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• scRNAseq of neuroblastoma PDX and cell lines

  This dataset contains the 22 bam files coresponding to the scRNAseq done in PDX models and cell lines.

  Dataset EGAD00001007870

• Characterizing the tumor immune microenvironment of ependymomas using targeted gene expression profiles and RNA-sequencing the pros and cons

  RNA sequencing data of a collection of 6 pediatric ependymoma cases

  Dataset EGAD00001009301

• NiCOL Study RNA-seq dataset

  15 samples sequenced in RNA-seq. This dataset contains their raw FASTQ data and the raw count table and the TPM count table.

  Dataset EGAD00001010912

• Paired bone marrow aspirates of ALL before and after treatment

  This dataset includes 16 paired bone marrow (BM) aspirates from patients with acute lymphoblastic leukemia (ALL). The samples are collected at diagnosis and 4 weeks later at the end of induction therapy.

  Dataset EGAD50000002324

• Bulk RNA sequencing of human T and B cells before and after interleukin-2 immunotherapy

  Bulk RNA sequencing of flow cytometry sorted human CD4+ regulatory T (Treg), CD4+ conventional T (Tcon), CD8+ T, and CD19+ B cells from systemic lupus erythematosus patients collected at baseline (day 0, before interleukin-2 immunotherpay), day 5 (after 1 treatment cycle of interleukin-2 immunotherapy), and day 68 (after 4 treatment cycles of interleukin-2 immunotherapy). The dataset comprises files from the above-mentioned 4 immune cell subsets, collected at 3 time points (day 0, day 5, and day 68) of 12 systemic lupus erythematosus patients. Due to technical reasons, day 5 samples of patient SLE_012 could not be processed and are thus missing. The complete dataset totals in 140 raw sequencing files (fastq format).

  Dataset EGAD50000000661

• Single-nuclei RNA sequencing of pheochromocytoma and paraganglioma arising from germline SDHB mutations

  10x genomics single-nuclei RNA sequencing of 9 SDHB-deficient non-metastatic and metastatic pheochromocytoma and paraganglioma. snRNA-seq was performed using the ‘Frankenstein’ protocol (dx.doi.org/10.17504/protocols.io.bqxymxpw). Briefly, nuclei were extracted from frozen tissues and subjected to fluorescence-activated nuclei sorting (FANS) using 4′,6-diamidino-2-phenylindole (DAPI). Sorting was performed using a BD FACSaria 2 instrument, sorting between 3000 and 10,000 nuclei per sample, capturing both diploid and tetraploid populations. FAN-sorted nuclei were immediately processed using either the 10x Chromium Single Cell 5’ (PN-1000006, 4 samples) or 3’ (PN-1000075, 4 samples) Library & Gel Bead Kit (10x Genomics, USA). Once processed, snRNA-seq libraries were sequenced on the Illumina Nova-Seq 6000 (Illumina, USA) using 150bp paired-end sequencing. This dataset contains raw sequencing reads in FASTQ format.

  Dataset EGAD50000000505

• NGS-Based Mutational Analysis of 87 PMBL Patients from the GAINED Cohort (Subset of 382 Sequenced Patients)

  Targeted DNA sequencing was performed on DNA extracted from 87 formalin-fixed paraffin-embedded (FFPE) samples, representing a subset of the 382 sequenced patients from the GAINED cohort. A custom “Lymphopanel” was used to identify mutations in 70 genes associated with lymphomagenesis. Library preparation, exome capture, sequencing, and analysis were conducted by IntegraGen SA (Evry, France). Sequencing was performed on an Illumina HiSeq4000 platform, with variant calling and annotation using established bioinformatics tools such as MuTect and VEP.

  Dataset EGAD50000001359

• WES and RNA-seq of pre-invasive lung adenocarcinoma

  The prevalence of lung adenocarcinoma (LUAD) has increased sharply in East Asia. Early diagnosis leads to better survival rates, but this requires an improved understanding of the molecular changes during early tumorigenesis, particularly in non-smokers. We performed whole exome-sequencing and RNA-sequencing of samples from 94 East Asian patients with precancerous lesions (25 with atypical adenomatous hyperplasia [AAH]; 69 with adenocarcinoma in situ [AIS]) and 73 patients with early invasive lesions (minimally invasive adenocarcinoma [MIA]). This datasets contains the sequencing raw data (FASTQ format).

  Dataset EGAD50000000637

• WGS data of fetal stem cells (15x) and culture-associated mutations of iPSCs and ISC

  This data set includes WGS data of the in vivo acquired mutations in fetal ISCs and HSPCs of 4 foetuses ( T21=2, D21= 2). In addition, this data set includes sub-clonal fetal ISCs to determine the culture-associated mutations of fetal ISCs. Also, it concludes clone +subclone WGS data of iPSCs derived of the fetal ISCs

  Dataset EGAD00001008475

• T-cell receptor targeting FLT3 D835Y mutation study

  We identified a T-cell receptor (TCR) reactive to the recurrent FLT3 D835Y mutation in the tyrosine-kinase domain. To validate the elimination efficacy of leukemia cells, we transplanted human acute myeloid leukemia (AML) cells with FLT3 D835Y mutations into NSG-SGM3 mice and treated either with TCR FLT3 D835Y redirected T cells, or control TCR (TCR 1G4). After treatment, we performed flow sorting of AML blasts (CD3-CD19-) and primary T cells (CD3+CD8+orCD4+CD19-CD33-) and performed whole-exome sequencing.

  Dataset EGAD00001011258