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• Longitudinal Single-Cell Profiling in Refractory Mantle Cell Lymphoma

  we performed sequential scRNA-seq of 21 specimens (discovery cohort) collected at baseline, during treatment, and/or at disease remission/progression from 3 ibrutinib-responsive (R) patients (Pt-V, C and D) and 2 non-responsive (NR) patients (Pt-B and E). In addition, the PBMC samples from two healthy donors (N1 and N2) were included as the normal controls.

  Dataset EGAD00001006994

• RCC Infiltrated Macrophages and Monocytes

  Tumor infiltrated Macrophages and Monocytes were sorted on Aria II (Becton Dickinson) into TRIzol LS and flash frozen. RNA was extracted with chloroform. Isopropanol and linear acrylamide were added, and the RNA was precipitated with 75% ethanol. Total RNA (0.649–1 ng) with RNA integrity numbers 6.8 to 10 underwent amplification using the SMART-Seq v4. Ultra Low Input RNA Kit (Clontech; cat. #63488). Amplified cDNA (15 ng) was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems, KK8504) using 8 cycles of PCR.

  Dataset EGAD00001009393

• RNA sequencing of skin tissue and peripheral blood mononuclear cells from patients with atopic dermatitis and healthy controls.

  We performed RNA-sequencing of skin tissue and peripheral blood mononuclear cells obtained from patients with atopic dermatitis along with healthy controls in Japanese population.

  Study JGAS000628

• TallFlow - multi-omics

  Single-cell Immune profiling 10X genomics protocol. This data includes 5' mRNA sequencing, TCR sequencing, and 204 AB sequencing. In total 15 pediatric T-ALL samples and 4 pediatric Thymus samples.

  Study EGAS50000000358

• 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

• SCANDARE HNSCC

  Prospective biobanking study in SCANDARE HNSCC (Head and Neck Squamous Cell Carcinoma) patients aiming at better understand the link between the molecular alterations of the tumor itself, its microenvironment and immune response.

  Study EGAS50000001158

• Etiology of congenital thyroid dysfunction in Down Syndrome: a multi-omics investigation

  The goal of this study was to investigate dfiferences in the thyroid DNA methylome and transcriptome between fetuses with Down syndrome and fetuses with no genetic/developmental abnormality.

  Study EGAS50000000264

• Deciphering novel TCF4-driven mechanisms underlying a common triplet repeat expansion-mediated disease

  short and long read data generated from cultured corneal endothelial cells (CECs) of unaffected controls, expansion positive Fuchs Endothelial Corneal Dystrophy (FECD) and expansion negative FECD individuals.

  Study EGAS50000000303

• Single-cell RNA-sequencing on malignant and benign tissue samples

  Single-cell RNA-sequencing on malignant and benign tissue samples from untreated donors with colorectal adenocarcinoma and liver metastasis was performed in order to deduce tissue adaptive expression patterns of the disease. Matching tissue from five donors with untreated CRC and liver metastasis were sampled.

  Dataset EGAD50000001203

• DNA sequences from adolescent and young adult patients with melanoma treated with immunotherapy

  Sequencing libraries were prepared and barcoded using the unique molecular identifier and index tagging following the VariantPlex Somatic Protocol (ArcherDx). Pool-library was loaded at 1.2 pM concentration with 20% PhiX and paired-end sequencing was performed using the NextSeq 500 Illumina sequencer using 300 cycle high output reagent kit.

  Dataset EGAD50000000353

• SNP_array

  33 ETMR samples were genotyped using Illumina HumanOmni2.5M array. Hybridization and scanning was done according to the manufacturer's instructions (Illumina). Copy number (Log R) and B allele frequency estimates were obtained sing the Genotyping module (v1.9.4) in GenomeStudio v2011.1 (Illumina). Normalized and log2-transformed copy number measurements were imported from genomestudio and analysed using R package CopyNumber to identify segments with similar copy number.

