Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

64 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nascent RNAseq of hESC.

ABSTRACT: Nascent RNAseq in conjunction with Illumina TRUseq method to sequence total RNAs including short lived RNAs using highly strand-specific next-generation sequencing (NGS) libraries

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Homo sapiens

SUBMITTER: Gregor Rot

PROVIDER: E-MTAB-5115 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

RNAseq libraries to study developmental alternative polyadenylation in human primitive streak progenitors derived from hESCs.

Project description:Illumina TRUseq method to generate highly strand-specific next-generation sequencing (NGS) libraries

2019-02-25 | E-MTAB-5099 | biostudies-arrayexpress

TDP-43 iCLIP in mESC and hESC

Project description:Genome-wide analysis of rna-TDP43 interactions at single nucleotide resolution in mouse and human embryonic stem cells

2019-03-31 | E-MTAB-5100 | biostudies-arrayexpress

QuantSeq libraries to study TDP-43 dependent alternative polyadenylation

Project description:QuantSeq-Rev method to generate highly strand-specific next-generation sequencing (NGS) libraries enabling transcript quantification and identification of the 3'end of polyadenylated RNAs

2019-02-25 | E-MTAB-5091 | biostudies-arrayexpress

RNAseq libraries to study TDP-43 dependent alternative polyadenylation

Project description:Illumina TRUseq method to generate highly strand-specific next-generation sequencing (NGS) libraries

2019-02-25 | E-MTAB-5097 | biostudies-arrayexpress

QuantSeq and RNAseq libraries to study developmental alternative polyadenylation

2019-02-25 | E-MTAB-5090 | biostudies-arrayexpress

EMpire: Deep isoform level integration of the transcriptome, translatome, and proteome

Project description:In this study, we make used of mRNA-seq and its ability to reliably quantify isoforms, integrating this data with ribosome profiling and LC-MS/MS, to assign ribosome footprints and peptides at the isoform level. We leverage the principle that most cell types, and even tissues, predominantly express a single principal isoform to set isoform-level mRNA-seq quantifications as priors to guide and improve allocation of footprints or peptides to isoforms. Through tightly integrated mRNAseq, ribosome footprinting and/or LC-MS/MS proteomics we demonstrate that a principal isoform can be identified in over 80% of gene products in homogenous HEK293 cell culture and over 70% of proteins detected in complex human brain tissue. Defining isoforms in experiments with matched RNA-seq and translatomic/proteomic data increases the functional relevance of such datasets and will further broaden our understanding of multi-level control of gene expression. In this PRIDE submission you will find the raw files for the HEK293 cell proteomics. Files for the human brain proteomics can be found at PXD005445. We have also uploaded a zip file that contains the input files for our HEK293 cell analysis, and the isoform level output files – there is a separate folder within the zip files for these. The data used to create the manuscript figures is in the Rdata file. Code for assigning peptides and footprints to isoforms can be found on Github here: https://github.com/rkitchen/EMpire

2018-08-21 | PXD008693 | Pride

Gene expression analysis of H9 hESC derived cardiomyocytes (CM) and neuron stem cells (NSC)

Project description:In this study, we generated wildtype H9 hESC derived cardiomyocytes (CM) and neural stem cells (NSC) by in vitro differentiation. Global gene expression profiles were compared among undifferentiated H9 hESC and the derived CM and NSC. Comparison of global gene expression profiles of undifferentiated H9 hESC and the derived CM and NSC populations.

2013-08-31 | E-GEOD-48257 | biostudies-arrayexpress

Induction of pluripotency in human somatic cells via a primitive streak-like state

Project description:During mammalian embryonic development, the primitive streak is initiates the differentiation of pluripotent epiblast cells into germ layers. Pluripotency can be reacquired in committed somatic cells using a combination of handful transcription factors, such as OCT3/4, SOX2, KLF4 and c-MYC (hereafter referred to as OSKM), albeit with low efficiency . Here we show that, during the OSKM-induced reprogramming process toward pluripotency in human cells, intermediate cells transiently show gene expression profiles resembling mesendoderm, which is a major component of the primitive streak. Based on these findings, we discover that forkhead box H1 (FOXH1), a transcription factor required for anterior primitive streak specification during early development, significantly enhances the reprogramming efficiency of human fibroblasts by promoting their maturation, including the mesenchymal to epithelial transition and the activation of late pluripotent markers. These results demonstrate that during the reprogramming process, human somatic cells go through a transient state that resembles mesendoderm. Human differentiated progeny derived from pluripotent stem cells, N=13 Human undifferentiated pluripotent stem cells, N=6 Transgenic ESC line, N=6 Human tissues, N=29 Human tissue-derived cells, N=20 Human nascent reprogrammed cells, N=95 Mouse cells, N=12

2014-04-24 | E-GEOD-50206 | biostudies-arrayexpress

RNAseq libraries to study early developmental progenitors (24hrs differentiation vs hESCs)

Project description:Illumina TRUseq method to generate highly strand-specific next-generation sequencing (NGS) libraries

2019-03-20 | E-MTAB-5114 | biostudies-arrayexpress

Cardiac precursor differentiation from hESCs by lentiviral promoter drug selection

Project description:Several of the essential core transcriptional control elements in human embryonic stem cells (ESCs) have been identified, but the production and function of alternative isoforms in self-renewal, pluripotency and tissue lineage specification remain largely unknown. We have modified the H9 ESC line to allow for drug selection of human pluripotent ESCs and cardiac progenitors. Exon-level microarray expression data from undifferentiated ESCs and day 40 cardiac precursors were used to identify differentially expressed and alternative splice isoforms during differentiation. Keywords: comparison RNA from a homogenous population of undifferentiated hESCs (REX1-neo promoter drug selection) and differentiated day 40 cardiomyocytes (alpha MHC-puro promoter drug selection) was isolated and profiled with exon-tiling arrays.

2008-10-24 | E-GEOD-13297 | 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