Exo-seq Tag Clusters Track Settings
 
Exo-seq Tag Clusters at Different Zeitgeber Times and Temperatures   (All Expression and Regulation tracks)

Display mode:       Reset to defaults   

Show only items with score at or above:   (range: 0 to 1000)

Select subtracks by temperature and zt: (help)
 All Temperature temp 18C  temp 25C  temp 29C 
ZT
zt3 
zt9 
zt15 
zt23 
List subtracks: only selected/visible    all    ()  
 
hide
 Configure
 zt3 temp_18C  Exo-seq Tag Clusters for Zeitgeber Time 3 at 18C   Schema 
 
hide
 Configure
 zt9 temp_18C  Exo-seq Tag Clusters for Zeitgeber Time 9 at 18C   Schema 
 
hide
 Configure
 zt15 temp_18C  Exo-seq Tag Clusters for Zeitgeber Time 15 at 18C   Schema 
 
hide
 Configure
 zt23 temp_18C  Exo-seq Tag Clusters for Zeitgeber Time 23 at 18C   Schema 
 
hide
 Configure
 zt3 temp_25C  Exo-seq Tag Clusters for Zeitgeber Time 3 at 25C   Schema 
 
hide
 Configure
 zt9 temp_25C  Exo-seq Tag Clusters for Zeitgeber Time 9 at 25C   Schema 
 
hide
 Configure
 zt15 temp_25C  Exo-seq Tag Clusters for Zeitgeber Time 15 at 25C   Schema 
 
hide
 Configure
 zt23 temp_25C  Exo-seq Tag Clusters for Zeitgeber Time 23 at 25C   Schema 
 
hide
 Configure
 zt3 temp_29C  Exo-seq Tag Clusters for Zeitgeber Time 3 at 29C   Schema 
 
hide
 Configure
 zt9 temp_29C  Exo-seq Tag Clusters for Zeitgeber Time 9 at 29C   Schema 
 
hide
 Configure
 zt15 temp_29C  Exo-seq Tag Clusters for Zeitgeber Time 15 at 29C   Schema 
 
hide
 Configure
 zt23 temp_29C  Exo-seq Tag Clusters for Zeitgeber Time 23 at 29C   Schema 
    

Description

These tracks show the interquantile widths of the promoters for D. melanogaster based on the Exo-seq data collected at different Zeitgeber Times (ZT) and temperatures. The Exo-seq datasets were obtained from the NCBI Sequence Read Archive database under the accession number SRP045351.

Methods

Each dataset was mapped to the D. melanogaster release 6 assembly using bwa with default parameters. The alignment results were analyzed by CAGEr. The tag counts were normalized by the normalizeTagCount function in CAGEr with the following parameters:

method = "powerLaw", fitInRange = c(10, 1000), alpha = 1.16, T = 1*10^6

The promoter widths were determined by the cumulativeCTSSdistribution and quantilePositions functions in CAGEr using the following parameters:

clusters = "tagClusters", qLow = 0.1, qUp = 0.9

Display Conventions

The span of each feature corresponds to the promoter width. The thin box within each span corresponds to the interquantile width (qLow = 0.1 to qUp = 0.9) that captures 80% of the CAGE signal. The thicker box denotes the position within the promoter with the highest CAGE signal.

Credits

Afik S, Bartok O, Artyomov MN, Shishkin AA, Kadri S, Hanan M, Zhu X, Garber M, Kadener S. Defining the 5′ and 3′ landscape of the Drosophila transcriptome with Exo-seq and RNaseH-seq. Nucleic Acids Res. 2017 Jun 20;45(11):e95.

Haberle V, Forrest AR, Hayashizaki Y, Carninci P, Lenhard B. CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses. Nucleic Acids Res. 2015 Apr 30;43(8):e51.