Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

81 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of E14Tg2a cells upon Zic3 knockdown after day1 and day2 of differentiation into epiblast-like stem cells

ABSTRACT: Identification of Zic3-dependent transcriptome at d1EpiLC and d2EpiLC. Gene expression was studied in the presence or absence of Zic3 (RNAi) in the Rex1GFPd2 mouse embryonic stem cell line (parental line; E14Tg2a) in d1- and d2-EpiLC differentiated states.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Mus musculus

SUBMITTER: Munazah Andrabi

PROVIDER: E-MTAB-7206 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

ChIP-seq of Zic3 in ES-E14Tg2a embryonic stem cells after 2 days of differentiation to epiblast-like cells

Project description:Identification of Zic3 cistrome at ESC, d1EpiLC and d2EpiLC. ChIPmentaion experiments were performed using ZIC3 (Abcam, ab222124) antibody in the Rex1GFPd2 mouse embryonic stem cell line (ESC; parental line; E14Tg2a) and d1- and d2-EpiLC differentiated states.

2019-05-11 | E-MTAB-7208 | biostudies-arrayexpress

Single cell RNAseq of embryonic stem cells at day1 and day2 of epiblast-like stem cells differentiated states

Project description:The single cell transcriptome in the Rex1GFPd2 mouse embryonic stem cell line (parental line; E14Tg2a) at ESC, d1- and d2-EpiLC differentiated states.

2019-05-13 | E-MTAB-7211 | biostudies-arrayexpress

syangRNAseq

Project description:Gene expression was studied in the presence or absence of Otx2 (RNAi) in the Rex1GFPd2 mouse embryonic stem cell line (parental line; E14Tg2a) in undifferentiated and differentiated states.

2014-06-24 | E-MTAB-2245 | biostudies-arrayexpress

RNA-seq of E14Tg2a cells upon Zic3 knockdown after day1 and day2 of differentiation into epiblast-like stem cells

Project description:RNA-seq of E14Tg2a cells upon Zic3 knockdown after day1 and day2 of differentiation into epiblast-like stem cells

| PRJEB28630 | ENA

ChIP-seq of Zic3 in ES-E14Tg2a embryonic stem cells after 2 days of differentiation to epiblast-like cells

Project description:ChIP-seq of Zic3 in ES-E14Tg2a embryonic stem cells after 2 days of differentiation to epiblast-like cells

| PRJEB28642 | ENA

Open chromatin profiling on ESC transition to day1- and day2-epiblast-like stem cells

Project description:Identification of open chromatin profiles at ESC, d1EpiLC and d2EpiLC. The accessible chromatin landscape of naive ESCs (Rex1GFPd2 mouse embryonic stem cell line; parental line; E14Tg2a) and their transition to EpiLCs over a two day period was determined using ATAC-seq.

2019-05-11 | E-MTAB-7207 | biostudies-arrayexpress

Whole heart transcriptional response to complete and epiblast-specfic deletion of Zic3 in 15.5 dpc mouse embryos

Project description:In order to better understand the molecular basis for the heart defects seen in Zic3 null and epiblast CKO embryos, we investigated whether complete or epiblast-specific deletion of Zic3 would impact later embryonic heart development at the transcriptional level by whole genome expression microarray. The whole heart was carefully dissected out from 15.5 dpc Zic3 +/y, Zic3 flox/y, Zic3 flox/y; Sox2-cre, and Zic3 -/y embryos, total RNAs were extracted and purified using RNeasy Mini Kit (QIAGEN). Spectrophotometry (NanoDrop-1000 Spectrophotometer, Thermo Fisher Scientific) and microfluidic electrophoresis (Experion Automated Electrophoresis System, Bio-Rad Laboratories) were used for RNA quality control. In vitro transcription was performed using Illumina TotalPrep RNA Amplification Kit (Applied Biosystems/Ambion). cRNAs were hybridized onto Illumina MouseWG-6 v2.0 Expression BeadChips (Illumina) per manufacturer’s instructions.

2012-12-12 | E-GEOD-41674 | biostudies-arrayexpress

Whole heart transcriptional response to complete and epiblast-specfic deletion of Zic3 in 15.5 dpc mouse embryos

2012-12-12 | GSE41674 | GEO

Zic3 interacts with distant regulatory elements to regulate zebrafish developmental genes

Project description:Zic3 regulates early embryonic patterning in vertebrates. Its loss-of-function disrupts gastrulation, left-right patterning, and neurogenesis. We use the zebrafish as a model to study the developmental role of Zic3 in vivo. Using a combination of two genomics approaches – ChIP-seq and microarray, we identified Zic3 targets, which include genes from the Nodal and Wnt pathways, and show for the first time cis-regulation of these genes by Zic3 using in vivo enhancer assay. We uncovered a previously unrecognized link between Zic3 and the non-canonical Wnt pathway in gastrulation and left-right patterning, and identified neural pre-pattern genes as Zic3 targets during the early steps of neural induction. Zic3 preferably binds to distal intergenic regions, some of which contain evolutionarily conserved functional enhancers. Our study establishes the zebrafish as an excellent model for genome-wide study of a transcription factor in vivo.

2014-02-27 | GSE41458 | GEO

Otx2 ChIP-seq in Rex1GFPd2 mouse embryonic stem cell line

Project description:Chromatin immunoprecipitation using Otx2 antibodies in Rex1GFPd2 mouse ES cells (parental line; E14Tg2a)

2014-06-24 | E-MTAB-2281 | biostudies-arrayexpress