Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Phosphorytomics analysis was conducted from NIH-3T3 cell lines cultured in standard substrate and Nanopore#3scaffold

ABSTRACT: Phosphorytomics analysis was conducted to examine the differentially expressed phosphorylated protein in NIH-3T3 cell lines cultured in standard substrate and Nanopore#3scaffold.

ORGANISM(S): Mus Musculus

SUBMITTER: Keqing Shi

PROVIDER: PXD060988 | iProX | Thu Feb 20 00:00:00 GMT 2025

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Similar Datasets

Proteomic analysis revealed the proteins witidiferential expression in NIH-3T3 cells samples clultured in stadard subtrate and Nanopore#3 scaffold

Project description:Proteomic analysis was conducted to examine the differentially expressed proteins in NIH-3T3 cell lines cultured in standard substrate and Nanopore#3 scaffold.

2025-02-20 | PXD060987 |

Phosphorylation of ZHP-3 expressed in cultured human cells

Project description:When we expressed C. elegans ZHP-3 in tissue-cultured human cells, we found that this protein was frequently phosphorylated, likely by human cyclin-dependent kinases (CDKs). This suggests that ZHP-3 in C. elegans may function as a substrate for CDKs.

2025-01-15 | PXD059805 |

Transcription profiling of hESCs cultured on cSAPs and flat control (TCPS) using RNAseq analysis

Project description:The biophysical cues in the fate determination of pluripotent stem cells (PSCs) have not been well-revealed. In the current study, we used a novel type of substrate called colloidal self-assembled patterns (cSAPs) as an artificial matrix for the expansion of human ESCs. Briefly, the cSAPs substrate was composed of SiO2 with 2 μm diameter and PS with 100 nm diameter within the 24-well tissue culture plates (TCPS, Falcon). H1 hESCs cultured on cSAPs and flat control (TCPS) for 2 passages (4 days/passage) were dissociated with 0.5 mM EDTA for RNAseq. Total RNA (each sample ~ 1 × 106 cells) was extracted by 1 ml TRIzol (Life Technologies) and purified according to the standard instruction. RNA Sequence analysis was conducted by BGI Tech (Shenzhen, China). The analysis of gene function was performed with the multi-group data mining system of Dr. Tom (http://report.bgi.com). Gene changes on cSAPs compare to TCPS over 2-fold were defined as the significant threshold. The result indicates that hESCs cultured on the cSAPs were highly pluripotent and induced up-regulation of Toll-like receptor, HIF-1a, and Notch and down-regulation of FAs, MAPK, JAK/STAT, and TGF-β signaling pathways. We further confirmed the RNAseq result for down-regulation of CAV1, CXCL14, PTK2, and VCL genes which are part of focal adhesion and MAPK signaling by qPCR analysis. These findings demonstrate that the complex cSAPs can generate specific biophysical cues for the pluripotency of PSCs and enhance the differentiation potential to hemopoietic cells. We further demonstrated that the cSAPs substrate can keep the pluripotency and increase the efficiency of hemopoietic differentiation of cultured PSCs in comparison with the cultured cells on the flat substrate.

2021-12-20 | E-MTAB-11123 | biostudies-arrayexpress

Expression data from cultured human ovarian carcinoma cell lines

Project description:The hallmark of human cancer is heterogeneity, mirroring the complexity of genetic and epigenetic alterations acquired during oncogenesis. We extracted RNA of 34 cultured human ovarian carcinoma cell lines and performed expression microarrays so that cultured cell lines can represent in vivo human tumors.

2013-05-21 | GSE28724 | GEO

Expression data from cultured human esophageal squamous cell carcinoma cell lines and cultured human fibroblasts.

Project description:Cancer cells express different sets of receptor type tyrosine kinases. These receptor kinases may be activated through autocrine or paracrine mechanisms. Fibroblasts may modify the biologic properties of surrounding cancer cells through paracrine mechansms. We used microarrays to obtain the global gene expression of human esophageal squamous cell carcinoma cell lines and various esophageal fibroblasts. A total of 22 human esophageal squamous cell carcinoma cell lines and fibroblasts were analyzed. 4 fibroblasts were obtained from surgically resected human esophagus. Cells were cultured under standard conditions, total RNA was extracted and hybridized on Affymetrix microarrays.

2014-12-09 | E-GEOD-63941 | biostudies-arrayexpress

RNA-Seq to validate the effect of substrate and format as drivers of transcriptional variance in human intestinal organoids

Project description:An initial comparison of RNA-sequencing datasets from 251 experiments on 35 human intestinal organoid lines revealed that differences in transcriptional signatures could be influenced by variations in the format (3D, monolayers on transwells, and monolayers on 96-well plates) as well as substrate (collagen and Matrigel) in which the organoid lines are cultured. While the organoid lines were a common to these datasets, there were differences in experimental approaches in different laboratories. To rule out potential confounding variables, we performed an RNA-Seq experiment using 5 jejunal organoid lines cultured at the same time in different formats and substrates to evaluate their roles in baseline transcriptional signatures and determine if key findings from the initial analysis could be validated.

2021-10-30 | GSE182437 | GEO

Substrate sample

Project description:Substrate soil microbial community diversity

| PRJNA593085 | ENA

substrate films

Project description:substrate films Raw sequence reads

| PRJNA792343 | ENA

Sphere cultured biliary tract cancer cell lines SNU245 and SNU1196

Project description:Sphere cultured biliary tract cancer cell lines SNU245 and SNU1196

| PRJNA978524 | ENA

Substrate selectivity for semisynthetic CK2 proteins with Pin1

Project description:Protein Ser/Thr kinase CK2 is involved in a myriad of cellular processes including cell growth and proliferation by phosphorylating hundreds of substrates, yet the regulation process of CK2 function is poorly understood. The CK2 catalytic subunit, CK2α, is phosphorylated at Thr344 and phosphorylation on the C-terminal tail of CK2α is required for interaction with Pin1 protein. The substrate selectivity for protein kinase CK2α was examined by performing kinase assays on protein microarrays spotted with 17,000 human proteins. Semisynthetic CK2α proteins were prepared to contain an unmodified C-terminal tail or phospho-Thr (pThr) at T344. These semisynthetic proteins were used to determine if the phosphorylation-dependent interaction of CK2α with Pin1 can modulate the substrate selectivity for CK2. The different semisynthetic CK2α proteins (unmodified and pThr344) were tested alone and in the presence of the recombinant Pin1 protein. Pin1 has been shown to interaction with CK2α only when CK2α is phoshorylated on its C-terminal site (including Thr344). In the study presented here, kinase assays were performed using two different semisynthetic CK2α proteins: unmodified C-terminal tail and phospho-Thr (pThr) at 344. The semisynthetic proteins were each tested alone and in the presence of the recombinant Pin1 protein. There were four different kinase conditions and each condition was performed in duplicate.

2011-10-24 | E-GEOD-33150 | 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