Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mouse GBM OptiMix single-cell RNA-seq (CTRL vs SLR)

ABSTRACT: Single-cell RNA-seq study of mouse GBM samples with OptiMix barcoding. Two multiplexed 10x Chromium libraries were generated (runs dated 2025-06-13 and 2025-07-30). Demultiplexed biological groups include CTRL1-CTRL4 and SLR1-SLR4.

ORGANISM(S): Mus musculus

PROVIDER: GSE324014 | GEO | 2026/09/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

SLR/IAA14-dependent auxin induced lateral root initiation

Project description:Lateral root initiation was used as a model system to study the mechanisms behind auxin-induced cell division. Genome-wide transcriptional changes were monitored during the early steps of lateral root initiation. Inclusion of the dominant auxin signaling mutant solitary root1 (slr1) identified genes involved in lateral root initiation that act downstream of the AUX/IAA signaling pathway. Interestingly, key components of the cell cycle machinery were strongly defective in slr1, suggesting a direct link between AUX/IAA signaling and core cell cycle regulation. However, induction of the cell cycle in the mutant background by overexpression of the D-type cyclin (CYCD3;1) was able to trigger complete rounds of cell division in the pericycle that did not result in lateral root formation. Therefore, lateral root initiation can only take place when cell cycle activation is accompanied by cell fate respecification of pericycle cells. The microarray data also yielded evidence for the existence of both negative and positive feedback mechanisms that regulate auxin homeostasis and signal transduction in the pericycle, thereby fine-tuning the process of lateral root initiation. Keywords: time-course wild type vs mutant comparison

2005-11-01 | GSE3350 | GEO

Mouse GBM OptiMix single-cell RNA-seq (CTRL vs SLR)

Project description:Mouse GBM OptiMix single-cell RNA-seq (CTRL vs SLR)

| PRJNA1432972 | ENA

Project description:Fish eDNA Barcoding 2025

| PRJNA1346814 | ENA

Single-cell RNA sequencing of EGFR/RB1/TP53-mutant LUAD cell lines with and without PHOX2B overexpression to assess neuroendocrine phenotype induction

Project description:EGFR/RB1/TP53-mutant LUAD cell lines (H1975 and PC9) with and without PHOX2B overexpression were profiled to assess induction of the neuroendocrine (NE) phenotype. Cell lines transduced with lentiviral PHOX2B cDNA or empty vector (LV105) were analyzed by single-cell RNA sequencing (10x Chromium) with hashtag oligo (HTO) multiplexing (CellPlex). Conditions include parental H1975 and PC9 LUAD cell lines as well as engineered TP53/RB1 double-knockout variants (CYW). Four biological replicates were performed across 8 pooled sequencing runs (32 demultiplexed samples total).

2026-08-19 | GSE339453 | GEO

SUMOylation of rice DELLA SLR1 modulates transcriptional responses and improves yield under salt stress.

Project description:This work aimed to characterize the molecular differences of SUMO1-SLR1 and SLR1 in rice (Oryza sativa cv. Nipponbare) shoots subjected to salt stress and to identify novel SLR1 interactors. Because DELLA proteins regulate gene expression, we exposed SLR1-OX, SUMO1SLR1-OX, and Nipponbare genetic background to high salt concentrations (120 mM NaCl) during 8 hours at the seedling stage and collected samples for subsequent RNA-seq analysis. Functional annotation of SLR1-OX DEGs showed enrichment of gene ontology (GO) terms associated with diterpenoid biosynthesis, highlighting the impact of SLR1 on GA metabolism. After functional annotation of DEGs specific to SUMO1SLR1-OX, we found a significant over-representation of GO terms associated with defense response and gibberellin dioxygenase activity. We also found a salt stress-dependent induction of GA20ox2 and GA2ox3 genes in SUMO1SLR1-OX. GA20ox2 and GA2ox3 encode enzymes involved in the regulation of active GA (GA4) levels. Therefore, it is reasonable to hypothesize that SLR1 SUMOylation could adjust active GA homeostasis upon exposure to salt stress.

