GEO DataSets

(Submitter supplied) RECQL4, a member of the RecQ helicase family, plays a role in maintaining genomic stability, but its precise function remains unclear. The N-terminus of RECQL4 has similarity to Sld2, a protein required for the firing of DNA replication origins in budding yeast. Consistent with this sequence similarity, Xenopus RECQL4 has been implicated in initiating DNA replication in oocyte extracts. To determine whether human RECQL4 is required for firing of DNA replication origins, we generated cells in which both RECQL4 alleles were targeted, resulting in either lack of protein expression (Knock-Out) or expression of a full-length, mutant protein lacking helicase activity (Helicase Dead). more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

31 Samples

Download data: BW, CSV

(Submitter supplied) Human-specific changes in specific Siglecs is one of the reasons put forth as molecular mechanisms that could explain human proneness to developing cancers. The SIGLEC12 gene, which encodes the Siglec-XII protein mainly found on epithelial cells, has a fixed homozygous missense mutation in a critical arginine renders unable to recognize its natural ligand. Additionally, the gene harbors a polymorphic frameshift mutation that eliminates expression of the full-length protein in most humans. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

5 Samples

Download data: TXT

(Submitter supplied) Human-specific changes in specific Siglecs is one of the reasons put forth as molecular mechanisms that could explain human proneness to developing cancers. The SIGLEC12 gene, which encodes the Siglec-XII protein mainly found on epithelial cells, has a fixed homozygous missense mutation in a critical arginine renders unable to recognize its natural ligand. Additionally, the gene harbors a polymorphic frameshift mutation that eliminates expression of the full-length protein in most humans. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: TXT

(Submitter supplied) Human-specific changes in specific Siglecs is one of the reasons put forth as molecular mechanisms that could explain human proneness to developing cancers. The SIGLEC12 gene, which encodes the Siglec-XII protein mainly found on epithelial cells, has a fixed homozygous missense mutation in a critical arginine renders unable to recognize its natural ligand. Additionally, the gene harbors a polymorphic frameshift mutation that eliminates expression of the full-length protein in most humans. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

8 Samples

Download data: TXT

(Submitter supplied) Lynch syndrome (LS) patients develop DNA mismatch repair deficient tumors which generate high loads of neoantigens (neoAgs), thus constituting a well-defined population that can benefit from cancer immune-interception strategies, including neoantigen-based vaccines. Using paired whole-exome sequencing and mRNAseq of colorectal cancers (CRC) (n=13) and pre-cancers (n=61) from our LS patient cohort (N=46), we performed in-silico prediction and immunogenicity ranking of highly recurrent frameshift-neoags, followed by their in-vitro validation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

34 Samples

Download data: TXT

(Submitter supplied) Analysis of Beat AML sequencing data revealed a recurrent frameshift variant (R939Pfs*Ter36) in Zinc Finger 687 (ZNF687) that was observed in ~1% of patients and has not been previously described. ZNF687 encodes a transcription factor containing DNA binding C2H2 zinc finger and has been studied in select other malignancies, including Paget’s disease of bone that is associated with giant cell tumor (PDB/GCT) and hepatocellular carcinoma. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

8 Samples

Download data: CSV

(Submitter supplied) Pathological activation of the PI3K/AKT pathway is among the most frequent defects in human cancer and is also the cause of rare overgrowth disorders. Yet, unlike the related oncogenic RAS/MAPK pathway, there is currently no systematic understanding of the quantitative flow of information within PI3K/AKT signalling and how it is perturbed by disease-causing mutations. Here, we develop scalable, single-cell approaches for systematic studies of signal processing within the PI3K pathway, enabling precise calculations of its information transfer for different growth factors. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

9 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21103 GPL24247

40 Samples

Download data: BW, CSV, NARROWPEAK

(Submitter supplied) It is not known why cancers arising in anatomically distinct locations but within the same tissue type can exhibit stark differences in molecular, pathological and clinical features. Cancers arising in proximal and distal sites of the colon are emblematic of these above differences as the proximal and distal colon cancers harbor differences in key molecular features, with BRAFV600E oncogene predominantly occurring in proximal colon cancers in the context of the increased promoter DNA methylation phenotype (CIMP-high), while distal colon cancers lack these molecular features. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

16 Samples

Download data: CSV

(Submitter supplied) Epidermolysis Bullosa Simplex (EBS) is the most common form of Epidermolysis Bullosa (EB) and it is mainly inherited in an autosomal dominant manner (prevalence 1/30000 – 1/50000). Several clinical variants have been described based on the mutated gene, the site of blister formation and the anatomical distribution, but the vast majority of the patients display dominant mutations in genes encoding keratin 5 (KRT5) and keratin 14 (KRT14). more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL15520

