Human non-small cell lung cancer cell line NCI-H661 DPPA2-4 immunoprecipitation mass spectrometry (LC-MSMS)
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Epithelial Cell, Cell Culture
DISEASE(S): Non-small Cell Lung Carcinoma
SUBMITTER: 
Janith Seneviratne
LAB HEAD: Melanie Eckersley-Maslin
PROVIDER: PXD070581 | Pride | 2026-03-31
REPOSITORIES: Pride
Dataset's files
Items per page: 5 1 - 5 of 25 |
Similar Datasets
Project description:Staufen-associated mRNAs were identified in early Drosophila embryos by RNA-co-immunoprecipitation followed by microarray analysis (RIP-Chip), using two complementary approaches: RIP-Chip from wild-type embryos using a synthetic anti-Staufen antibody, and RIP-Chip from transgenic GFP-Staufen-expressing embryos using an anti-GFP antibody. Genome-wide transcript expression in whole embryos was also assessed for the wild-type and GFP-Staufen lines. There are 18 samples in total. These include 3 replicates each of 1) gene expression profiling from total mRNA isolated from wild-type 0-3 hour embryos, 2) synthetic anti-Staufen antibody RNA co-immunoprecipitations of endogenous Staufen from wild-type 0-3 hour embryos, 3) control synthetic antibody RNA co-immunoprecipitations from wild-type 0-3 hour embryos, 4) gene expression profiling from total mRNA isolated from transgenic GFP-Staufen expressing 0-3 hour embryos, 5) anti-GFP RNA co-immunoprecipitations of GFP-Staufen from transgenic GFP-Staufen expressing 0-3 hour embryos, 6) anti-FLAG control RNA co-immunoprecipitations from transgenic GFP-Staufen expressing 0-3 hour embryos.
2013-09-05 | E-GEOD-43418 | biostudies-arrayexpress
Project description:HelQ is a 3’-5’ single stranded DNA (ssDNA) dependent helicase part of the Superfamily 2 helicases (SF2) which are characterised by the presence of two motor domains with a RecA-like fold which couples ATP hydrolysis to DNA translocation. The N-terminal domain of HelQ or N-HelQ (~300 amino acids) is non catalytically active, but sequence analysis has found a non-canonical PIWI-like motif (found in RNA splicing helicase Brr2) which is unable to bind DNA but is involved in displacement of RPA (Replication Protein A) from ssDNA 8. This study focussed on better understanding the role of this N-terminal domain of this helicase in vitro using BioID2. Biotin ligase protein interaction Identification generation 2 (BioID2) is a method for screening physiologically relevant protein interactions that occur in living cells originally developed by Roux et al.. BioID2 uses the promiscuous ability of Biotin ligase from A. aeolicus with a mutated catalytical domain (R40G) to biotinylate nearby proteins, these proteins can be pulled out of solution using streptavidin beads and protein identity discovered via LC-MS/MS. This method allows high throughput screening of the proteome surrounding HelQ and offers insight into potential DNA repair pathways involving HelQ.
2025-05-06 | PXD049246 | Pride
Project description:Ubiquitin ligases (E3s) embedded in the endoplasmic reticulum (ER) membrane regulate essential cellular activities including protein quality control, calcium flux, and sterol homeostasis. At least 25 different, transmembrane domain (TMD)-containing E3s are predicted to be ER-localised, but for most their organisation and cellular roles remain poorly defined. Using a comparative proteomic workflow, we mapped over 450 protein-protein interactions for 21 different stably expressed, full-length E3s. Bioinformatic analysis linked ER-E3s and their interactors to multiple homeostatic, regulatory, and metabolic pathways. Among these were four membrane-embedded interactors of RNF26, a polytopic E3 whose abundance is auto-regulated by ubiquitin-proteasome dependent degradation. RNF26 co-assembles with TMEM43, ENDOD1, TMEM33 and TMED1 to form a complex capable of modulating innate immune signalling through the cGAS-STING pathway. This RNF26 complex represents a new modulatory axis of STING and innate immune signalling at the ER membrane. Collectively, these data reveal the broad scope of regulation and differential functionalities mediated by ER-E3s for both membrane-tethered and cytoplasmic processes.
2020-07-06 | PXD019559 | Pride
Project description:Germline small RNA pathways initiate silencing of repetitive elements in animals and an interplay of nuclear small RNAs and chromatin modifications maintain this silencing, protecting the germline from spreading of transposable elements. In C. elegans germline, nuclear argonaute protein HRDE-1 initiates the transcriptional silencing pathway that is crucial for long term and heritable silencing of genes and repetitive regions. Here, we show that HRDE-1 interacts with components of the splicing machinery and the exon-junction complex. One such factor is the conserved RNA helicase EMB-4/AQR that binds introns and recruits the exon-junction proteins to newly spliced RNA. Our data shows that EMB-4/AQR is required for the transcriptional silencing pathway initiated by HRDE-1 and it functions by removing the intronic barriers to silencing thorugh its helicase function.
