Dataset Information

IP-MS target protein identification

ABSTRACT: To identify the target of the monoclonal antibody, Immuoprecipitation (IP) was performed to pull-down target protein from cell culture extraction, corn or zebrafish tissue lysate. The IP product was validated on silver-stained SDS-PAGE and Western blot. The target band was cut out and performed LC-MS/MS for target protein identification.

INSTRUMENT(S): LTQ Orbitrap Velos, Q Exactive

ORGANISM(S): Homo Sapiens (human) Danio Rerio (zebrafish) (brachydanio Rerio) Zea Mays (maize)

TISSUE(S): Heart, Seed, Cell Culture

SUBMITTER: Yang Li

LAB HEAD: Sheng-Ce Tao

PROVIDER: PXD011629 | Pride | 2020-05-26

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20160128_aibimate_10_1_BB4_01_14902.mgf	Mgf
	20160128_aibimate_11_2_GA6_01_14878.mgf	Mgf
	20160128_aibimate_20_2_GA3_01_14872.mgf	Mgf
	20160128_aibimate_23_1_GA4_01_14874.mgf	Mgf
	20160128_aibimate_31_GA1_01_14868.mgf	Mgf

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Publications

An array of 60,000 antibodies for proteome-scale antibody generation and target discovery.

Wang Zhaohui Z Li Yang Y Hou Bing B Pronobis Mira I MI Pronobis Mira I MI Wang Mingqiao M Wang Yuemeng Y Cheng Guangcun G Weng Weining W Wang Yiqiang Y Tang Yanfang Y Xu Xuefan X Pan Rong R Lin Fei F Wang Nan N Chen Ziqing Z Wang Shiwei S Ma Luyan Zulie LZ Li Yangrui Y Huang Dongliang D Jiang Li L Wang Zhiqiang Z Zeng Wenfang W Zhang Ying Y Du Xuemei X Lin Ying Y Li Zhiqing Z Xia Qingyou Q Geng Jing J Dai Huaping H Yu Yuan Y Zhao Xiao-Dong XD Yuan Zheng Z Yan Jian J Nie Qinghua Q Zhang Xiquan X Wang Kun K Chen Fulin F Zhang Qin Q Zhu Yuxian Y Zheng Susan S Poss Kenneth D KD Tao Sheng-Ce SC Meng Xun X

Science advances 20200311 11

Antibodies are essential for elucidating gene function. However, affordable technology for proteome-scale antibody generation does not exist. To address this, we developed Proteome Epitope Tag Antibody Library (PETAL) and its array. PETAL consists of 62,208 monoclonal antibodies (mAbs) against 15,199 peptides from diverse proteomes. PETAL harbors binders for a great multitude of proteins in nature due to antibody multispecificity, an intrinsic antibody feature. Distinctive combinations of 10,000 ...[more]

PMID: 32195335

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Project description:Genome-wide expression signatures detect specific perturbations in developmental programs and contribute to functional resolution of key regulatory networks. In maize (Zea mays) inflorescences, mutations in the RAMOSA (RA) genes affect determinacy of axillary meristems and thus alter branching patterns, an important agronomic trait. In this work, we developed and tested a framework for analysis of tag-based, digital gene expression (DGE) profiles using Illumina’s high-throughput sequencing technology and the newly-assembled B73 maize reference genome. We also used a mutation in the RA3 gene to identify putative expression signatures specific to stem cell fate in determinacy of axillary meristems. The RA3 gene encodes a trehalose-6-phosphate-phosphatase and may act at the interface between developmental and metabolic processes. Deep sequencing of DGE libraries, representing three biological replicate ear samples from wild-type and ra3 plants, generated 27 million 20-21nt reads with frequencies spanning four orders of magnitude. Unique sequence tags were anchored to 3´-ends of individual transcripts by DpnII and NlaIII digests, which were multiplexed during sequencing. We mapped 86% of non-redundant signature tags to the maize genome, which associated with 37,117 working gene models and un-annotated regions of expression. 66% of maize genes were detected at ? nine reads in immature maize ears. We used comparative genomics to leverage existing information from Arabidopsis and rice in functional analyses of differentially expressed maize genes. Results from this study provide a basis for analysis of short-read expression data in maize and resolved specific expression signatures that will help define mechanisms of action for the RA3 gene. 3' tag-based DGE libraries were generated using Illumina 1G technology. Libraries were prepared from 2mm ear samples and represent: 3 biological replicates of wild-type B73, 3 biological replicates of ramosa3 (ra3) mutants, and 1 technical replicate of a ra3 sample. Each sample was sequenced in a single lane of a flow cell. Each lane includes library preparations from both DpnII and NlaIII digests for that sample. Sequences from DpnII digests start with GATC and those from NlaIII digests start with ATG.