Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spatial proteomics based on laser capture micro-dissection (LCM) for investigating the impact of CD168+ TAM- coated tumor region (CCTR) on CD8+ T cells Function in colon cancer tissues

ABSTRACT: Multiplex immunofluorescence staining for CD11b, CD168, CD8, and Pan-CK was performed on three colon cancer specimens to identify CCTR regions. Subsequently, CD8+ T cells located at varying distances from the CCTR were subjected to single-cell resolution laser capture micro-dissection (LCM) and spatial proteomics analysis. These cells were categorized into three groups: the CCTR group (≤50 μm, n=393), the ad-CCTR group (>50 μm and ≤200 μm, n=375), and the non-CCTR group (>200 μm, n=383).

ORGANISM(S): Homo Sapiens

SUBMITTER: Jianjun Li

PROVIDER: PXD073051 | iProX | Wed Jan 14 00:00:00 GMT 2026

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq analysis on bioactive micelle PPP8 therapy for Hemin stimulated mouse neurons

Project description:To analyze the effect of micellar PPP treatment on hemin-stimulated neurons, HT22 cells were treated with PBS, 50 μM hemin, or 25 μg/mL micellar PPP8 plus 50 μM hemin for 6 h. HT22 cells treated with PBS (control group), hemin (experimental group), or the combination of PPP8 and hemin (intervention group) were then collected for transcriptome (RNA-seq) analysis.

2025-12-09 | GSE290286 | GEO

Expression data for HT29 cells treated with 5-aza-deoxy-cytidine [Affymetrix]

Project description:The RNA samples from HT-29 (ATCC) colon cancer cell line were reverse transcribed into cDNAs and categorized in 3 groups with different concentrations of 5-aza-deoxy-cytidine (5-Aza); in each group three replicative 150 mm cultures were treated with: 1) dimethyl sulfoxide (vehicle alone, 0 μM 5-Aza); 2) 5μM 5-Aza and 3) 10 μM 5-Aza; for five days We then used Affymetrix microarray platform to profile the gene expression of the 3 HT29 cell groups (3 replicates in each group) in order to search for differentially expressed genes

2013-09-17 | GSE41364 | GEO

Laser-capture microscopy coupled with Smart-seq2 (LCM-seq) for robust and efficient transcriptomic profiling of mouse and human tissues

Project description:Generally, when LCM is used in diverse transcriptomic analyses, several hundred, if not thousands, of cells are needed to obtain high quality of RNA-seq data. As some cellular populations are very small and tissue often in scarcity, we aimed to carefully document the lowest number of cells needed to retrieve sequencable libraries. We started with capturing 120 cells and subsequently scaled down to 50 cells, 30 cells, 10 cells, 5 cells, 2 cells and finally 1 cell. By optimizing multiple steps in the procedure, including direct lysis of cells without performing RNA isolation, we developed LCM-seq that couples LCM with Smart-seq2 for robust and efficient polyA-based RNA sequencing. We applied LCM-seq to mouse and human neuron samples, and demonstrated that LCM-seq can allow us to acquire high quality RNA-seq data from mouse and human tissues to conduct various transcriptomic studies.

2016-07-05 | GSE76514 | GEO

To measure extension longevity effect of soraprazan and identify the mechanism

Project description:Lipofuscin is known as intracellular waste substance produced by damaged mitochondrial incompleted decomposition. And it is a biomarker of aging. As aging, accumulation of the lipofuscin in retinal pigment epithelium induces blindness called Age-related macular degeneration. Soraprazan is developed to reduce the lipofuscin production and cure the age-related macular degeneration. Soraprazan reducing the age biomarker lipofuscin can be suggested to have effect of longevity extension. C.elegans were treated on NGM agar plate containing 0, 50, 100, 200 μM soraprazan and showed the lipofuscin reduction and extension of longevity. To identify the mechanism, 0 and 200 μM treated worms’ RNA expression was analyzed through microarray.

