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perl模块安装大全

今天又有小伙伴微信问我perl模块安装的问题,因为ENSEMBL发布的大多数数据库以及软件都是基于perl的,尤其是分量很重的VEP,所以即使你再如何如何的讨厌perl,也不得不与之打交道。

这种细节问题问我,我当然无法直接给出答案咯。毕竟,我的知识积累都不是靠死记硬背的。所以需要取回过头查看一下我的博客,才意识到,我竟然已经写了7篇教程,关于perl的模块。目录如下:

首先需要自己确定已经安装了哪些模块,都安装在哪里?还有新的模块需要安装到哪里?
然后再学习如何安装新的模块。

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文献阅读笔记-DIPG里面的Super-enhancers可能是治疗靶点

背景:
Diffuse intrinsic pontine glioma (DIPG) is a universally fatal pediatric cancer.
A histone-3 K27M mutation affects ∼80% of DIPGs and drives aberrant transcription.

早在2015年的83个药物对14个DIPG细胞系的筛选实验中,就发现哪怕是效果最好的multi-HDAC inhibitor panobinostat也会被某些DIPG细胞系产生耐药性。(http://www.biotrainee.com/thread-1599-1-1.htmlContinue reading

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文献阅读笔记-对肿瘤细胞系进行药物筛查

我看到一篇nature medicine文章里面提到了这个对肿瘤细胞系进行药物筛查文章链接:https://www.nature.com/nm/journal/v21/n6/full/nm.3855.html

首先,肿瘤细胞系是:

We assembled a panel of 14 patient-derived DIPG cell cultures, created using neurosphere and adherent models and obtained from both biopsy and autopsy samples (Fig. 1a), representing the breadth of DIPG cell cultures available worldwide at the initiation of the study. Continue reading

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文献阅读笔记-2014-K27M-H3.3-DIPG

DIPG和 adult glioblastomas (GBMs) 很大区别,不应该用同样的治疗方式。

测序策略是:

We integrated deep sequencing analysis of 36 tumor-normal pairs (20 whole-genome sequencing (Illumina HiSeq 2000) and 16 whole-exome sequencing (Applied Biosystems SOLiD 5500xl)) with comprehensive methylation (28 DIPGs; Illumina Infinium450k methylation array), copy number (45 DIPGs; Affymetrix SNP6.0) and expression (35 DIPGs; Illumina HT-12 v4) data (Supplementary Table 1).  Continue reading

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文献阅读笔记-2013-H3K27me3 and K27M mutation

这篇文章是Received 29 March 2013, Revised 9 August 2013, Accepted 4 October 2013, Available online 31 October 2013

同时还有17 MAY 2013一篇science文章提到了K27M mutant影响了PRC2活性

we performed IHC for H3K27me3 in a large cohort of pHGGs with known H3F3A mutation status (n = 104).

Strikingly, all K27M mutant pHGGs (n = 21) showed a strong reduction of overall H3K27me3 levels.

这篇文章就这一个目的,抢这个热点。
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文献阅读笔记-2012–Hotspot Mutations GBM

这篇文章最重要的观点是甲基化用来给GBM分组,分成了6组,至于突变什么的,随便讲了讲,反正数据也不给下载。

We identified six epigenetic and biological GBM subgroups displaying distinct global DNA methylation patterns, which harbor unique hotspot mutations, DNA copy-number alterations, and transcriptomic patterns.

分组如下: Continue reading

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文献阅读笔记,2012-Driver mutations-GBM

主要是做测序

To decipher the molecular pathogenesis of paediatric GBM, we undertook a comprehensive mutation analysis in protein-coding genes by performing whole-exome sequencing (WES) on 48 well-characterized paediatric GBMs, including 6 patients for whom we had matched non-tumour (germline) DNA.

只有6个患者有NT配对样本,用来找somatic的mutation,结果发现其中4个患者就有H3F3A的突变,但是H3F3A本身是非常保守的,所以这个现象值得研究。

to our knowledge no human disorders have specifically been associated with mutations in histones, including H3.3

所以才扩大了WES测序样本数量。 Continue reading