Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Pluripotency governed by Sox2 via regulation of Oct3/4 expression in mouse embryonic stem cells

ABSTRACT: To characterize the differentiation by Sox2 KO, we performed microarray analyses of mouse ES cell line 2TS22C during the time-course being induced of Sox2 KO Inducible Sox2 KO cell line 2TS22C were assigned to eight experimental groups and cultured in GMEM medium (SIGMA) with LIF at 37Â°C in an atmosphere of 5% CO2 until the specified time point before the harvest: (1)for controls, cultured in the absence of Tc; (2) for 3h after the administration of Tc; (3) for 6h; (4) for 12h; (5) for 24h; (6) for 48h; (7) for 72h; (8) for 96h.

ORGANISM(S): Mus musculus

SUBMITTER: Kazue Takahashi

PROVIDER: E-GEOD-5895 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Pluripotency governed by Sox2 via regulation of Oct3/4 expression in mouse embryonic stem cells.

Masui Shinji S Nakatake Yuhki Y Toyooka Yayoi Y Shimosato Daisuke D Yagi Rika R Takahashi Kazue K Okochi Hitoshi H Okuda Akihiko A Matoba Ryo R Sharov Alexei A AA Ko Minoru S H MS Niwa Hitoshi H

Nature cell biology 20070521 6

The pluripotency of embryonic stem (ES) cells is thought to be maintained by a few key transcription factors, including Oct3/4 and Sox2. The function of Oct3/4 in ES cells has been extensively characterized, but that of Sox2 has yet to be determined. Sox2 can act synergistically with Oct3/4 in vitro to activate Oct-Sox enhancers, which regulate the expression of pluripotent stem cell-specific genes, including Nanog, Oct3/4 and Sox2 itself. These findings suggest that Sox2 is required by ES cells ...[more]

PMID: 17515932

Similar Datasets

Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray (22k Linearity)

Project description:E12.5 mouse whole embryo and E12.5 placenta total RNA were pooled to create 25:75, 50:50, and 75:25 ratio mixtures, based on Bioanalyzer quantitation. These samples, along with the original unmixed RNAs, were used as templates for duplicate linear amplification labeling reactions. cRNA target mixtures were hybridized against a Universal Mouse Reference (Stratagene). Pairwise comparison using the NIA Microarray Analysis (ANOVA) software produced log ratios, which were compared to the expected log ratios for genes showing statistically significant (FDR<0.05) differential expression between unmixed embryo and placenta. Keywords: cell type comparison design,development or differentiation design,normalization testing design,reference design E12.5 mouse whole embryo and E12.5 placenta total RNA were pooled to create 25:75, 50:50, and 75:25 ratio mixtures, based on Bioanalyzer quantitation. These samples, along with the original unmixed RNAs, were used as templates for duplicate linear amplification labeling reactions. cRNA target mixtures were hybridized against a Universal Mouse Reference (Stratagene). Pairwise comparison using the NIA Microarray Analysis (ANOVA) software produced log ratios, which were compared to the expected log ratios for genes showing statistically significant (FDR<0.05) differential expression between unmixed embryo and placenta.

2010-06-09 | E-GEOD-3508 | biostudies-arrayexpress

Klf4 cooperates with Oct3/4 and Sox2 to activate the Lefty1 core promoter in embryonic stem cells

Project description:To characterize Klf4 downstream genes, we performed microarray analyses of the ES cells knocked down by siRNA of Klf4 gene. Keywords: individual genetic characteristic design ES cells grow without feeders on gelatin coated in complete ES medium. Cells were incubated at 37 0C; 5% CO2. ES cells were transfected with siRNA and pCAGEGFP-IP plasmid. After transfection, cells were cultured for 24 hours, following to drag selection for more 24 hours in the presence of puromycin to ensure concentration of transfectants. Total RNA were extracted with Trizol reagent (Sigma) according to the manufacturerâ??s instructions.

