Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq analysis of peripheral nerve with conditional knockout of H3K27 demethylases.

ABSTRACT: The goal of the experiment was to determine the role of H3 emethylases in the nerve injury response in peripheral nerve. A Schwann cell specific knockout of the H3K27 demethylases (Jmjd3 and Utx) was generated to compare with wild type mice in sham and injured mice at 1d and 7d timepoints after nerve injury.

ORGANISM(S): Mus musculus

PROVIDER: GSE178872 | GEO | 2021/06/25

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Chemical Inhibition of H3K27me3 demethylases during B cell differentiation

Project description:To understand the role of the H3K27me3 demethylases, UTX and JMJD3, in B cell differentiation. Naïve B cells were cultures ex vivo with LPS, IL-2,IL-5 in the presence of DMSO or GSK-J4, UTX/JMJD3 inhibitor. Plasmablasts and activated B cells were magnetically enriched after 3 days of culture.

2021-11-16 | GSE158139 | GEO

Transcriptomic and epigenomic profiling of H3K27me3 demethylases inhibitor GSK-J4 induced changes in colon cancer cells (ChIP-Seq)

Project description:H3K27me3 demethylases UTX and JMJD3 play vital roles in development and disease, including cancer. Therefore, we systematically investigated the impact of inhibition of these two demethylases using a small molecule inhibitor in colon cancer cells.

2020-09-21 | GSE146678 | GEO

Transcriptomic and epigenomic profiling of H3K27me3 demethylases inhibitor GSK-J4 induced changes in colon cancer cells (RNA-Seq)

2020-09-21 | GSE146676 | GEO

Characterizing the contrasting roles of JMJD3 and UTX histone demethylases in T cell acute lymphoblastic leukemia [shJMJD3_ChIP-seq]

2014-10-01 | E-GEOD-56692 | biostudies-arrayexpress

Characterizing the contrasting roles of JMJD3 and UTX histone demethylases in T cell acute lymphoblastic leukemia [short_hairpins_RNA-seq]

Project description:T-cell acute lymphoblastic leukemia (T-ALL) is an immature hematopoietic malignancy driven mainly by oncogenic activation of NOTCH1 signaling. In this study we abrogated the expression of JMJD3 (KDM6B) and UTX (KDM6A) H3K27me3 demethylases in human T-ALL lines and assayed for genome-wide expression changes using RNA sequencing. This piece of data was further integrated to ChIP-Sequencing analysis of H3K27me3 from the same treatment as well as H3K27me3 and JMJD3 genome-wide analysis from treatment of T-ALL lines with the GSKJ4 inhibitor. These results, coupled to genomic analysis of primary samples for the genomic status of the UTX gene in T-ALL, helped us to identify a hitherto unknown role of JMJD3as an oncogenice facilitator in leukemia whereas UTX seems to play a tumor suppressor role. Whole RNA was extracted from 1-5 million T-ALL (lines) cells or primary cells using the RNAeasy kit (Qiagen) according to the manufacturer’s protocol. Poly-A+ (magnetic oligodT-containing beads (Invitrogen)) or Ribominus RNA was used for library preparation. cDNA preparation and strand-specific library construction was performed using the dUTP method. Libraries were sequenced on the Illumina HiSeq 2000 using 50bp single-read method. Differential gene expression analysis was performed for each matched knockdown vs control pairs, separately in each biological or technical replicate in each of two cell lines (CUTLL1, CEM). Three types of comparisons were tested: (a) JMJD3 knockdown vs Renilla, (b) JMJD3 knockdown vs UTX knockdown, and (c) UTX knockdown vs Renilla. Analysis was performed using both DEGseq and Cufflinks packages leading to very similar conclusions.

2014-10-01 | E-GEOD-56689 | biostudies-arrayexpress

Characterizing the contrasting roles of JMJD3 and UTX histone demethylases in T cell acute lymphoblastic leukemia [shJMJD3_ChIP-seq]

2014-10-01 | GSE56692 | GEO

Gene expression signatures following nerve injury in a rat model (0d-14d)

Project description:We used microarrays to distinguish the gene expression differences among different time points after injury. We generated L4-6 dorsal root ganglia (DRG) tissues and proximal sciatic nerve (SN) tissues (0.5cm) at 0d, 1d, 4d, 7d and 14d after sciatic nerve resection.

2013-01-01 | E-GEOD-30165 | biostudies-arrayexpress

Impact of Jmjd3 and Utx histone demethylases on Histone H3 lysine 27 trimethylation (H3K27Me3) in mature CD4 SP thymocytes

Project description:While histone H3 lysine 27 trimethylation (H3K27Me3) is associated with gene silencing, whether H3K27Me3 demethylation affects transcription and cell differentiation in vivo has remained elusive. To investigate this, we conditionally inactivated the two H3K27Me3 demethylases, Jmjd3 and Utx, in non-dividing intrathymic CD4+ T cell precursors. We show that both enzymes redundantly promote H3K27Me3 removal at, and expression of, a specific subset of genes involved in terminal thymocyte differentiation, especially S1pr1, encoding a sphingosine-phosphate receptor required for thymocyte egress. Floxed alleles of the genes encoding Utx and Jmjd3 (Kdm6a and Kdm6b, respectively) were deleted in double positive (DP) thymocytes carrying a CD4 Cre transgene. Genome-wide H3K27Me3 ChipSeq was performed on (i) pre-selection (CD69lo) DP thymocytes from wild-type mice carrying an endogenous polyclonal TCR repertoire, (ii) mature (TCRhi CD24lo) CD4 SP thymocytes from wild type (Wt), Jmjd3KO, UtxKO and dKO mice carrying an endogenous polyclonal TCR repertoire and (iii) mature (Va2hi CD24lo) CD4 SP thymocytes from wild type and dKO mice carrying the OTII TCR transgene.

2015-09-02 | E-GEOD-70795 | biostudies-arrayexpress

RNA-seq of Injured Nerve in Schwann cell conditional knockout of Eed

Project description:The goal of the experiment was to determine the role of the polycomb repressive complex 2 in the nerve injury response in peripheral nerve. A Schwann cell specific knockout of the Eed subunit of PRC2 was generated to compare with wild type mice in sham and injured mice at 1d and 14d timepoints after nerve injury.

2018-01-01 | GSE106969 | GEO

Characterizing the contrasting roles of JMJD3 and UTX histone demethylases in T cell acute lymphoblastic leukemia [short_hairpins_RNA-seq]

2014-10-01 | GSE56689 | GEO