Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

30 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq Time Course of Developing Hydra Spheroids in Hydra Medium (HM) and isotonic medium (70mM sucrose) conditions

ABSTRACT: Probing the role of mechanical oscillations in Hydra regeneration by manipulating environmental osmotic properties. Single spheroids from a period of 22h were collected at 1h intervals and sequenced in both a normal hypotonic medium (HM), as well an isotonic medium (70mM sucrose).

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Hydra vulgaris

SUBMITTER: Panagiotis Papasaikas

PROVIDER: E-MTAB-9672 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of Hydra body segments and regenerated Hydra animals

Project description:Positional RNA-sequencing of isolated Hydra body pieces and RNA-sequencing of fully regenerated Hydra animal was combined with RNA-sequencing of actively regenerating spheroids (see submission E-MTAB-9672) in order to elucidate the role of tissue stretching on regeneration and body pattern formation.

2022-10-13 | E-MTAB-9676 | biostudies-arrayexpress

Cooperative blockade of CK2 and ATM kinases drives apoptosis in VHL-deficient renal carcinoma cells / RNA-seq (BRB-seq) of treated 786-O spheroids

Project description:Multicellular Tumor Spheroids (MCTS) were pre-formed for 3 days with 786-O cell line to better mimic the tumor microenviroenment. These spheroids were treated with either vehicle (DMSO), drugs alone (KU-60019 10 μM; CX-4945 5 μM) or in combination (KU + CX) for 48h before RNA extraction.

2021-02-04 | E-MTAB-9977 | biostudies-arrayexpress

RNA-seq of NvElav1::mOrange positive and NvElav1::mOrange negative cells from Nematostella vectensis

Project description:NvElav1::mOrange is a stable transgenic line that labels a large fraction of the nervous system of the sea anemone Nematostella vectensis (Nakanishi et al., Development 2012). Two week old primary polyps were dissociated and the NvElav1::mOrange positive cells were enriched by FACS.

2020-02-28 | E-MTAB-8794 | biostudies-arrayexpress

Introducing synthetic thermostable RNase inhibitors in single-cell RNA-seq

Project description:Single-cell RNA-sequencing (scRNAseq) is revolutionizing biomedicine, propelled by advances in methodology, ease of use, and cost reduction of library preparation. Over the past decade, there have been remarkable technical improvements in most aspects of single-cell transcriptomics. Yet, there has been little to no progress in advancing RNase inhibition despite that maintained RNA integrity is critical during cell collection, storage, and cDNA library generation. Here, we demonstrate that a synthetic thermostable RNase inhibitor yield single-cell libraries of equal or superior quality compared to ubiquitously used protein-based recombinant RNase inhibitors (RRIs). Importantly, the synthetic RNase inhibitor provide additional unique improvements in reproducibility and throughput, enable new experimental workflows including heat cycles, and can reduce the need for dry-ice transports. In summary, replacing RRIs represents a substantial advancement in the field of single-cell transcriptomics.

2024-07-29 | E-MTAB-13873 | biostudies-arrayexpress

LoRTIS: A long read method for analysis of large transposon mutant libraries

Project description:Transposon insertion site sequencing (TIS) is a powerful method for associating genotype to phenotype. However, all TIS methods described to date use short nucleotide sequence reads which cannot uniquely determine the locations of transposon insertions within repeating genomic sequences where the repeat units are longer than the sequence read length. To overcome this limitation, we have developed a TIS method using Oxford Nanopore sequencing technology that generates and uses long nucleotide sequence reads; we have called this method LoRTIS (Long Read Transposon Insertion-site Sequencing). This experiment data contains sequence files generated using Nanopore and Illumina platforms. Biotin1308.fastq.gz and Biotin2508.fastq.gz are fastq files generated from nanopore technology. Rep1-Tn.fastq.gz and Rep1-Tn.fastq.gz are fastq files generated using Illumina platform. In this study, we have compared the efficiency of two methods in identification of transposon insertion sites.

2022-05-30 | E-MTAB-11351 | biostudies-arrayexpress

PolyA-enriched RNA-seq of primary human hepatocyte spheroids treated with small molecule inhibitors targeting TEAD

Project description:TEAD1 emerged as an estrogen-sensitive gene that was upregulated in a HFD mouse model and in NAFLD patients. We investigated the roles of TEAD in NAFLD by treating primary human hepatocyte spheroids with two small molecule inhibitors blocking the TEAD/YAP interaction. One small molecule blocks the interaction by inhibiting TEAD autopalmitoylation (TEADap), the second small molecule blocks the interaction by binding to the surface of the TEAD protein (TEADsf).

2024-02-22 | E-MTAB-13207 | biostudies-arrayexpress

Single-cell transcriptome analysis of secretagogin mRNA expressing cells from the mouse hypothalamic paraventricular nucleus

Project description:The molecular mechanism regulating phasic corticotropin-releasing hormone (CRH) release from parvocellular neurons (PVN) remains poorly understood. Here, we find a cohort of parvocellular cells interspersed with magnocellular PVN neurons expressing secretagogin. Single-cell transcriptome analysis combined with protein interactome profiling identifies secretagogin neurons as a distinct CRH-releasing neuron population reliant on secretagoginM-bM-^@M-^Ys Ca2+ sensor properties and protein interactions with the vesicular traffic and exocytosis release machineries to liberate this key hypothalamic releasing hormone. single cells from the PVN region juvenile (21-28 days) mice were dissected and subject to whole transcriptome analysis

2014-11-20 | E-GEOD-63093 | biostudies-arrayexpress

Quantitative single-cell RNA-seq

Project description:Purpose: We applied cDNA molecule counting using unique molecular identifiers combined with high-throughput sequencing to study the transcriptome of individual mouse embryonic stem cells, with spike-in controls to monitor technical performance. We further examined transcriptional noise in the embryonic stem cells. One 96-well plate of single-stranded cDNA libraries generated from 96 single R1 mouse embryonic stem cells sequenced on two lanes, and one 96-well plate of the same libraries further amplified by 9 PCR cycles sequenced on one lane.

2013-12-20 | E-GEOD-46980 | biostudies-arrayexpress

Alternative platelet differentiation pathways initiated by non-hierarchically related hematopoietic stem cells

Project description:We performed single cell whole transcriptome (Smart-seq3) analysis of hematopoietic stem and progenitor cells long-term replenished by transplanted single Vwf-tdTomato+ P-HSCs (2290 total cells from 7 reconstituted mice) and Vwf-tdTomato Multi-HSCs (2478 total cells from 8 reconstituted mice), as well as control cells from normal mouse bone marrow.

2024-06-02 | E-MTAB-13935 | biostudies-arrayexpress

Chromatin profiling of dendritic cells in healthy and hyperglycaemic mice

Project description:The aim of the experiment was to compare chromatin states between healthy and hyperglycaemic mice. We focused on dendritic cells extracted from the lungs. Nuclei were extracted from 200.000 sorted dendritic cells per sample. H3K27me3 and H3K27ac were then profiled using CUT&RUN protocol.

2023-06-29 | E-MTAB-11390 | 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