Schema for Exosome RNAi CAGE - Exosome RNAi Knockdown CAGE TSS
  Database: dm6    Primary Table: GSE109588_kd_CTSS_minus    Row Count: 1   Data last updated: 2022-10-20
fieldexampleSQL type info
fileName /gbdb/dm6/bbi/exosome_CAGE/...varchar(255) values

This table points to a file in BigWig format.

Sample Rows
 
fileName
/gbdb/dm6/bbi/exosome_CAGE/GSE109588_CAGE_kd.CTSS.normalized.minus.bw

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

Exosome RNAi CAGE (GSE109588_CAGEr) Track Description
 

Description

These tracks show the combined normalized density of CAGE reads for exosome-depleted and control samples from D. melanogaster S2 cells. The CAGE datasets were obtained from the NCBI Sequence Read Archive database under the accession number SRP131270.

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(500, 50000), alpha = 1.07, T = 1*10^6

References

Rennie S, Dalby M, Lloret-Llinares M, Bakoulis S, Dalager Vaagensø C, Heick Jensen T, Andersson R. Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities. Nucleic Acids Res. 2018 Jun 20;46(11):5455-5469.

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.