生信菜鸟团 » roadmap http://www.bio-info-trainee.com 欢迎去论坛biotrainee.com留言参与讨论，或者关注同名微信公众号biotrainee Sat, 28 Jun 2025 14:30:13 +0000 zh-CN hourly 1 https://wordpress.org/?v=4.1.33 备忘录- Universal Human Reference RNA sample (HUR)-样本列表 http://www.bio-info-trainee.com/2273.html http://www.bio-info-trainee.com/2273.html#comments Thu, 12 Jan 2017 02:52:41 +0000 http://www.bio-info-trainee.com/?p=2273 Continue reading →]]> 大家不要点击，我把这个博客当做笔记本的，这个知识点对你们几乎木有用的！

Universal Human Reference RNA 似乎是agilent公司的，包含了10个不同的人类细胞系！roadmap对这些样本测了RNA-seq，我以后课题可能会用得着。

列表如下：

E000	Universal_Human_Reference
E003	H1_Cell_Line
E004	H1_BMP4_Derived_Mesendoderm_Cultured_Cells
E005	H1_BMP4_Derived_Trophoblast_Cultured_Cells
E006	H1_Derived_Mesenchymal_Stem_Cells
E007	H1_Derived_Neuronal_Progenitor_Cultured_Cells
E011	hESC_Derived_CD184+_Endoderm_Cultured_Cells
E012	hESC_Derived_CD56+_Ectoderm_Cultured_Cells
E013	hESC_Derived_CD56+_Mesoderm_Cultured_Cells
E016	HUES64_Cell_Line
E024	4star
E027	Breast_Myoepithelial_Cells
E028	Breast_vHMEC
E037	CD4_Memory_Primary_Cells
E038	CD4_Naive_Primary_Cells
E047	CD8_Naive_Primary_Cells
E050	Mobilized_CD34_Primary_Cells_Female
E053	Neurosphere_Cultured_Cells_Cortex_Derived
E054	Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived
E055	Penis_Foreskin_Fibroblast_Primary_Cells_skin01
E056	Penis_Foreskin_Fibroblast_Primary_Cells_skin02
E057	Penis_Foreskin_Keratinocyte_Primary_Cells_skin02
E058	Penis_Foreskin_Keratinocyte_Primary_Cells_skin03
E059	Penis_Foreskin_Melanocyte_Primary_Cells_skin01
E061	Penis_Foreskin_Melanocyte_Primary_Cells_skin03
E062	Peripheral_Blood_Mononuclear_Primary_Cells
E065	Aorta
E066	Adult_Liver
E070	Brain_Germinal_Matrix
E071	Brain_Hippocampus_Middle
E079	Esophagus
E082	Fetal_Brain_Female
E084	Fetal_Intestine_Large
E085	Fetal_Intestine_Small
E087	Pancreatic_Islets
E094	Gastric
E095	Left_Ventricle
E096	Lung
E097	Ovary
E098	Pancreas
E100	Psoas_Muscle
E104	Right_Atrium
E105	Right_Ventricle
E106	Sigmoid_Colon
E109	Small_Intestine
E112	Thymus
E113	Spleen
E114	A549
E116	GM12878
E117	HELA
E118	HEPG2
E119	HMEC
E120	HSMM
E122	HUVEC
E123	K562
E127	NHEK
E128	NHLF

来自于：http://egg2.wustl.edu/roadmap/web_portal/processed_data.html#ChipSeq_DNaseSeq

Expression quantification

Data format: Tab-delimited matrix

  • Download URL:
    http://egg2.wustl.edu/roadmap/data/byDataType/rna/expression/
  • EG.name.txt:is the header file containing order and names of epigenomes (columns) in the expression matrices listed below. The EG names and the RNA seq quantification include an E000 sample representing a Universal Human Reference RNA sample (HUR). Agilent's Universal Human Reference RNA is composed of total RNA from 10 human cell lines. The reference RNA is designed to be used as a reference for expression profiling experiments. Since RNA species differ in abundance between cell lines, an ideal reference sample should represent these different RNAs. Equal quantities of DNase-treated total RNA from each cell line were pooled to make the Universal Human Reference RNA. Stratagene also supplies a QPCR Human Reference Total RNA, suitable for QRT-PCR, which has undergone further DNase treatment. Further details are available at
    http://www.genomics.agilent.com/article.jsp?pageId=1452&_requestid=2183245 and
    http://www.chem.agilent.com/library/usermanuals/public/740000.pdf
  • Ensembl_v65.Gencode_v10.ENSG.gene_info: details and annotations for the ENSEMBL ids in the expression matrices
  • 57epigenomes.RPKM.pc: RPKM expression matrix for protein coding genes
  • 57epigenomes.N.pc: RNA-seq read counts matrix for protein coding genes
  • 57epigenomes.RPKM.nc: RPKM expression matrix for non-coding RNAs
  • 57epigenomes.N.nc: RNA-seq read counts matrix for non-coding RNAs
  • 57epigenomes.exon.RPKM.pc: RPKM expression matrix for protein coding exons
  • 57epigenomes.exon.N.pc: RNA-seq read counts matrix for protein coding exons
  • 57epigenomes.RPKM.intronic.pc: RNA-seq read count matrix for intronic protein-coding RNA elements
  • 57epigenomes.N.intronic.pc: RNA-seq read count matrix for intronic protein-coding RNA elements
  • 57epigenomes.N.rb: RNA-seq read counts matrix for ribosomal genes
  • 57epigenomes.RPKM.rb: RPKM expression matrix for ribosomal RNAs
  • 57epigenomes.exn.RPKM.rb: RPKM expression matrix for ribosomal gene exons
  • 57epigenomes.exn.N.rb: RNA-seq read counts matrix for ribosomal gene exons