2010-06-10 | E-GEOD-5930 | biostudies-arrayexpress

In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling: Part2

Project description:E12.5 mouse whole embryos and placentas were pooled within 3 litters and total RNA was extracted. Fluorescently-labeled, linearly-amplified cRNA targets were prepared from the RNA samples and compared on a novel microarray design to validate the system. A "self-versus-self" experimental design was used to assess the false-positive rates in the system. The in situ-synthesized 60-mer oligonucleotide microarray platform contains approximately 22,000 DNA features, and was designed to detect transcripts from the entire NIA cDNA clone collection. Keywords: self vs self design E12.5 mouse whole embryos and placentas were pooled within 3 litters and total RNA was extracted. Fluorescently-labeled, linearly-amplified cRNA targets were prepared from the RNA samples and compared on a novel microarray design to validate the system. A "self-versus-self" experimental design was used to assess the false-positive rates in the system. The in situ-synthesized 60-mer oligonucleotide microarray platform contains approximately 22,000 DNA features, and was designed to detect transcripts from the entire NIA cDNA clone collection.

2010-06-30 | E-GEOD-3513 | biostudies-arrayexpress

In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling: Part 3

Project description:E12.5 mouse whole embryos and placentas were pooled within 3 litters and total RNA was extracted. Fluorescently-labeled, linearly-amplified cRNA targets were prepared from the RNA samples at various input levels. A "full-scale" reference was prepared using the standard input level of 6.0 ug total RNA, and one round of amplification was performed with 250 ng and 50 ng total RNA inputs. For 10 ng and 2 ng inputs, two rounds of amplification were used. Targets were compared on a microarray platform designed for this test using a "dye-swapped" experimental design, and sets of significantly differential genes were compared to the full scale reference's list to determine specificity and sensitivity in terms of detection of significant expression differences. Keywords: dye swap design,quality control testing design E12.5 mouse whole embryos and placentas were pooled within 3 litters and total RNA was extracted. Fluorescently-labeled, linearly-amplified cRNA targets were prepared from the RNA samples at various input levels. A "full-scale" reference was prepared using the standard input level of 6.0 ug total RNA, and one round of amplification was performed with 250 ng and 50 ng total RNA inputs. For 10 ng and 2 ng inputs, two rounds of amplification were used. Targets were compared on a microarray platform designed for this test using a "dye-swapped" experimental design, and sets of significantly differential genes were compared to the full scale reference's list to determine specificity and sensitivity in terms of detection of significant expression differences.

2010-06-30 | E-GEOD-3507 | biostudies-arrayexpress

In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling: Part1

Project description:E12.5 mouse whole embryos and placentas were pooled within 3 litters and total RNA was extracted. Fluorescently-labeled, linearly-amplified cRNA targets were prepared from the RNA samples and compared on a novel microarray design to validate the system. A "dye-swapped" experimental design was used to assess the accuracy and precision of the system. The in situ-synthesized 60-mer oligonucleotide microarray platform contains approximately 22,000 DNA features, and was designed to detect transcripts from the entire NIA cDNA clone collection. Keywords: dye swap design,quality control testing design E12.5 mouse whole embryos and placentas were pooled within 3 litters and total RNA was extracted. Fluorescently-labeled, linearly-amplified cRNA targets were prepared from the RNA samples and compared on a novel microarray design to validate the system. A "dye-swapped" experimental design was used to assess the accuracy and precision of the system. The in situ-synthesized 60-mer oligonucleotide microarray platform contains approximately 22,000 DNA features, and was designed to detect transcripts from the entire NIA cDNA clone collection.

2010-06-30 | E-GEOD-3516 | biostudies-arrayexpress

ES, EC, NS, TS, Placenta and Neural induction (N2B27) comaprison

Project description:Comparison among ES, EC, TS, NS, differentiated neural cells derived from NS and placenta in addition to ES-N2B27 neural induction. Comparison among ES, EC, TS, NS, differentiated neural cells derived from NS and placenta in addition to ES-N2B27 neural induction.

