Pyrophosphoproteomics on NOLC1 / TCOF1 / IWS1 pulldown samples
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo Sapiens (human)
SUBMITTER: Dorothea Fiedler, Rashna Bhandari
PROVIDER: PXD038962 | JPOST Repository | Tue Mar 12 00:00:00 GMT 2024
REPOSITORIES: jPOST
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| IWS-KD.raw | Raw | |||
| IWS1_KA.raw | Raw | |||
| NOLC-KA.raw | Raw | |||
| NOLC-KD.raw | Raw | |||
| TCOF-KA.raw | Raw |
Items per page: 5 1 - 5 of 8 |
Similar Datasets
Project description:Goal is to analyze the expression profile of cells shortly after induction of mitochondrial double stranded breaks. ARPE-19 cells are transfected with constructs coding for mitochondrial TALENs, either active or dead. These constructs target two different locations of mtDNA (ATP8 and Dloop). Gene expression is then compared between untransfected and transfected cells (either active or dead TALENs), or between active TALEN (cells with mitochondrial double stranded breaks) and dead TALEN (expressing the same protein without cutting the mitochondrial genome)
2021-02-24 | GSE164979 | GEO
Project description:Background: The small RNAs that Transposable Elements generate are vastly different when they are transcriptionally silenced compared to when they are transcriptionally activated. We performed the deep sequencing of small RNAs in a number of small RNA biogenesis mutants in both Transposable Element-silenced and Transposable Element-active epigenome backgrounds. Results: We found that Transposable Elements generate large amounts of 21-22nt siRNAs only when they are transcriptionally active. These 21-22nt siRNAs are incorporated into the AGO6 protein. Conclusion: Ago6 is the key protein that bridges the post-transcriptional degradation of Transposable Element mRNAs and the establishment of DNA methylation. Examination of flower bud small RNAs from wild type and 5 single or double mutant combinations, many of which have biological replicates. In addition, IP purification of the AGO6 protein (and mock no-antigen controls) followed by sequencing of the incorporated small RNAs. Replicate A for Col and ddm1 are submitted in GSE41755
2014-11-14 | E-GEOD-57191 | biostudies-arrayexpress
Project description:DDX23 belongs to DEAD-box family of RNA helicases and plays crucial roles in spliceosome formation and pre-mRNA splicing. In this study, DDX23 was first identified as a key DEAD-box RNA helicase in ovarian cancer, and its overexpressed was associated with poor clinical outcomes. High expression of DDX23 was involved in the malignant proliferation and aggressiveness of ovarian cancer.
2021-07-31 | GSE181078 | GEO
Project description:T-47d breast cancer cells were transfected in 6 test/control replicates with biotinylated miR-190b mimic or biotinylated mimic negative control by Qiagen. After 48h cells were lysed and miRNA:mRNA complexes were pulled-down by double precipitation. Firstly by pulling down Ago2 with Dynabeads G with rad Ago2 antibody and secondly via streptavidin coated magnetic beads. The precipitation was carried out according to manufacturer protocol. RNA from the eluted samples was then isolated using phenol-chloroform-isoamyl alcohol mixure and suspended in RNAse free water. This experiment was implemented to assess direct targets bound by miR-190b in the ER-positive breast cancer subtype T-47d.
2022-03-16 | GSE198723 | GEO
Project description:R&D experiment 1 to optimize library preparation for array-based sequence capture
| PRJEB2023 | ENA
Project description:The goal of this study is to compare the different biological functions between nuclear (ICD)-TYRO3- and kinase dead (KD)-TYRO3-overexpressed cells by BRD3 occupancy profiling. We revel that ICD-TYRO3-overexpressed cell were particularly enriched in negatively regulate cell death, regulation of cell cycle, regulation of vascular permeability, positively regulation of EMT, cell-cell adhesion, and regulation of phosphorylation.
2024-11-08 | GSE188378 | GEO
Project description:We found that several deacetylase-dead HDAC3 mutants were able to rescue the metabolic phenotype of HDAC3-depleted livers. Here we profile the histone acetylation in the presence of different HDAC3 mutants in mouse liver. Deacetylase-dead HDAC3 mutants, including HAHA, KA, YF and HEBI, were introduced into HDAC3-depleted (Cre) mouse livers by virus along with wild-type (WT) HDAC3 as a control. Livers were harvested at 5 pm (ZT 10) and subjected to ChIP with anti-H3K9ac antibodies followed by deep sequencing.
