Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of mouse Rex-1 knockout cell lines was compared to that of J1 wild type cellsRex-1 knockout cell lines was compared to that of J1 wild type cells in the presence and absence of LIF

ABSTRACT: This study was undertaken in order to characterize the functions of Rex-1 and identify potential Rex-1 target genes.Both alleles of the Rex-1 gene were disrupted in J1 mouse embryonic stem cells. Gene expression levels in one of the resulting Rex-1 knockout cell lines was compared to that of J1 wild type cells. Experiment Overall Design: Gene expression in Rex-1 knockout mouse embryonic stem cells compared to that of J1 wild type cells. Cells were cultured in the presence and absence of LIF. This series utilized eight samples.There are two biological replicates per cell type cultured under this condition. The J1 samples serve as the control.

ORGANISM(S): Mus musculus

SUBMITTER: Kymora Scotland

PROVIDER: E-GEOD-9978 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

AICAR can modulate the expression of microRNA in J1 mESC

Project description:We have demonstrated AICAR can maintain J1 mouse ES cells pluripotency in our previous research, yet its effects on ES cells miRNAs expression remain a mystery. In this study, we performed small RNA (sRNA) High-throughput sequencing using Illumina HiSeq 2000 to investigate the influence of AICAR on J1 mouse ES cells miRNAs expression and further found the mechanism of how miRNAs affect ES cells pluripotency maintenance. Samples that treated by DMSO is used as a control. Compare microRNA expression of J1 mESC cultured with or without small molecule AICAR

2014-02-06 | E-GEOD-54586 | biostudies-arrayexpress

Deep sequencing identifies PD0325901 modulated microRNAs in the J1 mESCs

Project description:PD0325901 is involved in improving reprogramming efficiency during inducing pluripotent stem cells (iPSC) or maintain a blastocyst-like state in embryonic stem cells (ESC). However, the knowledge about this small molecule regulating miRNAs in ESC was limited. To understand the role of miRNAs during PD03-induced ESC maintenance and gain an insight how PD0325901 regulates miRNAs expression; we performed small RNA sequencing using Illumina HiSeq 2000 under the compounds treatment. The data show the miRNAs regulated by PD0325901. J1 mESCs maintained in medium containing 1000 U/mL LIF and supplemented with PD0325901 for 24 hours, J1 treated with DMSO was set as control. Then total RNA was extracted for analysis.

2016-05-17 | E-GEOD-67570 | biostudies-arrayexpress

Influence of SB431542 on J1 mouse embryonic stem cells growth

Project description:To know exactly how SB431542 contribute to mouse embryonic stem cells (mESCs) undifferentiated state maintenance, microarray experiment for DMSO mock treated and SB431542 treated J1 mESCs was performed J1 mESCs maintained in medium containing 1000 U/mL LIF and supplemented without or with SB431542 for 24 hours, then total RNA was extracted for analysis.

2014-10-29 | E-GEOD-55729 | biostudies-arrayexpress

Identifying PD0325901-regulated genes in the J1 mESCs

Project description:It has been demonstrated that PD0325901 promotes self-renewal of mouse embryonic stem cells, however, the target genes of PD0325901 are not fully understood. To better understand the downstream target genes of PD0325901, we performed Microarray analyses to identify their downstream targets. The data show the genes regulated by PD0325901. J1 mESCs maintained in medium containing 1000 U/mL LIF and supplemented without or with PD0325901 for 24 hours, then total RNA was extracted for analysis.

2016-05-17 | E-GEOD-67534 | biostudies-arrayexpress

Identifying CHIR99021 and AICAR-regulated genes in the J1 mESCs

Project description:It has been demonstrated that CHIR99021 promotes self-renewal of mouse embryonic stem cells, however, the target genes of CHIR99021 is not fully understood. AICAR is the activator of AMP-activated protein kinase. It is reported that AICAR plays important role in mouse embryonic stem cells, however the moleculor mechanism of this phenomenon is unknown. To better understand the downstream target genes of CHIR99021 and AICAR, we performed Microarray analyses to identify their downstream targets. The data show the genes regulated by CHIR99021 or AICAR. J1 mESCs maintained in medium containing 1000 U/mL LIF and supplemented without or with CHIR99021 or AICAR for 24 hours, then total RNA was extracted for analysis.

