Search Results - EGA European Genome-Phenome Archive

Development of Computational Approaches for Cell Hashing in scRNA-Seq

As a test of cell overloading after cell hashing, a sample of peripheral blood mononuclear cells (PBMC) from a single subject was separated into naive T cells, memory T cells, and non-T cell PBMC populations using fluorescence activated cell sorting (FACS). Each population was separated into two technical replicates, then stained with BioLegend TotalSeq-A antibodies. All 6 samples were pooled, then loaded into 6 wells of a 10X Genomics Chromium 3' RNA-seq v3 chip at increasing cell counts: 16,000 (k), 24k, 32k, 48k, 64, and 80k cells per well. We also included a single sample that was not hashed or pooled, as well as a single sample that was stained with hashing antibodies, but not pooled in two separate wells.

Study phs002695

Adult-type Granulosa Cell Tumour of the Ovary

A recurrent mutation in FOXL2 (c.402C>G; p.C134W) is present in over 95% of adult-type granulosa cell tumours (AGCTs). In contrast, various loss-of-function mutations in FOXL2 lead to the development of blepharophimosis, ptosis and epicanthus inversus syndrome (BPES). BPES is characterized by an eyelid malformation often accompanied with primary ovarian insufficiency but not granulosa cell tumours. Two recent studies suggest that FOXL2 C402G is a gain or change-of-function mutation with altered DNA-binding specificity. Another study proposes that FOXL2 C402G is selectively targeted for degradation inducing somatic haploinsufficiency suggesting its role as a tumour suppressor. The latter study relies on data indicative of an FOXL2 allelic imbalance in AGCTs. Here we present RNA-seq data as genetic evidence that no real allelic imbalance is observed at the transcriptomic level in AGCTs. Additionally, there is no loss of protein expression in tumours harboring the mutated allele. These data and other features of this mutation as compared to other oncogenes and tumour suppressor genes argue strongly against FOXL2 being a tumour suppressor in this context. Given the likelihood that FOXL2 C402G is oncogenic, targeting the variant protein or its downstream consequences is the most viable path forward to identifying an effective treatment for this cancer.

Study EGAS00001005414

RNA-seq of longitudinal human blood and nose swab samples from a controlled human infection experiment with SARS-CoV-2 virus

Controlled human infection experiments enable longitudinal profiling of immune responses to a pathogen. 36 healthy volunteers aged 18-29 years, with no evidence of previous infection or vaccination, were inoculated with SARS-CoV-2 virus and quarantined for 14 days. Blood samples for RNA sequencing were collected into PAXgene tubes before virus challenge, 6 hours after challenge, daily thereafter for 14 days and on day 28. Mid-turbinate nose swabs for RNA sequencing were collected before virus challenge, and on days 1, 3, 5, 7, 10 and 14 after challenge, preserved in RNAprotect.

Study EGAS50000000667

Glioblastoma stem cell lines RNA-seq (Guilhamon et al.)

RNA was extracted from GSCs using the Qiagen RNeasy Plus kit. RNA sample quality was measured by Qubit (Life Technologies) for concentration and by Agilent Bioanalyzer for RNA integrity. All samples had RIN above 9. Libraries were prepared using the TruSeq Stranded mRNA kit (Illumina). Two hundred nanograms from each sample were purified for polyA tail containing mRNA molecules using poly-T oligo attached magnetic beads, then fragmented post-purification. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using RNase H and DNA Polymerase I. A single “A” base was added and adapter ligated followed by purification and enrichment with PCR to create cDNA libraries. Final cDNA libraries were verified by the Agilent Bioanalyzer for size and concentration quantified by qPCR. All libraries were pooled to a final concentration of 1.8nM, clustered and sequenced on the Illumina NextSeq500 as a pair-end 75 cycle sequencing run using v2 reagents to achieve a minimum of ~40 million reads per sample.

Dataset EGAD00001006813

Counts: Brain transcriptome of hereditary cerebral haemorrhage with amyloidosisâ€“Dutch type (HCHWA-D)

These are the log2CPM (log2 counts per million) fragments per gene counts associated with the BAM files in EGAD00001003806, in tab separated format. Counts for 36 postmortem brain samples from 9 non-demented control subjects and 9 Hereditary cerebral hemorrhage with amyloidosis-Dutch type subjects are included (1 Frontal cortex sample and 1 Occipital cortex sample per subject). RNA samples were depleted for ribosomal RNA with the Ribo Zero Gold Human kit (Illumina) and strand specific RNA-Seq libraries were generated. Paired-end sequencing was performed on a HiSeq2500 Illumina system (2x50bp reads). Alignments were performed using GSNAP v2014-12-23 with setting "--npaths 1" on GRCh38 reference genome without the alternative contigs. Fragment per gene counting was performed using HTSeq-count v0.6.1p1 with setting "--stranded reverse". The gene annotation used for quantification were UCSC RefSeq genes for GRCh38 downloaded on 2015-07-13.

