Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

33 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-Seq and RNA Polymerase II ChIP-Seq of mouse spermatogenesis

ABSTRACT: To characterize gene expression in spermatogenesis we sequenced eight mRNA samples from testes of juvenile mice aged between 6 and 38 days post partum. We then classified gene expression profiles and found over 1,000 meiotically-expressed protein-coding genes that have not been previously reported in relation to spermatogenesis. Furthermore, we developed an in silico de-convolution approach to estimate cell type-specific gene expression from temporal gene expression profiles and applied it to our dataset. To further characterize transcription during spermatogenesis, we determined RNA polymerase II (RNAPII) distribution along the genome using ChIP-Seq. mRNA sequencing at 8 time points during spermatogenesis was used to characterize differential gene expression; RNA Pol II ChIP-Seq at two time points was used to estimate RNA Pol II accumulation at promoters.

ORGANISM(S): Mus musculus

SUBMITTER: Gennady Margolin

PROVIDER: E-GEOD-44346 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Integrated transcriptome analysis of mouse spermatogenesis.

Margolin Gennady G Khil Pavel P PP Kim Joongbaek J Bellani Marina A MA Camerini-Otero R Daniel RD

BMC genomics 20140118

<h4>Background</h4>Differentiation of primordial germ cells into mature spermatozoa proceeds through multiple stages, one of the most important of which is meiosis. Meiotic recombination is in turn a key part of meiosis. To achieve the highly specialized and diverse functions necessary for the successful completion of meiosis and the generation of spermatozoa thousands of genes are coordinately regulated through spermatogenesis. A complete and unbiased characterization of the transcriptome dynam ...[more]

PMID: 24438502

Similar Datasets

2) Twisting Urea- to Imide-Based Mass Spectrometry-Cleavable Cross-Linkers to Embed Affinity Tags

Project description:Disuccinimidyl dibutyric urea (DSBU) is a mass spectrometry (MS)-cleavable cross-linker that has been applied to multiple applications in structural biology, ranging from isolated protein complexes to comprehensive system-wide interactomics. DSBU facilitates a rapid and reliable identification of cross-links through the dissociation of its urea group in the gas-phase. In this study, we further advance the structural capabilities of DSBU by twisting the urea group into an imide, thus introducing a novel class of cross-linkers. This modification preserves the MS-cleavability of the amide bond, granted by the two acyl groups of the imide function. The central nitrogen atom enables the introduction of affinity purification tags. Here, we introduce disuccinimidyl dibutyric imide (DSBI) as prototype of this class of cross-linkers. It features a phosphonate handle for immobilized metal ion affinity chromatography (IMAC) enrichment. We detail DSBI synthesis and describe its behavior in solution and in the gas-phase while cross-linking isolated proteins and human cell lysates. DSBI and DSBU cross-links are compared at the same enrichment depths to bridge these two cross-linker classes. We validate DSBI cross-links by mapping them in high-resolution structures of large protein assemblies . The cross-links observed yield insights into the morphology of intrinsically disordered proteins (IDPs) and their complexes. The DSBI linker might spearhead a novel class of MS-cleavable and enrichable cross-linkers

2024-09-03 | PXD050960 | Pride

Genome wide profiling of the RNAPII, Î³H2AX, H3K4Me1, H3K4M2 and H3K4Me3 in MLL2 F/F and FC/FC MEF cells

Project description:We investigated the RNAPII and Î³H2AX occupancy genome wide by ChIP-Seq in MLL2 F/F and FC/FC80 MEF cells. We found that a week after MLL2 excision (FC/FC cells), a group of genes present higher levels of Î³H2AX and RNAPII near the TSS, as compared to the control (F/F cells). H3K4Me1, H3K4M2 and H3K4Me3 levels near the TSS were also studied. There is a total of 52 samples. 3 independent replicates for each experiment were performed. H3, H2AX and IgG ChIPs were used for normalisation or as controls.The experiments were performed using immortalised mouse embryonic fibroblasts (MEF) in which both MLL2 alleles were targeted by the loxp system (F/F cells). Tamoxifen treatment of the F/F cells for 24 hours results in the excision of both MLL2 alleles (FC/FC cells).

2016-04-13 | E-GEOD-73124 | biostudies-arrayexpress

RNA-Seq and RNA Polymerase II ChIP-Seq of mouse spermatogenesis

Project description:To characterize gene expression in spermatogenesis we sequenced eight mRNA samples from testes of juvenile mice aged between 6 and 38 days post partum. We then classified gene expression profiles and found over 1,000 meiotically-expressed protein-coding genes that have not been previously reported in relation to spermatogenesis. Furthermore, we developed an in silico de-convolution approach to estimate cell type-specific gene expression from temporal gene expression profiles and applied it to our dataset. To further characterize transcription during spermatogenesis, we determined RNA polymerase II (RNAPII) distribution along the genome using ChIP-Seq.

