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

Transcription profiling of human synovial tissue with ectopic lymphoid structures from patients with rheumatoid arthritis

ABSTRACT: Spots were selected that had an expression level higher than 1.6 the local background. The use of a common reference sample allows the comparison of the relative expression levels across the tissue samples. All genes were expressed relative to their median expression level across the arrays of the same microarray platform, allowing us to combine the data from the 2 platforms. Data from Lymphochip and Stanford Human cDNA arrays was combined per patient. Only genes with reliable datapoints in at least 80% of the samples were used. Subsequently, genes with the same unigene identifier were averaged in SMD. For all further analysis genes were selected that showed at least a two-fold difference in expression level in at least one array.

ORGANISM(S): Homo sapiens

SUBMITTER: Cornelis Verweij

PROVIDER: E-SMDB-4129 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Gene expression profiling of rheumatoid arthritis synovial tissues

Project description:Spots were selected that had an expression level higher than 1.6 the local background. The use of a common reference sample allows the comparison of the relative expression levels across the tissue samples. All genes were expressed relative to their median expression level across the arrays of the same microarray platform, allowing us to combine the data from the 2 platforms. Data from Lymphochip and Stanford Human cDNA arrays was combined per patient. Only genes with reliable datapoints in at least 80% of the samples were used. Subsequently, genes with the same unigene identifier were averaged in SMD. For all further analysis genes were selected that showed at least a two-fold difference in expression level in at least one array. A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied. Keywords: disease_state_design

2007-09-13 | GSE9027 | GEO

Gene expression profiling of rheumatoid arthritis synovial tissues

2007-09-13 | E-GEOD-9027 | biostudies-arrayexpress

Genome-wide analysis of cellular SMD or NMD substrates that regulated by Upf1 or PNRC2 in HeLa cell

Project description:Analysis of cellular SMD or NMD substrates that regulated by Upf1 and/or PNRC2 in HeLa cell. The hypothesis tested in the present study was that endogenous SMD or NMD substrates may co-regulated by Upf1 and PNRC2. Results provide important information that vast range of cellular SMD or NMD substrates are reqired PNRC2 for decay.

2012-02-28 | GSE26781 | GEO

Ectopic lymphoid structures in the aged lacrimal glands

Project description:To investigate the molecular pathways altered during aging of the lacrimal gland in C57BL/6J females, we compared the LG transcriptome at different time points.

2023-02-06 | GSE224596 | GEO

Ectopic lymphoid structures as microniches for tumor progenitor cells

Project description:Genomic copy number profiling of hepatocellular carcinomas (HCC) from IKKβ(EE)Hep mice (C57BL/6) constitutively expressing IKKβ in the liver without and after treatment with DEN (diethylnitrosamine) and of HCCs that developed in wild type mice (C57BL/6) after DEN treatment.

2015-09-25 | E-MTAB-3848 | biostudies-arrayexpress

Features of ectopic lymphoid-like structures in human uveitis.

Project description:Persistent non-infectious uveitis has a significant morbidity, but the extent to which this is accompanied by inflammation driven remodelling of the tissue is unclear. To address this question, we studied a series of samples selected from two ocular tissue repositories and identified 15 samples with focal infiltration. Eleven of fifteen contained lymphocytes, both B cells (CD20 positive) and T cells (CD3 positive). In 20% of the samples there was evidence of ectopic lymphoid like structures with focal aggregations of B cells and T cells, segregated into anatomically different adjacent zones. To investigate inflammation in the tissue, an analysis of 520 immune relevant transcripts was carried out and 24 genes were differentially upregulated, compared with control tissue. Two of these (CD14 and fibronectin) were increased in ocular inflammation compared to control immune tissue (tonsil). We demonstrate that in a significant minority of patients, chronic persistent uveitis leads to dysregulation of ocular immune surveillance, characterized by the development of areas of local ectopic lymphoid like structures, which may be a target for therapeutic intervention directed at antibody producing cells.

| S-EPMC7029346 | biostudies-literature

siRNA of human HeLa cells reveals Staufen1 regulates a variety of mammalian transcripts

