Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GRO-Seq analysis of in vitro activated B cells in early G1

ABSTRACT: Purpose: To detect the on-going transcription in early G1 B cells Methods: Primary B cells were isolated and in vitro activated by LPS, IL4 and Rp105, followed by nocodazole arrest and release. The early G1 population was then sorted and the nuclei was isolated for GRO-Seq. The sequenced reads were processed using Burrows–Wheeler Aligner (BWA) followed by HOMER. Results: The nascent transcription and the convergent transcription were determined in both unsynchronized and sorted early G1 population Conclusions: Convergent transcription is detected at Igh switch regions in early G1 cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE89464 | GEO | 2016/11/30

SECONDARY ACCESSION(S): PRJNA352264

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Oct4 ChIP-Seq at G1 and G2/M phase of cell cycle in mouse embryonic stem cells

Project description:We mapped the genome-wide occupancy of Oct4 at G2/M (nocodazole-treated cells) and G1 phase (release of nocodazole-treated cells) in E14 mouse embryonic stem cells.

2016-04-19 | GSE78073 | GEO

Mapping of CTCF occupancy in interphase and mitosis cells

Project description:To address whether CTCF is involved in the transcription of early G1 genes immediately after mitotic exit, we carried out ChIP sequencing (ChIP-seq) experiments to evaluate CTCF binding to genomic DNA in asynchronous cells and nocodazole-arrested mitotic cells. Of the 62,996 peaks identified in the asynchronous cells, 41,397 peaks (65.71%) were lost in the mitotic cells. However, the 21,599 peaks (34.29%) were identified in the both conditions, indicating that the enrichment level of CTCF is decreased in the mitotic cells. It has been reported that expression profiles of the first 2 hours of G1 phase in HeLa cells. A scatter plot comparison of the genes expressed in the early G1 phase indicated the reduced CTCF binding level in the mitotic phase. These results indicate that CTCF was dissociated or CTCF bound to chromosomes was reduced in the mitotic chromatin and then may be re-associated to chromatin in the early G1 phase.

2019-06-18 | GSE83579 | GEO

Triap1 upregulation promotes escape from mitotic slippage-induced G1 arrest

Project description:Proteomic analysis of G1-arrested human cells after treatment with nocodazole

2023-03-09 | PXD037143 | Pride

Two Distinct Sertoli Cell States are Regulated via Germ Cell Crosstalk [scRNA-seq]

Project description:We report single-cell RNA-sequencing data for RFPxAMH-Cre sorted Sertoli cells from unsynchronized adult testes.

2021-08-31 | GSE166563 | GEO

A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition [CaptureC]

Project description:Capture-C of G1E ER4 cell line in a nocodazole arrest-release experiment anchored at multiple gene promoters to quantify long-range chromatin interactions at the mitosis-G1 transition.

2016-06-15 | GSE83290 | GEO

Budding yeast cohesin (Mcd1) distribution in mitotically arrested cells

Project description:genomic localization of the budding yeast cohesin complex was mapped in mitotically arrested cells by Mcd1 ChIP followed by hybridization to high-density tiled microarrays Cells were synchronized first in G1 and then released into media containing the microtubule poison nocodazole. Cells were fixed and processed for ChIP once arrested as large-budded cells. Immunoprecipitated DNA and total genomic DNA not subjected to immunoprecipitation were competitively hybridized to Nimblegen whole genome arrays.

2009-09-30 | E-GEOD-18021 | biostudies-arrayexpress

Leukemia reconstitution in vivo is driven by cells in early cell cycle and low metabolic state

Project description:To characterize LICs in ALL irrespective of surface markers expression, we investigated leukemia initiating activities of cellular subfractions of patient-derived xenograft BCP-ALL cells sorted according to different cell cycle phases (i.e. G0/G1 and G2/M) followed by transplantation onto NOD/SCID mice. All cell fractions led to leukemia engraftment indicating LIC activity irrespective of cell cycle stage. Most importantly, cells isolated from G0/G1 cell cycle phases led to early leukemia engraftment in contrast to cells from late cell cycle (G2/M). To further characterize cells with different engraftment potential in vivo, we analyzed the gene expression profiles of early (G1b early) and late (G2/M) engrafting cells.

2018-03-18 | GSE71836 | GEO

PHF8 mediates histone demethylation events in cell cycle progression [ChIP-Seq]

Project description:While reversible histone modifications are linked to an ever-expanding range of biological functions, the demethylases for histone H4 lysine 20 and their potential regulatory roles remain unknown. Here, we report that the PHD and Jumonji C (JmjC) domain-containing protein, PHF8, while utilizing multiple substrates, including H3K9me1/2 and H3K27me2, also functions as an H4K20me1 demethylase. PHF8 is recruited to promoters by its PHD domain based on interaction with H3K4me2/3 and controls G1/S transition in conjunction with E2F1, HCF-1 and Set1A, at least in part, by removing the repressive H4K20me1 mark from a subset of E2F1-regulated gene promoters. Phosphorylation-dependent PHF8 dismissal from chromatin in prophase is apparently required for the accumulation of H4K20me1 during early mitosis, which might represent a component of the Condensin II loading process. Accordingly, the HEAT repeat clusters in two non-SMC Condensin II subunits, N-CAPD3 and N-CAPG2, are capable of recognizing H4K20me1, and ChIP-seq. analysis demonstrate a significant overlap of Condensin II and H4K20me1 sites in mitotic HeLa cells. Thus, the identification and characterization of an H4K20me1 demethylase, PHF8, has revealed an intimate link between this enzyme and two distinct events in cell cycle progression. unsynchronized HeLa cells were used to profile H3K4me2 and E2F1; unsynchronized or G1 or G1/S synchronized HeLa cells were used to profile PHF8; M phase synchronized HeLa cells were used to profile SMC4 and H4K20me1

2010-09-01 | E-GEOD-22478 | biostudies-arrayexpress

Genome wide analysis of genes expressed in early G1 phase of the cell cycle in PMCA4 wild type and PMCA4 knockout primary vascular smooth muscle cells

Project description:Husain lab cell proliferation in vitro experimental data showed a G1 arrest in PMCA4 knockout primary vascular smooth muscle cells (VSMC). This microarray documents the different gene expression profiles of PMCA4 wild type and knockout cells at the early G1 stage in serum synchronized cell populations (n=4 populations for each genotype). Serum synchronized cell populations were Hoechst labeled and flow sorted for early G1 sub-populations (PMCA4 WT n=4; PMCA4 KO n=4) and total RNA from sorted cells was used for microarray analysis.

2014-01-21 | E-GEOD-38318 | biostudies-arrayexpress

Two Distinct Sertoli Cell States are Regulated via Germ Cell Crosstalk

Project description:We report bulk RNA-sequencing for synchronized adult Sertoli cells in germ cell-sufficient (RFPxAMH-Cre) and germ cell-deficient (NANOS2 KO) mice. We also have single-cell RNA-sequencing data for RFPxAMH-Cre sorted Sertoli cells from unsynchronized adult testes (not included in this series).

2021-08-31 | GSE166187 | 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