Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Next Generation Sequencing Facilitates Quantitative Analysis of Bone Marrow Macrophages and Spleenic Macrophages Transcriptomes in mouse T cell acute lymphoblastic leukemia

ABSTRACT: The goals of this study aim to reveal functional and phenotypic diversity of leukemia-associated macrophages in response to the microenvironmental cues in mouse T cell acute lymphoblastic leukemia Compare Transcriptomes of macrophages in T cell acute leukemia which are suggested as leukemia-associated macrophages (LAMs) with homeostasis

ORGANISM(S): Mus musculus

SUBMITTER: Guo Guang Zheng

PROVIDER: E-GEOD-63751 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Organ-specific microenvironment modifies diverse functional and phenotypic characteristics of leukemia-associated macrophages in mouse T cell acute lymphoblastic leukemia.

Chen Sha-Yan SY Yang Xiao X Feng Wen-Li WL Liao Jin-Feng JF Wang Li-Na LN Feng Li L Lin Yong-Min YM Ren Qian Q Zheng Guo-Guang GG

Journal of immunology (Baltimore, Md. : 1950) 20150206 6

Tumor-associated macrophages are widely studied in solid tumors. The distribution of macrophages in lymph node samples was found to be associated with the prognosis of lymphoma patients. However, the role of macrophages in leukemia and their functional and phenotypic characteristics in hematopoietic malignancies have not been defined. In this study, we examined the distribution and functional and phenotypic characteristics of macrophages in a Notch1-induced mouse model of T cell acute lymphoblas ...[more]

PMID: 25662994

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Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study were to compare signals from competent and abnormal human embryos impacted differently on the expression of endometrial receptivity genes in mouse uteri using transcriptome profiling (RNA-seq). Methods: Immature female (25 d C57BL/6) mice were given a hormone treatment of a single dose 1 mg progesterone and 10 mg/kg/day ÃÂ²-estradiol for a total of 3d to prime the uterus for embryo transfer. The uterine horns of control and study mice were injected with an equal volume (50 ÃÂ¼l) of either unconditioned embryo culture medium (ECM), serving as controls, or pooled conditioned media from competent (n = 9) or arresting embryos (n = 18). Uterine mRNA profiles of 25-day-old wild-type (WT) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000 platform. The sequence reads that passed quality filters were analyzed with the following methods: Bowtie Alignment followed by TopHat (splice juntions mapper) and Cufflinks (transcript abundance). qRTÃ¢ÂÂPCR validation was performed using SYBR Green assays. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the uteri WT and NrlÃ¢ÂÂ/Ã¢ÂÂ mice with BWA workflow and 34,115 transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRTÃ¢ÂÂPCR. RNA-seq data had a linear relationship with qRTÃ¢ÂÂPCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 10% of the transcripts showed differential expression between the WT and NrlÃ¢ÂÂ/Ã¢ÂÂ retina, with a fold change Ã¢ÂÂ¥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRTÃ¢ÂÂPCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling. Conclusions: Our study represents the first detailed analysis of maternal uterine reponse to signals from competent and abnormal human embryos, with biological replicates, generated by RNA-seq technology. Supernatant from competent and abnormal human embryos were flushed into the uterine horns of 25d old C57BL/6 female mice. Uterine mRNA profiles of 21-day old mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000 platform (HiSeq).

Dataset Information

Next Generation Sequencing Facilitates Quantitative Analysis of Bone Marrow Macrophages and Spleenic Macrophages Transcriptomes in mouse T cell acute lymphoblastic leukemia

Publications

Organ-specific microenvironment modifies diverse functional and phenotypic characteristics of leukemia-associated macrophages in mouse T cell acute lymphoblastic leukemia.

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