Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1140057 | ENA |
REPOSITORIES: ENA
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Project description:To understand the effects of Hsp60 deficiency in developing vertebrates, we generated CRISPR/Cas9-mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf .
2024-09-27 | GSE254091 | GEO
Project description:Transcriptional Profile Analysis of RPGRORF15 frameshift mutation
| PRJNA120739 | ENA
Project description:Purpose: Genetic and clinical association studies have identified disrupted-in-schizophrenia 1 (DISC1) as a candidate risk gene for major mental illness. DISC1 is interrupted by a balanced chr(1;11) translocation in a Scottish family, in which the translocation predisposes to psychiatric disorders. We investigate the consequences of DISC1 interruption in human neural cells using TALENs or CRISPR-Cas9 to target the DISC1 locus. We sought to compare the gene expression profiles of human neural progenitor cells (NPCs) and neurons with interruption of the DISC1 gene in exon 2 (affecting all known coding transcripts) or exon 8 (near the site of the Scottish translocation, affecting longer transcripts). Methods: Wild-type and DISC1-targeted iPSCs (wild-type = "WT", exon 8 single allelic frameshift mutant = "ex8_wm", exon 8 biallelic frameshift mutant = "ex8_mm", exon 2 biallelic frameshift mutant = "ex2mm") were differentiated to NPCs and neurons using an embryoid aggregate method. NPC or neuronal cultures were used for RNA harvest and subsequent paired-end stranded sequencing of >50M reads/sample and 3-6 biological replicates per group. Results: We find that a subset of genes related to neuronal differentiation and development are dysregulated with DISC1 disruption at the NPC timepoint, whereas expression of genes related to neuronal function and signaling are altered at the neuronal timepoint. This study implicates DISC1 as a regulator of neuronal development. mRNA profiles of wild-type and DISC1-targeted human iPSC-derived neural progenitor cells (day 17) and neurons (day 50) by paired-end sequencing, with 3-6 biological replicates, using Illumina HiSeq
2015-09-14 | E-GEOD-71289 | biostudies-arrayexpress
Project description:RNA-seq of UPMM3 with restoration of BAP1 and BAP1 mutant proteins. Cell line UPMM3 contains a frameshift mutation in BAP1.
2018-01-31 | GSE97224 | GEO
Project description:The interaction of frameshift mutation-derived cancer neoantigens and cancer immunotherapy remains unknown. We found that live cell adjuvant or cDNA transfection in the muscle, which express MHC-class I and class II-restricted non-self-peptides, generated broad-spectrum anti-tumor immunity. Such chimeric peptides did not need to be tumor-neoantigens, but must be in a single chain (complete T cell antigen: CTA). Long product of frameshift mutation frequently contained CTA and the colon cancer patients with the long frameshift products (>120 amino acids) showed a good prognosis. Mechanistically, live cell adjuvant expressing CTA strengthened crosstalk between dendritic cells and CD8+ T cells in a CD4+ T cells-dependent manner. This cross talk suppressed CD8+ T cell exhaustion and produced stem-cell like progenitor CD8+ T cells in vivo. Combination of the live cell adjuvant conversed unresponsive tumors to responsive to PD-1 blockade therapy. Together, our findings provide a new broad-spectrum cancer immunotherapy, and clarify the type of frameshift neoantigens controlling the efficacy.
2024-10-16 | GSE245743 | GEO
Project description:To understand the effects of Hsp60 deficiency in developing vertebrates, we generated CRISPR/Cas9-mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the proteome changes in zebrafish larvae at 5 days post fertilization (DPF). Wildtype control and hspd1-/- larvae at 5dpf, were analyzed by TMT and nanoLC-MS/MS based proteomcis. For this purpose, we studied five pools from each genotype, and each pool consisted of five larvae.
2024-09-27 | PXD048920 | Pride
Project description:We found a high frequency of heterozygous Fanconi-BRCA pathway mutations in pediatric T-ALL. BRCA2 was the most commonly mutated gene. We transduced Cas9-expressing Jurkat cells, which lacked an identifiable BRCA2 mutation, with an integration-defective lentiviral guide RNA expression construct targeting exon 11 of BRCA2 (NM_000059). Single-cell cloning and sequencing analysis revealed two distinct clones harboring monoallelic BRCA2 frameshift mutations, termed clones W4 and W5. Each of these clones was subjected to RNA sequencing analysis.
2019-02-20 | GSE126780 | GEO
Project description:We identified a mutation that is a frameshift mutation in a mononucleotide run of eight consecutive T's in the coding region of the gene SSY1, which encodes a key component of a plasma-membrane sensor of extracellular amino acids.We introduced it into the S288c background and examined the effect on gene expression. Keywords: Total gene expression analysis S288C wt, S288C ssy1-t9 and S288C ssy1-ko were compared
2010-05-26 | E-GEOD-9875 | biostudies-arrayexpress
Project description:We report sequencing of 10 SCC_NodalMet samples from human subjects. Sequencing was done on an oncology targeted gene mutation panel consisting of 76 genes.
2022-02-28 | GSE196601 | GEO