概要: Diminishing potential to replace damaged tissues is a hallmark for ageing of somatic stem cells, but the mechanisms leading to ageing remain elusive. We present a proteome-wide atlas of age-associated alterations in human haematopoietic stem and progenitor cells (HPCs) along with five other cell types that constitute the bone marrow niche. For each, the abundance of a large fraction of the ~12,000 proteins identified was assessed in a cohort of healthy human subjects from different age. As the HPCs became older, pathways in central carbon metabolism exhibited features reminiscent of the Warburg effect where glycolytic intermediates are rerouted towards anabolism. Simultaneously, altered abundance of early regulators of HPC differentiation revealed a reduced functionality and a bias towards myeloid differentiation at the expense of lymphoid development. Ageing caused significant alterations in the bone marrow niche too, such as functionality of the pathways involved in HPC homing and lineage differentiation. The data represents a valuable resource for further in-depth mechanistic analyses, and for validation of knowledge gained from animal models.
项目整体设计: RNA-seq samples extracted from human bone marrow, from 6 cell populations (HPC, LYM, MON, ERP, GRA, MSC). Technical replicates are included for each donor and cell type. Technical replicates were produced by making independent libraries from the same RNA.
Bone marrow (BM) samples were harvested through puncture at the posterior iliac crest using a Yamshidi needle
处理方案:
BM aspirates were processed by FICOLL density fractionation for isolation of MNCs; stained with CD34-APC, CD45-FITC and CD14-PE; FACS-sorted and stored at -80℃
提取方案:
RNA was extracted with trizol (Invitrogen) using a linear acrylamide carrier. RNA was then treated with DNase I (Life technologies) and purified using Agencourt RNAClean XP beads (Beckman Coulter). RNA quality and concentration were assessed by using an RNA 6000 bioanalyzer pico kit (Agilent). Samples with concentrations less than 30 pg/μl and/or an RNA integrity number (RIN) less than 6 were excluded from further analysis.
建库方案:
A cDNA library was produced using the Smart-Seq 2 protocol. Sequencing was performed on an Illumina HiSeq4000 with 75 bp paired-end reads with the aim to achieve coverage of 25 million reads per sample.
测序信息
分子类型:
poly(A)+ RNA
库的片段类型:
PAIRED
库的链类型:
-
测序平台:
ILLUMINA
测序仪型号:
Illumina HiSeq 4000
链特异性:
Unspecific
样本
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生物条件:
实验变量:
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质量评估:
数据来源
GEN样本编号
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组织
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细胞亚型
细胞系
疾病
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发育阶段
突变/变异
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Condition Detail
生长方案
处理方案
提取方案
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分子类型
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加标（Spike-In）
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碱基数
平均测序片段长度_1
平均测序片段长度_2
唯一比对率
多重比对率
覆盖度
文章
Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline.
