9d27d7a2-6da5-4e0f-bd7a-cd66a94b7a93 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001007716 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:We included 3 BAM files of the genome sequencing data: 2 of 3 are from tumour samples, namely 1 repaired-FFPE and 1 unrepaired FFPE; the third BAM file is from normal tissue of FFPE block. There is also a VCF file containing all somatic mutations in the dataset.
| EGAD00001007723 | EGA
Project description:Three SpCas9-ABE (R785X/R785X) and three xCas9-ABE-repaired organoid clones (F508del/R553X) and their respective unrepaired control organoids were paired-end whole genome sequenced using Illumina Novaseq 6000 system. The reads were mapped to hg19 genome assembly and data is provided as BAM files.
| EGAD00001005427 | EGA
Project description:Plant BZR1-BAM transcription factors contain a β-amylase (BAM)-like domain, characteristic of proteins involved in starch breakdown. The enzyme-derived domains appear to be non-catalytic, but determine the function of the Arabidopsis thaliana BZR1-BAMs (BAM7 and BAM8) during transcriptional initiation. Microarray experiments with plants overexpressing different mutant versions of the proteins show that only functional BZR1-BAM variants deregulate gene expression and cause leaf developmental abnormalities. Transcriptional changes caused by overexpression of the BZR1 domain alone indicate that the BAM domain increases selectivity for the preferred cis-regulatory element BBRE (BZR1-BAM Responsive Element). In this study, we used the ATH1 GeneChip microarray to investigate transcript abundance in different Arabidopsis thaliana genotypes.
2014-06-10 | GSE58370 | GEO
Project description:Understanding gene expression diversity across human populations is essential for accurate genome annotation and disease interpretation. However, existing annotations are primarily based on European-derived transcriptomic data, potentially limiting their applicability to other populations. This study aims to assess population-specific transcript diversity and its impact on gene annotation. To achieve this, we performed long-read RNA sequencing on lymphoblastoid cell lines from 43 individuals across eight globally diverse populations. Our workflow included RNA extraction, cDNA synthesis, and sequencing using Oxford Nanopore long-read technology, followed by transcript assembly and comparison with existing gene annotations. We also integrated novel transcripts into reference annotations to evaluate their effect on allele-specific transcript usage detection. This work provides a critical step toward improving transcriptome annotation across diverse populations, ensuring a more comprehensive representation of human genetic variation. We provide here unprocessed, unaligned BAMs (just basecalled; uploaded file names end with *.bam) along with (ONT duplex read resolution, chimeric read splitting, UMI-based deduplication, adapter trimming, and basecalling quality >= 10; uploaded file names end with *preprocessed_Q10.fastq.gz) for each sample.
2026-02-14 | E-MTAB-14935 | biostudies-arrayexpress
Project description:Plant BZR1-BAM transcription factors contain a M-NM-2-amylase (BAM)-like domain, characteristic of proteins involved in starch breakdown. The enzyme-derived domains appear to be non-catalytic, but determine the function of the Arabidopsis thaliana BZR1-BAMs (BAM7 and BAM8) during transcriptional initiation. Microarray experiments with plants overexpressing different mutant versions of the proteins show that only functional BZR1-BAM variants deregulate gene expression and cause leaf developmental abnormalities. Transcriptional changes caused by overexpression of the BZR1 domain alone indicate that the BAM domain increases selectivity for the preferred cis-regulatory element BBRE (BZR1-BAM Responsive Element). In this study, we used the ATH1 GeneChip microarray to investigate transcript abundance in different Arabidopsis thaliana genotypes. Arabidopsis thaliana (accession Columbia) were grown in a nutrient-rich, medium-grade, peat-based compost in Percival AR95 growth chambers (CLF Plant Climatics) at a constant temperature of 20M-BM-0C, 70% humidity and a 12-h light period with constant, uniform light intensity of 150 M-NM-<molM-bM-^@M-"m-2M-bM-^@M-"s-1. Three-week-old plants were harvested 4 h after onset of the light period and immediately frozen in liquid nitrogen. Fourteen individual plants were pooled per replicate.
2014-06-10 | E-GEOD-58370 | biostudies-arrayexpress
Project description:The vertebrate central nervous system (CNS) is protected by the blood brain barrier (BBB) and meningeal membranes, which ensure immune privilege. In the mammalian brain, microglia and border associated macrophages (BAMs) provide immune surveillance and scavenge wastes, yet how evolution shaped immune-cell diversity and function is not understood. In zebrafish, a vascular-derived mural lymphatic endothelial cell (muLEC) lineage fulfils scavenger cell functions at CNS borders. Here, we identify the transcription factor odd-skipped related 2 (osr2) as a specific marker and regulator of muLEC differentiation and maintenance. osr2 controls the transition of muLECs from interconnected endothelial cells to individual scavenger cells in part via control of cadherin-6 (cdh6). muLECs are more transcriptionally similar to BAMs than to other mammalian meningeal cells and share several functions in tissue homeostasis. However, BAMs are absent from zebrafish and muLECs from mice and humans. Analysis of osr2, LEC and BAM markers in diverse vertebrate species reveals muLECs as an ancient lineage and BAMs a recent mammalian specialisation. muLECs and BAMs share functional analogies but are not homologous, providing an example of convergent evolution. This highlights the physiological importance of meningeal scavenger cells and the developmental plasticity of LECs in generating specialised cell types throughout evolution.
2025-11-07 | GSE270486 | GEO