Ontology highlight
ABSTRACT:
PROVIDER: PRJNA641132 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:Unaligned bam of 31 samples derived from blood
| EGAD00001001263 | EGA
Project description:<p>The purpose of this study was to obtain tissue specimens derived from patients with melanoma to generate research tools to advance our understanding of the genetics, pathogenesis, and therapeutics of melanoma. Briefly, tissue was obtained from metastatic lesions and used to generate clonal primary cell lines from melanoma cells and fibroblasts from the tumor microenvironment. RNA was extracted from low passage cell lines using Trizol reagent. cDNA libraries were prepared using the TruSeq mRNA sample preparation kit, v2 (Illumina) and sequenced on the HiSeq 2000 platform (Illumina). The submitted files are bam files that contain both unaligned and aligned reads (human genome, build hg19). </p>
| phs001115 | dbGaP
Project description:Unaligned bam of 31 samples derived from primary tumor
| EGAD00001001262 | EGA
Project description:To identify the molecular mechanisms of reduced pain response in Twik-1 knockout mice, we performed bulk RNA-sequencing on lumbar DRGs from WT and Twik-1 knockout mice. Thirty days after sciatic nerve injury, the ipsilateral L4-L6 DRGs were manually sectioned into ~150 µm slices using a razor blade. RNAs were extracted from the sliced DRGs using PicoPure™ RNA Isolation Kit. RNA libraries were constructed using the SMART-Seq v4 Ultra Low Input RNA Kit. High-quality libraries were pooled and sequenced on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads. Image analysis was performed using the NovaSeq 6000 Control Software (v1.8.2), and base calling data were demultiplexed using bcl2fastq (v2.20.0.422), generating FASTQ files. Raw sequencing reads were aligned to the Mus musculus reference genome (GRCm39) using STAR aligner (version 2.7.11a). The genome index was built from the primary assembly FASTA file (Mus_musculus.GRCm39.dna.primary_assembly.fa.gz) and the corresponding gene annotation file (Mus_musculus.GRCm39.113.gtf.gz), ensuring accurate mapping across exon–intron boundaries. Resulting SAM/BAM files were then processed, sorted, and indexed with Samtools (version 1.18). Gene-level counts were generated using htseq-count (version 2.0.3) with the corresponding GTF annotation file.
2026-04-14 | GSE316192 | GEO
Project description:Purpose:The goal of this study was to evalute gene expression patterns of equine chorioallantoic membrane during different stages of the pregnancy Method: mRNA profile of equine chorioallantoic membrane (CAM) from 45days, 4months, 6months and 10months (4 samples for each time points) generated by RNA-sequencing,using a Illumina HiSeq 4000 ( HiSeq 4000 sequencing kit version 1). The sequence reads were trimmed for adapters and quality using TrimGalore Version 0.4.4,and then mapped to EquCab2.0 using STAR-2.5.2b. Final quantification at the gen level was performed by analyzing the BAM files in cufflinks using the Equus_caballus_ENSEMBL_88 gtf file as Guide.
2018-11-19 | GSE108279 | GEO
Project description:This experiment was conducted to generate targeted resequencing data covering a region associated with osteosarcoma in greyhounds. 8 greyhounds diagnosed with osteosarcoma and 7 greyhounds without tumors were sequenced. DNA from the 15 dogs was used to prepare libraries and hybrid capture performed to enrich the region of interest prior to paired-end sequencing using Illumina Genome Analyzer II. The reads were aligned to the dog-genome CanFam2.0 using bwa and pre-processed using Picard and GATK. Variant discovery was performed using GATK. The resulting list of variants were used in the study to finemap the associated region and look for causal variants. We submit the preprocessed BAM-files that still have all reads although some reads are flagged. We also submit the resulting vcf-file with called and filtered variants in all individuals.
2013-11-16 | E-MTAB-1984 | biostudies-arrayexpress
Project description:Here we present HDX-MS data to study the conformational dynamics of BAM, BAM(T434A) and BAM(LVPR).
2025-10-13 | PXD057055 | Pride