2017-06-30 | PXD004416 | Pride
Project description:Viruses interact with numerous host factors to facilitate viral replication and to dampen antiviral defense mechanisms. We currently have a limited mechanistic understanding of how SARS-CoV-2 binds host factors and the functional role of these interactions. Here, we uncover a novel interaction between the viral NSP3 protein and the fragile X mental retardation proteins (FMRPs: FMR1 and FXR1-2). SARS-CoV-2 NSP3 mutant viruses preventing FMRP binding have slightly attenuated replication in vitro and reduced levels of viral antigen in lungs during early stages of infection. We show that a unique peptide motif in NSP3 binds directly to the two central KH domains of FMRPs and that this interaction is disrupted by the I304N mutation found in a patient with fragile X syndrome. NSP3 binding to FMRPs disrupts their interaction with the stress granule component UBAP2L through direct competition with a peptide motif in UBAP2L to prevent FMRP incorporation into stress granules. Collectively, our results provide novel insight into how SARS-CoV-2 hijacks host cell proteins and provides molecular insight to the possible underlying molecular defects in fragile X syndrome.
2023-12-28 | PXD047232 | Pride
Project description:Vitamin D induces anti-proliferative and differentiating effects in prostate cancer. Thus calcitriol, the hormonally active form of Vitamin D, and its analogs have been extensively studied in prostate cancer cells. Yet despite its importance, relatively little is known about the genome-scale mechanisms by which Vitamin D, through its cognate nuclear vitamin D receptor (VDR), exerts its regulatory functions at the genomic level. In this study, we defined VDR transcriptional networks in the LNCaP prostate cancer cell line by mapping the genomic binding sites of VDR and by identifying differentially expressed genes upon calcitriol treatment. We found that VDR and androgen receptor (AR) antagonistically regulate a subset of cell cycle-related genes that are over-expressed in prostate cancer tumors. The expression balance of these genes is partially regulated through the competition dynamics between AR and VDR binding to shared cis-regulatory elements. On such shared elements, we found that FOXA1 mediates this competition by serving as a pioneering factor for both AR and VDR binding. We also found significant enrichment of AR-, VDR-, and AR/VDR overlapping binding sites in prostate cancer-associated single-nucleotide polymorphism (SNP) intervals identified from genome-wide association studies (GWAS), providing genetic evidence to link AR, VDR and their crosstalk to prostate cancer susceptibilities. In particular, we found that in a cis-regulatory element of the RFX6 gene implicated in prostate cancer progression, an allelic variant increases prostate cancer risk by switching the antagonism between AR and VDR into a synergistic interaction. Examination of AR, VDR, and FOXA1 binding in LNCaP cells, in biological replicates
2015-08-01 | E-GEOD-64656 | biostudies-arrayexpress
Project description:We profiled two repressive histone modifications (H3K9m3 and H3K27m3) using ChIP-Seq in normal urothelial cells and cell lines representing non-invasive and invasive tumors. Two bladder cancer cell lines (RT112 and EJ/T24 from ATCC) and normal human urothelial (NHU) cells were treated according to standard ChIP-Seq protocols using antibodies against the histone modifications H3K9m3 and H3K27m3 (from Millipore). The sequencing reads were mapped against the human genome (GRCh37/hg19).
2011-08-03 | E-GEOD-31125 | biostudies-arrayexpress
Project description:Immunoprecipitation of SLX/SLXL1 from mouse testis and mass spec.
2019-10-24 | PXD014276 | Pride
Project description:A mutation within FASTKD2 causes a rare form of Mendelian mitochondrial encephalomyopathy. To investigate whether and how RNA binding of FASTKD2 contributes to the disease phenotype, we identified the RNA targets of FASTKD2 by iCLIP.
