Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Microarray analysis of PPIF knockdown in human dermal fibroblasts and keratinocytes

ABSTRACT: To determine the effect of CyD knockdown through gapmer-mediated knockdown of PPIF gene in pathogenic functions related to wound healing

INSTRUMENT(S): Punch biopsy - fibroblasts; commercial stock - HEKa, CL2 lab

ORGANISM(S): Homo sapiens

SUBMITTER: Matthew Hunt

PROVIDER: E-MTAB-13920 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of AMO-1 multiple myeloma cell line silenced for lncRNA NEAT1 expression and relative control condition

Project description:The aim of this experiment was to identify NEAT1-dependent transcriptional program in multiple myeloma. AMO-1 cell line was silenced for NEAT1 expression using antisense oligonucleotide gapmeR (g#N1_E). Not-targeting gapmeR was used as control (g#SCR). RNA was collected 96 hours after gapmeR delivery.

2026-03-06 | E-MTAB-13925 | biostudies-arrayexpress

Effects of CEBPA isoform expression on NB4 cells

Project description:Here we investigated the effects of CEBPA transcription factor expression on myeloid NB4 cells. The sequence of rat CEBPA was C-terminally fused to a promiscuous biotin ligase tag (BirA*) and NB4 cell lines were engineered to express the fusion protein under the control of a doxycycline inducible promoter. Three different NB4 cell lines were investigated that expressed (i) BirA* tag alone (ii) full length CEBPA isoform (P42) fused to BirA* (iii) truncated CEBPA isoform (P30) fused to BirA*. Cells were seeded in media supplemented with or without doxycycline.

2021-06-26 | E-MTAB-9947 | biostudies-arrayexpress

Treatment-free remission and relapse in chronic myeloid leukaemia (CML) patients

Project description:Peripheral blood from 70 individuals (31 CML patients who subsequently relapsed after discontinuation of tyrosine kinase inhibitors (TKI) treatment, 29 CML patients who maintained treatment-free remission, and 10 healthy donors) was profiled to investigate transcriptional programs associated with sustained control versus relapse. Samples from CML patients were collected on the last day of TKI treatment within the EURO-SKI trial, and leukocytes were isolated for RNA extraction. Genome-wide expression profiling was performed using Clariom D microarrays (Applied Biosystems). The resulting dataset aims to define peripheral blood molecular signatures and biomarkers that predict treatment-free remission in CML.

2026-06-01 | E-MTAB-16324 | biostudies-arrayexpress

Comparison of Azithromycin treated and non-treated human lung fibroblasts

Project description:Azithromycin has been shown to have anti-fibrotic effects on idiopathic lung fibroblasts (IPF). We thus wanted to investigate involved genes and pathways by microarray analysis. We treated normal human lung fibroblasts with Azithromycin (50uM) for 24h and compared them to non-treated samples.

2019-11-07 | E-MTAB-8488 | biostudies-arrayexpress

Targeting oncogenic microRNAs from the miR-371~373 and miR-302/367 clusters in malignant germ cell tumours causes growth inhibition through cell cycle disruption

Project description:Background. MiR-371~373 and miR-302/367 cluster over-expression occurs in all malignant- GCTs, regardless of age (paediatric/adult), site (gonadal/extragonadal), or subtype [seminoma, yolk sac tumour (YST), embryonal carcinoma (EC)]. Six of eight microRNAs from these clusters contain the seed ‘AAGUGC’, determining mRNA targeting. Here we sought to identify the significance of these observations by targeting these microRNAs functionally. Methods. We targeted miR-371~373 and/or miR-302/367 clusters in malignant-GCT cell lines, using CRISPR-Cas9, gapmer primary miR-302/367 transcripts inhibition, and peptide- nucleic-acid (PNA) or locked-nucleic-acid (LNA)-DNA inhibition targeting miR-302a-d-3p, and undertook relevant functional assays. Results. MiR-302/367 cluster microRNAs made the largest contribution to AAGUGC seed abundance in malignant-GCT cells, regardless of subtype (seminoma/YST/EC). Following unsuccessful use of CRISPR-Cas9, gapmer, and PNA systems, LNA-DNA-based targeting resulted in growth inhibition in seminoma and YST cells. This was associated with de- repression of multiple mRNAs targeted by ‘AAGUGC’ seed-containing microRNAs, with pathway analysis confirming predominant disruption of Rho-GTPase signaling, vesicle organization/transport, and cell-cycle regulation, findings corroborated in clinical samples. Further LNA-DNA inhibitor studies confirmed direct cell-cycle effects, with increase of cells in G0/G1-phase and decrease in S-phase. Conclusion. Targeting of specific miR-371~373 and miR-302/367 microRNAs in malignant- GCTs demonstrated their functional significance, with growth inhibition mediated through cell-cycle disruption.

