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• Epigenomic analysis of the human placenta and endometrium constituting the fetal-maternal interface

  This study aims to determine the reference epigenomes of the human placenta and endometrium, which constitute the fetal-meternal interface, for future use in studies of human diseases associated with reproduction and development. In the placenta, we focus on cytotrophoblast and syncytiotrophoblast cells (both at first trimester and at term) and, in the endometrium, we focus on epitherial cells (at the follicular and secretory phases) and stroma cells. These reference epigenomic data will be of valuable resource in studying disease-associated differences in epigenomic modification in the reproductive system. JGA submission accessions: JGA000117,JGA00000000117

  Study JGAS000107

• Ancient genomes reveal insights into ritual life at Chichén Itzá

  To better understand the origin and biological relationships of the sacrificed children from Chichén Itzá to each other and to present-day inhabitants of the region, here we used a combined bioarchaeological and genomics approach to investigate 64 subadults interred within a chultún near the Sacred Cenote and compare them to 68 present-day Maya inhabitants of the nearby town of Tixcacaltuyub, as well as to other available ancient and contemporary genetic data from the region. The community of Tixcacaltuyub has been collaborating with our research team for many years, and their perspectives informed the development of this project.

  Study EGAS50000000296

• Accurate Genome-Wide Germline DNA Profiling from Decade-Old Archival Tissue Specimens

  We evaluate the validity of repurposing archival tissue specimens for germline genetic studies. We performed lc-WGS and imputed genotypes on 10 pairs of matching blood and tumor tissue and benchmarked the accuracy of genome-wide genotypes, HLA haplotypes, and several polygenic risk scores (PRSs). The reported results indicate the high accuracy of germline genotypes and haplotypes obtained from archival tissue DNA. Using this methodology, we estimate breast cancer PRS in 36 Ductal carcinoma in situ (DCIS) patients and demonstrate its association with breast cancer subsequent event (BCSE).  

  Study phs002865

• Gene expression data of 2D duodenum organoids with or without continuous flow

  We developed a monolayer culture system for small intestinal organoids, and then placed the culture plate on a rotator to generate a constant flow in the overlay medium. This mechanical stimulation facilitated the formation of villus-like structures from the monolayer of small intestinal organoids. We analyzed gene expression of 2D normal duodenum organoids with or without medium rotation. Total RNA was extracted from organoids with or without a four-day medium rotation, and after 0, 1, 2 or 4 days of medium rotation, and sequenced with HiSeq X Ten (Illumina).

  Study JGAS000256

• Transcriptional effect of 4HTBZ on Caco-2 cells

  This study was performed to investigate the transcriptional effect of the H2S donor 4HTBZ on intestinal epithelial cells upon inflammatory stimulation. Caco-2/TC7 cells were pre-stimulated with interferon gamma (IFNG, 2.5 ng/mL) and tumor necrosis factor alpha (TNF, 10 ng/mL), followed by treatment with 4HTBZ (50 µM) or vehicle (0.1% DMSO) for 72 hours. Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany), and cDNA libraries were prepared with the QuantSeq 3′ mRNA-Seq Kit (Lexogen, Inc.) and sequenced on an Illumina HiSeq4000 system.

  Study EGAS50000001237

• Sequencing data of multiple sarcoma samples for personalized medicine and endotype identification

  Sequencing data derived from multiple patient samples was used to guide multiple patient-specific experiments and identify potential therapeutic options. These diseases are rare and high-risk (undifferentiated pleomorphic sarcoma, rhabdomyosarcoma) and thus have few available validated clinical options. This leaves the population of patients with few options if, and when, standard therapy fails to cure or control disease. An aspect of the personalize therapy design included the identification of broader disease endotypes (a combination of genetic and clinical data describing patient status) to identify subgroups of the individual disease that could better define treatments and could segment patient populations for deeper preclinical research.

  Study EGAS00001003981

• Dataset for NSCLC samples

  This dataset contains 10x scRNA sequencing data of 16 NSCLC samples. Sequencing was performed on Illumina HiSeq 4000. The sequencing was always paired.

  Dataset EGAD50000000185

• Melanoma exome profiling

  This dataset includes whole exome profiling of 65 early-passage metastatic melanoma cell lines. The data are provided as BAM files for tumor and normal samples.

  Dataset EGAD00001006271

• Processed RNAseq data

  This dataset contains log2(TPM + 1) transformed counts for the 823 tumor samples profiled by RNAseq.

  Dataset EGAD00001006618

• Tumor from individual with germline POLD1 L474P

  This dataset includes WXS sequencing for 1 tumor FFPE sample and adjacent normal tissue from the individual from one family member.

  Dataset EGAD00001009281