Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-Seq and ChIP-Seq from Tbr2+ and Tbr2- nuclei

ABSTRACT: RNA-Seq and ChIP-Seq from Tbr2+ and Tbr2- nuclei

PROVIDER: PRJNA706762 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13860367.fastq.gz	Fastqsanger.gz
	SRR13860368.fastq.gz	Fastqsanger.gz
	SRR13860369.fastq.gz	Fastqsanger.gz
	SRR13860370.fastq.gz	Fastqsanger.gz
	SRR13860371.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 29

Similar Datasets

RNA-Seq and ChIP-Seq from Tbr2+ and Tbr2- nuclei

Project description:We performed RNA-Seq and H3K9ac ChIP-Seq from Tbr2+ and Tbr2- nuclei sorted by FACS from E16.5 embryonic cortex treated with either vehicle or HDAC inhibitor (TSA).

2021-03-05 | GSE168298 | GEO

Transcriptome analysis of E15.5 wild-type (Tbr2-f/+) andTbr2-Isl1/+ retinae

Project description:Isl1 encodes a member of the LIM/homeodomain family of transcription factors. During retinal development. Isl1 plays a critical role in RGC fate specification. Tbr2 is essential for the formation and maintaining the survival of ipRGCs. In this study, we tested whether ectopically expressing Isl1 in Tbr2-expressing cells affects the developmental program of Tbr2-expressing retinal neurons, including ipRGCs and a subset of wide-field displaced amacrine cells. We generated a Tbr2-Isl1 knock-in allele using gene targeting technique, and then used RNA-seq approach to compare transcriptome profiles between E15.5 wild-type (Tbr2-flox/+) and Tbr2-Isl1/+ retinas to uncover how Isl1 affects Tbr2-regulated genes.

2025-04-30 | GSE149791 | GEO

Identification of ChIP-seq and RIME grade antibodies for Estrogen Receptor alpha

Project description:Estrogen Receptor alpha (ERα) is a key driver of most breast cancers, and it is the target of endocrine therapies used in the clinic to treat women with ERα positive (ER+) breast cancer. The two methods ChIP-seq (chromatin immunoprecipitation coupled with deep sequencing) and RIME (Rapid Immunoprecipitation of Endogenous Proteins) have greatly improved our understanding of ERα function during breast cancer progression and in response to anti-estrogens. A critical component of both ChIP-seq and RIME protocols is the antibody that is used to pull down the bait protein. To date, most of the ChIP-seq and RIME experiments for the study of ERα have been performed using the sc-543 antibody from Santa Cruz Biotechnology. However, this antibody has been discontinued, thereby severely impacting the study of ERα in normal physiology as well as diseases such as breast cancer and ovarian cancer. Here, we compare the sc-543 antibody with other commercially available antibodies, and we show that 06-935 (EMD Millipore) and ab3575 (Abcam) antibodies can successfully replace the sc-543 antibody for ChIP-seq and RIME experiments.

2019-03-21 | PXD012930 | Pride

Ultra-parallel ChIP-seq by barcoding of intact nuclei

Project description:Ultra-parallel ChIP-seq by barcoding of intact nuclei

| PRJNA435556 | ENA

Tbr2 and Neurog2 transcription factor binding sites in E14.5 WT cerebral cortices

Project description:To date, speculations on the molecular roles of Tbr2 transcription factor during specification, maintenance and differentiation of cortical specific Intermediate Neural Progenitors are coming from the analysis of loss- and gain-of-function experiments. However since its capacity to bind the DNA to extert its function we did Chromatin Immuno-Precipitation followed by deep sequencing to profile its target on the genome. We performed this approach directly in vivo to respect the physiological and peculiar enviroment of its action during cortical development. Moreover we did the same approach for Neurogenin 2 proneural gene. Interestingly the vast majority of the Neurog2 peaks are in common with Tbr2 dataset suggesting a co-operation between the two factors confirmed by biochemical and functional assays. Finally we compared Tbr2 dataset with the DNA regions bound by the H3K27me3 histone demethylase Jmjd3 (NCBI:Kdm6b) obtained by others. Interestingly we were able to find regions in common linked to important genes for neuronal differentiation. 3 samples, one input chromatin, one ChIP for Tbr2 and one ChIP for Neurog2

2016-09-08 | E-GEOD-63620 | biostudies-arrayexpress

Single nuclei RNA-seq using droplet microfluidics (DroNc-seq)

Project description:Single nuclei RNA-seq using droplet microfluidics (DroNc-seq)

| PRJNA413529 | ENA

ChIP-seq analysis of control and DOT1L HET cortical nuclei.

Project description:ChIP-seq analysis of control and DOT1L HET cortical nuclei.

| PRJNA1240293 | ENA

Transcriptional profiling of E14.5 control and Tbr2 fl/fl;Foxg1::Cre cortices

Project description:The abscence of TBR2 gene in human leads to microcephaly. This condition is mimicked by the specific ablation of the murine gene in developing cerebral cortex. Herein we compared gene expression in control and Tbr2 cKO in E14.5 cerebral cortices. This approach represents a useful tool to identify the molecular mechanisms at the basis of the phenotype. 6 samples, 3x Tbr2 +/+;Foxg1::Cre (control) and 3x Tbr2 fl/fl;Foxg1::Cre

2016-09-08 | E-GEOD-63619 | biostudies-arrayexpress

Single nuclei RNA-seq from adult mouse Hippocampus

Project description:We report RNA-seq of single nuclei isolated from the adult C57BL/6 male mouse Hippocampus region. Majority of the nuclei were isolated from 12 weeks old mice (4 different animal), with an additional set of nuclei from 3 months and 2 years old animals. In addition a set of GFP labeled nuclei driven by a VGAT promoter . Microdissections of dentate gyrus, CA1 and CA2/3 regions of the Hippocampus were placed into ice-cold RNA-later for fixation and stored at 4âc overnight, then stored in -80âc. Nuclei were isolated by sucrose gradient centrifugation and kept on ice until sorting using Fluorescence Activated Cell Sorting (FACS) into 96 well plates containing RNA lysis buffer. Single nucleus RNA was first purified then derived cDNA libraries were generated following a modified Smart-seq2 protocol. For VGAT nuclei: high titer AAV1/2 of pAAV-EF1a-DIO-EYFP-KASH-WPRE-hGH-polyA was injected into dorsal and/or ventral Hippocampus, animals were sacrificed two weeks after injections, and GFP labeled nuclei were sorted into plates and processed as described above.

2016-08-16 | E-GEOD-85721 | biostudies-arrayexpress

Gene expression in Tbr2 lineage neurons in the murine cerebral cortex

Project description:During cortical development neurons are generated from basal progenitors (BPs) which specifically express the transcription factor Tbr2. We used fluorescent-activated cell sorting (FACS) to isolate Tbr2-lineage neurons (GFP+) from mice brain at postnatal day 2 (P2) and determined mRNA expression profiles using microarray (Illumina MouseWG-6 v2). Role of transcription factor Tbr2 in neurodevelopment.

2019-10-18 | GSE121470 | 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