6 Samples

Download data: TXT

(Submitter supplied) Epidermolysis Bullosa Simplex (EBS) is the most common form of Epidermolysis Bullosa (EB) and it is mainly inherited in an autosomal dominant manner (prevalence 1/30000 – 1/50000). Several clinical variants have been described based on the mutated gene, the site of blister formation and the anatomical distribution, but the vast majority of the patients display dominant mutations in genes encoding keratin 5 (KRT5) and keratin 14 (KRT14). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

2 Samples

Download data: MTX, TSV

(Submitter supplied) Pathogenic variants in multiple X-linked genes have been implicated in syndromic and non- syndromic intellectual disability disorders. The gene ZFX on Xp22.11 encodes a transcription factor that has been linked to diverse processes including oncogenesis and development, but germline variants have not previously been reported in association with disease. Here, we present clinical and molecular characterization of 18 patients with germline ZFX variants. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

8 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Pathogenic variants in multiple X-linked genes have been implicated in syndromic and non- syndromic intellectual disability disorders. The gene ZFX on Xp22.11 encodes a transcription factor that has been linked to diverse processes including oncogenesis and development, but germline variants have not previously been reported in association with disease. Here, we present clinical and molecular characterization of 18 patients with germline ZFX variants. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

18 Samples

Download data: TXT

(Submitter supplied) Hypertrophic cardiomyopathy (HCM) is often associated with heterozygous mutations in sarcomeric genes. One of the most commonly affected genes encodes for myosin binding protein C (cMyBP-C, MYBPC3). Interestingly, most mutations in MYBPC3 lead to premature termination codons which could result in truncated fragments of cMyBP-C. However, truncated cMyBP-C has not been detect, but rather a reduction of total wildtype cMyBP-C. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

16 Samples

Download data: TAB

(Submitter supplied) The intermediate hPRLr (hPRLrI) is produced by alternative splicing which induces a frameshift, resulting in a novel 13 amino acid tail ("I-Tail") gain and a premature stop codon. hPRLrI induces significant proliferation and anchorage-independent growth of normal mammary epithelia when co-expressed with long form hPRLr (hPRLrL). hPRLrL and hPRLrI co-expression are necessary to induce the transformation of mammary epithelia. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: CSV

(Submitter supplied) Appendiceal neoplasms include a heterogeneous group of epithelial and non-epithelial tumors with varying malignant potential. Despite the rise in incidence of appendiceal neoplasms in recent years, limited progress has been made in the understanding, management and therapeutic treatment. To comprehensively characterize the cell types and molecular mechanisms driving cellular remodeling in epithelial appendiceal neoplasms, we performed an integrated scRNA-seq study. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

16 Samples

Download data: MTX, RDS, TSV

(Submitter supplied) TP63 (p63) is strongly expressed in lower-grade carcinomas of head-and-neck, skin, breast, urothelium, etc. to maintain the well-differentiated phenotype. TP63 has two transcription start sites at exon 1 and exon 3’ to produce TAp63 and DeltaNp63 isoforms, respectively. The major protein, DeltaNp63alpha, functions as a core factor to organize super enhancers of genes essential for epidermal/craniofacial differentiation and for self-activation of DeltaNp63. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL18573

2 Samples

Download data: XLSX

(Submitter supplied) TP63 (p63) is strongly expressed in lower-grade carcinomas of head-and-neck, skin, breast, urothelium, etc. to maintain the well-differentiated phenotype. TP63 has two transcription start sites at exon 1 and exon 3’ to produce TAp63 and DeltaNp63 isoforms, respectively. The major protein, DeltaNp63alpha, epigenetically activates genes essential for epidermal/craniofacial differentiation, including DeltaNp63 itself. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL20844

3 Samples

Download data: TXT, XLSX

(Submitter supplied) Idiopathic fertility disorders are associated with mutations in various genes. Here, we report that coiled-coil glutamate-rich protein 1 (CCER1), a germline-specific and intrinsically disordered protein (IDP), mediates post-meiotic sperm differentiation, while CCER1 deficiency results in defective sperm chromatin compaction and infertility in mice. CCER1 increases transition protein (Tnp1/2) and protamine (Prm1/2) transcription and serves as a multifaceted mediator for multiple epigenetic modification events of histones during the histone to protamine transition (HTP). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL21273 GPL17021

11 Samples

Download data: HIC, TXT

(Submitter supplied) First, we compared gene expression and alternative splicing changes between differentially-localized P633L-RBM20, WT-RBM20, and R634Q-RBM20 in iPSC-CMs. Using ICS, we sorted iPSC-CMs with differentially-localized RBM20 based on correlation with nuclear staining. This was followed by RNA-sequencing of the sorted populations. Second, we analysed gene expression and splicing changes in iPSC-CMs overexpressing of WT-, R634Q-, or NLS-tagged R634Q-RBM20 in splice deficient cells carrying the homozygous frameshift mutation (S635FS). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL18573

60 Samples

Download data: CSV, TXT