Sample Summary Fetal Lung Summary Track Settings
 
Roadmap Epigenome Fetal Lung Summary for 10 assay type(s)

Track collection: Sample Summary

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     FL DGF 66 24  Fetal Lung Digital Genomic Footprinting (HOTSPOT_SCORE=0.6416 Pcnt=60)    Data format 
     FL DNase 19 73  Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3539 Pcnt=41)    Data format 
     FL DNase 27 17  Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6099 Pcnt=90 DonorID:H-22727)    Data format 
     FL DNase 47 66  Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.389 Pcnt=30 DonorID:H-23247)    Data format 
     FL DNase 4B 07  Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4924 Pcnt=60 DonorID:H-22934B)    Data format 
     FL DNase 65 27  Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3588 Pcnt=17 DonorID:H-23365)    Data format 
     FL DNase 66 24  Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6395 Pcnt=92 DonorID:H-23266)    Data format 
     FL DNase 66 51  Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5007 Pcnt=65 DonorID:H-23266)    Data format 
     FL DNase 76 46  Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4301 Pcnt=52 DonorID:H-22676)    Data format 
     FL DNase 84 09  Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5432 Pcnt=77 DonorID:H-23284)    Data format 
     FL DNase 84 20  Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.494 Pcnt=62 DonorID:H-23284)    Data format 
     FL DNase 90 85  Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3625 Pcnt=20 DonorID:H-23090)    Data format 
     FL DNase 99 61  Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4228 Pcnt=67)    Data format 
     FL H3K27me3 27  Fetal Lung H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1037 Pcnt=17 DonorID:H-22727)    Data format 
     FL H3K27me3 72  Fetal Lung H3K27me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.2539 Pcnt=55)    Data format 
     FL H3K27me3 H22772  Fetal Lung H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad    Data format 
     FL H3K36me3 27  Fetal Lung H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1924 Pcnt=25 DonorID:H-22727)    Data format 
     FL H3K36me3 84  Fetal Lung H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1892 Pcnt=27)    Data format 
     FL H3K4me1 27  Fetal Lung H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2044 Pcnt=14 DonorID:H-22727)    Data format 
     FL H3K4me1 66  Fetal Lung H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.4642 Pcnt=71)    Data format 
     FL H3K4me1 72  Fetal Lung H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.4224 Pcnt=46)    Data format 
     FL H3K4me1 H22772  Fetal Lung H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad    Data format 
     FL H3K4me3 27  Fetal Lung H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1892 Pcnt=3 DonorID:H-22727)    Data format 
     FL H3K4me3 76  Fetal Lung H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2218 Pcnt=13 DonorID:H-22676)    Data format 
     FL H3K9ac 27  Fetal Lung H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1557 Pcnt=23 DonorID:H-22727)    Data format 
     FL H3K9ac 72  Fetal Lung H3K9ac Signal from REMC/Broad (HOTSPOT_SCORE=0.2297 Pcnt=33)    Data format 
     FL H3K9ac H22772  Fetal Lung H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad    Data format 
     FL H3K9me3 27  Fetal Lung H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0411 Pcnt=7 DonorID:H-22727)    Data format 
     FL H3K9me3 66  Fetal Lung H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1397 Pcnt=50)    Data format 
     FL Input 66  Fetal Lung Input Signal from REMC/Broad (Hotspot_Score=0.006 Pcnt=30)    Data format 
     FL Input 72  Fetal Lung Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0417 Pcnt=75)    Data format 
     FL Input 84  Fetal Lung Input Signal from REMC/Broad (Hotspot_Score=0.0054 Pcnt=27)    Data format 
     FL Input H22772  Fetal Lung Input Histone Modification by Chip-seq Signal from REMC/Broad    Data format 
     FL RRBS 27  Fetal Lung DNA Methylation by RRBS Signal from REMC/Broad    Data format 
     FL RRBS 66  Fetal Lung DNA Methylation by RRBS Signal from REMC/Broad    Data format 
    
Assembly: Human Feb. 2009 (GRCh37/hg19)

Vizhub @ Wash U built this track, and Roadmap Epigenomics Consortium is responsible for its contents.

Description

These tracks are genome-wide DNA methylation maps generated by Roadmap Epigenomics Project. Each track is collection of DNA methylation experiment data on one sample type.

DNA methylation of human DNA mostly happens on cytosine bases of CpG dinucleotides. The methylated DNA usually prevent accessibility of regulatory proteins and hampers transcription, while unmethylated DNA is usually indicative of open chromatin. The MeDIP-Seq and MRE-Seq experiments are usually performed on same sample to identify genome-wide DNA methylation pattern. MeDIP-Seq (methylated DNA immunoprecipitation and sequencing) is a ChIP-based approach utilizing antibody against methylated cytosine. This method enriches methylated DNA and high read count indicates high likelihood of underlying region is methylated. The MRE-Seq (methylation restriction enzyme sequencing) uses methylation-sensitive restriction enzymes to digest DNA, and only cut at unmethylated restriction sites. The cut restriction sites will be detected by sequencing where reads aligned to a restriction site on reference genome means the restriction site is unmethylated.

The MethylC-Seq (MethylC sequencing) uses bisulfite to convert methylated cytosines to thymines before sequencing. The percentage of reads with a T versus a C indicates the percentage methylation at the cytosine. Details can be found in this paper Lister R, et al., Nature. 2009 Nov 19;462(7271):315-22. .

RRBS (Reduced-Representation-Bisulfite-Sequencing) is similar to MethylC-seq except RRBS uses restriction enzyme to fragment the genome into fragments suitably-sized for sequencing. While RRBS produces percent methylation similar to MethylC-seq, it is limited to cytosines that are within restriction fragments of a suitable size and tend to measure CpG dense regions only. Details can be found in this paper: Meissener, A. et al., Nucleic Acids Res. 2005; 33(18): 5868-5877. .

Display conventions

Each track can be turned on/off individually. Inside each track, sub-tracks are displayed in same vertical space and are overlayed with transparent colors for contrast. All tracks displays read density data in form of wiggle plots. Number of aligned reads is counted at each base pair, and a summarized value is computed for each 20 bp interval for display. Sub-tracks sharing same space use same scale.

Methods

Experimental protocols: follow this link for experimental protocols.

Data processing: EDACC carried out data processing and quality assessment. Details are fully explained here . In brief, sequencing reads were aligned with 'Pash' program to derive read density data. The read density data is prepared into 'wiggle' format files with fixed step length of 20 bp. Data in wiggle and other formats have been deposited in NCBI Gene Expression Omnibus database for public access.

Quality control: the HotSpot was one of the methods used to assess quality of MeDIP-Seq experiments. The long track name includes a "Hotspot_Score" field indicates the percentage of sequencing reads found inside hotspot regions. The "Pcnt" field shows the percentile of current experiment score in all MeDIP-Seq experiments. This value is subject to change in next Data Release. The most comprehensive and up-to-date description on QC Metrics used by the consortium can be found here .

Release Notes

The data is combination of Release II, III, IV, V, VI, VII, VIII and IX which were mapped to human reference genome version hg19. The data is production of Roadmap Epigenomics Project.

Please follow the link for Roadmap Epigenomics data access policy

Credits

These data were generated in labs from three institutions: UCSF, UBC, UCSD as part of Roadmap Epigenomics Project.

Useful links