2014-01-22 | GSE44346 | GEO

PRDM11 ChIP in U2932 cells

Project description:The PR-domain family e(PRDMs) encodes transcriptional regulators, several of which are deregulated in cancer. We found that loss of Prdm11 accelerates MYC-driven lymphomagenesis in the Eµ-Myc mouse model. Moreover, we show that patients with PRDM11-deficient diffuse large B cell lymphomas (DLBCLs) have poorer overall survival and belong to the non-Germinal Center B cell (GCB)-like subtype. Mechanistically, genome-wide mapping of PRDM11 binding sites coupled with transcriptome sequencing in human DLBCL cells evidenced that PRDM11 associates with transcriptional start sites of target genes and regulates important oncogenes such as FOS and JUN. Hence, we characterize PRDM11 as a novel tumor suppressor controlling the expression of key oncogenes and add new mechanistic insight into B-cell lymphomagenesis. 5 samples: PRDM11 Ab1, PRDM11 Ab2, RNA Polymerase II, IgG and input

2015-03-02 | E-GEOD-56064 | biostudies-arrayexpress

CDK8 ChIP-seq from HCT116 cells in normoxia and hypoxia

Project description:To test if CDK8 acts directly at HIF1A target genes, we performed ChIP-seq experiments in HCT116 cells under normoxic and hypoxic conditions. ChIP-seq for CDK8 versus Input under normoxia and 24hrs hypoxia (1% O2).

2013-03-01 | E-GEOD-38258 | biostudies-arrayexpress

Peroxynitrite-mediated post-translational modification of human glutamine synthetase

Project description:The aim of the project was to understand the mechanisms that underlie the oxidative inactivation of human glutamine synthetase (HsGS). For that purpose, we expressed and purified recombinant HsGS, exposed it in phosphate buffer to peroxynitrite (ONOO-) and assessed the functional and structural consequences. To characterize the oxidative post-translational modifications induced by ONOO-, several approaches were carried out (e.g. SDS-PAGE, western-blot, amino acid quantification by LC, etc). The most detailed characterization was performed through LC-MS/MS analysis after trypsin digestion of the ONOO--treated protein, which allowed us to identify the amino acid residues that are modified and to estimate the extent of such modifications.

2023-05-10 | PXD037583 | Pride

BMP signaling in mouse embryonic stem cells (ESCs) in the naÃ¯ve and primed pluripotent states [ChIP-Seq]

Project description:Carrying out both RNA-seq and Smad1/5 genome-wide chromatin immunoprecipitation and sequencing (ChIP-seq) analyses of mESCs in the naÃ¯ve or primed states, we revisit the roles of BMP signaling in mESCs. Smad1/5 binding sites in 2 cell types; mESCs and ES-derived EpiSC (ESD-EpiSCs).

2015-12-04 | E-GEOD-70579 | biostudies-arrayexpress

Cross-linking of mouse laminin 111

Project description:Laminin, a ~800 kD heterotrimeric protein, is a major functional component of the extracellular matrix, contributing to tissue development and maintenance. We used cross-linking and mass spectrometry to determine the order of subunits in the ~750 Å trimeric coiled-coil oligomerization domain of laminin and to achieve an estimate of the register of the three subunits along the length of the coiled coil.

2016-12-22 | PXD004898 | Pride

Gene silencing triggers Polycomb Repressive Complex 2 recruitment to CpG islands genome-wide [ChIP-seq_drugs]

Project description:Polycomb group (PcG) proteins are required for normal differentiation and development, and their activity is found deregulated in cancer. PcG proteins are involved in gene silencing, however, whether they initiate or maintain transcriptional repression is a subject of debate. Here, we show that knockout of the Polycomb repressive complex 2 (PRC2) does not lead to significant gene expression changes in mouse embryonic stem cells (mESCs), and that it is dispensable for initiating silencing of target genes during differentiation. Transcriptional inhibition in mESCs is sufficient to induce genome-wide ectopic PRC2 recruitment to endogenous PcG target genes found in other tissues. PRC2 binding analysis shows that it is restricted to nucleosome-free CpG islands (CGIs) of un-transcribed genes. Our results show that it is the transcriptional state that governs PRC2 binding, and we propose that it binds by default to non-transcribed CGI genes to maintain their silenced state and to protect cell identity. Suz12, H3K27me3 and RNAPII ChIP-seq experiments before and after transcriptional inhibition with either DRB (0h, 6h and 12h) or Triptolide (0h, 3h and 9h) treatment of Mus musculus wild-type E14 Embryonic Stem Cells with up to two biological replicates per condition.

2014-07-03 | E-GEOD-58019 | biostudies-arrayexpress

A network including TGFÎ²/Smad4, Gata2 and p57 regulates proliferation of mouse hematopoietic stem/progenitor cells [ChIP-seq]

Project description:Transforming growth factor-Î² (TGFÎ²) is a potent inhibitor of hematopoietic stem cell (HSC) proliferation. However, the precise mechanism for this effect is unknown. Here, we have identified the transcription factor Gata2, previously described as an important regulator of HSC function, as an early and direct target gene for TGFÎ²-induced Smad signaling in hematopoietic stem and progenitor cells (HSPCs). Interestingly, TGFÎ²-induced Gata2 upregulation is critical for subsequent transcriptional activation of the TGFÎ² signaling effector molecule p57 and resulting growth arrest of HSPCs. Importantly, both Gata2 and p57 are abundantly expressed in freshly isolated highly purified HSCs, demonstrating the relevance of this circuit in HSC regulation within the HSC niche. Our results connect key molecules involved in HSC self-renewal and reveal a functionally relevant network regulating proliferation of primitive hematopoietic cells. To identify TGFÎ² targets downstream of Gata2, we carried out a ChIP-Seq experiment on TGFÎ²-induced Lhx2 cells. Interestingly, there was a large overlap between the GATA2-bound genes and genes differentially expressed after 2h TGFÎ² induction. One sample of 1x10^8 cells (treated with 10 ng/ml TGFÎ² for 2h) was sequenced.

2016-09-01 | E-GEOD-73641 | 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