Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

18 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DNA-microarray of human breast cancer cell line MCF10A harboring PSD4 knock-out and wild-type control

ABSTRACT: To address the mechanism of action of EFA6B we have knocked-out its gene PSD4 using the CRISPR/Cas9 technology. The MCF10A human mammary cell line was used for the knock-out as it is a well-characterized normal human mammary cell line and thus enabled us to study the effect of deleting PSD4 in a non-transformed genetic background.

ORGANISM(S): Homo sapiens

SUBMITTER: Finetti Pascal

PROVIDER: E-MTAB-10063 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome profiling of MED1 wild-type and knockout human pre-B ALL cell line 697 (RNA-seq)

Project description:CRISPR/Cas9 system was used to generate mediator complex subunit 1 (MED1) knockout human pre-B ALL cell line 697. RNA-seq was performed to observe the effects of MED1 deletion on gene expression in 697.

2020-05-13 | E-MTAB-8178 | biostudies-arrayexpress

Genome-wide profiling of MED1 and RUNX1 binding in MED1 wild-type and knockout human pre-B ALL cell line 697 (ChIP-seq)

Project description:CRISPR/Cas9 system was used to generate mediator complex subunit 1 (MED1) knockout human pre-B ALL cell line 697. ChIP-seq was performed to identify genomic regions responsible for recruitment of MED1 and RUNX1.

2020-05-13 | E-MTAB-8177 | biostudies-arrayexpress

RNA-Seq of monoclonal cell lines after CRISPR/Cas9-mediated editing of box C/D snoRNA genes (SNORDs)

Project description:In this study monoclonal cell lines carrying mutations in snoRNA genes (SNORD74, SNORD75, SNORD77, SNORD80) were obtained. Next, whole transcriptome analysis of obtained cell lines was performed on an Illumina NextSeq 500 platform. RNA-seq libraries was constructed on PolyA mRNA-enriched fraction. The comparison of the expression levels of genes and transcripts in RNA-Seq experiments was carried out using CuffDiff tool. Mutations in SNORD75 in the obtained monoclonal cell line were shown to result in aberrant splicing of Gas5.

2019-10-14 | E-MTAB-8269 | biostudies-arrayexpress

Single-cell RNAseq of Mixl1 knockout chimeric mouse embryos at embryonic day 8.5 of mouse development.

Project description:Chimeric embryos were generated to investigate the effect of Mixl1 knockout in mouse embryos by single-cell RNA-sequencing. Mixl1 is an essential transcription factor for mesendoderm development. Chimeric embryos contain tissue that is Mixl1+/+, which prevents global developmental failures. Embryos were generated by blastocyst injection of tdTomato-labelled, Mixl1-/- mouse embryonic stem cells into wild type embryos. After blastocyst harvest, cells were flow-sorted before 10X Genomics library preparation and single-cell RNA-sequencing.

2023-10-26 | E-MTAB-13409 | biostudies-arrayexpress

Single-cell RNAseq of Brachyury knockout chimeric mouse embryos at embryonic days 8.5 and 7.5 of mouse development.

Project description:Chimeric embryos were generated to investigate the effect of T knockout in mouse embryos by single-cell RNA-sequencing. T is an essential transcription factor for axial embryonic patterning. Chimeric embryos contain tissue that is T+/+, which prevents global developmental failures. Embryos were generated by blastocyst injection of tdTomato-labelled, Tal1-/- mouse embryonic stem cells into wild type embryos. After blastocyst harvest, cells were flow-sorted before 10X Genomics library preparation and single-cell RNA-sequencing.

2020-08-31 | E-MTAB-8811 | biostudies-arrayexpress

Functional validation of a gene regulatory element as a candidate cancer driver using RNA-seq in HEK293 cells

Project description:Functional validation of regulatory element as a putative non-coding cancer driver

2020-01-18 | E-MTAB-8631 | biostudies-arrayexpress

RNA-Seq of monoclonal cell lines after CRISPR/Cas9-mediated editing of the small nucleolar RNA host-gene GAS5

Project description:In this study monoclonal cell lines carrying mutations in the small nucleolar RNA host-gene GAS5 were obtained. Next, Poly(A) RNA-seq and Small RNA-seq analyses of obtained cell lines were performed on an Illumina NextSeq 500 platform. Poly(A) RNA-seq libraries was constructed on polyA mRNA-enriched fraction. Small RNA-seq libraries was constructed on small RNA fraction (<200 nucleotide length). The reads were aligned via STAR to the human genome (GRCh37). The comparison of the mRNA levels of genes and small RNA levels in RNA-Seq experiments was carried out using CuffDiff tool. Sashimi plots for RNA-Seq analyses of isoform expression were generated by IGV. It was shown that specific mutations in SNORD74 led to the downregulation of all GAS5-encoded SNORDs and GAS5 lncRNA. Obtained results demonstrate the SNORD-dependent manner of the GAS5 maturation.

2023-11-14 | E-MTAB-13515 | biostudies-arrayexpress

TETs controls maintenance DNA methylation via the regulation of Dppa3

Project description:Dissection of catalytic and non-catalytic functions of Tet1 and Tet2. Transcriptome profiling of wild type, Tet1 catalytic mutants, Tet2 and Tet1/2 catalytic mutant catalytic during EpiLC differentiation.

2020-10-05 | E-MTAB-6797 | biostudies-arrayexpress

Human pluripotent stem cell-derived kidney organoids reveal tubular epithelial pathobiology of heterozygous HNF1B-associated dysplastic kidney malformations - cell line dataset

Project description:Hepatocyte nuclear factor 1B (HNF1B) encodes a transcription factor expressed in developing human kidney epithelia. Heterozygous HNF1B mutations are the commonest monogenic cause of dysplastic kidney malformations (DKMs). To understand their pathobiology, we generated heterozygous HNF1B mutant kidney organoids from CRISPR-Cas9 gene-edited human ESCs and iPSCs reprogrammed from a family with HNF1B-asscociated DKMs. Mutant organoids contained enlarged malformed tubules and displayed deregulated cell turnover. This submission is RNAseq of organoids from MAN13 embryonic stem cells.

2024-04-29 | E-MTAB-12824 | biostudies-arrayexpress

Single-cell RNAseq of Tal1 knockout chimeric mouse embryos at embryonic day 8.5 of mouse development

Project description:Chimeric embryos were generated to investigate the effect of Tal1 knockout in mouse embryos by single-cell RNA-sequencing. Tal1 is an essential transcription factor for the formation of the embryonic blood. Embryo chimerism permits the analysis of the effects of Tal1 knockout without the confounding effects of the absence of embryonic blood, which results in global developmental failures. Embryos were generated by blastocyst injection of tdTomato-labelled, Tal1-/- mouse embryonic stem cells into wild type embryos. After blastocyst harvest, cells were flow-sorted before 10X Genomics library preparation and single-cell RNA-sequencing.

2018-12-05 | E-MTAB-7325 | 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