Project description:Human dataset, collected 2015-2016, consisting of gastrointestinal mucosal biopsy samples and stool. Files with the aqueous and organic extraction fractions are included. Metabolite extraction was carried out based on a modified protocol as previously published by Elizabeth J. Want et al. in Nature Protocols, 2013, Global Metabolic profiling of animal and human tissues via UPLC-MS.
Project description:Phenol Toluol extraction (PTex) carried out two steps organic-phase separation: first pH neutral phenol–Toluol extraction separated RNA and protein from DNA: RNA and proteins to the top aqueous phase but DNA and membranes in the interface. Aqueous phase then went through two rounds acid-phenol extraction, resulting RNA in the top aqueous phase, proteins bottom organic phase and RNA-protein complexes in the interface. After carefully isolated the interface, ethanol precipitation was carried on for purifying RNA-protein adducts (Urdaneta et al, 2019; Smith et al, 2020)
Project description:Total RNA-seq data from samples produced using conventional TRIzol RNA extraction (control), using the semi-extractability assay (PMID: 28404604) or Orthogonal Organic Phase Separation (OOPS; PMID: 30607034, PMID: 32651564) in naive mESCs (nPSCs). Control samples RNA was extracted from the aqueous phase of non-heated and non-sheared TRIzol samples. The semi-extractability assay samples were prepared by heating and needle-shearing TRIzol samples prior to extraction. For OOPS, the RNA was extracted from the TRIzol interphase of UV-crosslinked cells (254 nm, 400 mJ/cm2). Total RNA-seq libraries were prepared using the CORALL Total RNA-Seq Kit with RiboCop (Dual Indexing, UDI12A) - version 2.
Project description:Total RNA-seq data from samples produced using conventional TRIzol RNA extraction (control), using the semi-extractability assay (PMID: 28404604) or Orthogonal Organic Phase Separation (OOPS; PMID: 30607034, PMID: 32651564) in naive mESCs (nPSCs), primed pluripotent stem cells (pPSCs) and 1-day Wnt-differentiated cells (dPSCs). Control samples RNA was extracted from the aqueous phase of non-heated and non-sheared TRIzol samples. The semi-extractability assay samples were prepared by heating and needle-shearing TRIzol samples prior to extraction. For OOPS, the RNA was extracted from the TRIzol interphase of UV-crosslinked cells (254 nm, 400 mJ/cm2). Total RNA-seq libraries were prepared using the CORALL Total RNA-Seq Kit with RiboCop (Single Indexing) - version 1.
Project description:Total RNA-seq data from samples produced using conventional TRIzol RNA extraction (control), using the semi-extractability assay (PMID: 28404604) or Orthogonal Organic Phase Separation (OOPS; PMID: 30607034, PMID: 32651564) in naive mESCs (nPSCs) after the cells were exposed to 10 μM thapsigargin for 30 minutes. Control samples RNA was extracted from the aqueous phase of non-heated and non-sheared TRIzol samples. The semi-extractability assay samples were prepared by heating and needle-shearing TRIzol samples prior to extraction. For OOPS, the RNA was extracted from the TRIzol interphase of UV-crosslinked cells (254 nm, 400 mJ/cm2). Total RNA-seq libraries were prepared using the CORALL Total RNA-Seq Kit with RiboCop (Dual Indexing, UDI12A) - version 2.
Project description:50,000 cells were injected orthotopically into the inguinal fat pad of a Nod-Scid-Gamma (NSG) immuno-compromised mouse. Injected cells were 80% unlabelled 4T1 cells (parental population), and 20% ZsGreen-labelled 4T1-T cells (clone isolated in Wagenblast et Al, Nature, 2015). Tumour were allowed to develop for 20 days, and then collected during necropsy. Disaggegated cells were processed through the 10X genomics Single Cell 3' gene expression pipeline. This data is intended as an example dataset for a novel virtual reality viewer for single-cell data described in Bressan et Al, Nat. Cancer, 2021 (submitted)
Project description:The 50 and 75% aqueous EtOH fractions (YHI-I-1-3 and YHI-I-1-4, respectively) obtained from the aqueous layer of A. kurodai collected at Azuri-hama (Mie Prefecture, Japan) on April 2018.
Project description:The miRNAs were purified from paraffin embedded liver biopsy samples of HCV and HCC patients, using an miRNeasy mini kit (Qiagen) according to manufacturer’s instructions. First, 25mg of liver biopsy tissues was homogenized in 700μl QIAzol lysis reagent, mixed, and shaken with chloroform. After that, the phases were separated by centrifugation at 12000´g for 15 min. The upper aqueous phase was collected in a fresh tube and the remaining DNA and organic protein organic phases was stored at -70°C until required. The RNA aqueous phase was washed further on the column and finally RNA was eluted into DEPC water (Ambion). Purified miRNAs were reverse transcribed into first strand cDNA using a miRNA first strand kit. (Qiagen). The reaction was carried out at 37ºC for 2 hours followed by heating at 95ºC for 5 min.