Schema for MACE TSS - TSS Identified by 5' Massive Amplification of cDNA Ends (5' MACE)
  Database: dm6    Primary Table: MACE_S2DRSC_tagClusters    Row Count: 8,496   Data last updated: 2022-10-20
fieldexampleSQL type info
bin 585smallint(5) unsigned range
chrom chr2Lvarchar(255) values
chromStart 66540int(10) unsigned range
chromEnd 66541int(10) unsigned range
name .varchar(255) values
score 0int(10) unsigned range
strand +char(1) values
thickStart 66540int(10) unsigned range
thickEnd 66541int(10) unsigned range
reserved 0int(10) unsigned range
blockCount 1int(10) unsigned range
blockSizes 1longblob  
chromStarts 0longblob  

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStarts
585chr2L6654066541.0+66540665410110
585chr2L6704067043.0+6704067041022,10,2
585chr2L7173771739.0+7173771738021,10,1
585chr2L7252172522.0+72521725220110
585chr2L7261072612.0+72611726120120
585chr2L7338473385.0+73384733850110
585chr2L7344273443.0+73442734430110
585chr2L7437774378.0+74377743780110
585chr2L102379102381.0+1023801023810120
585chr2L106699106703.0-106700106701021,30,1

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.