Schema for Exo-seq Tag Clusters - Exo-seq Tag Clusters at Different Zeitgeber Times and Temperatures
  Database: dm6    Primary Table: ExoCAGE_29C_zt23_tagClusters    Row Count: 25,974   Data last updated: 2022-10-20
fieldexampleSQL type info
bin 585smallint(5) unsigned range
chrom chr2Lvarchar(255) values
chromStart 59241int(10) unsigned range
chromEnd 59244int(10) unsigned range
name .varchar(255) values
score 0int(10) unsigned range
strand -char(1) values
thickStart 59243int(10) unsigned range
thickEnd 59244int(10) unsigned range
reserved 0int(10) unsigned range
blockCount 1int(10) unsigned range
blockSizes 3longblob  
chromStarts 0longblob  

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStarts
585chr2L5924159244.0-59243592440130
585chr2L6704367046.0+67043670440130
585chr2L7259972631.0+72599726000218,10,31
585chr2L7342673441.0+734267342701150
585chr2L9473494743.0+9474194742021,50,4
585chr2L102380102429.0+102385102386031,38,10,2,48
585chr2L102459102464.0+1024591024600150
585chr2L106697106729.0-10672810672901320
585chr2L107756107797.0+107760107761031,1,10,4,40
585chr2L107926107952.0+10792610792701260

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Exo-seq Tag Clusters (tss_exoseq_tagClusters) Track Description
 

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.