Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

53 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNAseq of combined LUAD and SCLC tumors to look at gene expression changes

ABSTRACT: For in-depth characterization of neuroendocrine transformation, we analyzed clinical specimens consisting of combined lung adenocarcinoma (LUAD)/small cell lung carcinoma (SCLC) histology exhibiting clear spatial separation. Microdissection was performed for RNA sequencing.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Homo sapiens

SUBMITTER: Triparna Sen

PROVIDER: E-MTAB-10399 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

MicroRNA expression contributes to the poor prognosis of human small cell lung cancer

Project description:MicroRNAs are important cellular components and their dysfunctions are associated with various disease.Small-cell lung cancer (SCLC) is an aggressive disease with a poor prognosis, but little is know about the underlying machinery that leads to rapid tumor growth and early metastases.In this study, clinical outcome prediction miRNAs were successfully found through expression profiling of a total of 924 miRNA genes in 42 SCLC cases. 42 patients with respectable very limited disease (training set) were enrolled. All the patients underwent surgical resection followed by adjuvant chemotherapy according to the standard of care. Total RNA was extracted from formalin-fixed paraffin-embedded （FFPE）specimens, low molecular weight RNA was seperate and labeled , and then hybridized to capitalbio V3 biochip representing about 924 microRNA . three chip were test in each group, and the procedure was repeated twice.

2011-02-22 | E-GEOD-27435 | biostudies-arrayexpress

miRNA Lisbon

Project description:Proteomic analysis of differentially expressed proteins in MDA-MB-231 and MCF-10A cell lines when miR-200c and miR-203 were transiently expressed or inhibited, respectively.

2022-02-28 | PXD007210 | Pride

Identification of a novel ESR1 transcript variant in breast cancer cells by RNA capture-sequencing

Project description:RNA capture-sequencing analysis was carried out to study the usage of ESR1 exons and transcripts in different breast cancer models, including both ERα(+) and ERα(-) cell lines. Total RNA was extracted and processed for the analysis.

2022-08-29 | E-MTAB-10733 | biostudies-arrayexpress

Isolation of Circulating Tumor Cells from Small Cell Lung Cancer patients using CD56+ as a marker

Project description:We have isolated Circulating Tumor Cells from four Small Cell Lung Cancer Patients at diagnosis and relapse using a two-step method developed in the laboratory. Subsequently, Whole-Exome sequencing was performed on these samples as well as on the corresponding biopsies.

2023-01-11 | E-MTAB-10766 | biostudies-arrayexpress

Proteomics identifies ubiquitin-proteasome targets and new roles for chromatin-remodelling in the Arabidopsis response to phosphate starvation

Project description:In order to identify new regulators of the phosphate (Pi) starvation signaling pathway in plants, we analyzed variation in the abundance of nuclear-enriched nuclear proteins isolated from Arabidopsis roots that depends on Pi supply. We used 2-D Fluorescence Difference Gel Electrophoresis and MALDI-TOF/TOF techniques for nuclear proteome separation, visualization and relative protein abundance quantification and identification. Pi-controlled proteins identified in our analysis included components of the chromatin remodeling, DNA replication, and mRNA splicing machineries. In addition, by combining Pi starvation conditions with proteasome inhibitor treatments, we characterized the role of the ubiquitin- (Ub)-proteasome system (UPS), a major mechanism for targeted protein degradation in eukaryotes, in the control of the stability of Pi-responsive proteins. Among Pi-responsive proteins, the histone chaperone NAP1;2 was selected for further characterization, and was shown to display differential nucleo-cytoplasmic accumulation in response to Pi deprivation. We also found that mutants affecting three members of the NAP1 family accumulate lower Pi levels and display reduced expression of Pi starvation-inducible genes, reflecting a regulatory role for these chromatin-remodelling proteins in Pi homeostasis.

2020-01-22 | PXD000305 | Pride

The Phytoestrogen Genistein Is a Tissue-Specific Androgen Receptor Modulator

Project description:We report that the phytoestrogen genistein acts as a tissue-specific androgen receptor modulator in mouse using a novel androgen reporter mouse line and gene expression profiling. Genistein is a partial androgen agonist/antagonist in prostate, brain, and testis but not in skeletal muscle or lung. Gene expression profiling has been done from prostates of intact and castrated male mice treated with genistein or vehicle. Gene expression profiling was also done from prostates of estradiol-treated intact male mice. Gene expression profiling from prostates of castrated and intact male mice after 5-day genistein- or vehicle-treatment or after 4-day estradiol- or vehicle-treatment.

2011-08-18 | E-GEOD-31341 | biostudies-arrayexpress

Expression Profiling and Array Comparative Genomic Hybridization of Pancreatic Xenografts and Cell Lines

Project description:This SuperSeries is composed of the following subset Series: GSE25273: Array Comparative Genomic Hybridization of Pancreatic Xenografts and Cell Lines GSE26088: Expression Profiling of Pancreatic Xenografts and Cell Lines Refer to individual Series

2011-12-15 | E-GEOD-26089 | biostudies-arrayexpress

Whole genome gene expression analysis of clear-cell renal cell carcinoma samples

Project description:Analysis of gene expression of 23 T1 or T3 clear-cell renal cell carcinoma samples. Unsupervised clustering divided this group into three clusters, two of them contained pure T1 or T3 samples while one contained a mixed group. We defined a group of 35 genes that discriminate the mixed cluster. This gene set could be associated with tumor classification into a higher stage and it contained significant number of genes coding for molecular transporters, channel and transmembrane proteins.

2019-05-04 | E-MTAB-6118 | 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