  Dataset EGAD00010001667

• Clonal_human_oesophagus_punches

  We wish we perform whole genome sequencing on known clonal libraries of human oesophagus to provide a detailed investigation into differences in mutational burden, copy number and mutational signatures both within and between individuals.

  Study EGAS00001007696

• Histone Acetylome-wide Association Study of Autism Spectrum Disorder

  H3K27ac ChIP-seq were performed on postmortem samples from autism spectrum disorder and matched control brains. Tissues were chosen from three brain regions: prefrontal cortex, temporal cortex and cerebellum.

  Study EGAS00001001943

• Single-cell T-cell receptor sequencing of intraepithelial gammadelta T-cells in celiac disease

  Single-cell paired TCR sequencing of intraepithelial γδ T-cells in gluten-free diet treated and untreated celiac disease patients and in controls. (Paired end, amplicon sequencing).

  Study EGAS00001003897

• Dynamic N6-methyladenosine Epitranscriptomic Landscape in Lung Adenocarcinoma

  Systematically evaluate the global effect of dysregulated m6A regulators on the m6A epitranscriptome in patient tumors, and identify prognostic m6A markers by linking with patients' clinicopathological and outcome information.

  Study EGAS00001005524

• Genome-wide characterization of Arabian Peninsula populations

  The screening of 741,000 variants in 420 individuals from Arabian Peninsula (100 from Saudi Arabia, 100 from Yemen, 100 from Oman and 120 from UAE) and 80 individuals from Iran.

  Study EGAS00001003335

• Chronic lymphocytic leukemia patient-derived xenografts recapitulate clonal evolution to Richter transformation

  Whole-genome sequencing (WGS) and RNA-seq data from patient-derived xenografts (PDXs) obtained from CLL and RT primary samples as described in Playa-Albinyana et al.

  Study EGAS00001006965

• PhIP-Seq LLD

  Bacteriophage Immunoprecipitation Sequencing (PhIP-Seq) of LLD participants. Libraries and protocol were developed in the Weizmann Institute of Science. Two different libraries were used, containing microbial and other immunological peptides respectively.

  Study EGAS00001006999

• MPRA-SCZ

  RNA-Seq and ATAC-Seq of iPSC derived neurons under baseline and KCl stimulation conditions from 10 distinct donors, including 5 healthy controls and 5 schizophrenic individuals. scATAC of human post mortem prefrontal cortex from 4 adult individuals including 2 neurotypical individuals and 2 schizophrenic individuals.

  Dataset EGAD00001011335

• 340 human whole genome sequences from Angola and Mozambique

  CRAM files of 340 human genomes from Angola and Mozambique. Paired-end reads were generated in an Illumina-X Ten and were mapped against the human reference genome build hg19/GRCh37. More details about the sequencing and the samples in Tallman et al. 2023. Nature Communications.

  Dataset EGAD00001011992

• RNA-seq iNKT, T and C1R cells

  RNA-seq (Ribodepleted Directional -75 PE- Hiseq 4000) data of purified and expanded iNKt and T cells from normal donor, and RNA-seq (poly-A 100-PE Hiseq 2500) data from C1R cell line. Data set consist of 3 pairs of fastq files, one pair per sample

  Dataset EGAD00001004331

• cfDNA mutation analysis using TAPAS in plasma and urine

  A 2.077Mb (57306 probes) personalised capture panel [Tailored Panel Sequencing (TAPAS)] was designed based upon the somatic SNVs identified by WES of RCC patient FF and FFPE tissue samples and applied to cfDNA in plasma and urine.

  Dataset EGAD00001005813

• Gene expression profiling of SLE and healthy control samples

  mRNA-sequencing study of 141 patients with SLE and 48 healthy control samples.

  Study EGAS00001005701

• Bulk RNA-seq of Human Epiglottis and Subglottis

  This study contains bulk and single nucleus RNA-seq of human epiglottis and subglottis tissue.