2010-06-11 | E-GEOD-4077 | biostudies-arrayexpress

Defining a developmental path to neural fate by global expression profiling of mouse ESCs and adult NS cells

Project description:Defining a developmental path to neural fate by global expression profiling of mouse embryonic stem cells and adult neural stem/progenitor cells. This SuperSeries is composed of the following subset Series: GSE4075: Neural induction (Embrioid bodies-Retinoic acid) GSE4076: Neural induction (N2B27 monolayer cluture) GSE4077: ES, EC, NS, TS, Placenta and Neural induction (N2B27) comaprison Keywords: SuperSeries Refer to individual Series

2010-06-11 | E-GEOD-4082 | biostudies-arrayexpress

Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray (WGA 2.1 Spike Test)

Project description:E12.5 mouse whole embryo, E12.5 placenta, embryonic stem (ES) cells, and trophoblast stem (TS) cells were compared on a novel microarray design to validate the system. The in situ-synthesized 60-mer oligonucleotide microarray platform contains approximately 44,000 DNA features, and was designed to detect transcripts from all known genes, as well as about 5,000 potential genes, as identified by the NIA Mouse Gene Index 2.0. Seven external RNA controls were derived from intronic and intergenic yeast genome sequences, and 60-mer probes were spotted 10 time each on the slides. These spike-in RNA controls were diluted to cover 7 orders of magnitude in initial concentration, and used to define a function relating signal intensity to transcript abundance. Keywords: cell type comparison design,development or differentiation design,normalization testing design,reference design E12.5 mouse whole embryo, E12.5 placenta, embryonic stem (ES) cells, and trophoblast stem (TS) cells were compared on a novel microarray design to validate the system. The in situ-synthesized 60-mer oligonucleotide microarray platform contains approximately 44,000 DNA features, and was designed to detect transcripts from all known genes, as well as about 5,000 potential genes, as identified by the NIA Mouse Gene Index 2.0. Seven external RNA controls were derived from intronic and intergenic yeast genome sequences, and 60-mer probes were spotted 10 time each on the slides. These spike-in RNA controls were diluted to cover 7 orders of magnitude in initial concentration, and used to define a function relating signal intensity to transcript abundance.

2005-10-28 | E-GEOD-3509 | biostudies-arrayexpress

Thyroid Hormone (TH) Controls The Remodeling Of The Pancreas And The Liver, Part B

Project description:Thyroid hormone (TH) controls the remodeling of the pancreas and the liver. TH-induces dedifferentiation of the exocrine pancreas to a progenitor state (Proc. Nat. Acad Sci. 105, 8962-8967 (2008)) and it remodels the endocrine pancreas (Dev. Biol. 328, 384-391 (2009)). The redifferentiated frog pancreas resembles closely the pancreas of other typical vertebrates. Two pancreas arrays were carried out. The first one studied gene expression changes at different developmental stages of Xenopus laevis during metamorphosis. The second array studies gene expression changes at varying times after the addition of TH to premetamorphic tadpoles. Keywords: co-expression design,development or differentiation design,reference design,time series design Overall design: Thyroid hormone (TH) controls remodeling of the liver. The microarray was carried out to identify changes in gene expression at different stages of development during metamorphosis. This is part 2, done on the 22K Xenopus platform version 1. This dataset was from livers of Xenopus tadpoles (NF52, NF62, and NF66). Each was made in triplicate. Samples in all 3 parts of the study received the same thyroid hormone levels.

2010-05-16 | E-GEOD-16017 | biostudies-arrayexpress

Thyroid Hormone (TH) Controls The Remodeling Of The Pancreas And The Liver, Part A

Project description:Thyroid hormone (TH) controls the remodeling of the pancreas and the liver. TH-induces dedifferentiation of the exocrine pancreas to a progenitor state (Proc. Nat. Acad Sci. 105, 8962-8967 (2008)) and it remodels the endocrine pancreas (Dev. Biol. 328, 384-391 (2009)). The redifferentiated frog pancreas resembles closely the pancreas of other typical vertebrates. Two pancreas arrays were carried out. The first one studied gene expression changes at different developmental stages of Xenopus laevis during metamorphosis. The second array studies gene expression changes at varying times after the addition of TH to premetamorphic tadpoles. Keywords: cell cycle design,co-expression design,reference design,time series design Thyroid hormone (TH) controls remodeling of the pancreas. The micro array was carried out to identify changes in gene expression between the tadpole and frog pancreas. This is part 1, done on the 44K Xenopus platform. This dataset was used only for one pancreas experiment with several data points (control, 12h, 24h, 48h and frog). Each was made in triplicate. Samples in all 3 parts of the study received the same thyroid hormone levels.

2010-05-16 | E-GEOD-16074 | 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