2020-01-23 | GSE144059 | GEO

Timeseries RNA-Seq analysis of low phosphorus-induced adventitious root formation in Populus ussuriensis

Project description:For RNA-seq, new cuttings from 3-week-old in vivo plants were cultured on the solid Woody Plant Medium (WPM) containing 20 g/L sucrose and 3 g/L Gelrite (Duchefa). After 5 days of culture, the root primordium formed cuttings were transferred to modified liquid WPM containing 10 μM or 200 μM KH2PO4, and harvested the basal ends of stem cuttings containing root primordium with its surrounding tissues using 11# scalpel after 2h, 4h, 8h, 12h and 24h culture. Samples were collected from two biological replicates (50 cuttings each).

2022-08-16 | GSE174726 | GEO

Laser-capture microscopy coupled with Smart-seq2 (LCM-seq) for robust and efficient transcriptomic profiling of mouse and human tissues

2016-07-05 | E-GEOD-76514 | biostudies-arrayexpress

Laser Capture Microdissection-based RNAseq for Profiling Mouse and Human Sebaceous Gland Transcriptomes

Project description:We describe the use of laser capture microdissection (LCM) to isolate human and murine sebaceous glands (SGs) for transcriptomic analysis and publish this SG transcriptomic data for reference. We show that compared to whole skin RNA sequencing, LCM RNA sequencing allows for high resolution in identifying and describing SG genes at homeostasis. Lastly, we compare this LCM of sebaceous glands to published SG clusters from single cell RNA sequencing of skin, and show that we achieve greater resolution and depth with the LCM approach.

2024-01-26 | GSE230682 | GEO

Laser Capture Microdissection of Hyperlipidemic Mouse Aorta Atherosclerosis

Project description:Atherosclerosis is a transmural chronic inflammatory condition of small and large arteries that is associated with adaptive immune responses at all disease stages. However, impacts of adaptive immune reactions on clinically apparent atherosclerosis such as intima lesion (plaque) rupture, thrombosis, myocardial infarction, and aneurysm largely remain to be identified. It is increasingly recognized that leukocyte infiltrates in plaque, media, and adventitia are distinct but their specific roles have not been defined. To map these infiltrates, we employed laser capture microdissection (LCM) to isolate the three arterial wall laminae using apoE-/- mouse aorta as a model. RNA from LCM-separated tissues was extracted and large scale whole genome expression microarrays were prepared. We observed that the quality of the resulting gene expression maps was compromised by tissue RNA carried over from adjacent laminae during LCM. To account for these flaws, we established quality controls and algorithms to improve the predictive power of LCM-derived microarray data. Our approach creates robust transcriptome atlases of normal and atherosclerotic aorta. Assessing LCM transcriptomes for immunity-related mRNAs indicated markedly distinctive gene expression patterns in the three laminae of the atherosclerotic aorta. These mouse mRNA expression data banks can now be mined to address a wide range of questions in cardiovascular biology.

2011-11-03 | GSE21419 | GEO

Transcriptome study of Caco-2 human intestinal cells following exposure to empty or S-nitrosoglutathione-loaded polymeric nanoparticles

Project description:To further study the transcriptome of Caco-2 human colon epithelial-like cells after exposure to S-nitrosoglutathione (GSNO, 1.4 μM), or Eudragit RL PO polymeric nanoparticles (NP-ERL, 50 μg/mL) or GSNO loaded nanoparticles (NP-GSNO, 50 μg/mL corresponding to (1.4 μM GSNO) we investigate whole genome microarray to identify genes regulates by exposure or not to GSNO (1.4 μM) or Eudragit RL PO polymeric nanoparticles (NP-ERL, 50 μg/mL) or GSNO loaded nanoparticles (NP-GSNO, 50 μg/mL corresponding to (1.4 μM GSNO).

2015-12-31 | GSE69551 | GEO

Laser-capture microdissected invasive micropapillary carcinomas of the breast

Project description:The purpose of this study was to identify differentially expressed genes in laser-capture microdissected (LCM) invasive mammary carcinomas (IMCs).

2011-04-25 | GSE28821 | GEO

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