Project description:It is currently unknown how extensively the double-stranded RNA binding protein Staufen (Stau)1 is utilized by mammalian cells to regulate gene expression. To date, Stau1 binding to the 3â untranslated region (3âUTR) of ARF1 mRNA has been shown to target ARF1 mRNA for Stau1-mediated mRNA decay (SMD). ARF1 SMD depends on translation and recruitment of the nonsense-mediated mRNA decay factor Upf1 to the ARF1 3âUTR by Stau1. Here, we use microarray analyses to examine changes in the abundance of cellular mRNAs that occur when Stau1 is depleted. Results indicate that 1.1% and 1.0% of the 11,569 HeLa-cell transcripts that were analyzed are, respectively, upregulated and downregulated at least two-fold in three independently performed experiments. Additionally, we localize the Stau1 binding site to the 3âUTR of four mRNAs that we define as natural SMD targets. Together, these and substantiating results suggest that Stau1 influences the expression of a wide variety of physiologic transcripts and metabolic pathways. Experiment Overall Design: We report the results of three independently performed microarray analyses that examined changes in the abundance of transcripts from HeLa-cell genes upon Stau1 depletion. HeLa cells were transiently transfected with either a nonspecific Control small interfering (si)RNA or Stau1 siRNA. Stau1 siRNA reduced the level of cellular Stau1 to as little as 4% of normal, where normal is defined as the level in the presence of Control siRNA (data not shown). RNA from three independently performed transfections was separately hybridized to microarrays.

2008-06-15 | E-GEOD-6679 | biostudies-arrayexpress

Homo sapiens

Project description:Kidney transplantation (SMD set)

| PRJNA114471 | ENA

Protruding structures on caterpillars are controlled by ectopic Wnt1 expression.

Project description:Spine-like or protruding structures, which may be aposematic for predators, are often observed in multiple segments of lepidopteran larvae (caterpillars). For example, the larvae of the Chinese wheel butterfly, Byasa alcinous, display many protrusions on their backs as a warning that they are toxic. Although these protrusions are formed by an integument lined with single-layered epidermal cells, the molecular mechanisms underlying their formation have remained unclear. In this study, we focused on a spontaneous mutant of the silkworm, Bombyx mori, Knobbed, which shows similar protrusions to B. alcinous and demonstrates that Wnt1 plays a crucial role in the formation of protrusion structures. Using both transgene expression and RNAi-based knockdown approaches, we showed that Wnt1 designates the position where epidermal cells excessively proliferate, leading to the generation of knobbed structures. Furthermore, in the B. alcinous larvae, Wnt1 was also specifically expressed in association with the protrusions. Our results suggest that Wnt1 plays a role in the formation of protrusions on the larval body, and is conserved broadly among diverse species in Lepidoptera.

| S-EPMC4376876 | biostudies-literature

SMD-IPTL 4-plex yeast and BSA-yeast

Project description:Isobaric peptide termini labeling (IPTL) is an attractive protein quantification method, because it provides more accurate and reliable quantification information than traditional isobaric labelling methods (TMT, iTRAQ) by making use of the entire fragment ion series instead of only a single reporter ion. The multiplexing capacity of published IPTL implementations is, however, limited to three. Here, we present a selective maleylation-directed isobaric peptide termini labelling (SMD-IPTL) approach for quantitative proteomics of LysC protein digests. SMD-IPTL extends the multiplexing capacity to 4-plex with the potential for higher levels of multiplexing using commercially available 13C/15N-labelled amino acids. SMD-IPTL is achieved in a one-pot reaction in three consecutive steps: 1) selective maleylation at the N-terminus; 2) labelling at the ԑ-NH2 group of the C-terminal Lys with isotopically labelled acetyl alanine; 3) thiol Michael addition of an isotopically labelled acetyl cysteine at the maleylated N-terminus. The isobarically labelled peptides are fragmented into sets of b- and y-ion clusters upon LC-MS/MS, which not only convey sequence information but also quantitative information for every labelling channel and avoid the issue of ratio distortion observed with reporter-ion-based approaches. We demonstrate the SMD-IPTL approach with a 4-plex labelled sample of BSA and yeast lysates mixed at different ratios. Utilizing SMD-IPTL for labelling and a narrow precursor isolation window of 0.8 Th with an offset of -0.2 Th, accurate ratios were measured across a 10-fold mixing range of BSA in a background of yeast proteome. With the yeast proteins mixed at ratios of 1:5:1:5, BSA was detected at ratios 0.94:2.46:4.70:9.92 when spiked at 1:2:5:10 ratios with an average standard deviation of peptide ratios of 0.34.

2020-04-27 | PXD018589 | Pride

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