Ontology highlight
ABSTRACT:
PROVIDER: PRJNA629061 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11637891_1.fastq.gz | Fastqsanger.gz | |||
| SRR11637891_2.fastq.gz | Fastqsanger.gz | |||
| SRR11637892_1.fastq.gz | Fastqsanger.gz | |||
| SRR11637892_2.fastq.gz | Fastqsanger.gz | |||
| SRR11637893_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 8 |
Similar Datasets
Project description:We generated a comprehensive collection of zebrafish neurexin knockout lines covering all family members, including alleles with transmembrane domain disruptions and deletions covering full genomic locus and partial gene region. All homozygous mutants were viable and showed no gross developmental abnormalities, enabling molecular profiling despite later‑onset behavioural phenotypes. This resource includes defined nrxn1a-nrxn1b, nrxn2a-nrxn2b, and nrxn3a-nrxn3b double gene mutant lines and provides a vertebrate model to investigate paralog‑specific consequences of neurexin loss of function. The RNA‑seq FASTQ files deposited in this GEO submission were generated from these neurexin mutant and matched control zebrafish and support analysis of transcriptional changes associated with neurexin deficiency.
2026-06-28 | GSE324987 | GEO
Project description:Potocki-Shaffer syndrome (PSS) is a rare contiguous gene deletion syndrome marked by haploinsufficiency of genes in chromosomal region 11p11.2p12. Approximately 50 cases of PSS have been reported; however, a syndrome with a PSS-like clinical phenotype caused by 11p11.12p12 duplication has not yet been reported. We first report the 11p11.12p12 duplication in a family with intellectual disability and craniofacial anomalies. 11p11.12p12 duplication syndrome was identified by karyotype analysis. Next-generation sequencing (NGS) analysis clarified the location of the chromosomal variations, which was confirmed by chromosome microarray analysis (CMA). Whole-exome sequencing (WES) was performed to exclude single nucleotide variations (SNVs). The raw data of NGS analysis and WES have been submitted to SRA, the accession number is PRJNA713823.
2021-03-24 | GSE169469 | GEO
Project description:Background and Aims: Evidence for a genetic contribution to eosinophilic esophagitis (EoE) exists from family and genome-wide association studies. Extensive investigation into rare variants contributing to EoE has not been performed. The Aim is to evaluate families with multiple cases of EoE by genomic and transcriptomic sequencing to identify genes predisposing to EoE. Methods: We whole exome sequenced (WES) distant relative pairs (e.g., cousins) in extended EoE pedigrees and other affected relatives to identify rare, shared, potentially pathologic variants. Whole-transcriptome sequencing by RNA-Seq was performed in nuclear families with multiple EoE cases. We compared the overlap of genes from DNA and RNA sequencing for relevance to disease manifestations. Results: WES was performed in 50 familial cases in 21 EoE extended pedigrees. We observed 219 rare, candidate predisposition variants in 210 genes with complete sharing among all affected family members. Transcriptome sequencing was performed for 43 EoE cases in 18 nuclear kindreds, including 6 relatives without EoE. We observed 10,070 total differentially expressed genes compared to controls. We identified three genes (MUC16, ADGRE1, and TENM3) with evidence of rare variant sharing and differential gene expression among all affected family members. We identified 43 other genes with partial sharing of rare variants among affected family members and with differential gene expression. Several genes identified as prominent in EoE were also differentially expressed in unaffected relatives. Conclusions: Multiple genes related to immune response, barrier dysfunction, and cell adhesion were identified in familial EoE cases and unaffected family members supporting a genetic familial predisposition and a possible multi-hit background to disease pathophysiology.
2025-01-24 | GSE250595 | GEO
Project description:Single Gland Whole-exome sequencing: building on our prior description of multi-region WES of colorectal tumors and targeted single gland sequencing (E-MTAB-2247), we performed WES of multiple single glands from different sides (right: A and left: B) of two tumors in this study (tumor O and U) on the illumina platform using the Agilent SureSelect 2.0 or illumina Nextera Rapid Capture Exome kit (SureSelect or NRCE, as indicated in the naming of fastq files). Colorectal Cancer Xenograft Whole-exome sequencing: The HCT116 and LoVo Mismatch-Repair-deficient colorectal adenocarcinoma cell lines were obtained from the ATCC and cultured under standard conditions. For both cell lines, a single âfoundingâ cell was cloned and expanded in vitro to ~6M cells. Two aliquots of ~1M cells were subcutaneously injected into opposite flanks (right and left) of a nude mouse and tumors allowed to reach a size of ~1B cells (1cm3) before the animal was sacrificed. Tumor tissue was collected separately from the right and left lesions and DNA was extracted for WES using the illumina TruSeq Exome kit or Nextera Rapid Capture Exome expanded Kits (Truseq or NRCEe), as was DNA from the first passage population (a polyclonal tissue culture for HCT116 and a polyclonal xenograft sample for LoVo), which were employed as a control to study mutation accumulation in culture and post xenotransplantation.
2017-05-01 | E-MTAB-5547 | biostudies-arrayexpress
Project description:Colorectal cancer (CRC) represents the third most common cancer worldwide. Next generation sequencing (NGS) appearance has allowed us to produce huge amount of data and, in order to fully exploit its usage, copy number variants (CVN) detection software have been developed. In this study, we analyze germline DNA whole-exome sequencing (WES) data from 38 families with strong CRC aggregation without alterations in known hereditary genes to detect rare candidate CNVs to CRC predisposition using ExomeDepth and CoNIFER tools. Variants shared between family members were compared to Database of Genomic Variants (DGV) catalogue and our Spanish database. CNVs finally selected were validated and segregation analysis were performed using Comparative Genome Hybridization (CGH). Gene expression arrays and qRT-PCR were conducted in both germline and tumor cDNA to check possible effects at transcription level. Immunohistochemistry (IHC) studies were also carried out. Whith this, 21 candidate CNV corresponding to 16 duplications and 5 deletions were detected by calling tools. After multiple filtering steps, only the duplication in chromosome 1 in family 7 stood out as interesting. Validation by CGH confirmed the duplication and correct family segregation. TTF2, TRIM45, VTCN1 and miR942 are embedded in chromosome 1 duplication. Expression studies pointed to TTF2 and miR942 overexpression in carriers, and tumor IHC showed TTF2 protein overexpression and underexpression of the TMEM158 protein. Also known as RIS1, TMEM158 is a predicted target of miR942 and has been claimed to be a candidate tumor-supressor. All in all, chromosome 1 duplication may correspond to the mutational event involved in CRC predisposition in the carrier family by overexpressing TTF2 and miR942, leading to TMEM158 underexpression. Keywords: colorectal cancer, next generation sequencing, copy number variant, duplication, predisposition.
2019-03-01 | GSE96597 | GEO