  Dataset EGAD50000001278

• Single-nucleus RNA-sequencing of normal adrenal cortex and adrenocortical tumors

  BAM generated using Cell Ranger v3.1.0 and Space Ranger v1.3.1 and anonymized using BAMBoozle

  Dataset EGAD50000000835

• Genomic characterization of pancreatic tumours and matched xenograft and organoid models - WGS mapped reads

  Whole Genomes Define Concordance in Matched Primary, Xenograft, and Organoid Models of Pancreas Cancer - WGS mapped reads

  Dataset EGAD00001003586

• A110632A

  Whole genome sequencing for single cells for library A110632A 1151 cells; filetype=bam

  Dataset EGAD00001007094

• A110632B

  Whole genome sequencing for single cells for library A110632B 892 cells; filetype=bam

  Dataset EGAD00001007095

• A118833A

  Whole genome sequencing for single cells for library A118833A 919 cells; filetype=bam

  Dataset EGAD00001007096

• A118833B

  Whole genome sequencing for single cells for library A118833B 1147 cells; filetype=bam

  Dataset EGAD00001007097

• A118845B

  Whole genome sequencing for single cells for library A118845B 1209 cells; filetype=bam

  Dataset EGAD00001007098

• A118869A

  Whole genome sequencing for single cells for library A118869A 1165 cells; filetype=bam

  Dataset EGAD00001007099

• A118869B

  Whole genome sequencing for single cells for library A118869B 1124 cells; filetype=bam

  Dataset EGAD00001007100

• A95626A

  Whole genome sequencing for single cells for library A95626A 1040 cells; filetype=bam

  Dataset EGAD00001007103

• A95634B

  Whole genome sequencing for single cells for library A95634B 1335 cells; filetype=bam

  Dataset EGAD00001007105

• A95646A

  Whole genome sequencing for single cells for library A95646A 1071 cells; filetype=bam

  Dataset EGAD00001007106

• A95653B

  Whole genome sequencing for single cells for library A95653B 1342 cells; filetype=bam

  Dataset EGAD00001007107

• A95663B

  Whole genome sequencing for single cells for library A95663B 1364 cells; filetype=bam

  Dataset EGAD00001007108

• A95675A

  Whole genome sequencing for single cells for library A95675A 668 cells; filetype=bam

  Dataset EGAD00001007109

• A95731B

  Whole genome sequencing for single cells for library A95731B 1307 cells; filetype=bam

  Dataset EGAD00001007110

• A96115B

  Whole genome sequencing for single cells for library A96115B 1201 cells; filetype=bam

  Dataset EGAD00001007112

• A96118A

  Whole genome sequencing for single cells for library A96118A 1193 cells; filetype=bam

  Dataset EGAD00001007113

• A96130B

  Whole genome sequencing for single cells for library A96130B 1267 cells; filetype=bam

  Dataset EGAD00001007114

• A96178A

  Whole genome sequencing for single cells for library A96178A 788 cells; filetype=bam

  Dataset EGAD00001007115

• A96178B

  Whole genome sequencing for single cells for library A96178B 846 cells; filetype=bam

  Dataset EGAD00001007116

• A96181C

  Whole genome sequencing for single cells for library A96181C 1216 cells; filetype=bam

  Dataset EGAD00001007117

• A96225B

  Whole genome sequencing for single cells for library A96225B 959 cells; filetype=bam

  Dataset EGAD00001007119

• A96225C

  Whole genome sequencing for single cells for library A96225C 1034 cells; filetype=bam

  Dataset EGAD00001007120

• A96240A

  Whole genome sequencing for single cells for library A96240A 1493 cells; filetype=bam

  Dataset EGAD00001007121

• A98172A

  Whole genome sequencing for single cells for library A98172A 898 cells; filetype=bam

  Dataset EGAD00001007123