Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ChIP-Seq and RNA-Seq of mouse E12.5

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Mus musculus

SUBMITTER: Sten Linnarsson

PROVIDER: E-GEOD-82100 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

A PBX1 transcriptional network controls dopaminergic neuron development and is impaired in Parkinson's disease.

Villaescusa J Carlos JC Li Bingsi B Toledo Enrique M EM Rivetti di Val Cervo Pia P Yang Shanzheng S Stott Simon Rw SR Kaiser Karol K Islam Saiful S Gyllborg Daniel D Laguna-Goya Rocio R Landreh Michael M Lönnerberg Peter P Falk Anna A Bergman Tomas T Barker Roger A RA Linnarsson Sten S Selleri Licia L Arenas Ernest E

The EMBO journal 20160628 18

Pre-B-cell leukemia homeobox (PBX) transcription factors are known to regulate organogenesis, but their molecular targets and function in midbrain dopaminergic neurons (mDAn) as well as their role in neurodegenerative diseases are unknown. Here, we show that PBX1 controls a novel transcriptional network required for mDAn specification and survival, which is sufficient to generate mDAn from human stem cells. Mechanistically, PBX1 plays a dual role in transcription by directly repressing or activa ...[more]

PMID: 27354364

Similar Datasets

ChIP-Seq for Pbx1 in the mouse E12.5 ventral midbrain

Project description:Investigations into the roles for Pbx1 and its transcriptional network in dopaminergic neuron development and Parkinson's Disease One sample each for Pbx1, IgG, and input

2016-07-22 | E-GEOD-82098 | biostudies-arrayexpress

RNA-Seq of mouse E12.5 brain regions

Project description:Investigations into the roles for Pbx1 and its transcriptional network in dopaminergic neuron development and Parkinson's Disease Three samples each from dorsal midbrain, forebrain, hindbrain, Alar plate, and ventral midbrain

2016-07-22 | E-GEOD-82099 | biostudies-arrayexpress

Program specificity for Ptf1a in PancreasM-BM- versusM-BM- Neural Tube DevelopmentM-BM- correlates with distinctM-BM- collaborating cofactors and chromatin accessibility

Project description:Ptf1a is a lineage-specific basic-helix-loop-helix transcription factor critical in the development of both the pancreas and nervous system. How one transcription factor controls diverse programs of gene expression is a fundamental question in developmental biology. To uncover molecular strategies for the program-specific functions of Ptf1a, we identified bound genomic regions in vivo during development of both tissues. A majority of regions bound by Ptf1a are tissue-specific, lie near genes needed for proper formation and maturation of each tissue, and reflect regions of open chromatin.M-BM- M-BM- Information for the specificity of Ptf1a binding and function is encoded in the DNA surrounding the Ptf1a-bound sites, since Ptf1a-bound regions are sufficient to direct tissue-restricted reporter expression when tested in transgenic mice. Fox and Sox factors were identified as lineage specific modifiers ofM-BM- Ptf1a binding, sinceM-BM- binding motifs for these factors are enriched in Ptf1a-bound regions in pancreas and neural tube, respectively. Although Ptf1a and Foxa2 co-localize to sites in embryonic pancreas and can act synergistically in cell transfection assays, biochemical experiments detected no physical interaction between the two factors. These findingsM-BM- indicateM-BM- that lineage-specific chromatin landscapes likely constrain the functions of Ptf1a, and identify Fox and Sox gene families as part of this process. RNA-Seq: Examination of gene expression in Ptf1a expressing cells (NT E.12.5, Pancreas E15.5) ChIP-Seq: Examination of chromatin occupancy in 2 tissue types (E12.5 NT and 17.5 Pancreas). Faire-Seq: Examination of open chromatin in 2 tissue types (E12.5 NT and 17.5 Pancreas).

2013-08-15 | E-GEOD-47459 | biostudies-arrayexpress

Otx2 controls regional patterning within the MGE and regional identity of the septum [ChIP-Seq]

Project description:The Otx2 homeobox transcription factor is essential for gastrulation and early neural development. We generated Otx2 conditional knockout (cKO) mice to investigate its roles in telencephalon development after E9.0. We conducted transcriptional profiling and in situ hybridization to identify genes de-regulated in Otx2 cKO ventral forebrain. In parallel, we used ChIP-seq to identify enhancer elements, OTX2 binding motif, and which de-regulated genes are likely direct targets of Otx2 transcriptional regulation. We found that Otx2 was essential in septum specification; regulation of Fgf signaling in the rostral telencephalon; and medial ganglionic eminence (MGE) patterning, neurogenesis, and oligodendrogenesis. Within the MGE, Otx2 was required for ventral but not dorsal identity; this is the first demonstration of a transcription factor that contributes to regional patterning within the MGE. Microdissected subpallium (septum, MGE, and LGE ) from wildtype E12.5 CD-1 embryos was used in three independentanti-OTX2 ChIP-seq experiments.

