Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Total RNA-seq in the A549 cell line after glucocorticoid re-induction

ABSTRACT: We performed total RNA-seq in the A549 cell line. Cells were treated with either 100 nM dexamethasone or 0.1% ethanol. After 4 hours, cells were washed 2x with PBS and cultured in hormone-free medium for 24 hours, after which cells were treated again for 4 hours with either 100 nM dexamethasone or 0.1% ethanol.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Homo sapiens

SUBMITTER: Melissa Bothe

PROVIDER: E-MTAB-9923 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq data of LP1 multiple myeloma cell line treated for 6h or 24h with Tasquinimod

Project description:Tasquinimod is a new immunomodulatory treatment for MM that is in phase I/II clinical evaluation in patients with relapsed/refractory MM. In the present study, we evaluated the effect of tasquinimod on MM cells using RNA sequencing to provide more mechanistic insights into the observed tasquinimod-mediated anti-tumor effects.

2023-01-25 | E-MTAB-11787 | biostudies-arrayexpress

Post-transplant (non-alcoholic steatohepatitis) NASH compared with transplanted normal controls

Project description:Non-alcoholic fatty liver disease (NAFLD) encompasses a spectrum of disease that ranges from simple steatosis, to inflammatory form non-alcoholic steatohepatitis (NASH), cirrhosis, and up to hepatocellular carcinoma. While NASH usually takes decades to develop at a rate of one stage per seven years, in the case of post-trasplant NASH (pt-NASH) develops fibrosis much more rapidly, with almost 50% of liver transplant recipients presenting stage 3 fibrosis by 5 years post-transplant. Archived fresh-frozen transplanted liver biopsy samples from four liver biopsy samples with evidence of NASH (2 recurrent and 2 de novo), two with simple steatosis (both de novo), and five with normal histology as controls had their transcriptome sequenced in two batches for deeper coverage.

2022-05-09 | E-MTAB-11688 | biostudies-arrayexpress

Transcriptional profile of cerebellar tissues gained from 4 weeks old mice that carry aberrant variants of splicing factor Prpf8 (Prpf8Y2334N and Prpf8Δ17).

Project description:We compared the transcriptome of cerebellar tissues gained from 4 weeks old mice that carry either the Prpf8Y2334N or Prpf8Δ17 mutant variant of splicing factor Prpf8. In both RNA-Seq runs, homozygous animals were analysed along with wt controls (both genders).

2023-03-31 | E-MTAB-10753 | biostudies-arrayexpress

Transcriptional changes occurring in end-stage human SCA1 cerebellum.

Project description:RNA-Seq was performed in post-mortem SCA1 cerebellum at the end stage of the disease and an age/sex-matched control tissue from a healthy individual.

2020-02-18 | E-MTAB-7714 | biostudies-arrayexpress

RNA sequencing of MOLM-13 and KG-1a cell lines after inhibition of S100A9 and BCL2

Project description:The aim is investigate the alterations in the transcriptome after combined inhibition of S100A9 and BCL2 in AML cell lines.

2023-12-01 | E-MTAB-13095 | biostudies-arrayexpress

Mosaic BRAF fusions are a recurrent cause of congenital melanocytic naevi targetable by MEK inhibition

Project description:Among children with multiple congenital melanocytic naevi (CMN), 25% have no established genetic cause. Here, we study 169 CMN patients, 38 of whom were double wild-type for NRAS/BRAF mutations. Nineteen of these 38 patients had sufficient tissue to undergo RNAseq, which revealed mosaic BRAF fusions in 11/19 patients and mosaic RAF1 fusions in 1/19. These findings offer a genetic diagnosis to an additional group of patients opening the possibility for treatment options.

2023-09-30 | E-MTAB-13182 | biostudies-arrayexpress

Retinitis pigmentosa-linked mutation in DHX38 modulates its splicing activity

Project description:We analyzed function of DHX38 helicase in RNA splicing. We downregulated DHX38 in HEK293 cells by RNAi and compared the transcriptome of DHX38 knockdown cells with cells treated with negative control siRNA.

2022-03-11 | E-MTAB-11127 | biostudies-arrayexpress

Transcriptome profiling (RNA-seq) of human acute leukemias and healthy donors

Project description:Total RNA-seq of blasts derived 100 adult T-ALL cases, 211 AML cases and 13 mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). In addition, CD34+ HSPCs derived from 9 healthy donors are used as a control. Due to patient confidentiality considerations, the raw data files for this dataset have been deposited to the EGA controlled-access archive under the accession numbers EGAS00001007094 (study); EGAD00001011054, EGAD00001007646, EGAD00001007581 (datasets).

2023-08-31 | E-MTAB-13121 | biostudies-arrayexpress

RNA-seq of MUTZ3 cells in experiments to investigate EVI1 regulation

Project description:We investigated whether GATA2 enhancer-driven transcription of EVI1 in inv(3)/t(3;3) is reversible in leukemia cells. In primary inv(3)/t(3;3) AML, immature CD34+CD15- cells can be discriminated from more mature CD34-CD15- and CD34-CD15+ cells. Besides, we also investigated the effect of deleting a MYB binding site on these cells using CRISPR/Cas9.

2021-07-26 | E-MTAB-9939 | biostudies-arrayexpress

Identification of LEC1 target genes

Project description:The transcription factor (TF) LEAFY COTYLEDON1 (LEC1) acts as an essential regulator of Arabidopsis embryogenesis and seed development. It controls aspects of early embryogenesis such as cotyledon identity and suspensor morphology, as well as seed maturation processes such as storage compound accumulation, acquisition of desiccation tolerance and dormancy. To identify downstream components of the LEC1 regulon, dexamethasone-regulated expression of LEC1 and ChIP/chip were applied and revealed the enrichment of phytohormone- as well as elongation-related genes among LEC1 target genes. Two weeks old 35S::LEC1::GR seedlings were treated with DEX or ethanol for 24 hours before cross-linking and chromatin isolation. Four biological replicates were performed, using an ethanol-treated sample as control (LEC1_EtOH versus LEC1_DEX). After data normalization, statistical analysis and exclusion of putative false negatives, a number of 356 target promoter regions were identified.

2012-03-30 | E-GEOD-22352 | 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