2024-09-01 | E-MTAB-14289 | biostudies-arrayexpress

Sialidase NEU3 action on GM1 ganglioside is neuroprotective in GM1 Gangliosidosis

Project description:Three runs for each sample for quantitation (MS1 spectra only) which are dated 20230716. One run for each sample for identification with UVPD. Peak area was quantified using the Genesis algorithm in QualBrowser.

2023-08-30 | MSV000092791 | MassIVE

The ImmgenT Open-Source project

Project description:This SuperSeries is composed of the SubSeries listed below. Supplementary files current as of 7/8/2025. v1 - 5/14/2025 v2 - 7/8/2025

2025-05-14 | GSE297097 | GEO

Transcriptome analysis of gibberellin-signaling mutants in rice

Project description:This Series is composed of the following Samples: GSM375647: Taichung 65_shoot_replicate 1 GSM375648: Taichung 65_shoot_replicate 2 GSM375649: Taichung 65_shoot_replicate 3 GSM375765: gid1-3_ shoot_replicate 1 GSM375766: gid1-3_ shoot_replicate 2 GSM375767: gid1-3_ shoot_replicate 3 GSM375769: gid2-1_ shoot_replicate 1 GSM375770: gid2-1_ shoot_replicate 2 GSM375772: gid2-1_ shoot_replicate 3 GSM375773: slr1 (k1001)_ shoot_replicate 1 GSM375775: slr1 (k1001)_ shoot_replicate 2 GSM375777: slr1 (k1001)_ shoot_replicate 3 12 samples were used in this experiment

2009-04-21 | E-GEOD-15046 | biostudies-arrayexpress

Metastable Intermediates Identified in Epithelial to Mesenchymal Transition are Regulated by G-quadruplex DNA Structures

Project description:Cancer is a heterogenous disease, with multiple cellular subpopulations present within a single tumour mass that differ genetically and morphologically, and thus respond differently to chemotherapeutics. Epithelial-to-Mesenchymal transition (EMT) has been shown to play a role in tumour heterogeneity. Single-cell sequencing is critical to identify cell-type-specific transcriptomic differences with multiplexing methods increasing experimental scope with reduced cost. Cell hashing with barcoded antibodies is commonly used to multiplex samples but is limited to samples expressing target antigens. Antigen-independent methods of barcoding cells, such as barcoded lipid-anchors, have gained traction but present substantial populations that cannot be unambiguously demultiplexed. Herein we report a multiplexed single-cell transfection-enabled cell hashing sequencing (scTECH-seq) platform, which uses antigen-independent endocytic uptake to barcode cells, resulting in efficient, uniform barcoding with high cell recovery. We apply this methodology to identify distinct metastable cell states in human mammary cells undergoing EMT and show that stabilisation of G-quadruplex DNA has the potential to inhibit EMT.

2024-07-01 | GSE225155 | GEO

Nitrogen fertilizer reduces salicylic acid-mediated immunity by activating gibberellin signaling in rice

Project description:The environment plays important role in the interaction between plant hosts and pathogens. The application of chemical fertilizer is a crucial breeding technology to enhance crop yield since last century. As the most abundant fertilizer, nitrogen often increases disease susceptibility for crop plants. The underlying mechanism for nitrogen induced disease susceptibility is elusive. Here we found that nitrogen application activate gibberellin signaling by degradation of SLR1, the repressor protein in gibberellin signaling, which result in simultaneously promoting plant growth and disease susceptibility. SLR1, physically interacts with OsNPR1 and consequently facilitate OsNPR1 mediated defense responses. Transcriptome analysis showed that OsNPR1-SLR1 module plays a vital role in transcriptional reprogramming for both disease resistance and plant growth. Increase of SLR1 protein level in gibberellin deficient rice plants neutralizes disease susceptibility but sacrifice yield enhancement under high nitrogen supply. Mutation in SD1, encoding OsGA2ox2, produced more grains than WT，and maintains disease resistance under high nitrogen supply. Taken together, our work reveals the molecular mechanism underlying nitrogen-induced disease susceptibility, and demonstrates that the application of sd1 rice varieties prevent the tradeoff between disease susceptibility and yield increase under high nitrogen supply.

2024-08-01 | GSE171646 | 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