Schema for scRNAs (S2 Cells) - Short Capped RNAs (scRNAs) in S2 Cells
  Database: dm6    Primary Table: scRNA5pr_untreated_tagClusters    Row Count: 10,498   Data last updated: 2022-10-21
fieldexampleSQL type info
bin 585smallint(5) unsigned range
chrom chr2Lvarchar(255) values
chromStart 67042int(10) unsigned range
chromEnd 67044int(10) unsigned range
name .varchar(255) values
score 0int(10) unsigned range
strand +char(1) values
thickStart 67043int(10) unsigned range
thickEnd 67044int(10) unsigned range
reserved 0int(10) unsigned range
blockCount 1int(10) unsigned range
blockSizes 2longblob  
chromStarts 0longblob  

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStarts
585chr2L6704267044.0+67043670440120
585chr2L7241372427.0-724267242701140
585chr2L7259972631.0+725997260001320
585chr2L7264872669.0-726567265701210
585chr2L7338773407.0+734067340701200
585chr2L7344073484.0+73468734690238,10,43
585chr2L7386573876.0-738707387101110
585chr2L7405774115.0+7408874089021,520,6
585chr2L8736987400.0-8738187382031,7,10,6,30
585chr2L9473494752.0+947349473501180

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

scRNAs (S2 Cells) (scRNAs_S2) Track Description
 

Description

These tracks show the normalized read density for the 5′ and 3′ ends of short capped RNAs (scRNAs) in D. melanogaster S2 cells. Most of the scRNAs are produced by paused polymerases. The 5′ ends of the scRNAs demarcate the transcription start site while the 3′ ends of the scRNAs demarcate where RNA Polymerase II have paused.

Datasets from Nechaev S et al., 2010

This study analyzed the 5′ and 3′ scRNAs found in untreated S2 cells and in TFIIS-depleted S2 cells. The datasets were retrieved from the Gene Expression Omnibus database at NCBI under the accession number GSE18643.

Datasets from Henriques T et al., 2013

In addition to analyzing the 3′ scRNAs found in whole S2 cells, this study also analyzed the 3′ scRNAs that are associated with chromatin and 3′ scRNAs that are detergent-soluble. The datasets were retrieved from the Gene Expression Omnibus database at NCBI under the accession number GSE49078.

Methods

Each dataset was mapped to the D. melanogaster release 6 assembly using bwa with default parameters. The alignment results were analyzed by CAGEr.

For the Nechaev S et al. study, the tag counts were normalized by the normalizeTagCount function in CAGEr with the following parameters:

method = "powerLaw", fitInRange = c(10, 1000), alpha = 1.10, T = 1*10^6

For the Henriques T et al. study, 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 = 1*10^7

Note that the orientation of the features identified by the CAGEr analysis of the 3′ scRNAs were flipped to facilitate data interpretations.

References

Nechaev S, Fargo DC, dos Santos G, Liu L, Gao Y, Adelman K. Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. Science. 2010 Jan 15;327(5963):335-8.

Henriques T, Gilchrist DA, Nechaev S, Bern M, Muse GW, Burkholder A, Fargo DC, Adelman K. Stable pausing by RNA polymerase II provides an opportunity to target and integrate regulatory signals. Mol Cell. 2013 Nov 21;52(4):517-28.

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.