 

RNA-seq signal tracks

Data format: BIGWIG

 

 

]]> http://www.bio-info-trainee.com/2273.html/feed 0 4种方式下载roadmap计划的所有数据 http://www.bio-info-trainee.com/1830.html http://www.bio-info-trainee.com/1830.html#comments Thu, 28 Jul 2016 14:52:16 +0000 http://www.bio-info-trainee.com/?p=1830 Continue reading →]]> roadmap的官网是：http://www.roadmapepigenomics.org/
精选的129个细胞系，细胞系的介绍如下：http://www.broadinstitute.org/~anshul/projects/roadmap/metadata/EID_metadata.tab
对每个细胞系，都至少处理了5个核心组蛋白修饰数据，还有其它若干转录因子数据。
官网介绍的很详细，我就不翻译了：

The NIH Roadmap Epigenomics Mapping Consortium was launched with the goal of producing a public resource of human epigenomic data to catalyze basic biology and disease-oriented research. The Consortium leverages experimental pipelines built around next-generation sequencing technologies to map DNA methylation, histone modifications, chromatin accessibility and small RNA transcripts in stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease. The Consortium expects to deliver a collection of normal epigenomes that will provide a framework or reference for comparison and integration within a broad array of future studies. The Consortium also aims to close the gap between data generation and its public dissemination by rapid release of raw sequence data, profiles of epigenomics features and higher-level integrated maps to the scientific community. The Consortium is also committed to the development, standardization and dissemination of protocols, reagents and analytical tools to enable the research community to utilize, integrate and expand upon this body of data.
首先是这个网站：
矩阵很容易看懂roadmap处理了哪些细胞系，进行了什么样的处理，数据可以直接下载。
4

然后我比较首先推崇broad研究所的下载方式

里面还列出了他们用过的peaks caller 工具：
http://www.broadinstitute.org/~anshul/projects/encode/preprocessing/peakcalling/  可以看到，主要有MACS，peakranger，quest，sicer，peakseq，hotspot等等
直接进入broad分析好的peaks结果：
[DIR] Parent Directory
-
[DIR] broadPeak/ 08-Feb-2015 21:00 -
[DIR] gappedPeak/ 08-Feb-2015 21:00 -
[DIR] lowq/ 31-Aug-2014 20:42 -
[DIR] narrowPeak/ 08-Feb-2015 20:59 -

这里面有3种peaks，我现在还没有搞懂是什么意思。

接着是 iHEC存放的数据：

我还是第一次看到这个数据接口，也是以文件夹文件的形式直接浏览，根据自己的需求下载即可：
除了ENCODE计划的数据，还有Blueprint计划和roadmap计划的数据都可以下载。

最后可以从圣路易斯华盛顿大学里面下载

圣路易斯华盛顿大学Washington University in St. Louis，简称（Wash U，WU）以美国国父乔治·华盛顿命名，始建于1853年2月22日，位于美国密苏里州圣路易斯市，是美国历史上建校最早也是最负盛名的“华盛顿大学”，该校在美国新闻和世界报道（US News & World Report）2014大学综合排名中名列14位。
里面有一个非常详细的页面来介绍roadmap的各种数据:http://egg2.wustl.edu/roadmap/web_portal/processed_data.html
如果你已经了解了roadmap计划，就很容易找到自己的数据，从而直接浏览器或者wget下载即可。
首先是序列比对结果下载。
onsolidated Epigenomes:36 bp mappability filtered, pooled and subsampled read alignment files:
http://egg2.wustl.edu/roadmap/data/byFileType/alignments/consolidated/
Unconsolidated Epigenomes (Uniform mappability): 36 bp mappability filtered primary alignment files:
http://egg2.wustl.edu/roadmap/data/byFileType/alignments/unconsolidated/
包括各种peaks记录文件下载
    • Broad domains on enrichment for histone ChIP-seq and DNase-seq)

http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/

      • Data format: GappedPeak (subset of domains containing at least one narrow peaks)

http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/gappedPeak/

     

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