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• Transcriptome Sequencing PPGL

  RNA library preparation of samples with RNA Integrity Number (RIN) > 5.5 (median 7.1; range 5.6-8.9) was performed as described in the TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101). Briefly, 0.7-1 µg total RNA PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters. Adapter-ligated library was completed by PCR with Illumina PE primers. The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina HiSeq2500 on a 51bp single-read format following manufacturer's protocols. cDNA libraries from FFPE tumors and low integrity RNA’s (RIN<5.5) from FF tumors (median 2.4; range 1-5.5) but % of fragments > 200 nucleotides higher than 20% (median 57.5; range 20-96) were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, 015) with a UMI Second Strand Synthesis Module for QuantSeq FWD (Lexogen, 081), vendor’s protocol for low input/ low quality/ FFPE RNA using 200-500 ng of total RNA, according to availability, was used as starting material. PCR Add-on Kit for Illumina (Lexogen, 020) was used to adjust the library amplification number of cycles. Libraries were applied to an Illumina flow cell for cluster generation and sequenced on NovaSeq6000. Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software. Demultiplexing of BCL files to FASTQ format was performed with the bcl2fastq Software (Illumina).

  Study EGAS00001006044

• Profiling of gene expression and epigenomics in the fetal brain

  scRNA-seq and Cut&Tag from a sample of the human fetal brain. To compare neurogenesis in the primary human brain with that in organoids, we profiled transcriptome and chromatin accessibility (10X multiome) as well as bulk Cut&Tag of histone modifications H3K27me3, H3K27ac and H3K4me3. We used a human brain sample from GW 19 for all experiments.

  Dataset EGAD50000000225

• Whole Genome DNA Methylation

  Whole Genome Bisulfite Sequencing on normal primary human uveal melanocytes. WGBS libraries were prepared using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences 30024), the EZ DNA Methylation-Gold Kit (Zymo D5005), and DNA Clean & Concentrator-5 (Zymo D4013), following the instruction manual Accel-NGS Methyl-Seq DNA Library (Revision 160510). Paired-end (2 x 150 bp) libraries were sequenced on a DNBSEQ-T7 instrument (MGI) after library conversion.

  Dataset EGAD50000000766

• Indonesian Genome Diversity Project 3

  Low coverage whole genome sequences (1-3x) were collected to study human genetic history across Wallacea archipelago and West Papuan Region of Indonesia . We collected 254 newly sequenced genomes mostly from previously undocumented populations including 9 communities in Wallacea and 3 in West Papuan regions. Out of 254, there are 8 high coverage whole genome sequences were produce in the study (L4).

  Dataset EGAD50000000647

• scRNAseq of endothelial cells from human iPSC-derived kidney organoids transplanted in the coelomic cavity of chicken embryos compared to untransplanted controls

  This dataset includes scRNA-seq fastq files and Seurat counts and metadata for 6 samples of endothelial cells enriched from hiPSC-derived kidney organoids cultured in vitro or transplanted in chicken embryos. Samples were obtained at 2 timepoints: d7+13 (1 day after transplantation) and day 7+20 (8 days after transplantation).

  Dataset EGAD50000001555

• WGS soft tissue sarcoma tumoroid biobank

  Dataset EGAD00001008466

• RNAseq

  Libraries for sixty-eight cases (23 EATL and 45 MEITL) were prepared starting from 1 µg of total RNA using the TruSeq Stranded total RNA Gold kit from Illumina (San Diego, California, USA) and were sequenced in three batches on a HiSeq 4000 machine from Illumina with an average output of 63 million reads per sample (range 49-126).

  Dataset EGAD50000001619

• colorectal_epigenome

  Three different types of samples were used: 19 normal adjacent, 17 adenoma and 19 colorectal tumor tissue samples. This included 10 pairs of colorectal cancer and normal samples and 1 pair of adenoma-normal samples of the same patient. Tissue specimens were formalin-fixed paraffin-embedded (FFPE). DNA was isolated using the QIAamp FFPE Tissue kit (Qiagen, Hilden, DE) according to the manufacturer’s instructions. The processed DNA was run on the Illumina Human MethylEPIC® v1.0 BeadChip array.

  Dataset EGAD00010002726

• Transcriptome analysis of human muscle/myofibers carrying the human nemaline myopathy type 6-associated KBTBD13-R408C variant.

  This dataset contains mRNA-seq results from eleven samples from human donors, each sample being composed of 5-10 rebulked fiber type-specific myofibers. This sample set includes; 1) Three FT-I and three FT-IIa rebulked samples from control individuals 2) Three FT-I and two FT-IIa rebulked samples from NEM6 patients with a KBTBD13R408C variant (NP_001094832.1: p.Arg408Cys)

  Dataset EGAD50000002408

• BAM-format HiFi whole genome sequencing reads (PacBio Revio) from stabilized human saliva

  HiFi whole‑genome sequencing data from a single human saliva sample collected and stabilized using an Oragene device. Sequencing was performed on a SMRT® Cell using PacBio Revio™ SPRQ chemistry. Sequencing produced >100 Gb of HiFi reads yielding >30× genome coverage suitable for comprehensive variant and methylation analysis. Dataset includes long‑read HiFi sequences in BAM format, containing both aligned and unaligned reads.

  Dataset EGAD50000002398