Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of CN, CN/AML, and CN/AML BAALC KO iPSCs-derived HSPCs

ABSTRACT: RNA-seq of CN, CN/AML, and CN/AML BAALC KO iPSCs-derived HSPCs

PROVIDER: PRJEB43341 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of CN, CN/AML, and CN/AML BAALC KO iPSCs-derived HSPCs

Project description:Severe congenital neutropenia (CN) is a pre-leukemia syndrome that, in the majority of patients, is caused by heterogeneous ELANE mutations encoding neutrophil elastase (NE). To study leukemogenesis associated with CN we generated CN and CN/AML patient-specific induced pluripotent stem cells (iPSCs). Additional mutations in leukemia-relevant genes, CSF3R and RUNX1, were introduced using CRISPR/Cas9 gene-editing. Consequently, we performed in vitro embryoid body (EB)-based hematopoietic and myeloid differentiation of generated iPSC lines. On day 14-17 of EB-based differentiation, iPSC-derived CD45+CD34+ cells were harvested and mRNA was isolated using RNeasy Mini- or Micro Kit (Qiagen). Sequencing libraries were prepared using the TruSeq RNA Sample Prep Kit (Illumina). Poly (A) selected single-read and pair-read sequencing libraries were sequenced on the Illumina platform in order to compare the transcriptomes of CN and CN/AML iPSCs-derived HSPCs from 2 CN/AML patients. Next, we identified that BAALC knockout resulted in a dramatic induction of granulocytic differentiation and a significant reduction in proliferation of CN/AML iPSC-derived HSPCs. To identify BAALC-dependent leukemia-associated gene expression, we compared the transcriptomes of CN/AML iPSCs before and after BAALC KO using a similar approach described above for CN and CN/AML iPSCs-derived HSPCs.

2021-03-08 | E-MTAB-10162 | biostudies-arrayexpress

Modeling Down syndrome AML by introducing disese-specific mutations in iPSCs

Project description:Down syndrome AML is characterized by the presence of the pathgnonomic mutation in GATA1, which cooperates with other somatic mutations. In this study, we utilzed iPSCs derived from Down syndrome individuals bearing trisomy 21 and introduced disease-specific mutations using CRISPR-Cas9. Hematopoeitic stem and progenitor cells (HSPCs) obtained by hematopoeitic differentiation of these iPSCs, and megakaryocytes generated from the HSPCs (by culturing in megakaryocyte-specific media) were used for RNA sequencing analysis.

2022-03-02 | GSE188568 | GEO

HBV-KMT2B integrated human induced pluripotent stem cells (KMT2B-Int iPSCs) vs heterozygous mutated KMT2B iPSCs (KMT2B-HT iPSCs) vs homozygous mutated KMT2B iPSCs (KMT2B-KO iPSCs) vs their original iPSCs (KMT2B-WT iPSCs)

Project description:Transcriptional profiling of all KMT2B-WT, HT, KO, Int iPSCs. KMT2B-HT, KO, and Int iPSCs were generated by gene editing using CRISPR/Cas9 and Cre recombinase technologies.

2023-11-15 | GSE217994 | GEO

RNA-seq of CD33 KO and control HSPCs

Project description:RNA-seq of CD33 KO and control HSPCs

| PRJNA453558 | ENA

Transcriptome profiling of quiescent and cytokine induced normal human haematopoietic CD34+ HSPCs, and AML blast cells

Project description:Control group is an essential part of the research design which provide a baseline by elimating variables, bias and other factors that skew the data. Human CD34+ cells are generally used as controls to study myeloid malignancies. This study determines whether fresh or short term cytokine induced CD34+ HSPCs can provide a more appropriate normal control (compared to AML blasts) for target discovery studies. We here determine that the GEP of CD34+ cells that do not undergo ex vivo expansion best match the GEP of minimally differentiated AML blasts and would serve as a better control to identify novel targets in the AML blast population.

2015-12-09 | E-MTAB-3328 | biostudies-arrayexpress

Gene expression signature associated with ASXL1 mutations in cytogenetically normal acute myeloid leukemia (CN-AML)

Project description:We studied gene expression profiles from 65 patients with CN-AML, who all had wild-type NPM1 and no FLT3-ITD. We identified an ASXL1 mutation-associated gene expression signature by comparing 26 ASXL1-mutated and 39 ASXL1-wild type patients. Only NPM1 wild type/FLT3-ITD-negative patients were included in this analysis to avoid potential confounding due to the effects of these two mutations on gene expression.

2012-10-10 | E-TABM-1208 | biostudies-arrayexpress

Herminiimonas sp. CN strain:CN

Project description:Herminiimonas sp. CN strain:CN Genome sequencing and assembly

| PRJNA209422 | ENA

Prognostic gene signature for normal karyotype AML

Project description:Patients with cytogenetically normal acute myeloid leukemia (CN-AML) show heterogeneous treatment outcomes. We used gene expression profiling to develop a gene signature that predicts overall survival (OS) in CN-AML. Based on data from 163 patients treated in the German AMLCG 1999 trial and analyzed on oligonucleotide microarrays, we used supervised principal component analysis to identify 86 probe sets (representing 66 different genes) which correlated with OS, and defined a prognostic score based on this signature. When applied to an independent cohort of 79 CN-AML patients, this continuous score remained a significant predictor for OS (hazard ratio [HR], 1.85; P=0.002), EFS (HR, 1.73; P=0.001), and RFS (HR, 1.76; P=0.025). It kept its prognostic value in multivariate analyses adjusting for age, FLT3 ITD and NPM1 status. In a validation cohort of 64 CN-AML patients treated on CALGB study 9621, the score also predicted OS (HR, 4.11; P<0.001), EFS (HR, 2.90; P<0.001), and RFS (HR, 3.14, P<0.001) and retained its significance in a multivariate model for OS. In summary, we present a novel gene expression signature that offers additional prognostic information for patients with CN-AML. Keywords: clinical outcome

2008-08-22 | GSE12417 | GEO

Differential methylation in CN-AML preferentially targets non-CGI regions and is dictated by DNMT3A mutational status and associated with predominant hypomethylation of HOX genes

Project description:The study investigated the abberrent DNA methylation in correlation with gene expression in cytogenetic normal acute myeloid leukemia. CN-AML blasts isolated from patient bone marrow aspriation were compared to CD34+ cell population from healthy donors by DNA methylation array and affymetrix gene expression microarray.

2014-07-31 | GSE58477 | GEO

Expression and Prognostic impact of LncRNAs in AML

Project description:Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides located within the intergenic stretches or overlapping antisense transcripts of protein coding genes. LncRNAs are involved in numerous biological roles including imprinting, epigenetic regulation, apoptosis and cell-cycle. To determine whether lncRNAs are associated with clinical features and recurrent mutations in older patients (aged M-bM-^IM-%60 years) with cytogenetically normal (CN) acute myeloid leukemia (AML), we evaluated lncRNA expression in 148 untreated older CN-AML cases using a custom microarray platform. We analyzed 148 older cytogenetically normal(CN)-AML patients samples using a custom microarray platform and describe the expression of lncRNAs among the AML samples.

2014-11-26 | E-GEOD-63614 | 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