Journal: Cancer cell

Article Title: CDK7 Inhibition Potentiates Genome Instability Triggering Anti-Tumor Immunity in Small Cell Lung Cancer

doi: 10.1016/j.ccell.2019.11.003

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Cell Ranger (v1.3) , Cell Ranger Single Cell Software Suite , https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger.

Techniques: Control, Recombinant, Blocking Assay, Gene Expression, Lysis, Red Blood Cell Lysis, SYBR Green Assay, Polymer, BrdU Staining, Bicinchoninic Acid Protein Assay, Multiplex Assay, Software

Journal: Developmental cell

Article Title: Dynamic transcriptional responses to injury of regenerative and non-regenerative cardiomyocytes revealed by single-nucleus RNA sequencing

doi: 10.1016/j.devcel.2020.02.019

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: The Cell Ranger Single-Cell Software Suit ( https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines/latest/what-is-cell-ranger ) was used to perform sample demultiplexing, barcode processing and single-cell 3′ gene counting.

Techniques: Produced, Virus, Recombinant, Modification, Protease Inhibitor, Multiplex Assay, TUNEL Assay, In Situ, Reverse Transcription, Software

Journal: Frontiers in Animal Science

Article Title: Gene expression profiling indicates a shift in ammonia assimilation capacity along the hepatic acinus induced by different forms of selenium in vitamin–mineral mixes fed to beef steers grazing on toxic endophyte-infected tall fescue

doi: 10.3389/fanim.2023.1165321

Figure Lengend Snippet: FIGURE 4 Overview of main glutamine/glutamate cycle and ammonia metabolism pathways in periportal and perivenous hepatocytes. The assignment of a process and its related enzyme and transporter expression is based on rodent model literature. The activities of critical enzymes and transporters responsible for a plethora of metabolic pathways have been found to be heterogeneously expressed along the hepatic acini of mice and rats (Boon et al., 1999). Collectively, this portrayal of metabolic zonation between the periportal and pericentral hepatocytes gives rise to the separation of urea (periportal) and glutamine (pericentral) synthesis (Jungermann and Sasse, 1978; Gebhardt, 1992). Briefly, from a glutamate/glutamine and ammonia metabolism perspective, glutamine and ammonia from portal blood are absorbed and metabolized for urea synthesis in periportal hepatocytes, whereas glutamate and excess ammonia are taken up by pericentral hepatocytes, and used as substrates (glutamine synthetase) for glutamine synthesis. More detailed decriptions of these metabolic pathways, as well as exprimental results, supporting the existence of this zonation pattern are presented in the text. Not all steps are shown. All transporters are in pink font. All enzymes are in blue font. The red arrow indicates the treatment effect of both MIX and OSe. SNAT2, glutamine transporter encoded by SLC38A2; SNAT3, glutamine transporter encoded by SLC38A3; SNAT5, glutamine transporter encoded by SLC38A5; EAAC1, glutamate/aspartate transporter encoded by SLC1A1; GLT1, glutamate/aspartate transporter encoded by SLC1A2; RHBG, ammonia transporter encoded by SLC42A2; GLS2, liver mitochondria glutaminase 2 encoded by GLS2; GDH, glutamate dehydrogenase encoded by GLUD1; CPS1, carbamoyl phosphate synthetase encoded by CPS1; NAGS, N-acetylglutamate synthase encoded by NAGS; OCT, ornithine carbamoyltransferase encoded by OCT; ARG1, arginase 1 encoded by ARG1; ORNT1, ornithine/arginine exchanger encoded by SLC25A15; ARG2, arginase 2 encoded by ARG2; OAT, ornithine aminotransferase encoded by OAT; GS, glutamine synthetase encoded by GLUL.

Article Snippet: ARG1 arginase 1 ARG2 arginase 2 CPS1 carbamoyl phosphate synthetase 1 DEG differentially-expressed genes EAAC1 high affinity Na+-dependent, glutamate/aspartate transporters, SLC1A1 FDR false discovery rate GCOS GeneChip operating software GDH glutamate dehydrogenase 1 GEO gene expression omnibus GLT1 high affinity Na+-dependent, glutamate/aspartate transporters, SLC1A2 GLS2 glutaminase 2, liver mitochondria GLUL glutamine synthetase IPA Ingenuity pathway analysis MIAME minimum information about a microarray experiment NAGS N-acetylglutamate synthase OCT ornithine carbamoyltransferase ORNT1 ornithine/arginine exchanger, SLC25A15 OAT ornithine aminotransferase PGS Partek genomics suite software PRODH proline dehydrogenase 1 (a.k.a. proline oxidase) PYCR1 pyrroline-5-carboxylate reductase 1 PYCR2 pyrroline-5-carboxylate reductase 2 P5C synthetase pyrroline-5-carboxylate synthetase, encoded by gene ALDH18A1 P5C dehydrogenase pyrroline-5-carboxylate dehydrogenase, encoded by gene ALDH4A1 RHBG ammonia transporter, SLC42A2 RIN RNA integrity number SNAT2 glutamine transporter, SLC38A2 SNAT3 glutamine transporter, SLC38A3 SNAT5 glutamine transporter, SLC38A5.

Techniques: Expressing