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

RNA-seq of a cardiac differentiation timecourse from human embryonic stem cells

ABSTRACT: Bulk RNA-seq data of HES3 hESCs sampled through a differentiation timecourse. Sample collection was at day 0, 3.75, 4.75, 5.75 and 12. There are additional day 5.75 samples with MYC transgene overexpression (activated from day 4.75).

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Homo sapiens

SUBMITTER:

PROVIDER: E-MTAB-14248 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): ERP162149

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

RNA-seq of sorted cells at day 3 of cardiac differentiation based on HAND1 level

Project description:The aim of the experiment was to identify HAND1 target genes and its impact on chromatin accessibility in relation to cardiac development. A HAND1-null hESC line was used, in which a doxycycline-inducible HAND1-T2A-BFP transgene had been integrated in approximately half of the cells for HAND1 rescue / overexpression. The hESCs were differentiated with BMP4, Activin A and CHIR. On day 2.5, doxycycline was added. On day 3, cells were dissociated and sorted by BFP level using FACS. Samples were immediately processed for RNA-seq and ATAC-seq.

2025-02-13 | E-MTAB-14278 | biostudies-arrayexpress

RNA-seq of sorted cells at day 7.5 of cardiac differentiation from human embyronic stem cells

Project description:The experiment aimed to resolve cellular heterogeneity in cardiac differentiation through the purification of different cell populations by lineage markers and analysis of their transcriptomes and chromatin accessibility. The differentiation protocol was designed to promote cell diversity. The addition of SB at day 2, inhibited SMAD2/3 phosphorylation and created a high BMP signalling bias to restrict cardiac differentiation in favour of other mesodermal lineages, whereas the addition of DMH1 at day 2, inhibited SMAD1/5/8 phosphorylation to create a high Activin signaling bias to promote the co-differentiation of endoderm. Cells were sorted based on SOX17-tomato and NKX2-5-GFP knock-in reporters into their major classes: Pop1 = SB_G0_T0 Pop2 = SB_G1_T0 Pop3 = CTRL_G0_T0 Pop4 = CTRL_G1_T0 Pop5 = DM_G0_T0 Pop6 = DM_G1_T0 Pop7 = DM_G1_T1 Pop8 = DM_G0_T1

2025-02-13 | E-MTAB-14276 | biostudies-arrayexpress

RNA-seq comparing wild-type and MEIS1/2 knockout cells in cardiac differentiation

Project description:Bulk RNA-seq data from differentiating embryoid bodies made from wild-type and MEIS1/2 knockout HES3 hESCs, collected at day 5 and 7 of differentiation. The aim of the experiments was to identity differentially expressed genes and therefore putative MEIS targets.

2025-01-31 | E-MTAB-14250 | biostudies-arrayexpress

Combining transcriptome and proteome analysis to identify and characterize the RpoS regulon in Pseudomonas fluorescens

Project description:Background: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s matrix.

2019-11-12 | PXD010845 | Pride

RIP-seq of translation initiation factors eIF2γ, eIF3b and two RBPs involved in the process of mRNA degradation and storage, Pat1p and Lsm1p

Project description:The aim of this experiment is to determine the RNA binding partners of the translation initiation factors eIF2γ (GCD11), eIF3b (PRT1) and Pat1p and Lsm1p two RNA binding proteins (RBPs) involved in mRNA degradation and storage.

2023-09-06 | E-MTAB-13033 | biostudies-arrayexpress

H2S regulation the metabolism of cucumber in response to salt-stress through transcriptome and proteome analysis

Project description:In a previous study, we found that H2S alleviates salinity stress in cucumber by maintaining the Na+/K+ balance and by regulating H2S metabolism and the oxidative stress response. However, little is known about the molecular mechanisms behind H2S-regulated salt-stress tolerance in cucumber. Here, an integrated transcriptomic and proteomic analysis based on RNA-seq and 2-DE was used to investigate the global mechanism underlying H2S-regulated salt-stress tolerance. In total, 11 761 differentially expressed genes (DEGs) and 61 differentially expressed proteins (DEPs) were identified. Analysis of the pathways associated with the DEGs showed that salt stress enriched expression of genes in primary and energy metabolism, such as photosynthesis, carbon metabolism and biosynthesis of amino acids. Application of H2S significantly decreased these DEGs but enriched DEGs related to plant-pathogen interaction, sulfur-containing metabolism, cell defense and signal transduction pathways. Notably, changes related to sulfur-containing metabolism and cell defense were also observed through proteome analysis, such as Cysteine synthase 1, Glutathione S-transferase U25-like, Protein disulfide-isomerase and Peroxidase 2. We present the first global analysis of the mechanism underlying H2S regulation of salt-stress tolerance in cucumber through tracking changes in the expression of specific proteins and genes.

2021-09-09 | PXD020642 | Pride

Differential expression analysis for RNA-seq data between cardiac progenitor and uncommitted cells at day 4.75

Project description:We report the differential expression between cardiac progenitor and uncommitted cells at day 4.75

2014-07-09 | GSE58363 | GEO

ATAC-seq of sorted cells at day 3 of cardiac differentiation based on HAND1 level

2025-02-13 | E-MTAB-14279 | biostudies-arrayexpress

Transcriptome of 3 developmental stages of Colletotrichum graminicola during infection of Zea mays leaf sheaths

Project description:Transcriptome of 3 developmental stages of Colletotrichum graminicola during infection of Zea mays leaf sheaths 3 biological replicates per stage. The three stages are: pre-penetration appressoria (PA), early biotrophic phase (BP), and the switch from biotrophy to necrotrophy (NP). Each biological replicate of the first stage, the pre-penetration appressoria, was sequenced to a 2-fold greater depth due to its lower representation in the samples.

2012-06-04 | E-GEOD-34632 | biostudies-arrayexpress

Single cell RNA-seq to resolve heterogeneity in a cardiac differentiation timecourse

Project description:Differentiation of HES3 hESCs using BMP4, Activin A and CHIR99021. 5 timepoints of sample collection (day 3-12). Differentiations were started sequentially and collected and processed on the same day. Sample1 = day 3 + day3.75 (50:50 mix); Sample2 = day 4.75; Sample3 = day 5.75; Sample 4 = day 12.

2025-01-31 | E-MTAB-14249 | 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