Project description:A 244 K genome-wide array based comparative genomic hybridization study was carried out in a familial translocation t(2;6)(p25;p21) balanced in the mother (SDM) and unbalanced in her daughter (SD). In the past, this translocation has allowed to localize the HLA multigene cluster to chromosome 6. With microarray technology, confirmation of the chromosome localization of HLA system was easily obtained, showing that such approach may be applied to the breakpoint localizations of other familial structural changes when they are unbalanced. Of interest was the breakage of genes at the breakpoint localization, without any phenotypic consequence to the parent and allowing to constitute a map of « haplotolerant genes ». In addition, many genomic variants were detected with this technology, enlarging the possibility of analyzing their possible contribution to phenotypic diversity.

2008-12-31 | E-TABM-308 | biostudies-arrayexpress

AML Sequencing Project

Project description:AML Sequencing Project

| PRJNA74781 | ENA

Leucegene: AML sequencing

Project description:RNA sequencing of human leukemia The goals of this project are to obtain a comprehensive study of mutations and gene expression in human acute myeloid leukemia (AML). Methods: AML cells were thawed. DNA and RNA (polyA) was extracted and sequences were obtained with an Illumina HiSeq 2000 sequencer.

2013-11-06 | E-GEOD-49642 | biostudies-arrayexpress

RNA-seq of engineered K562 cell line by CRISPR/Cas9 generation of t(7;12)(q36;p13) chromosomal translocation

Project description:We recreated the t(7;12) translocation in K562 cells by CRISPR/Cas9 to understand its effects on haematopoietic cells, which is of relevance to understand how this cytogenetic abnormalities causes and promotes acute leukaemia in infants. Wild-type K562 were edited by electroporation of ribonucleoprotein complexes consisting of Cas9 enzyme and two guide RNAs targeting patient-specific breakpoint loci. K562 electroporated with Cas9 enzyme only were used as control. Edited K562 harbouring the t(7;12) were single-cell cloned to obtain homogeneous populations (hereby referred to as K562-t(7;12)). We performed RNA sequencing analysis of K562-t(7;12) compared to K562 control to uncover transcriptional changes associated with the translocation.

2022-09-06 | E-MTAB-11851 | biostudies-arrayexpress

Whole Genome Sequencing of Tongue cancer samples and cell line

Project description:Whole genome sequencing (WGS) of tongue cancer samples and cell line was performed to identify the fusion gene translocation breakpoint. WGS raw data was aligned to human reference genome (GRCh38.p12) using BWA-MEM (v0.7.17). The BAM files generated were further analysed using SvABA (v1.1.3) tool to identify translocation breakpoints. The translocation breakpoints were annotated using custom scripts, using the reference GENCODE GTF (v30). The fusion breakpoints identified in the SvABA analysis were additionally confirmed using MANTA tool (v1.6.0).

2024-02-17 | E-MTAB-12534 | biostudies-arrayexpress

Transcription profiling of hepatocyes from Zucker fa/fa obese rats vs controls

Project description:Analysis of the gene signature of steatosis associated to obesity in hepatocytes of Zucker fa/fa obese rats and their controls; identifying target genes linked to steatosis progression. or Obesity and insulin resistance-associated steatosis can be a non-inflammatory condition affecting hepatocytes or progress to steatohepatitis: a condition that can result in end-stage liver disease. Although molecular events leading to accumulation of lipid droplets in the liver have been identified individually, the complexity of the condition suggested that emergent target would be uncovered by a more comprehensive examination. Then, this study was aimed at establishing a gene signature of steatosis in hepatocytes and at identifying target genes linked to steatosis progression. Using Affymetrix oligonucleotide arrays, we compared transcriptomes of hepatocytes isolated from Zucker "fa/fa" obese rats with three different age-related grades of steatosis with those of their counterpart non-steatotic cells.

2008-07-31 | E-MEXP-1414 | biostudies-arrayexpress

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