Dataset Information

PRM quantification of XRCC4 and Xkr4 peptides that were immunoprecipitated with SPOT-Xkr4-Flag

ABSTRACT: Several selected peptides of human XRCC4 and mouse Xkr4 were measured by PRM. LC-MS/MS analysis was performed on an EASY-nLC 1200 UHPLC connected to a Q Exactive Plus mass spectrometer through a nanoelectrospray ion source (Thermo Fisher Scientific). Targeted MS/MS scans were acquired by a time-scheduled inclusion list at a resolution of 70,000, an isolation window of 4.0 m/z, a maximum injection time of 2 sec, and a normalized collision energy of 27. Time alignment and relative quantification of the transitions were performed with PinPoint version 1.4 (Thermo Fisher Scientific).

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Hidetaka Kosako

PROVIDER: PXD023537 | JPOST Repository | Tue Jan 12 00:00:00 GMT 2021

REPOSITORIES: jPOST

ACCESS DATA

Dataset's files

Source:

Items per page:

1 - 5 of 5

Publications

Caspase cleavage releases a nuclear protein fragment that stimulates phospholipid scrambling at the plasma membrane.

Maruoka Masahiro M Zhang Panpan P Mori Hiromi H Imanishi Eiichi E Packwood Daniel M DM Harada Hiroshi H Kosako Hidetaka H Suzuki Jun J

Molecular cell 20210315 7

Phospholipid scrambling in dying cells promotes phosphatidylserine exposure, a critical process for efferocytosis. We previously identified the Xkr family protein Xkr4 as a phospholipid-scrambling protein, but its activation mechanisms remain unknown. Here we show that Xkr4 is activated in two steps: dimer formation by caspase-mediated cleavage and structural change caused by activating factors. To identify the factors, we developed a new screening system, "revival screening," using a CRISPR sgR ...[more]

PMID: 33725486

Similar Datasets

Project description:Purpose: Zinc Finger MIZ-Type Containing 1 (Zmiz1) is a member of the PIAS family of protein and function as a transcriptional coactivator of Notch, Androgen Receptor (AR), p53, Estrogen Receptor (ER), and Smad3/4 . Despite Zmiz1 critical role in angiogenesis, its role in lymphatic vasculature is unknown. Here, we use HDLECs cell line to profile transcriptional changes upon Zmiz1 knockdown using siRNA. Methods: Total RNA was extracted from control and Zmiz1 siRNA transfected HDLECs using GeneJET RNA Purification Kit (Thermo Fisher Scientific, K0732) following the manufacturer instructions. RNA concentration and RNA integrity (RIN) number were determined using Qubit RNA High Sensitivity Assay Kit (Thermo Fisher Scientific, Q32852) and Bioanalyzer RNA 6000 Nano assay kit (Agilent, 5067-1511) respectively. RNA library was prepared using TruSeq RNA Library Prep Kit v2 (Illumina, RS-122-2001) according to the manufacturer instructions. mRNA library was quantified using Qubit dsDNA High Sensitivity Assay Kit (Thermo Fisher Scientific, Q32851) and verified using the Bioanalyzer DNA1000 assay kit (Agilent, 5067-1505). Verified samples were sequenced using the NextSeq1000/2000 P2 Reagents (200 Cycles) v3 (Illumina, 20046812) on a Nextseq1000/2000. Sequenced reads were aligned to the human (hg19) reference genome with RNA-Seq alignment tool (STAR aligner). The aligned reads were used to quantify mRNA expression and determine differentially expressed genes using the RNA-Seq Differential Expression tool (version 1.0.1). Both alignment and differential expression analysis were performed using the tools in the illumina BaseSpace Sequence Hub. Results: We found 2,228 differentially expressed genes of which 1,115 genes were upregulated while 1,113 genes were downregulated. Downregulated genes were enriched in biological processes such as lymph vessel development, cell migration and heart valve development. Conclusions: We identify Zmiz1 regulates Prox1 in lymphatic endothelial cells

			Action	DRS
	1_XRCC4_WT_minus_PRM.raw	Raw
	2_XRCC4_WT_STS_PRM.raw	Raw
	3_XRCC4_R270A_minus_PRM.raw	Raw
	4_XRCC4_R270A_STS_PRM.raw	Raw
	XRCC4_PRM.xlsx	Xlsx