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The SETD3 interacting protein was identified and screened by TurboID method, and Search for potential histidine methylation modification sites

ABSTRACT: we employed a TurboID approach that utilized a modified promiscuous biotin ligase BirA for proximity labeling by fusing SETD3 with this enzyme, By introducing biotin, cellular fractions of SETD3-TurboID-transfected cells, both cytosolic and chromatin fractions, underwent immunoprecipitation, followed by MS analysis to identify SETD3-interacting proteins. We conducted two experiments, first time we tested four samples, the RAW data of cyto_Vec and chr_Vec represented cells experssing emptry vector soluble fraction and chromatin fraction respectively. the RAW data of cyto_SET and chr_SET represented cells experssing SETD3-TurboID soluble fraction and chromatin fraction respectively. And PSMs.xlsx described the analysis of mass spectrum data. Second time we tested three samples. The RAW data of 21010704_DHG_VEC, 21010704_DHG_WT and 21010704_DHG_YA represented cells experssing emptry vector, SETD3-WT-TurboID or SETD3-Y313A-TurboID respectively. 21010704_DHG_Protein-compare.xlsx described the proteins identification of mass spectrum data. 21010704_DHG_Methyl-H.xlsx listed the histidine methylation identification of mass spectrum data.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell, Cell Culture

DISEASE(S): Cervix Carcinoma

SUBMITTER: D HG

LAB HEAD: Du Haining

PROVIDER: PXD050556 | Pride | 2024-04-16

REPOSITORIES: Pride

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The SETD3 interacting protein was identified and screened by TurboID method, and Search for potential histidine methylation modification sites

Project description:we employed a TurboID approach that utilized a modified promiscuous biotin ligase BirA for proximity labeling by fusing SETD3 with this enzyme, By introducing biotin, cellular fractions of SETD3-TurboID-transfected cells, both cytosolic and chromatin fractions, underwent immunoprecipitation, followed by MS analysis to identify SETD3-interacting proteins. We conducted two experiments, first time we tested four samples, the RAW data of cyto_Vec and chr_Vec represented cells experssing emptry vector soluble fraction and chromatin fraction respectively. the RAW data of cyto_SET and chr_SET represented cells experssing SETD3-TurboID soluble fraction and chromatin fraction respectively. And PSMs.xlsx described the analysis of mass spectrum data. Second time we tested three samples. The RAW data of 21010704_DHG_VEC, 21010704_DHG_WT and 21010704_DHG_YA represented cells experssing emptry vector, SETD3-WT-TurboID or SETD3-Y313A-TurboID respectively. 21010704_DHG_Protein-compare.xlsx described the proteins identification of mass spectrum data. 21010704_DHG_Methyl-H.xlsx listed the histidine methylation identification of mass spectrum data.

2024-03-12 | PXD046472 | Pride

Expression data from ectopic PTHLH over-expression in Ca9-22 cells

Project description:To exmaine the PTHLH stimulated genes in Ca9-22 cells, we preformed the Affymetrix Human Genome U133 Plus 2.0 Array with empty vector or PTHLH expression vector. The raw data were normalized by GeneSpring GX software and up-load with raw values.

2017-03-08 | GSE81471 | GEO

20 human soft-tissue sarcomas (TMT)

Project description:SCX fractiond, TMT labeled pleomorphic soft-tissue sarcomas. 32 raw files (8x4) plus 8 pools (also TMT labeled) corresponding to each SCX fraction are submitted. The latter were used to propagate identifications across the runs.

2020-01-27 | PXD000617 | Pride

Microarray analysis of the oocyte quality

Project description:Microarray analysis was performed in ooplast samples to identify gene expression profiles associated with the embryo capacity to develop to blastocyst stage A fraction of the cytoplasm from in vitro matured oocytes was collected and snap frozen. The oocytes were chemically activated and presumptive zygotes were in vitro cultured in individual medium microdrops. The embryo development was recorded and oocytes classified according to the stage of embryo development. Oocyte was considered of good quality if the development proceeded to blastocyst stage, whereas it was considered of bad quality if there was a development block between 8-16 cells stage and morula formation.

