Schema for MACE TSS - TSS Identified by 5' Massive Amplification of cDNA Ends (5' MACE)
  Database: dm6    Primary Table: MACE_embryos_tagClusters    Row Count: 8,319   Data last updated: 2022-10-20
fieldexampleSQL type info
bin 585smallint(5) unsigned range
chrom chr2Lvarchar(255) values
chromStart 21827int(10) unsigned range
chromEnd 21841int(10) unsigned range
name .varchar(255) values
score 0int(10) unsigned range
strand +char(1) values
thickStart 21827int(10) unsigned range
thickEnd 21828int(10) unsigned range
reserved 0int(10) unsigned range
blockCount 1int(10) unsigned range
blockSizes 14longblob  
chromStarts 0longblob  

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStarts
585chr2L2182721841.0+218272182801140
585chr2L4471544716.0+44715447160110
585chr2L5924359245.0-59244592450120
585chr2L7173471741.0+7173771738031,1,10,3,6
585chr2L7387373874.0-73873738740110
585chr2L7564475645.0+75644756450110
585chr2L9472194743.0+947219472201220
585chr2L101502101503.0+1015021015030110
585chr2L106692106757.0-106731106732021,570,8
585chr2L107757107759.0+1077571077580120

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

MACE TSS (tss_MACE) Track Description
 

Description

These tracks show the transcription start sites identified by 5' Massive Amplification of cDNA Ends (5' MACE) in D. melanogaster S2-DRSC cells and 0-16 hour embryos. The MACE datasets were obtained from the NCBI Gene Expression Omnibus database under the accession number GSE24521.

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 = 1.05, T = 2*10^6

References

Enderle D, Beisel C, Stadler MB, Gerstung M, Athri P, Paro R. Polycomb preferentially targets stalled promoters of coding and noncoding transcripts. Genome Res. 2011 Feb;21(2):216-26.

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.