Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

42 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single Cell gene expression profile of MDA-MB-231 TGL cells

ABSTRACT: Baseline MDA-MB-231 TGL cells were processed by scRNA-Seq.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Francesca Nadalin

PROVIDER: E-MTAB-13896 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single Cell gene expression and DNA accessibility profile of barcoded SUM159PT cells

Project description:Cancer is a heterogeneous disease, where multiple, phenotypically distinct subpopulations co-exist. Tumour evolution is a result of a complex interplay of genetic and epigenetic factors. To predict the molecular drivers of distinct cancer responses, we apply single-cell lineage tracing (scRNA-Seq of barcoded cells) on a triple-negative breast cancer model. SUM159PT cells infected with a lentiviral barcode library (Perturb-seq Library) were sorted according to the presence of BFP signal, treated or not with paclitaxel (PTX), and then processed by scRNA-Seq or Multiome.

2024-05-24 | E-MTAB-13064 | biostudies-arrayexpress

Multiplexed Single Cell gene expression profile of barcoded SUM159PT cells

2024-05-24 | E-MTAB-13066 | biostudies-arrayexpress

Single-cell RNA and BCR sequencing of naive B cells cultured in IgG class-switching polarising conditions

Project description:Naive B cells (CD27-IgD+) were obtained from 3 healthy controls and cultured in vitro under anti-IgM, CD40L and IFN-gamma to polarise class-switching towards IgG isotypes. Single-cell RNA and BCR sequencing libraries were prepared at Day 0 (before addition of stimuli), Day 3 and Day 6 of the cell culture time-course. This is intended as a dataset to validate a new computational method sciCSR in enumerating productive and sterile immunoglobulin transcripts as indicators of B cell class switching and maturation dynamics.

2023-07-01 | E-MTAB-13050 | biostudies-arrayexpress

Single-cell Gene Expression Flex analysis on PC9 cells co-cultured with NIH-3T3 cells

Project description:The goal of the experiment is to determine whether it is feasible to use the 10x Genomics Gene Expression Flex solution in samples containing a mixture of human and mouse cells. First we tested how the presence of mouse cells impacted the data recovered by the use of the human whole trasnscriptome amplification (WTA) probe sets. Then we profiled a mixed species sample by using human and mouse probe sets in the same reaction. Finally, for samples with lower amounts of human cells we tried to correct the amount of cells recovered by the human and mouse probe sets by adjusting the amount of cells loaded from the respective hybridizations.

2024-04-15 | E-MTAB-13962 | biostudies-arrayexpress

Single-cell Gene Expression Flex analysis on patient derived xenografts (PDX) of lung cancer cells with minimal host tumor microenvironment (TME) cells

Project description:To goal of the experiment is to assess whether we can profile enough cells corresponding to the host TME. In this PDX model, most of the cells correspond to the xenograft material, with limited amounts of host TME cells. To this aim we loaded 16 times more cells hybridized with the mouse probe set compared to the human hybridization.

2024-04-15 | E-MTAB-13968 | biostudies-arrayexpress

Single-cell Gene Expression Flex analysis on cell line derived xenografts of PC9 cells treated with Osimertinib

Project description:The goal of the experiment is determine whether the mixing of human and mouse probe sets of the 10x Genomics Gene Expression Flex allows to profile cell line derived xenograft (CDX) samples. We profiled a CDX vehicle sample and a CDX sample after 10 days of treatment with Osimertinib at 25mg/kg.

2024-04-15 | E-MTAB-13963 | biostudies-arrayexpress

Single-cell mRNA-seq from a healthy skeletal muscle cell derived from human induced pluripotent stem cell

Project description:1 healthy cell - 1 time point (Day 17 of differentiation) - 1 replicate

2020-10-04 | E-MTAB-9510 | biostudies-arrayexpress

10X Chromium Single-cell RNA sequencing of the female reproductive tract during aging in C57BL/6 mice

Project description:The aim of the study was to assess the cellular composition and transcriptional changes at single-cell resolution of the female reproductive tract during ageing in ovary, oviduct and uterus. Tissues of aged mice were collected at the age of 9,12 and 15 months. All tissues were collected and digested using a collagenase and trypsin protocol to obtain single cell suspension. Libraries were prepared using the 10x scRNA-seq protocol.

2024-01-31 | E-MTAB-12889 | biostudies-arrayexpress

10X Chromium Single-cell RNA sequencing of the female reproductive tract in young, pregnant and aged C57BL/6 mice

Project description:The aim of the study was to assess the cellular composition and transcriptional changes at single-cell resolution of the female reproductive tract across the four stages of estrus cycle in young adult mice (ovary, oviduct, uterus, cervix and vagina, with spleen as a comparison) and compared this with similar analyses of decidualization (uterus) and ageing (ovary, oviduct, uterus, cervix, vagina and spleen). Vaginal smears were used to stage the estrus cycle in young mice. To collect the decidualized uteri mice were mated and uterine tissue was collected from pregnant mice at day 5.5 after mating. Tissues of aged mice were collected at the age of 18 months. All tissues were collected and digested using a collagenase and trypsin protocol to obtain single cell suspension. Libraries were prepared using the 10x scRNA-seq protocol.

2023-02-01 | E-MTAB-11491 | biostudies-arrayexpress

Mapping the functional impact of non-coding regulatory elements in primary T cells through single-cell CRISPR screens

Project description:The vast majority of complex disease associations cannot be cleanly mapped to a gene, as they often lie within the non-cding fraction of the genome. Immune disease-associated variants are enriched within regulatory elements, such as distal enhancers, found in T cell-specific open chromatin regions. To identify the genes modulated by these regulatory elements, we developed a CRISPRi-based single-cell functional screening approach in primary human CD4+ T cells. We performed a proof-of-concept screen targeting 45 non-coding regulatory elements and 35 transcription start sites, each targeted by 4 different gRNAs. We profiled approximately 250,000 CD4+ T cell single-cell transcriptomes using 3' 10X Genomics.

2024-01-08 | E-MTAB-13324 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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