Dataset EGAD00010001457

RNA-Seq of human longitudinal whole blood samples from PCR-positive and PCR-negative recent household contacts of COVID-19 index cases.

Little is known about the transcriptomic profile of individuals who are exposed to SARS-CoV-2 yet resist becoming PCR positive. To investigate this, longitudinal whole-blood samples were taken (0, 7, 14, and 28 days after enrolment) from PCR positive and PCR negative SARS-CoV-2-naïve household contacts who were recently exposed to a COVID-19 index. Samples were also taken from pre- and post-pandemic unexposed controls. Total RNA was extracted from PAXgene tubes before undergoing poly(A) selection followed by globin and rRNA depletion. DNA libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina. All samples were then sequenced across 2 flowcells of an Illumina HiSeq 4000.

Dataset EGAD50000000684

Single-Nuclei RNA Sequencing and Spatial Transcriptomics of Human Heart Right Atrial Appendage and Pericardial Fluid in Cardiovascular Disease

This dataset includes single-nuclei RNA sequencing (snRNA-seq) and spatial transcriptomics data from biopsies of the right atrial appendage and pericardial fluid, collected during open-heart surgeries. The samples represent various clinical contexts, including control, ischemic heart disease, heart failure, and myocardial infarction. For each biopsy, nuclei were isolated, and RNA sequencing libraries were prepared using the 10x Genomics Chromium v3 platform. Additionally, spatial transcriptomics was performed on the heart samples. The dataset provides raw sequencing data, which includes fastq files generated from these libraries, offering valuable insights into the cellular composition of heart tissues and associated fluids across different disease states.

Dataset EGAD50000000927

bulk RNAseq analysis of tumor from 3 non-muscle-invasive bladder cancer patients

We performed screenings of patient-specific neo-epitopes by tumor-infiltrating CD8+ T lymphocytes of 4 non-muscle invasive bladder cancer patients. After the tumor resection, these patients went on to receive BCG treatment as they had high-risk disease. In order to select the neo-epitopes, we performed bulk RNAseq of the bladder tumor to select the mutated genes that were expressed in the tumor (TPM >1). For patient UC2, 3 different tumors were resected at the same time and RNA from these 3 tumors were sent separately for RNAseq. For patient UC4, no RNA was available, so this patient is not included in this study.

Study EGAS50000001383

RNAseq data of metastatic breast cancer samples

Paired-end RNA sequencing data from 28 metastatic breast cancer samples. Sequencing was performed on the Illumina NovSeq 6000 and HiSeq 4000 using TruSeq Stranded mRNA Kit.

Dataset EGAD50000000818

PAMELA - 142 patients with HER2+ breast cancer

RNA sequencing data of 141 samples from 141 patients with HER2+ breast cancer treated withletrozole or tamoxifen (SOLTI-1114 PAMELA trial)

Dataset EGAD00001009054

RNA-seq TPM matrices

Matrices of TPM-normalized counts from RNAseq data for the three phase II clinical trials (IMvigor210, POPLAR, IMmotion150) and the phase I clinical trial PCD4989g.

Dataset EGAD00001006741

Whole-exome and whole-genome sequencing data

Multi-omic data for lung neuroendocrine neoplasms, including the first multi-omic sequencing data for the understudied lung atypical carcinoids. The data includes Whole-exomes, whole-genomes, RNA-seq, and EPIC 850K methylation array data.

Dataset EGAD00001005087

Single cell mRNA sequencing of primary GBM - SF 10345

We collected fresh tissue from an untreated GBM (SF10345) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.

Dataset EGAD00001002271

Single cell mRNA sequencing of primary GBM - SF 10360

We collected fresh tissue from an untreated GBM (SF10360) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.

Dataset EGAD00001002272

Single cell mRNA sequencing of primary GBM - SF 10282

We collected fresh tissue from an untreated GBM (SF10282) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.

Dataset EGAD00001002270