2013-12-27 | E-GEOD-29191 | biostudies-arrayexpress

Stable pausing by RNA polymerase II provides an opportunity to target and integrate regulatory signals

Project description:Metazoan gene expression is often regulated after the recruitment of RNA polymerase II (Pol II) to promoters, through the controlled release of promoter-proximally paused Pol II into productive RNA synthesis. Despite the prevalence of paused Pol II, very little is known about the dynamics of these early elongation complexes or the fate of short transcription start site-associated (tss) RNAs they produce. Here, we demonstrate that paused elongation complexes can be remarkably stable, with half-lives exceeding 15 minutes at genes with inefficient pause release. Promoter-proximal termination by Pol II is infrequent and released tssRNAs are targeted for rapid degradation. Further, we provide evidence that the predominant tssRNA species observed are nascent RNAs held within early elongation complexes. We propose that stable pausing of polymerase provides a temporal window of opportunity for recruitment of factors to modulate gene expression and that the nascent tssRNA represents an appealing target for these interactions. This submission includes 13 raw data files. Four samples (chromatin, soluble, mock-treated, and Rrp40-depleted) are represented by two biological replicate raw data files, while five samples (cells, DMSO, FP, mock-treated + FP, and Rrp-40depleted + FP) are represented by single raw data files.

2013-10-31 | E-GEOD-49078 | biostudies-arrayexpress

Prospective Collection of PillCam SB3 Videos and Raw Data Files for Future Developments (SODA)

Project description:Observational, Multicenter, Post-market, Minimal risk, Prospective data collection of PillCam SB3 videos (including PillCam reports) and raw data files and optional collection of Eneteroscopy reports

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Screening of the targeted mRNAs of ER-anchored PARN by transcriptome sequencing.

Project description:The goals of this study are to identify the potential targets and then elucidate the function of ER-anchored PARN. After overexpressing the empty vector, PARN(wild type) or D28A(the enzyme-dead mutant of PARN) in HEK-293T cell respectively and the following fractionation of the cytosol and ER fraction, we performed the high-throughput RNA sequencing for each fraction. After comparing the abundance of detected transcripts in different samples we found ER-anchored PARN only affects a small subset of mRNAs in HEK-293T cell.

2021-09-19 | GSE120209 | GEO

Bivalency - Histone H3 Lysine4 and Histone H3 Lysine27 Methylation Dynamics

Project description:The molecular signature at histone H3K4me3 and H3K27me3 involved in epigenetic regulation of normal (MCF10A) and transformed (MCF7, MDA-MB-231) breast cells using ChIP-Seq technology. This study examines the dynamic distribution of H3K4me3, associated with active chromatin, and H3K27me3, associated with repressed chromatin, histone modifications to provide an understanding of the changes in epigenetic regulation associated with the unique breast cancer subtypes. histone H3K4me3 and H3K27me3 ChIP-seq normal (MCF10A) and transformed (MCF7, MDA-MB-231) breast cells Please note that the 'H3K4me3' and 'input' data are duplicated records of the samples represented in GSE69377 for the convenient retrieval of the complete raw data from SRA.

2016-03-24 | E-GEOD-77772 | biostudies-arrayexpress

Mass-spectrometry based proteomics reveals a regulatory role for DYRK1A in DNA double-strand break repair

Project description:This data set contains RAW, and related result files from immunopurification mass-spectrometry experiments run on Orbitrap Lumos instruments from Thermo Fisher. Each biological replicate was done from either HeLa S3, cytoplasm, nuclear extract, or chromatin bound fraction using either DYRK1A or RNF169 as a bait. RAW files are labelled by replicate, cellular fraction, antibody that was used for each DYRK1A immunopurification and date.

2018-08-31 | MSV000082881 | MassIVE

Transcriptome information of RAW-Rv3722c and RAW-Vector cell lines

Project description:RAW-Rv3722c and RAW-Vector cells were collected for RNA extraction and subject to transcriptome sequencing. Expression levels of all genes in the two cell lines were determined by Next Generation Sequencing (NGS)

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