Ontology highlight
ABSTRACT:
PROVIDER: PRJNA806768 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18012878_1.fastq.gz | Fastqsanger.gz | |||
| SRR18012878_2.fastq.gz | Fastqsanger.gz | |||
| SRR18012879_1.fastq.gz | Fastqsanger.gz | |||
| SRR18012879_2.fastq.gz | Fastqsanger.gz | |||
| SRR18012880_1.fastq.gz | Fastqsanger.gz |
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Project description:We perform transcriptomic sequencing of rumen, reticulum, omasum, and abomasum epithelial tissues from developing lambs.
2024-05-17 | GSE200295 | GEO
Project description:Tuft cells are required for an effective immune response to gastrointestinal parasitic nematodes in mice, but little is known about tuft cells in other animals. Using scRNA-seq, we profiled the transcriptome of tuft cells and other mucosal cell types from the sheep abomasal epithelium following nematode infection. Cells were isolated from abomasum mucosal tissue of two sheep and processed using 10x Genomics Chromium Single Cell 3’ Reagent kit (v.3) using a total of 20,000 input cells. cDNA libraries were sequenced on an Illumina NextSeq 500 system to a depth of 50,000 read pairs per cell. Sequences were mapped to the genomes for ovine (Ovis aries Oar_v3.1; https://www.ensembl.org/Ovis_aries/Info/Index) and bovine (Bos taurus ARS-UCD1.2; https://www.ensembl.org/Bos_taurus/Info/Index) and gene count matrices generated using the Cell Ranger software (v.3.1.0) and analysed using Seurat package (v.3.1) with R version 3.6.0. The “Find Markers” function identified a tuft cell cluster and other distinct epithelial (Epcam+) and immune (Ptprc+) cell clusters.
2021-11-16 | E-MTAB-10231 | biostudies-arrayexpress
Project description:We perform transcriptomic sequencing of rumen, reticulum, omasum, and abomasum epithelial tissues from developing lambs. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points (day5 and day10).
2024-05-17 | GSE227043 | GEO
Project description:Our objective was to investigate differences in gene expression between 24 parasite-resistant hair and 24 susceptible wool lambs to determine genetic mechanisms involved in resistance to H. contortus. Half of the animals of each breed were infected and sacrificed at 3 or 27 days post-infection; the remaining animals were uninfected controls. Breed differences in abomasum and abomasal lymph node tissue gene expression were assessed using bovine cDNA microarrays. Over 60 transcripts differed between breeds for each tissue and infection status. Genes differentially expressed between hair and wool sheep 3 days PI were assessed for gene function and mechanisms for greater immune cell infiltration, abomasal tissue repair, Th17 response, and anticoagulation were present in parasite-resistant hair sheep. By 27 days PI, hair sheep had greater expression of genes involved in gut motility, inflammatory cytokines, and cell proliferation and differentiation compared to wool sheep. Changes in these processes indicate Caribbean hair sheep have a stronger inflammatory response when infected with H. contortus which may facilitate the increased parasite resistance observed in these sheep.
2009-03-31 | GSE14667 | GEO
Project description:Organoid models provide powerful tools to study tissue biology and development in a dish. Here, we established first-time organoid models from early-postnatal (postnatal day 7) mouse molar and incisor, capable of differentiation toward ameloblast-like cells in vitro. To more in detail characterise organoids from mouse molar and incisor, bulk RNA-sequencing was performed on the following (1) early passage (passage 0) organoids from both tooth types grown in basal tooth organoid medium (TOM) with or without addition of exogenous epidermal growth factor (EGF); and (2) late passage (passage 5) organoids grown in TOM+EGF or differentiation medium (DM).
2023-04-19 | E-MTAB-12557 | biostudies-arrayexpress
Project description:A patient-derived epithelium-only colon rectal organoid, also referred to as a colonoid, was generated from an adenoma (associated with a resection surgery of an invasive moderately differentiated colorectal adenocarcinoma) as part of the development of an on-going organoid biobank at the Michigan Medicine Translational Tissue Modeling Laboratory (TTML, www.UmichTTML.org). The genomic variant signature of this adenoma colonoid was characterized using whole exome sequencing in order to access genomic concordance between the source patient tissue (adenoma and histologically normal tissue 10 cm from lesion) and the in vitro culture, as well as to access genomic stability of the culture over time at 2 and 6.5 months in culture.
