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• Serum Proteome Profiling Identifies Early Markers of Therapeutic Response to Neoadjuvant Chemotherapy of Breast Cancer

  We performed a proteomic serum profiling of patients with non-metastasized breast cancer (BC) who received neoadjuvant chemotherapy (NACT). Samples were collected at three timepoints during NACT. Furthermore, we compared serum samples of BC patients pre-NACT to a control group of healthy volunteers.

  Dataset EGAD00010002330

• RNA-Seq Profiles from CA017-003 Clinical Trial

  The dataset contains RNAseq profiles of 182 patients from the CA017-003 clinical trial. The Allprep DNA/RNA FFPE kit was used to simultaneously purify genomic DNA and total RNA from formalin-fixed, paraffin embedded (FFPE) tissue sections. RNAseq libraries (50PE, 50M) were constructed using Illumina TruSeq RNA Access method. Fastq files are included.

  Dataset EGAD50000000991

• Total RNA sequencing of fibroblasts from an individual with fragile X syndrome

  Total RNA sequencing of fibroblasts from an individual with a methylated CGG repeat >200x in the FMR1 5'UTR. Libraries were prepared with total RNA with Ribo-Zero ribosomal RNA depletion (illumina), and sequenced paired-end, 75bp on a NextSeq 550 system. This dataset contains three RNA-sequencing replicates from the same cell line.

  Dataset EGAD50000000920

• McQuillin_Global_WES_Schizophrenia

  This research project was a collaboration between University College London, UK and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 1,623 Schizophrenia, Bipolar and Control samples from collaborators in UK. Genomic DNA from each sample was sequenced to a mean depth of 20x. The exome used Twist capture and samples were sequenced on Illumina HiSeqX machines producing CRAM files.

  Dataset EGAD50000001316

• RNA-Seq profiles from the CheckMate-649 Clinical Trial

  This dataset contains RNA sequencing (RNAseq) data of 814 patients from the CheckMate 649 clinical trial whose ICF allows data deposition into a public repository. Gene expression profiling was performed retrospectively using RNAseq on a subset of baseline tumor samples. Paired-end FASTQ files were processed on Seven Bridges platform (Seven Bridges Genomics).

  Dataset EGAD50000001105

• Spatial transcriptomics

  This dataset contains raw sequencing and processed data of spatially resolved transcriptomes. The data were generated with 10x Visium probe-based assay on FFPE tissues of 30 ST-EPN tumour resections. Raw data contain two-lane fastq files of the sequencing. Processed data contain aligned and filtered .h5 counts matrices as well as positional files as generated by 10x SpaceRanger.

  Dataset EGAD50000001876

• RNA-seq data: Histone mutations in human Pre-Leukemic HSC and AML

  RNA-seq data from TEX cells transduced with HIST1H3H WT, HIST1H3H K27M, HIST1H3F WT, HIST1H3F K27I and Luc2 control in triplicate. In addition, RNA-Seq was performed on untransduced TEX cells. Libraries [rRNA-depleted stranded (HMR)] were sequenced on an Illumina Hiseq 4000 platform to generate 100 bp paired-end reads.

  Dataset EGAD00001004437

• Genomic and transcriptomic profiling of carcinogenesis in patients with familial adenomatous polyposis

  Whole-exome sequencing (WES) and whole-genome sequencing (WGS) were performed on matched adjacent normal tissues, multiregionally sampled adenomas at different stages and carcinomas from 5 patients with FAP and 1 patient with MUTYH-associated polyposis (MAP) (n=56 exomes; n=56 genomes; n=8,757 single cells).

  Dataset EGAD00001005457

• SARS-CoV2 nasal epithelium

  Single cell RNA sequence generated from human primary nasal epithelium differentiated at air-liquid interface. This dataset comprises tissue from two donors, with cultures either unexposed or exposed to SARS-CoV2. Libraries were prepared using the 10X Genomics pipeline as per manufacturer's instructions.

  Dataset EGAD00001008159

• Single-cell RNA sequencing on 5063 single T cells from six hepatocellular carcinoma patients

  T cells isolated from peripheral blood, tumors and adjacent normal tissues from six hepatocellular carcinoma patients. SmartSeq2 and Tang2009 protocol were used to amplify RNA from single T cells. High depth enables simultaneously expression profiling and TCR assembling.

  Dataset EGAD00001003337