2013-01-01 | E-GEOD-40959 | biostudies-arrayexpress

Identifying vitamin C and RA-regulated genes in the J1 mESCs

Project description:It has been demonstrated that vitamin C enhances reprogramming efficiency during inducing pluripotent stem cells, however, the underlying mechanisms are not fully understood. To find the downstream target genes of vitamin C and investigate the mechanism of vitamin C on reprogramming promotion, we performed Microarray analyses to identify its downstream targets. Retinoic acid (RA), a stimulus molecule for cellular differentiation, is set as negative control. The data show the genes regulated by vitamin C or RA. J1 mESCs maintained in medium containing 1000 U/mL LIF and supplemented without or with vitamin C or RA for 24 hours, then total RNA was extracted for analysis.

2014-01-21 | E-GEOD-43405 | biostudies-arrayexpress

ChIP-seq of RNase J1 null strain

Project description:RNase J1 is the first nuclease with 5’-3’ exonuclease activity in bacteria and plays an important role in the maturation and degradation of mRNA. RNase J1 could also play a role in transcription termination of aberrant complexes. RNase J1 could bind to nascent RNA in such complexes, degrade the nascent RNA, and upon catching up with RNA polymerase (RNAP) dissociate the complex. Similar model was showed in eukaryotes. We did ChIP-seq to confirm our hypothesis.

2019-12-31 | E-MTAB-5659 | biostudies-arrayexpress

RNA-seq of Bacillus subtilis wild type and RNase J1 null strains

Project description:RNase J1 is the first nuclease with 5-3 exonuclease activity in bacteria and plays an important role in the maturation and degradation of mRNA. Absence of RNase J1 in cells has effect on cell morphology and growth rate. We did RNA-seq of Bacillus subtilis wild type and RNase J1 null strains (triplicates) to obtain more information about cellular role of this nuclease in cells. Complmentary ChIP-seq data have also been deposited in ArrayExpress under accession number E-MTAB-5659 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5659 ).

2019-12-31 | E-MTAB-5660 | biostudies-arrayexpress

Transcriptional analysis of live and hybridized J1 and NIH-3T3 cells

Project description:J1 mouse embryonic stem cells (mESCs) and NIH-3T3 fibroblasts were grown in standard media conditions. Hybridized cells were fixed with 4% paraformaldehyde; incubated for 12 hours at 30C in an RNA preserving hybridization (RPH) buffer (300 mM Sodium chloride, 30mM Sodium citrate, 2.1M Ammonium sulfate, 25% formamide, 10 mM EDTA, 1 mg/ml E. Coli tRNA, 500 μg/ml BSA); and reverse cross-linked for 1 hour at 50C in with Sodium dodecyl sulfate (SDS) and Proteinase K (100 mM NaCl, 10 mM pH 8.0 Tris, 1 mM EDTA, 0.5% SDS, 500 μg/ml Proteinase K). one replicate per sample

2014-03-20 | E-GEOD-55919 | biostudies-arrayexpress

Comparisons between fully and partially reprogrammed iPS cells induced by pMX-Klf4, pMX-Oct4 and pMX-Sox2 retroviruses

Project description:Induced pluripotent stem (iPS) cell reprogramming is a gradual epigenetic process that reactivates the pluripotent transcriptional network by erasing and establishing heterochromatin marks. Here, we characterize the physical structure of heterochromatin domains in full and partial mouse iPS cells by correlative Electron Spectroscopic Imaging (ESI). In somatic and partial iPS cells, constitutive heterochromatin marked by H3K9me3 is highly compartmentalized into chromocenter structures of densely packed 10 nm chromatin fibers. In contrast, chromocenter boundaries are poorly defined in pluripotent ES and full iPS cells, and are characterized by unusually dispersed 10 nm heterochromatin fibers in high Nanog-expressing cells, including pluripotent cells of the mouse blastocyst prior to differentiation. This heterochromatin reorganization accompanies retroviral silencing during conversion of partial iPS cells by Mek/Gsk3 2i inhibitor treatment. Thus, constitutive heterochromatin reorganization serves as a novel biomarker with retroviral silencing for identifying iPS cells in the very late stages of reprogramming. We compared the expression profiles of partially and fully reprogrammed iPS cell lines derived from CD1 mouse embryonic fibroblasts (MEFSs) by retroviral reprogramming (pMX-Oct4, pMX-Klf4 and pMX-Sox2). to the differentiated MEFS and the J1 embryonic stem cell line. We also studied the effect of a 2i cocktail treatment in partially reprogrammed iPS cells.

2011-09-21 | E-GEOD-21595 | biostudies-arrayexpress

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