LFQ shotgun proteomic analysis of HAP1 NatC KO cells
Ontology highlight
ABSTRACT: The impact of NatC subunits NAA30, NAA35 and NAA38 on the human proteome (protein abundance). Analysis of HAP1 WT, NAA30 KO, NAA35 KO and NAA38 KO cells
Project description:The impact of NatC subunits NAA30, NAA35 and NAA38 on the human N-terminal acetylome. Analysis of HAP1 WT, NAA30 KO, NAA35 KO and NAA38 KO cells
Project description:The impact of NatC and UBR4 on the human proteome (protein abundance). Analysis of HAP1 WT siCtr, HAP1 WT siUBR4, HAP1 NAA30 KO siCtr, and HAP1 NAA30 KO siUBR4 cells.
Project description:The transcript levels of 560 genes were decreased (less than two-fold), while those of 312 genes were increased (more than two-fold) in the KO-HsfA1d/A1e plants compared with the wild-type plants. The transcript levels of HsfA2, HsfA7a, HsfA7b, HsfB1, and HsfB2a were down-regulated in the KO-HsfA1d/A1e Arabidopsis thaliana ecotype Columbia plants were grown (16 h light, 25°C/8 h dark, 22°C) on MS medium under a light intensity of 100 µE m-2 sec-1. Two-week-old seedlings were subjected to high-light stress (400 µE m-2 sec-1, 25°C).
Project description:Arabidopsis Nudix hydrolases, AtNUDX6 and 7, exhibit pyrophosphohydrolase activities toward NADH and contribute to the modulation of various defense responses, such as the poly(ADP-ribosyl)ation (PAR) reaction and salicylic acid (SA)-induced Nonexpresser of Pathogenesis-Related genes 1 (NPR1)-dependent defense pathway, against biotic and abiotic stresses. To identify genes (NRGs) whose expression levels positively and negatively correlated with NADH levels, a transcriptome analysis using KO-nudx6, KO-nudx7, and double KO-nudx6/7 plants, in which intracellular NADH levels increased in a step-wise manner. Arabidopsis wild-type, KO-nudx6, KO-nudx7, and double KO-nudx6/7 plants were grown on MS medium in a growth chamber kept at 23°C during 16 h of light (100 µmol/m2/s) and at 22°C during 8 h of darkness. Two-week-old cotyledons were collected as samples for microarray analysis.
Project description:Gene knockdown of NAT12/NAA30 led to decreased proliferation, sphere forming ability and mitochondrial hypoxia tolerance in the GSC T65 culture. Intracranial transplantation of these cells into SCID mice showed that the decreased NAT12/NAA30 expression correlated with the prolonged animal survival and reduced tumor size
Project description:Gene knockdown of NAT12/NAA30 led to decreased proliferation, sphere forming ability and mitochondrial hypoxia tolerance in the GSC T65 culture. Intracranial transplantation of these cells into SCID mice showed that the decreased NAT12/NAA30 expression correlated with the prolonged animal survival and reduced tumor size Total RNA isolated from GSC cultures featuring NAT12/NAA30 gene knock-down (shRNA) was compared to total RNA from non-silencing control GSC cultures (NS-shRNA).
Project description:To screen mRNAs specifically regulated by mTORC1, a global mRNA expression profile in colon epithelial cells (CECs) from mice with or without CECs-specific TSC1 knockout (KO) was developed using microarray. Wile-type or CECs-specific TSC1 KO mice with experimental colitis were sacrificed, with CECs harvested and subjected to total RNA extraction.
Project description:Chronic viruses and cancers thwart immune responses in humans by inducing T cell dysfunction. Using a murine chronic virus that models human infections, we investigated the function of the adhesion molecule, P-selectin glycoprotein ligand-1 (PSGL-1) that is upregulated on responding T cells. PSGL-1-deficient mice unexpectedly cleared the virus due to dramatic increases in the intrinsic survival of multifunctional effector T cells that had downregulated PD-1 and other inhibitory receptors. Notably, this response resulted in CD4+ T cell-dependent immunopathology. Mechanistically, PSGL-1 ligation on exhausted CD8+ T cells inhibited TCR and IL-2 signaling, and upregulated PD-1, leading to diminished survival with TCR stimulation. In models of malignant melanoma where T cell dysfunction occurs, PSGL-1-deficiency led to PD-1 downregulation, improved T cell responses, and tumor control. Thus, PSGL-1 plays a fundamental role in balancing viral control and immunopathology, and also functions as a checkpoint that regulates T cell responses in the tumor microenvironment. WT or PSGL-1 KO mice were infected with 2 x 10^6 PFU LCMV Clone 13. Spleens from 10 WT or 10 PSGL-1 KO animals were pooled and processed. CD8+ T cells were negatively enriched from WT or PSGL-1 KO spleens (EasySep Stemcell). Purified T cells were stained with propidium iodide (PI) for 10 minutes on ice, cells were washed. CD8+ T cells were stained with H2-Db-GP33-41 tetramers (NIH) and FACS sorted (BD FACS Aria). Sorted tetramer+ cells were PI negative and purity was >98%. Experiment was repeated twice to generate 2 WT (WT 1; WT 2) and 2 PSGL-1 KO (KO 1; KO 2) samples that represented 10 pooled spleens per sample.
Project description:We found that the E3 ubiquitin ligase Itch significantly affects early B-cell differentiation. To explore the role of Itch in late B-cell differentiation, we sorted B cells from WT and Itch KO mice. To explore the effect of Itch deficency on gene expression, we determined mRNA profiles in B cells from WT and Itch KO mice by RNA-seq. RNA-seq was done with an Illumina HiSeq 2500 instrument at GENEWIZ, Suzhou, China.
Project description:We examined ubiquitin-linkages on Nrf1 purified from cell lysates of NGLY1-KO cells overexpressing Nrf1-FLAG with HA-FBS2. The ubiquitin linkage types were quantified using the LC-MS/MS-based absolute quantification method, ubiquitin parallel reaction monitoring (Ub-AQUA/PRM).