Project description:Molecular stratification using gene-level transcriptional data has identified subtypes with distinctive genotypic and phenotypic traits, as exemplified by the consensus molecular subtypes (CMS) in colorectal cancer (CRC). Here, rather than gene-level data, we make use of gene ontology and biological activation state information for initial molecular class discovery. In doing so, we defined three pathway-derived subtypes (PDS) in CRC; PDS1 tumours are canonical/LGR5+ stem-rich, highly proliferative and display good prognosis. PDS2 which is regenerative/ANXA1+ stem-rich, with elevated stromal/immune tumour microenvironmental lineages. PDS3 tumours represent a previously overlooked slow-cycling subset of tumours within CMS2, with reduced stem populations and increased differentiated lineages, particularly enterocytes and enteroendocrine cells, yet display the worst prognosis in locally advanced disease. These PDS3 phenotypic traits are evident across numerous bulk and single-cell datasets, and demark a series of subtle biological states that are under-represented in pre-clinical models currently and are not identified using existing subtyping classifiers Mutations: https://www.s-cort.org/sites/default/files/exports/scort_spinal_focus_paper/ws4_spinal_mutations.txt, CNA per gene : https://www.s-cort.org/sites/default/files/exports/scort_spinal_focus_paper/ws4_spinal_cna_gene_subselection_for_paper.txt, CNA segments SPINAL https://www.s-cort.org/sites/default/files/exports/scort_spinal_focus_paper/ws4_spinal_cna.zip, CNA segments FOCUS https://www.s-cort.org/sites/default/files/exports/scort_spinal_focus_paper/ws2.focus_cna.zip
Project description:Transcriptional profiling of human lymphoblastoid TK6 cells comparing mock irradiated cells with cells exposed 24 hours previously to 1.67 Gy HZE (1 GeV/amu iron ions accelerated at the NASA Space Research Laboratory (NSRL) of Brookhaven National Laboratory) or 2.5 Gy 137Cs gamma rays.
Project description:Transcriptional profiling of human lymphoblastoid TK6 cells comparing mock irradiaed cells resuspended in fresh untreated RPMI 1640 medium with cells resuspended in medium activated by exposure to 2.5 Gy HZE (1 GeV/amu iron ions accelerated at the NASA Space Research Laboratory (NSRL) of Brookhaven National Laboratory).
Project description:The study compared the protein composition of supraspinatus muscle from the spaceflight mice subjected to either the 13-day NASA STS-135 mission or the 30-day Bion-M1 mission and their corresponding ground control mice.
Project description:Liver stage of malaria parasite exports SLTRiP and PB268 to the cytosol of parasite infected host cell. To know the host genes perturbed by WT-PBANKA, SLTRiP-KO and PB268-KO parasite growth, we did transcriptomic sequencing of infected host cells. We did mRNA sequencing of four samples for comparative analysis of WT and PB-knockout parasites infected host cells at 22 hours of post sporozoites infection.
Project description:The purpose of the present work was to examine gene expression patterns in a rat keratinocyte line exposed to a 56Fe ion beam Experiment Overall Design: The cells were exposed to 1.01 geV/nucleon 56Fe ions generated by the NASA Space Radiation Laboratory facility. Data from Affymetrix rat microarrays (RAT 230_2) were processed by BRB ArrayTools 3.3.0 software, and the Gene Ontogeny (GO) database was utilized to categorize significantly responding genes.
Project description:Liver stage of malaria parasite exports SLTRiP and PB268 to the cytosol of parasite infected host cell. To know the host genes perturbed by WT-PBANKA, SLTRiP-KO and PB268-KO parasite growth, we did transcriptomic sequencing of infected host cells. We did mRNA sequencing of four samples for comparative analysis of WT and PB-knockout parasites infected host cells at 22 hours of post sporozoites infection. mRNA profiles of Plasmodium PBANKA, PBSLTRiP-KO, PB268-KO parasite infected and uninfected HepG2 cells after 22hrs of sporozoites infections were generated by deep sequencing using Illumina GAIIx.