Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genomic and transcriptomic profiling of clonal populations derived from homotypic cell-cell fusion in triple-negative breast cancer

ABSTRACT: To investigate the genomic and transcriptomic impact of homotypic cell-cell fusion, we compared copy number variation (CNV) of eight single-cell isolated clonal cell populations (controls) to eight fusion-derived clonal populations (fusions) via low-pass whole-genome sequencing (WGS) in two triple-negative breast cancer (TNBC) cell lines (HCC1806 and MDA-MB-231). Additionally, we co-cultured pairs of control clonal populations and single-cell isolated spontaneously arising fusion events to generate clonal fusion populations with matched parental controls, referred to as matched fusion-parent trios. All fusion clonal populations from matched trios were also profiled using WGS to analyze CNV versus matched parents, and all surviving fusion and control clonal populations from the matched trios were profiled in biological triplicate by TagSeq (3' tag-based RNA-seq) for transcriptomic analysis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE346002 | GEO | 2026/09/08

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genome-wide copy number variation in Chinese schizophrenia trios

Project description:To reveal the risk CNVs of SZ in Chinese population, we recrited and enrolled 100 Chinese family trios with a schizophrenia affected children and both of their father and mother. SZ was diagnosed according to DSM-IV criteria by two independent psychiatrists. There gDNA we screen the genome-wide CNV using Agilent SurePrint G3 Human CGH Microarray Kit (1x1M) and Agilent sex-matched human DNA was used as reference. The CNV were called by ADM-2 statistical algorithms with a threshold of 6.0. We compared the burden of large rare CNVs and found that SZ probands carried more duplications and less deletions. Furtherly, we performed familial inheritance analysis of transmission disequilibrium and de novo CNV detection, validated several associated CNV loci with SZ susceptibility and also identify eight novel loci conferring risk of SZ

2021-10-01 | E-MTAB-8075 | biostudies-arrayexpress

Profiling of Sarcomas from Archival Tissues [snRNA-Seq]

Project description:We performed single nuclei RNA-sequencing (snRNA-seq) with matched T cell receptor sequencing (TCR-seq), and pool matched low pass whole genome sequencing (WGS) of eight specimens from six patients, encompassing four undifferentiated polymorphic sarcomas (UPS) and four intimal sarcomas (INS), and paired specimens from two patients (one UPS and INS each) treated with immune checkpoint blockade (ICB).

2024-06-21 | GSE243380 | GEO

Profiling of Sarcomas from Archival Tissues [TCR-Seq]

2024-06-21 | GSE243379 | GEO

Profiling of Sarcomas from Archival Tissues [lp-WGS]

2024-06-21 | GSE243377 | GEO

Evaluation of copy number variation detection between high-resolution array CGH and low-coverage short-insert and mate-pair whole-genome sequencing

Project description:In principle, whole-genome sequencing (WGS) of the human genome even at low coverage offers higher resolution for genomic copy number variation (CNV) detection compared to array-based technologies, which is currently the first-tier approach in clinical cytogenetics. There are, however, obstacles in replacing array-based CNV detection with that of low-coverage WGS such as cost, turnaround time, and lack of systematic performance comparisons. With technological advances in WGS in terms of library preparation, instrument platforms, and data analysis algorithms, obstacles imposed by cost and turnaround time are fading. However, a systematic performance comparison between array and low-coverage WGS-based CNV detection has yet to be performed. Here, we compared the CNV detection capabilities between WGS (short-insert, 3kb-, and 5kb-mate-pair libraries) at 1X, 3X, and 5X coverages and standardly used high-resolution arrays in the genome of 1000-Genomes-Project CEU genome NA12878. CNV detection was performed using standard analysis methods, and the results were then compared to a list of Gold Standard NA12878 CNVs distilled from the 1000-Genomes Project. Overall, low-coverage WGS is able to detect drastically more (approximately 5 fold more on average) Gold Standard CNVs compared to arrays and is accompanied with fewer CNV calls without secondary validation. Furthermore, we also show that WGS (at ≥1X coverage) is able to detect all seven validated deletions larger than 100 kb in the NA12878 genome whereas only one of such deletions is detected in most arrays. Finally, we show that the much larger 15 Mbp Cri-du-chat deletion can be clearly seen at even 1X coverage from short-insert WGS.

2018-06-26 | GSE105092 | GEO

Whole Genome Sequencing of Tongue cancer samples and cell line

Project description:Whole genome sequencing (WGS) of tongue cancer samples and cell line was performed to identify the fusion gene translocation breakpoint. WGS raw data was aligned to human reference genome (GRCh38.p12) using BWA-MEM (v0.7.17). The BAM files generated were further analysed using SvABA (v1.1.3) tool to identify translocation breakpoints. The translocation breakpoints were annotated using custom scripts, using the reference GENCODE GTF (v30). The fusion breakpoints identified in the SvABA analysis were additionally confirmed using MANTA tool (v1.6.0).

2024-02-17 | E-MTAB-12534 | biostudies-arrayexpress

Transcriptomic deconvolution of human endometrial cell types

Project description:The human endometrium is a highly heterogeneous tissue comprising multiple cell-types and cellular states that change in cycle-dependent manner. This tissue heterogeneity is a major drawback when interpreting bulk (whole biopsy) transcriptomic data. To address this hurdle, RNA-seq analysis was performed on four isolated stromal cell populations [SUSD2+ perivascular stromal cells (PVCs), endometrial stromal cells (EnSCs), SUSD2+ clonal cells (MSCs), and clonal transit amplifying cells (TAs)], glandular epithelial cells, uNK cells, and matched whole tissue. Transcriptomic data were obtained for 3 whole endometrial biopsies and 6 matched, purified cell populations.

2020-10-09 | GSE159266 | GEO

Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription.

Project description:Transcriptome sequencing (RNA-seq) experiment of 14 human lymphoblastoid cell line samples from the 1000 Genomes sample set (http://www.1000genomes.org/). Dataset includes two parent-daughter trios (CEU and YRI populations) and additional eight unrelated individuals (CEU population). This accession contains raw and mapped RNA-seq read data, other assays in this study are available under accession E-MTAB-1884 (ChIP-seq, https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1884) and E-MTAB-1885 (GRO-seq, https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1885).

2013-10-17 | E-MTAB-1883 | biostudies-arrayexpress

Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription.

Project description:ChIP-seq experiment of 14 human lymphoblastoid cell line samples from the 1000 Genomes sample set (http://www.1000genomes.org/). Dataset includes two parent-daughter trios (CEU and YRI populations) and additional eight unrelated individuals (CEU population). This accession contains raw and mapped ChIP-seq read data, other assays in this study are available under accession E-MTAB-1883 (RNA-seq, https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1883) and E-MTAB-1885 (GRO-seq, https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1885/).

2013-10-17 | E-MTAB-1884 | biostudies-arrayexpress

Custom array CGH validation of de novo CNVs in asthma samples

Project description:This is the validation data for candidate de novo CNV calls made in the asthma trios by Itsara et al., Genome Research 2010. In this study, de novo CNV calls in the asthma data set were initially made with Illumina 550K SNP arrays. Validation was performed with custom Nimblegen array CGH for which DNA was available. de novo CNVs would be expected to validate in the child of each trio tested, and not be detected in either parent.

2010-09-01 | GSE23572 | 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