2024-08-01 | E-MTAB-13323 | biostudies-arrayexpress

Microarray analysis of macrophages derived from mouse bone marrow cells with or without metformin treatment

Project description:In this study, we investigated the effects of metformin on the differentiation of bone marrow-derived macrophages (BMDMs) and their potential role in cancer immunity. BMDMs were generated from bone marrow cells extracted from C57BL/6N mice and differentiated in the presence or absence of metformin. Our transcriptomic analysis, performed using the Clariom S Mouse microarrays, revealed changes in gene expression profiles between metformin-treated and untreated macrophages.

2025-06-13 | E-MTAB-14199 | biostudies-arrayexpress

Microarray analyses of fibroblast cell lines derived from a pain insensitive individual and 4 gender-matched controls

Project description:We have identified a pain insensitive individual carrying a microdeletion in the FAAH-OUT gene and a hypomorphic SNP in FAAH. A punch skin biopsy was taken from the individual and 4 gender matched controls and primary cultures of dermal fibroblasts were passaged. Total RNA was isolated from each cell line and analysed using microarrays to identify dysregulated genes.

2023-05-01 | E-MTAB-11809 | biostudies-arrayexpress

RNA-seq analysis of HeLa cells treated with GapmeR antisense oligonucleotides

Project description:The experiment was carried out to provide insights into biological function of a newly identified long noncoding RNA, PNCTR. HeLa cells were transfected with either a PNCTR-specific GapmeR antisense oligonucleotide or a non-targeting GapmeR control. Total RNAs were extracted at 24 hours post transfection, QC'd and hybridized with oligo(dT) magnetic beads to isolate the poly(A) RNA fraction. Stranded mRNA sequencing libraries were then prepared using the Illumina TruSeq Stranded mRNA Library Kit and sequenced using an Illumina HiSeq 2500 instrument.

2018-10-12 | E-MTAB-6529 | biostudies-arrayexpress

microRNA profiling of primary human keratinocytes and primary human dermal fibroblasts

Project description:In search for factors, overexpression of which in human dermal fibroblasts causes direct conversion to cells similar to keratinocytes, micro RNA expression profiles of human primary keratinocytes and human primary dermal fibroblasts are investigated. Skin samples obtained from 3 different sites of 1 subject were used for establishment of 3 primary keratinocytes and 3 primary dermal fibroblasts. Thus obtained 3 primary keratinocytes and primary dermal fibroblasts underwent micro RNA profiling.

2016-09-30 | E-MTAB-5055 | biostudies-arrayexpress

Trancriptome analysis of peripheral leukocytes from SARS-CoV-2 infected patients and healthy uninfected individuals during the first wave of COVID-19 pandemic in Brazil

Project description:To evaluate the gene expression profiling of peripheral leukocytes in different outcomes of SARS-CoV-2 infections, whole blood samples were collected from individuals with positive SARS-CoV-2 nasopharyngeal swab by RT-PCR (54 patients) and healthy uninfected individuals (12 volunteers). Infected patients were classified into mild, moderate, severe and critical groups according to a modified statement in the Novel Coronavirus Pneumonia Diagnosis and Treatment Guideline. Blood were collected into EDTA tubes and the buffy coat samples were stored in TRIzol reagent at -80 °C until use for RNA extraction. Affymetrix Clariom S array was used to perform the high-throughput gene expression profiling. Microarray analyses were performed using APT Affymetrix software, R packages and Bioconductor libraries. This systemic view of SARS-CoV-2 infections through blood transcriptomics will foster the understanding about molecular mechanisms and immunopathological processes involved in COVID-19 disease and its different outcomes.

2022-04-29 | E-MTAB-11240 | biostudies-arrayexpress

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