cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs.
cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs.
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DOI：
10.1186/s13148-016-0287-1
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发表时间：
2016
影响因子：
5.7
通讯作者：
Keller A
中科院分区：
文献类型：
--
作者：
Fehlmann T;Reinheimer S;Geng C;Su X;Drmanac S;Alexeev A;Zhang C;Backes C;Ludwig N;Hart M;An D;Zhu Z;Xu C;Chen A;Ni M;Liu J;Li Y;Poulter M;Li Y;Stähler C;Drmanac R;Xu X;Meese E;Keller A
我们使用基于组合探针-锚定合成（cPAS）的BGISEQ-500测序仪提供了第一个测序数据。应用cPAS，我们研究了人类小的非编码RNA的库，并将其与其他技术进行了比较。从不同标本的重复测量开始，包括实体组织（大脑和心脏）和血液，我们每个样本产生了3010万个读数的中位数。24.1 100万个映射到人类基因组，2330万个映射到miRBase。在大脑样本的六个技术重复中，我们观察到的相关性中位数为0.98。将BGISEQ-500与HiSeq进行比较，我们计算出相关性为0.75。BGISEQ-500和HiSeq与微阵列的可比性相似，第一个显示相关性为0.58，而后者显示相关性为0.6。至于血细胞中检测到的表达分布的潜在偏倚，98.6%的HiSeq读数与93.1%的BGISEQ-500读数匹配于具有最高读数计数的10种miRNA。在使用miRDeep 2并采用严格的选择标准预测新的miRNA后，我们在实体组织中普遍存在的cPAS测序读数中检测到74个高可能的候选者，并在血液中普遍存在36个候选者。虽然显然没有适合miRNome分析所有挑战的理想平台，但cPAS显示出高技术重现性，并补充了迄今可用的平台。本文的在线版本（doi：10.1186/s13148-016-0287-1）包含补充材料，可供授权用户使用。
We present the first sequencing data using the combinatorial probe-anchor synthesis (cPAS)-based BGISEQ-500 sequencer. Applying cPAS, we investigated the repertoire of human small non-coding RNAs and compared it to other techniques. Starting with repeated measurements of different specimens including solid tissues (brain and heart) and blood, we generated a median of 30.1 million reads per sample. 24.1 million mapped to the human genome and 23.3 million to the miRBase. Among six technical replicates of brain samples, we observed a median correlation of 0.98. Comparing BGISEQ-500 to HiSeq, we calculated a correlation of 0.75. The comparability to microarrays was similar for both BGISEQ-500 and HiSeq with the first one showing a correlation of 0.58 and the latter one correlation of 0.6. As for a potential bias in the detected expression distribution in blood cells, 98.6% of HiSeq reads versus 93.1% of BGISEQ-500 reads match to the 10 miRNAs with highest read count. After using miRDeep2 and employing stringent selection criteria for predicting new miRNAs, we detected 74 high-likely candidates in the cPAS sequencing reads prevalent in solid tissues and 36 candidates prevalent in blood. While there is apparently no ideal platform for all challenges of miRNome analyses, cPAS shows high technical reproducibility and supplements the hitherto available platforms. The online version of this article (doi:10.1186/s13148-016-0287-1) contains supplementary material, which is available to authorized users.
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影响因子：
9.3
作者：
Meder, Benjamin;Backes, Christina;Keller, Andreas
通讯作者：
Keller, Andreas
影响因子：
4.5
作者：
Burgos, Kasandra Lovette;Javaherian, Ashkan;Van Keuren-Jensen, Kendall
通讯作者：
Van Keuren-Jensen, Kendall
影响因子：
14.9
作者：
Griffiths-Jones S;Grocock RJ;van Dongen S;Bateman A;Enright AJ
通讯作者：
Enright AJ
影响因子：
12.3
作者：
Leidinger P;Backes C;Deutscher S;Schmitt K;Mueller SC;Frese K;Haas J;Ruprecht K;Paul F;Stähler C;Lang CJ;Meder B;Bartfai T;Meese E;Keller A
通讯作者：
Keller A
影响因子：
64.5
作者：
LEE, RC;FEINBAUM, RL;AMBROS, V
通讯作者：
AMBROS, V