2015-06-10 | E-GEOD-69724 | biostudies-arrayexpress

The Gene Expression Analysis in E12.5 Mouse Hearts with GATA4-FOG2 Interaction Loss

Project description:In order to identify the targets of GATA4-FOG2 action in mammalian heart development we performed Affymetrix microarray comparisons of gene expression in normal and mutant at embryonic (E) day E12.5 hearts. We compared RNA samples from both Fog2-null and Gata4ki/ki mutant E12.5 hearts to the wild-type control E12.5 hearts. We reasoned that as the phenotypes of the Fog2 knockout and Gata4ki/ki mutation (a V217G mutation that specifically cripples the interaction between GATA4 and FOG proteins) are similar, we should expect to identify a similar set of differentially expressed genes in both experiments. As an additional control, we expected to find the Fog2 gene expression absent in the mutant (null) Fog2 cardiac sample, but not Gata4ki/ki sample. We have analyzed 6 RNA samples total (3 from control hearts, 2 from FOG2 null hearts and 1 from GATA4ki hearts)

2010-02-21 | E-GEOD-14906 | biostudies-arrayexpress

RNA-seq of mid-gestation mouse mammary tissues from E12.5 stage organs

Project description:RNA sequencing of embryonic mammary tissue from mid-gestation E12.5 mouse mammary glands, using SMARTer amplification. Mammary epithelium, mammary mesenchyme, ventral surface epithelium were micro dissected from E12.5-stage C57BL/6 mouse embryos.

2018-11-30 | E-MTAB-6859 | biostudies-arrayexpress

E12.5 distal forelimb embryonnic transcriptome

Project description:Analysis of gene expression in the distal forelimbs RNA-Seq polyA on transcripts extracted from the dissection of three pairs of embryonnic forelimbs at E12.5

2015-10-26 | E-GEOD-72285 | biostudies-arrayexpress

In vivo RNA-Seq analysis of Foxa1 and Foxa2 transcriptional target at E12.5

Project description:E12.5 wild-type and NestinCre Foxa1/2 Flox/ Flox mutant embryos were quickly snap-frozen, then 10um-thick cryostat coronal sections of the midbrain were cut and mounted on membrane slides (Zeiss) and the floor plate was Laser Capture Microdissected. RNA was extracted using the Picopure RNA Isolation Kit RNA sequencing library was prepared using the Ovation RNA-Seq system (Nugen). RNA-Seq libraries were sequenced on the Illumina GAIIx.

2015-02-19 | E-MTAB-3333 | biostudies-arrayexpress

Transcriptomes of mouse PGCLCs isolated from 6-day culture embryoid bodies were compared with transcriptomes of their precur cells (ESCs, iPSCs, and EpiLCs) and E12.5 in vivo mouse PGCs

Project description:Transcriptomes of mouse E12.5 primordial germ cells (PGCs), primordial germ cell-like cells (PGCLCs) isolated from 6-day culture embryoid bodies, and the precursor pluripotent stem cells [embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs)] and epiblast-like cells (EpiLCs) Total RNA was isolated from FACS-enriched, SSEA1+/CD61+ double-positive PGCs and PGCLCs. RNA was also isolated from ESC, iPSC, and EpiLC cultured without enrichment. Transcriptomes were determined using Affymetrix microarray.

2016-08-22 | E-GEOD-80983 | biostudies-arrayexpress

RNA-seq profiling of transcriptomes of control and Hif1a mutant E12.5 hearts

Project description:Purpose: to identify genes aberrantly expressed upon myocardial ablation of Hif1a Methods: a floxed Hif1a allele was deleted in mouse embryonic hearts using a NXK2.5Cre line. Total RNA was extracted from E12.5 hearts (n=3 for controls and mutants) usinz Trizol and processed for RNA-seq. Reads were mapped to Mm10 reference genome using TopHat2 and Bowtie2. Transcript expression values were determined after transcript normalization with AltAnalyze Results: this analysis revealed a total of 1451 genes significantely (|Fold| > 20% and P<0.05) modulated in Hif1a cKO hearts 6 total RNAseq runs with 3 experimental samples and 3 controls samples

2015-04-29 | E-GEOD-61209 | 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