FoxM1 loss markedly down-regulates the expression of orphan nuclear receptor Nurr1, known to regulate HSC quiescence. We found that FoxM1 directly bound the promoter region of Nurr1 and induced transcriptional activity of Nurr1 promoter in vitro, and forced expression of Nurr1 rescued FoxM1-deletion-induced G0 loss of HSC-enriched population in vitro. Thus, our studies show a previously unrecognized role of FoxM1 as a critical regulator of HSC quiescence and self-renewal by controlling Nurr1-mediated pathways. The Hematopoietic Stem Cells (HSCs) were sorted from FoxM1[fl/fl] and Tie2-Cre FoxM1[fl/fl] mice, then amplified with Ovation Pico WTA System V2 before microarray analysis. There are 3 samples from FoxM1[fl/fl]mice and 3 samples from Tie2-Cre FoxM1[fl/fl] mice.

2015-06-15 | E-GEOD-62360 | biostudies-arrayexpress

Mouse Muscle Stem Cell Proteome during Activation and CPEB1 Dependent Proteome in Mouse Muscle Stem Cell

Project description:Muscle Stem Cells or satellite cells (SCs) are required for muscle regeneration. In resting muscles, SCs are kept in quiescence. After injury, SCs undergo rapid activation, proliferation and differentiation to repair damaged muscles. The transcriptome alteration during SC activation is well characterized. While transcriptome is not exactly represent proteome because of post-transcriptional regulations such as miRNA induced gene silencing. However, little is known about SC proteome. We obtained quisecent SCs (QSCs) and freshly isolated SCs (fiSCs, early activated SCs) and activated SCs (ASCs) for high resolution mass spectrometry Bruker timsTOF Pro. Thus, we uncovered the QSC proteome. By comparison of QSC proteome to fiuSCs proteome or ASCs proteome, we identified the pathways that are differentially expressed between them. Forthermore, we characterized a translational regulator CPEB1 reprogrammed translation landscape for SC activation.

2021-11-05 | PXD018865 | Pride

Next Generation Sequencing Facilitates Quantitative Analysis of Control and FoxM1-knockdown C2C12 Transcriptomes

Project description:Purpose:To identify FoxM1-dependent genes and the molecular pathways involved in the regulation of muscle stem cells function, we performed RNA-Sequence of C2C12 from shControl and shFoxM1 cells. Methods: C2C12 mRNA and lncRNA profiles of shControl and shFoxM1 cells (quiescent or activated states) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000. Results:Using an optimized data analysis workflow, we mapped about 80 million sequence reads per sample to the mouse genome (build mm10) and identified 49,586 transcripts in the control C2C12 and FoxM1-knockdown C2C12 with BWA workflow. Conclusions: Our results represents the first detailed analysis of C2C12 transcriptomes and found that knockdown of FoxM1 perturbed multiple mRNA pathways, as well as for novel lncRNA pathways.

2017-09-01 | GSE102685 | GEO

3 days injured in vivo ASCs proteome

Project description:Muscle Stem Cells or satellite cells (SCs) are required for muscle regeneration. In resting muscles, SCs are kept in quiescence. After injury, SCs undergo rapid activation, proliferation and differentiation to repair damaged muscles. The transcriptome alteration during SC activation is well characterized. While transcriptome is not exactly represent proteome because of post-transcriptional regulations such as miRNA induced gene silencing. However, little is known about SC proteome. We obtained in vivo activated SCs (ASCs) from 3 days post injured muscles for high resolution mass spectrometry Bruker timsTOF Pro. Compared with QSC proteome,, we identified the pathways that are differentially expressed between them.

2021-11-04 | PXD023656 | Pride

Microarray analysis of U87 glioma cells after transient knockdown of FOXM1

Project description:FOXM1 plays a key role in M phase in normal cells and is overexpressed in human glioma. We found that FOXM1 deprivation could sensitize the glioma cells to TMZ chemotherapy. To find out the mechanistic regulation of FOXM1 in chemo-resistant genes, we used microarrays to select the potential genes regulated by FOXM1 which dominates in glioma chemo-resistance. U87 glioma cells were transiently transfected with none-target siRNA or FOXM1 siRNA. Total RNA were extracted after 48 hours and subjected to the microarray.

2012-08-10 | E-GEOD-40051 | biostudies-arrayexpress

Retinoic Acid Related Receptor Orphan Receptor a (RORa) expressing T regulatory cells thwart type-2 cutaneous allergic inflammation

Project description:We used RNA-sequencing to profile gene expression differences between Tregs from skin and LNs of Foxp3 cre-efyp WT mice. We further compared skin Tregs from control and Foxp3 cre Rora fl/fl (Rora cKO) mice in the steady state and after allergic inflammation was induced using MC903.

2018-03-26 | GSE99086 | GEO

RNA seq of vhlfl/fl cd4 cre, hif1afl/fl vhlfl/fl cd4 cre and WT CD4 T cells before and after anti-CD3/CD28 stimulation

Project description:Purpose: We compared the transcriptomes of murine CD4 T cells lacking either the vhl gene ( vhlfl/fl cd4 cre (vhl cKO) ) or both vhl and hif1a (hif1afl/fl vhlfl/fl cd4 cre (dcKO)) with WT controls before and 24 h after T cell receptor stimulation using anti-CD3/CD28. Results: Using an optimized data analysis workflow, about 45-60 million sequence reads per sample to the mouse genome (build mm10) and identified ca 12500 transcripts in the CD4 T cells of WT and mutant mice after performing HISAT2 alignements to the mm10 reference. Conclusion: the segregation of the transcriptome of unstimulated WT CD4 T cells as compared to the other groups. Within the TCR-stimulated groups the gene expression of vhl cKO CD4 T cells differed to that of WT and vhl hif1a dcKO CD4 T cells which showed in comparison important similarity between them

2022-06-01 | GSE190791 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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