Search Results - EGA European Genome-Phenome Archive

Investigating differential diagnostic and prognostic biomarkers in primary cutaneous follicle center lymphoma and follicular lymphoma using low-coverage whole-genome sequencing

In this study, we analyzed 28 primary cutaneous follicle center lymphoma samples from 20 patients and compared the copy number profiles to a cohort of diagnostic samples of 64 nodal follicular lymphoma patients using low-coverage whole genome sequencing (lcWGS).

Dataset EGAD50000000199

WTCCC2 case-control study for Ulcerative Colitis

WTCCC2 project genome-wide case-control association study for Ulcerative Colitis (UC) using the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

Study EGAS00000000084

NanoSeq of buccal swab samples

16 buccal swab samples were analyzed by Nanoseq. S3 in the file names indicates 28 mm^2 swab size, and S5 indicates 254 mm^2 swab size. We analyzed 28 mm^2 swab samples using paired 254 mm^2 swab samples as controls. The files were generated by the Nanoseq pipeline using GRCh37 as the reference genome.

Dataset EGAD50000000999

Whole Exome Sequencing Data of indolent primary renal B-Cell lymphomas

We used sequenced 34 iNHL samples using whole exome sequencing (WES) data to evaluate possible mutational signatures and driver mutations associated with the patient’s clinical and cytogenetic characteristics.

Study EGAS50000000774

Whole genome sequencing data of pediatric hypodiploid B cell acute lymphoblastic leukemia

The dataset includes FASTQ and BAM files from diagnostic and matched remission (control) bone marrow samples of one hypodiploid ALL patient (ALLT-351). Sequencing library was made using NEB Next® Ultra™ DNA Library Prep Kit. Both diagnostic (60x) and remission (30x) samples were sequenced using HiSeq X.

Dataset EGAD50000001856

Impact of DIS3 Aso on BCR repertoir in human buffy coat purified B-Cells

The aim is to identify difference in the BCR of Aso DIS3 treated cells compared to Control Aso. Using extracted DNA from human B-cells

Study EGAS50000001107

WGS data of paediatric B-other B cell acute lymphoblastic leukemia (set4)

The dataset includes FASTQ and CRAM files from diagnostic and matched remission (control) samples of two B-other ALL patients (ALLT-389, ALLK-124). Sequencing library was made using Novogene NGS DNA Library Prep Set. Both diagnostic (90x) and remission (30x) samples were sequenced using Illumina NovaSeq 6000.

Dataset EGAD50000002159

Whole Exome Sequencing of 5 FFPE prostate samples (normal and tumour pairs) to identify mutations

Whole Exome Sequencing was performed on radical prostatectomy formalin-fixed paraffin-embedded sample pairs (n = 6). Library prep was done by exon capture using the Illumina Truseq Exome kit and sequenced as 75bp paired end on Illumina NextSeq 500. Sequences were aligned to the human genome (hg38) using BWA.

Dataset EGAD00001006107

Abnormal foetal development exome trios

This project is to explore the contribution of de novo mutations to severe structural malformations diagnosed prenatally using ultrasound. These malformations include heart, CNS, renal and GI abnormalities. In this pilot project we aim to exome sequence 30 parent-foetus trios to ~50X mean coverage and identify de novo functional variants using an algorithm developed in the Hurles group

Dataset EGAD00001001442

GWAS genotype data of Japanese

GWAS genotype data of the Japanese population (N=2,380) were collected at Osaka University and the affiliated medical institutes. GWAS genotyping was performed using Infinium Asian Screening Array (Illumina, USA).

Study EGAS00001006423

WGS data of paediatric hyperdiploid B cell acute lymphoblastic leukemia (set4)

The dataset includes FASTQ and CRAM files from diagnostic and matched remission (control) samples of one hyperdiploid ALL patient (ALLK-134). Sequencing libraries were made using Novogene NGS DNA Library Prep Set (Cat No. PT004). Both diagnostic (90x) and remission (30x) samples were sequenced using Illumina NovaSeq X Plus.

Dataset EGAD50000002429

Multimodal epigenetic sequencing analysis for colon cancer

Targeted methylation sequencing (enzymatic conversion) data of plasma samples collected from colon cancer patients and non-cancer subjects.

Study EGAS50000000052

scMethylation data of 5 regionally sampled GBM tissue for 2 patients

This dataset contains snRNA-seq data of 5 regionally sampled GBM tissue (peritumoral region, tumor edge, and tumor core). Regionally sampled GBM patient tissue was dissociated and nuclei were processed in an unbiased manner without any sorting procedure. Nuclei dissociation was performed following the nuclei isolation for single-cell ATAC-seq (10x Genomics; CG000169) with matched peri-tumoral and tumor core samples. Subsequent single-cell methylation sample preparation followed Scale Biosciences single-cell methylation kit protocol v1.0. mplification adaptors through ligation and adding a second barcode though indexed PCR reaction following Scale Biosciences single-cell methylation kit protocol v1.0. We employed the TWIST human methylome panel for targeted enrichment of informative methylation sites.

Dataset EGAD50000001837

Gremlin 1 + fibroblastic niche maintains dendritic cell homeostasis in lymphoid tissues

Although cross-species transcriptional analysis has been generated for DCs37, transcriptomic conservation between mouse and human FRCs at single-cell resolution has been unclear. To test whether GREM1+ FRCs might also play a role in DC homeostasis in humans, we performed scRNA-seq of CD45–PDPN+ stromal cells, as well as CD45+CD11c+ immune cells from healthy human LNs of three donors.

Study EGAS00001006211

15016 results for "cancer studies using rna-seq"

in 17.80 milliseconds.