2013-11-25 | E-GEOD-49365 | biostudies-arrayexpress
Project description:Protein kinases are frequently dysregulated and/or mutated in cancer and represent essential targets for therapy. Accurate quantification is essential. For breast cancer treatment, the identification and quantification of the protein kinase ERBB2 is critical for therapeutic decisions. While immunohistochemistry (IHC) is the current clinical diagnostic approach, it is only semiquantitative. Mass spectrometry-based proteomics offers quantitative assays that, unlike IHC, can be used to accurately evaluate hundreds of kinases simultaneously. The enrichment of less abundant kinase targets for quantification, along with depletion of interfering proteins, improves sensitivity and thus promotes more effective downstream analyses. Multiple kinase inhibitors were therefore deployed as a capture matrix for kinase inhibitor pulldown (KiP) assays designed to profile the human protein kinome as broadly as possible. Optimized assays were initially evaluated in 16 patient derived xenograft models (PDX) where KiP identified multiple differentially expressed and biologically relevant kinases. From these analyses, an optimized single-shot parallel reaction monitoring (PRM) method was developed to improve quantitative fidelity. The PRM KiP approach was then reapplied to low quantities of proteins typical of yields from core needle biopsies of human cancers. The initial prototype targeting 100 kinases recapitulated intrinsic subtyping of PDX models obtained from comprehensive proteomic and transcriptomic profiling. Luminal and HER2 enriched OCT-frozen patient biopsies subsequently analyzed through KiP-PRM also clustered by subtype. Finally, stable isotope labeled peptide standards were developed to define a prototype clinical method. Data are available via ProteomeXchange with identifiers PXD044655 and PXD046169.
| S-EPMC10790396 | biostudies-literature
Project description:Investigation of cell-to-cell variability holds critical physiological and clinical implications. Thus, numerous new techniques have been developed for studying cell-to-cell variability, and these single-cell techniques can also be used to investigate rare cells. Moreover, for studying protein-protein interactions (PPIs) in single cells, several techniques have been developed based on the principle of the single-molecule pulldown (SiMPull) assay. However, the applicability of these single-cell SiMPull (sc-SiMPull) techniques is limited because of their high technical barrier and special requirements for target cells and molecules. Here, we report a highly innovative nanobead-based approach for sc-SiMPull that is based on our recently developed microbead-based, improved version of SiMPull for cell populations. In our sc-SiMPull method, single cells are captured in microwells and lysed in situ, after which commercially available, pre-surface-functionalized magnetic nanobeads are placed in the microwells to specifically capture proteins of interest together with their binding partners from cell extracts; subsequently, the PPIs are examined under a microscope at the single-molecule level. Relative to previously published methods, nanobead-based sc-SiMPull is considerably faster, easier to use, more reproducible, and more versatile for distinct cell types and protein molecules, and yet provides similar sensitivity and signal-to-background ratio. These crucial features should enable universal application of our method to the study of PPIs in single cells.
| S-EPMC10679481 | biostudies-literature
Project description:Background: As degradation of formalin-fixed paraffin-embedded (FFPE) samples limits ability to expression profile, we explored factors predicting success for FFPE profiling and investigated an approach overcoming this limitation. Methods: Bladder (n=141, stored 3-8 years) and cervix (n=160, stored 8-23 years) carcinoma FFPE samples were hybridised to Affymetrix Exon1.0ST arrays. Percent detection above background (%DABG) measured technical success. Biological signal was assessed by distinguishing cervix squamous cell carcinoma (SCC) and adenocarcinoma (AC) using a gene signature. Precursor mir-205 was measured by Exon array and mature miR-205 by qRT-PCR. Eight-old and -young cervix samples were compared using Affymetrix miRNA 2.0 arrays. For comparison, the 'cervix_tumour_cs1_113' (previsously submitted GSM677307) was included and re-analyzed with the samples from the current study (total 161 Cervix samples). Results: RNA quality controls (e.g. RNA integrity number) failed to predict profiling success, but sample age correlated with %DABG in bladder (R2=-0.30, p<0.01) and cervix (R2=-0.69, p<0.01). Biological signal was lost in older samples and neither a signature nor precursor mir-205 separated samples by histology. miR-205 qRT-PCR discriminated SCC from AC, validated by miRNA profiling (26-fold higher in SCC; p=1.10x10-5). Median miRNA probeset expression of eight-old and eight-young cervix samples correlated well (R2=0.95) overcoming the age-related bias of mRNA probesets, suggesting miR-205 stability generalises across microRNA. Conclusions: microRNA profiling overcomes the limitation of degraded FFPE samples
2012-07-04 | GSE39016 | GEO