2015-11-09 | E-MTAB-4010 | biostudies-arrayexpress
Project description:LC-MS/MS proteomics analysis (Ig-Seq) of human sera collected before and after GII.4 monovalent oral HuNoV vaccination. Here is a brief description of MS files: VX101-160 day29 FT_2MUrea PF8302 8302_JP_1a_psms.txt 8302_JP_1a.raw VX101-160 day29 FT_2MUrea PF8302 8302_JP_1b_psms.txt 8302_JP_1b.raw VX101-160 day29 FT_2MUrea PF8302 8302_JP_1c_psms.txt 8302_JP_1c.raw VX101-160 day29 Elu_2MUrea PF8302 8302_JP_2a_psms.txt 8302_JP_2a.raw VX101-160 day29 Elu_2MUrea PF8302 8302_JP_2b_psms.txt 8302_JP_2b.raw VX101-160 day29 Elu_2MUrea PF8302 8302_JP_2c_psms.txt 8302_JP_2c.raw VX101-160 day1 FT PF8286 8286_1a_psms.txt 8286_1a.raw VX101-160 day1 FT PF8286 8286_1b_psms.txt 8286_1b.raw VX101-160 day1 FT PF8286 8286_1c_psms.txt 8286_1c.raw VX101-160 day1 Elu PF8286 8286_2a_psms.txt 8286_2a.raw VX101-160 day1 Elu PF8286 8286_2b_psms.txt 8286_2b.raw VX101-160 day1 Elu PF8286 8286_2c_psms.txt 8286_2c.raw VX101-003 day29 G11_FT PF8507 8507_1a_psms.txt 8507_1a.raw VX101-003 day29 G11_FT PF8507 8507_1b_psms.txt 8507_1b.raw VX101-003 day29 G11_FT PF8507 8507_1c_psms.txt 8507_1c.raw VX101-003 day29 G11_Elu PF8507 8507_2a_psms.txt 8507_2a.raw VX101-003 day29 G11_Elu PF8507 8507_2b_psms.txt 8507_2b.raw VX101-003 day29 G11_Elu PF8507 8507_2c_psms.txt 8507_2c.raw VX101-003 day29 G23_FT PF8507 8507_3a_psms.txt 8507_3a.raw VX101-003 day29 G23_FT PF8507 8507_3b_psms.txt 8507_3b.raw VX101-003 day29 G23_FT PF8507 8507_3c_psms.txt 8507_3c.raw VX101-003 day29 G23_Elu PF8507 8507_4a_psms.txt 8507_4a.raw VX101-003 day29 G23_Elu PF8507 8507_4b_psms.txt 8507_4b.raw VX101-003 day29 G23_Elu PF8507 8507_4c_psms.txt 8507_4c.raw VX101-003 day29 G24_FT PF8507 8507_5a_psms.txt 8507_5a.raw VX101-003 day29 G24_FT PF8507 8507_5b_psms.txt 8507_5b.raw VX101-003 day29 G24_FT PF8507 8507_5c_psms.txt 8507_5c.raw VX101-003 day29 G24_Elu PF8507 8507_6a_psms.txt 8507_6a.raw VX101-003 day29 G24_Elu PF8507 8507_6b_psms.txt 8507_6b.raw VX101-003 day29 G24_Elu PF8507 8507_6c_psms.txt 8507_6c.raw VX101-003 day1 G11_FT PF8521 8521_1a_psms.txt 8521_1a.raw VX101-003 day1 G11_FT PF8521 8521_1b_psms.txt 8521_1b.raw VX101-003 day1 G11_FT PF8521 8521_1c_psms.txt 8521_1c.raw VX101-003 day1 G11_Elu PF8521 8521_2a_psms.txt 8521_2a.raw VX101-003 day1 G11_Elu PF8521 8521_2b_psms.txt 8521_2b.raw VX101-003 day1 G11_Elu PF8521 8521_2c_psms.txt 8521_2c.raw VX101-003 day1 G23_FT PF8521 8521_3a_psms.txt 8521_3a.raw VX101-003 day1 G23_FT PF8521 8521_3b_psms.txt 8521_3b.raw VX101-003 day1 G23_FT PF8521 8521_3c_psms.txt 8521_3c.raw VX101-003 day1 G23_Elu PF8521 8521_4a_psms.txt 8521_4a.raw VX101-003 day1 G23_Elu PF8521 8521_4b_psms.txt 8521_4b.raw VX101-003 day1 G23_Elu PF8521 8521_4c_psms.txt 8521_4c.raw VX101-003 day1 G24_FT PF8521 8521_5a_psms.txt 8521_5a.raw VX101-003 day1 G24_FT PF8521 8521_5b_psms.txt 8521_5b.raw VX101-003 day1 G24_FT PF8521 8521_5c_psms.txt 8521_5c.raw VX101-003 day1 G24_Elu PF8521 8521_6a_psms.txt 8521_6a.raw VX101-003 day1 G24_Elu PF8521 8521_6b_psms.txt 8521_6b.raw VX101-003 day1 G24_Elu PF8521 8521_6c_psms.txt 8521_6c.raw
2025-07-27 | PXD047876 | Pride