Dataset Information

A Multi-Omic Analysis of Human Naive CD4 T cells

ABSTRACT: Technological advances in genomics, epigenomics, transcriptomics and proteomics have enabled massively parallel measurements across thousands of genes and gene products. Such high-throughput technologies have been extensively used to carry out genome-wide studies particularly in the context of diseases. Nevertheless, a unified analysis of the genome, epigenome, transcriptome, and proteome of a single mammalian cell type to obtain a coherent view of the complex interplay between omes has not yet been undertaken. Here, we report the first multi-omic analysis of human primary naïve CD4+ T cells, revealing hundreds of unannotated mRNA transcripts, miRNAs, pseudogenes, and noncoding RNAs. Additionally, we carried out a comparative analysis of naïve CD4+ T cells with primary resting memory CD4+ T cells, which have provided novel insights into T cell biology. Overall, our data will serve as a baseline reference of a single pure population of cells for future systems level analysis of other defined cell populations.

INSTRUMENT(S): LTQ Orbitrap Velos, LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): T Cell

SUBMITTER: Akhilesh Pandey

LAB HEAD: Akhilesh Pandey

PROVIDER: PXD000376 | Pride | 2015-11-12

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	01BR1_PAGE_IOB.pep.xml	Pepxml
	01BR1_PAGE_IOB.prot.prot.xml	Xml
	02BR1_PAGE_Core.pep.pep.xml	Pepxml
	02BR1_PAGE_Core.prot.xml	Xml
	03BR1_PAGE_AP.pep.xml	Pepxml

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Publications

A multi-omic analysis of human naïve CD4+ T cells.

Mitchell Christopher J CJ Getnet Derese D Kim Min-Sik MS Manda Srikanth S SS Kumar Praveen P Huang Tai-Chung TC Pinto Sneha M SM Nirujogi Raja Sekhar RS Iwasaki Mio M Shaw Patrick G PG Wu Xinyan X Zhong Jun J Chaerkady Raghothama R Marimuthu Arivusudar A Muthusamy Babylakshmi B Sahasrabuddhe Nandini A NA Raju Rajesh R Bowman Caitlyn C Danilova Ludmila L Cutler Jevon J Kelkar Dhanashree S DS Drake Charles G CG Prasad T S Keshava TS Marchionni Luigi L Murakami Peter N PN Scott Alan F AF Shi Leming L Thierry-Mieg Jean J Thierry-Mieg Danielle D Irizarry Rafael R Cope Leslie L Ishihama Yasushi Y Wang Charles C Gowda Harsha H Pandey Akhilesh A

BMC systems biology 20151106

<h4>Background</h4>Cellular function and diversity are orchestrated by complex interactions of fundamental biomolecules including DNA, RNA and proteins. Technological advances in genomics, epigenomics, transcriptomics and proteomics have enabled massively parallel and unbiased measurements. Such high-throughput technologies have been extensively used to carry out broad, unbiased studies, particularly in the context of human diseases. Nevertheless, a unified analysis of the genome, epigenome, tra ...[more]

PMID: 26542228

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Project description:Several versions of SWI/SNF complexes, BAF and PBAF, have been described based on unique subunit composition. We find that T cell development in the thymus and lymphoid periphery is largely normal in the absence of the PBAF-specific component BAF180. However, BAF180-deficient Th2 cells express high levels of the immunoregulatory cytokine IL-10. BAF180 binds directly to regulatory elements in the Il-10 locus but is replaced by BAF250 BAF complexes in the absence of BAF180, resulting in increased histone acetylation and CBP recruitment to the IL-10 locus. These results demonstrate that BAF180 is a repressor of IL-10 transcription in Th2 cells and suggest that the differential recruitment of different SWI/SNF subtypes can have direct consequences on chromatin structure and gene transcription. mouse primary T helper lymphocytes, naïve and Th2 cells, resting and stimulated, comparison of wild-type and BAF180/Pbrm1 deficient cells RNA from T helper cells was compared in the presence (WT) and absence (KO) of the Pbrm1/BAF180 gene. Comparison was made in 2 T helper subsets (Naive and Th2), each under 2 condtions (resting and stimulated), in triplicate (A,B,C). Resting naïve CD4+ T cells (N) were purified to 95% purity from the spleens and lymph nodes of 4-6 week old Balb/c mice (WT, or BAF180 cKO) using CD4+CD62L+ T cell Purification Kit II per manufacturer’s instructions (Miltenyi). Stimulated Naive cells (S) were prepared from resting naive cells by stimulation for 24 hours on anti-CD3 (1ug/ml), anti-CD28 (2 ug/ml) coated plates at 1-2 x 106/ml. Resting Th2 cells (2U) were prepared from resting naive cells by plating onto anti-CD3 (1ug/ml), anti-CD28 (2 ug/ml) coated plates at 1-2 x 106/ml in the presence of 10ng/ml IL-4, 10ug/ml anti-IFN-gamma. IL-2 (100U/ml) was added 24 hours later. Cultures were expanded in IL-2 (100U/ml) three days after initial culture. Stimulated Th2 cells (2S) were prepared from resting Th2 cells, stimulated with PMA (50ng/ml) and Ionomycin (500ng/ml) for 1.5 hours. RNA was harvested from 3 replicates of the primary Th cells under each condition. RNA was isolated using RNAeasy Kit (Qiagen), Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips. RNA was labeled using the standard Illumina protocol and Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) Biotin labeled cRNA was hybridized to Illumina’s Sentrix MouseRef-8,v2 Expression BeadChips.