2020-12-22 | E-MTAB-9936 | biostudies-arrayexpress
Project description:Organoid technology has provided unique insights into human organ development, function, and diseases. Patient derived organoids are increasingly used for drug screening, modeling rare disorders, designing regenerative therapies, and understanding pathological changes associated with disease progression. However, the use of Matrigel to grow organoids represents a major challenge in the clinical translation of organoid technology. Matrigel is a poorly defined cocktail of extracellular matrix proteins and growth factors extracted from the Engelbreth Holm Swarm mouse tumor. The extracellular matrix is a major driver of multiple cellular processes and differs significantly between tissues as well as in healthy and diseases states of the same tissue. Therefore, we envisioned that extracellular matrix derived from a native healthy tissue would be sufficient to support organoid growth akin to organogenesis in vivo. Here, we have developed hydrogels from decellularized human and bovine endometrium. These hydrogels supported the growth of mouse and human endometrial organoids, which was comparable to Matrigel. Organoids grown in endometrial hydrogels were proteomically more similar to the native tissue than the organoids cultured in Matrigel. Proteomic and Raman spectroscopy analyses showed that the method of decellularization affects the biochemical composition of hydrogels and subsequently, their ability to support organoid growth. The amount of laminin in hydrogels correlated with the number and the shape of organoids. We also demonstrated the utility of endometrial hydrogels in developing solid scaffolds for supporting high throughput cell culture-based applications. In summary, endometrial hydrogels overcome a major limitation of organoid technology and greatly expand the applicability of organoids to understand endometrial biology and associated pathologies.
2022-03-14 | MSV000089054 | MassIVE
Project description:RNA-Sequencing was performed on mechanically dissociated, epithelial-enriched samples, of human extrahepatic biliary tissue from Gallbladder, Common Bile Duct, and Pancreatic Duct tissues. Sequencing was also performed on in vitro cultures of Organoid cell lines at passage 5 that were derived from human Gallbladder, Common Bile Duct, Pancreatic Duct, or Intrahepatic Bile Ducts.
2019-01-20 | E-MTAB-7569 | biostudies-arrayexpress
Project description:Background & Aims Patient-derived gastrointestinal organoids are powerful tools for studying human physiology and disease. However, generating organoids requires prompt isolation and culture of fresh tissue, which is labor and time intensive, placing restraints on basic and clinical research. For example organoid biobanking efforts, or the ability to obtain specimens from distant locations that lack the expertise to culture organoids, is limited by current approaches. We sought to develop a method by which tissue biopsies from patients could be cryo-preserved, stored, or shipped, and later thawed in order to establish live organoid cultures. Methods A method for freezing and recovery, along with straightforward isolation methods using readily available materials were developed. Epithelial isolation and culture conditions were optimized to promote cell survival and the establishment of long-term culture post-thawing. Results Patient biopsies from stomach, duodenum, ileum, colon and from adenomateous colonic polyps were frozen, subsequently thawed and used to successfully establish patient-specific epithelium-only organoid cultures with 100% efficiency (n=31 independent patient biopsies from different regions of the GI tract). Frozen tissue could be shipped internationally and across the United States and used to establish successful organoid cultures. Organoid cultures could be expanded, passaged and frozen down for long-term storage. RNA-sequencing demonstrates that organoids derived from fresh tissue or from frozen biopsies are >99% transcriptionally identical. Conclusions Cryo-preservation of human tissue biopsies followed by the establishment of long-term, expandable cultures has negligible effect on transcription when compared to freshly prepared organoids, and will be of immense benefit to research and for clinical applications. This technique will allow for the establishment of biobanks of human tissues that can be revived and cultured in the future as well as transported across the globe for research, therapeutic or diagnostic use in remote labs and/or clinics.
2018-06-30 | E-MTAB-6516 | biostudies-arrayexpress