Chu Wang Similar Datasets
Project description:Identification of LEC1 binding sites in Arabidopsis seedlings
| PRJNA388705 | ENA
Project description:Following the identification of the 80S ribosome as a putative target of the tetracycline analogs Col3 and doxycycline, we next sought to identify the precise binding sites for these tetracyclines within the ribonucleoprotein complex. We incorporated dual bioorthogonal handles into tetracycline-based probes, containing both a photoactive diazirine to enable direct probe crosslinking to the human ribosome and an azide handle to allow selective enrichment of crosslinked biomolecules via copper-free click chemistry. The Col-3 and doxycycline probes were each incubated with A375 cells, followed by irradiation at 365 nm to induce photolysis of the diazirine moiety and subsequent crosslinking to adjacent ribosomal components. Pulldown and RNA-Seq of the crosslinked RNAs from our experiments were used to identify enrichment of reverse transcription (RT) stops at ribosomal RNA sites caused by local crosslinking of our probes. This RNA-Seq based RT stop enrichment analysis was compared to results using an non-specific aniline control probe and untreated controls.
2018-08-30 | E-MTAB-7147 | biostudies-arrayexpress
Project description:we report an alkynyl-functionalized bioorthogonal chemical probe, Cr-alkyne, for the detection and identification of protein lysine crotonylation in mammalian cells.
2024-07-04 | PXD053632 |
Project description:Identification Arabidopsis T-DNA insertion sites by whole-genome resequencing
| PRJNA785137 | ENA
Project description:Identification of LEC1 binding sites in Arabidopsis bent cotyledon stage seeds
| PRJNA388934 | ENA
Project description:We revisited the transcriptomes of Arabidopsis seedlings by analyzing alternatively spliced variants during early photomorphogenesis. Half of the expressed transcripts have alternatively spliced forms; many were previously uncharacterized. Light regulated AS for 19.2% of the genes expressed, intron retention being the most prevalent type of alternative splicing. We observed distinct groups of transcripts with differential expression levels or with AS, which implies that transcription and AS target different sets of genes. More than one-third of the AS transcripts with retained introns were translatable. In summary, these AS variants could play regulatory roles and increase the proteome complexity in photomorphogenic Arabidopsis
2025-10-10 | GSE89002 | GEO
Project description:Hydrogen peroxide (H2O2) reacts, directly or indirectly, with cysteines to form cysteine sulfenic acid, also known as S-sulfenylation. This cysteine oxidation steers diverse cellular processes by altering protein interactions, trafficking, conformation, and function. We present a method to identify S-sulfenylated cysteines sites in proteins using a genetic probe based on the yeast AP-1–like (YAP1) transcription factor that specifically reacts with sulfenic acid sites to form mixed disulfides. After a tryptic digest and with the help of an antibody directed against a 7-amino-acid YAP1C-derived peptide that contains the redox-active cysteine, we enriched for disulfide-linked peptides. The mass spectral characteristics for fragment ions of the mixed disulfides made it possible to identify 1,747 S-sulfenylation protein sites in Arabidopsis under H2O2 stress. Furthermore, cross-study comparison shows that 55% of cross-linked sites match with previously reported S-sulfenylated, S-nitrosylated and reversibly oxidized cysteines in Arabidopsis. These include well-characterized redox-sensitive cysteines, such as Cys20 of DEHYDROASCORBATE REDUCTASE 2 (DHAR2) and Cys181 of MAP KINASE 4 (MAPK4). Altogether, we describe a novel approach to identify S-sulfenylated sites in situ using the YAP1C probe, thereby offering a non-invasive manner to study site-specific cysteine oxidation and which can be applied for identification of S-sulfenylated sites at the organellar level.
2020-12-15 | PXD016723 | Pride
Project description:Human infection with Mycobacterium tuberculosis results in a continuum of ill-defined, clinical manifestations with stable latent M. tuberculosis infection (LTBI) and severe active disease at the ends. Identifying different states of infection is of importance to tuberculosis (TB) control since risk of developing active disease varies among different asymptomatic states while infectiousness varies among patients with different bacterial burden. We investigated changes in proteome-scale antibody responses during disease progression in a non-human primate model of tuberculosis. We probed M. tuberculosis proteome microarrays with serial sera collected from three infection-outcome groups (active, reactivation, and latent). We found that each infection outcome is associated with characteristic changes in the antibody levels and number of antigenic targets, which suggested an association between antibody responses and bacillary burden. Additional proteome-scale serological profiling of > 400 human TB suspects established that antibody responses are positively associated with bacterial load. Thus tuberculosis-specific antibody levels and number of antigenic targets increases with disease progression. Serum samples collected from adult patients with suspected tuberculosis during a multi-site study was used to probe whole proteome microarrays. Subject recruitment was conducted under uniform protocols approved by the institutional ethics committee at each site. Final diagnosis of active TB was based on positive M. tuberculosis culture results. The active TB patients were further subdivided into smear-positive and negative disease based on results of Ziehl-Neelsen staining of sputum smears for acid fast bacilli. Active TB was excluded as a diagnosis (Non-TB Disease [NTBD] patients) based on having negative M. tuberculosis culture and smear results and on having an alternate diagnosis. All subjects were presumably negative for HIV infection given the very low incidence of HIV infection in the study sites. Sera from 169 TB and 242 NTBD patients were selected for microarray probing. The control sera (n = 14) which was used to generate negative control distribution for each protein were negative to latent M. tuberculosis infection, as indicated by negative results to tuberculin skin test.
2012-07-05 | E-GEOD-30722 | biostudies-arrayexpress
Project description:Chemoproteomic profiling by a bioorthogonal probe reveals cell growth inhibition by histone H4 dopaminylation
| PRJNA1130375 | ENA
Project description:Genome-wide identification of FHY3 binding sites in Arabidopsis floral organ (RNA-Seq)
| PRJNA289555 | ENA